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diff --git a/docs/diagrams/Structure_BayesInf.drawio b/docs/diagrams/Structure_BayesInf.drawio
index ddabd26efb05c7db4ee7a49855f1a3585a883d58..783474b98e936e431d275fece17bd39645f0e6ba 100644
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+ <mxCell id="JXjM7l_erEiZMkSmYBvl-21" value="_normpdf" style="html=1;whiteSpace=wrap;" vertex="1" parent="1">
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diff --git a/examples/model-comparison/bayesvalidrox/__init__.py b/examples/model-comparison/bayesvalidrox/__init__.py
deleted file mode 100644
index 8e865af80652b8dd29203c2c85f8d1c717e335bc..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/__init__.py
+++ /dev/null
@@ -1,25 +0,0 @@
-# -*- coding: utf-8 -*-
-__version__ = "0.0.5"
-
-from .pylink.pylink import PyLinkForwardModel
-from .surrogate_models.surrogate_models import MetaModel
-#from .surrogate_models.meta_model_engine import MetaModelEngine
-from .surrogate_models.engine import Engine
-from .surrogate_models.inputs import Input
-from .post_processing.post_processing import PostProcessing
-from .bayes_inference.bayes_inference import BayesInference
-from .bayes_inference.bayes_model_comparison import BayesModelComparison
-from .bayes_inference.discrepancy import Discrepancy
-
-__all__ = [
- "__version__",
- "PyLinkForwardModel",
- "Input",
- "Discrepancy",
- "MetaModel",
- #"MetaModelEngine",
- "Engine",
- "PostProcessing",
- "BayesInference",
- "BayesModelComparison"
- ]
diff --git a/examples/model-comparison/bayesvalidrox/__pycache__/__init__.cpython-310.pyc b/examples/model-comparison/bayesvalidrox/__pycache__/__init__.cpython-310.pyc
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deleted file mode 100644
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diff --git a/examples/model-comparison/bayesvalidrox/bayes_inference/__init__.py b/examples/model-comparison/bayesvalidrox/bayes_inference/__init__.py
deleted file mode 100644
index df8d935680f96ab487cf087866e8bfd504762945..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/bayes_inference/__init__.py
+++ /dev/null
@@ -1,9 +0,0 @@
-# -*- coding: utf-8 -*-
-
-from .bayes_inference import BayesInference
-from .mcmc import MCMC
-
-__all__ = [
- "BayesInference",
- "MCMC"
- ]
diff --git a/examples/model-comparison/bayesvalidrox/bayes_inference/__pycache__/__init__.cpython-310.pyc b/examples/model-comparison/bayesvalidrox/bayes_inference/__pycache__/__init__.cpython-310.pyc
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diff --git a/examples/model-comparison/bayesvalidrox/bayes_inference/bayes_inference.py b/examples/model-comparison/bayesvalidrox/bayes_inference/bayes_inference.py
deleted file mode 100644
index 1898a8ae619597d92bc355ac4249f57019f0aed7..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/bayes_inference/bayes_inference.py
+++ /dev/null
@@ -1,1532 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-import numpy as np
-import os
-import copy
-import pandas as pd
-from tqdm import tqdm
-from scipy import stats
-import scipy.linalg as spla
-import joblib
-import seaborn as sns
-import corner
-import h5py
-import multiprocessing
-import gc
-from sklearn.metrics import mean_squared_error, r2_score
-from sklearn import preprocessing
-from matplotlib.patches import Patch
-import matplotlib.lines as mlines
-from matplotlib.backends.backend_pdf import PdfPages
-import matplotlib.pylab as plt
-
-from .mcmc import MCMC
-
-# Load the mplstyle
-plt.style.use(os.path.join(os.path.split(__file__)[0],
- '../', 'bayesvalidrox.mplstyle'))
-
-
-class BayesInference:
- """
- A class to perform Bayesian Analysis.
-
-
- Attributes
- ----------
- MetaModel : obj
- Meta model object.
- discrepancy : obj
- The discrepancy object for the sigma2s, i.e. the diagonal entries
- of the variance matrix for a multivariate normal likelihood.
- name : str, optional
- The type of analysis, either calibration (`Calib`) or validation
- (`Valid`). The default is `'Calib'`.
- emulator : bool, optional
- Analysis with emulator (MetaModel). The default is `True`.
- bootstrap : bool, optional
- Bootstrap the analysis. The default is `False`.
- req_outputs : list, optional
- The list of requested output to be used for the analysis.
- The default is `None`. If None, all the defined outputs for the model
- object is used.
- selected_indices : dict, optional
- A dictionary with the selected indices of each model output. The
- default is `None`. If `None`, all measurement points are used in the
- analysis.
- samples : array of shape (n_samples, n_params), optional
- The samples to be used in the analysis. The default is `None`. If
- None the samples are drawn from the probablistic input parameter
- object of the MetaModel object.
- n_samples : int, optional
- Number of samples to be used in the analysis. The default is `500000`.
- If samples is not `None`, this argument will be assigned based on the
- number of samples given.
- measured_data : dict, optional
- A dictionary containing the observation data. The default is `None`.
- if `None`, the observation defined in the Model object of the
- MetaModel is used.
- inference_method : str, optional
- A method for approximating the posterior distribution in the Bayesian
- inference step. The default is `'rejection'`, which stands for
- rejection sampling. A Markov Chain Monte Carlo sampler can be simply
- selected by passing `'MCMC'`.
- mcmc_params : dict, optional
- A dictionary with args required for the Bayesian inference with
- `MCMC`. The default is `None`.
-
- Pass the mcmc_params like the following:
-
- >>> mcmc_params:{
- 'init_samples': None, # initial samples
- 'n_walkers': 100, # number of walkers (chain)
- 'n_steps': 100000, # number of maximum steps
- 'n_burn': 200, # number of burn-in steps
- 'moves': None, # Moves for the emcee sampler
- 'multiprocessing': False, # multiprocessing
- 'verbose': False # verbosity
- }
- The items shown above are the default values. If any parmeter is
- not defined, the default value will be assigned to it.
- bayes_loocv : bool, optional
- Bayesian Leave-one-out Cross Validation. The default is `False`. If
- `True`, the LOOCV procedure is used to estimate the bayesian Model
- Evidence (BME).
- n_bootstrap_itrs : int, optional
- Number of bootstrap iteration. The default is `1`. If bayes_loocv is
- `True`, this is qualt to the total length of the observation data
- set.
- perturbed_data : array of shape (n_bootstrap_itrs, n_obs), optional
- User defined perturbed data. The default is `[]`.
- bootstrap_noise : float, optional
- A noise level to perturb the data set. The default is `0.05`.
- just_analysis : bool, optional
- Justifiability analysis. The default is False.
- valid_metrics : list, optional
- List of the validation metrics. The following metrics are supported:
-
- 1. log_BME : logarithm of the Bayesian model evidence
- 2. KLD : Kullback-Leibler Divergence
- 3. inf_entropy: Information entropy
- The default is `['log_BME']`.
- plot_post_pred : bool, optional
- Plot posterior predictive plots. The default is `True`.
- plot_map_pred : bool, optional
- Plot the model outputs vs the metamodel predictions for the maximum
- a posteriori (defined as `max_a_posteriori`) parameter set. The
- default is `False`.
- max_a_posteriori : str, optional
- Maximum a posteriori. `'mean'` and `'mode'` are available. The default
- is `'mean'`.
- corner_title_fmt : str, optional
- Title format for the posterior distribution plot with python
- package `corner`. The default is `'.2e'`.
-
- """
-
- def __init__(self, engine, MetaModel = None, discrepancy=None, emulator=True,
- name='Calib', bootstrap=False, req_outputs=None,
- selected_indices=None, samples=None, n_samples=100000,
- measured_data=None, inference_method='rejection',
- mcmc_params=None, bayes_loocv=False, n_bootstrap_itrs=1,
- perturbed_data=[], bootstrap_noise=0.05, just_analysis=False,
- valid_metrics=['BME'], plot_post_pred=True,
- plot_map_pred=False, max_a_posteriori='mean',
- corner_title_fmt='.2e'):
-
- self.engine = engine
- self.MetaModel = engine.MetaModel
- self.Discrepancy = discrepancy
- self.emulator = emulator
- self.name = name
- self.bootstrap = bootstrap
- self.req_outputs = req_outputs
- self.selected_indices = selected_indices
- self.samples = samples
- self.n_samples = n_samples
- self.measured_data = measured_data
- self.inference_method = inference_method
- self.mcmc_params = mcmc_params
- self.perturbed_data = perturbed_data
- self.bayes_loocv = bayes_loocv
- self.n_bootstrap_itrs = n_bootstrap_itrs
- self.bootstrap_noise = bootstrap_noise
- self.just_analysis = just_analysis
- self.valid_metrics = valid_metrics
- self.plot_post_pred = plot_post_pred
- self.plot_map_pred = plot_map_pred
- self.max_a_posteriori = max_a_posteriori
- self.corner_title_fmt = corner_title_fmt
-
- # -------------------------------------------------------------------------
- def create_inference(self):
- """
- Starts the inference.
-
- Returns
- -------
- BayesInference : obj
- The Bayes inference object.
-
- """
-
- # Set some variables
- MetaModel = self.MetaModel
- Model = self.engine.Model
- n_params = MetaModel.n_params
- output_names = Model.Output.names
- par_names = self.engine.ExpDesign.par_names
-
- # If the prior is set by the user, take it.
- if self.samples is None:
- self.samples = self.engine.ExpDesign.generate_samples(
- self.n_samples, 'random')
- else:
- try:
- samples = self.samples.values
- except AttributeError:
- samples = self.samples
-
- # Take care of an additional Sigma2s
- self.samples = samples[:, :n_params]
-
- # Update number of samples
- self.n_samples = self.samples.shape[0]
-
- # ---------- Preparation of observation data ----------
- # Read observation data and perturb it if requested.
- if self.measured_data is None:
- self.measured_data = Model.read_observation(case=self.name)
- # Convert measured_data to a data frame
- if not isinstance(self.measured_data, pd.DataFrame):
- self.measured_data = pd.DataFrame(self.measured_data)
-
- # Extract the total number of measurement points
- if self.name.lower() == 'calib':
- self.n_tot_measurement = Model.n_obs
- else:
- self.n_tot_measurement = Model.n_obs_valid
-
- # Find measurement error (if not given) for post predictive plot
- if not hasattr(self, 'measurement_error'):
- if isinstance(self.Discrepancy, dict):
- Disc = self.Discrepancy['known']
- else:
- Disc = self.Discrepancy
- if isinstance(Disc.parameters, dict):
- self.measurement_error = {k: np.sqrt(Disc.parameters[k]) for k
- in Disc.parameters.keys()}
- else:
- try:
- self.measurement_error = np.sqrt(Disc.parameters)
- except TypeError:
- pass
-
- # ---------- Preparation of variance for covariance matrix ----------
- # Independent and identically distributed
- total_sigma2 = dict()
- opt_sigma_flag = isinstance(self.Discrepancy, dict)
- opt_sigma = None
- for key_idx, key in enumerate(output_names):
-
- # Find opt_sigma
- if opt_sigma_flag and opt_sigma is None:
- # Option A: known error with unknown bias term
- opt_sigma = 'A'
- known_discrepancy = self.Discrepancy['known']
- self.Discrepancy = self.Discrepancy['infer']
- sigma2 = np.array(known_discrepancy.parameters[key])
-
- elif opt_sigma == 'A' or self.Discrepancy.parameters is not None:
- # Option B: The sigma2 is known (no bias term)
- if opt_sigma == 'A':
- sigma2 = np.array(known_discrepancy.parameters[key])
- else:
- opt_sigma = 'B'
- sigma2 = np.array(self.Discrepancy.parameters[key])
-
- elif not isinstance(self.Discrepancy.InputDisc, str):
- # Option C: The sigma2 is unknown (bias term including error)
- opt_sigma = 'C'
- self.Discrepancy.opt_sigma = opt_sigma
- n_measurement = self.measured_data[key].values.shape
- sigma2 = np.zeros((n_measurement[0]))
-
- total_sigma2[key] = sigma2
-
- self.Discrepancy.opt_sigma = opt_sigma
- self.Discrepancy.total_sigma2 = total_sigma2
-
- # If inferred sigma2s obtained from e.g. calibration are given
- try:
- self.sigma2s = self.Discrepancy.get_sample(self.n_samples)
- except:
- pass
-
- # ---------------- Bootstrap & TOM --------------------
- if self.bootstrap or self.bayes_loocv or self.just_analysis:
- if len(self.perturbed_data) == 0:
- # zero mean noise Adding some noise to the observation function
- self.perturbed_data = self._perturb_data(
- self.measured_data, output_names
- )
- else:
- self.n_bootstrap_itrs = len(self.perturbed_data)
-
- # -------- Model Discrepancy -----------
- if hasattr(self, 'error_model') and self.error_model \
- and self.name.lower() != 'calib':
- # Select posterior mean as MAP
- MAP_theta = self.samples.mean(axis=0).reshape((1, n_params))
- # MAP_theta = stats.mode(self.samples,axis=0)[0]
-
- # Evaluate the (meta-)model at the MAP
- y_MAP, y_std_MAP = MetaModel.eval_metamodel(samples=MAP_theta)
-
- # Train a GPR meta-model using MAP
- self.error_MetaModel = MetaModel.create_model_error(
- self.bias_inputs, y_MAP, Name=self.name
- )
-
- # -----------------------------------------------------
- # ----- Loop over the perturbed observation data ------
- # -----------------------------------------------------
- # Initilize arrays
- logLikelihoods = np.zeros((self.n_samples, self.n_bootstrap_itrs),
- dtype=np.float16)
- BME_Corr = np.zeros((self.n_bootstrap_itrs))
- log_BME = np.zeros((self.n_bootstrap_itrs))
- KLD = np.zeros((self.n_bootstrap_itrs))
- inf_entropy = np.zeros((self.n_bootstrap_itrs))
-
- # Compute the prior predtions
- # Evaluate the MetaModel
- if self.emulator:
- y_hat, y_std = MetaModel.eval_metamodel(samples=self.samples)
- self.__mean_pce_prior_pred = y_hat
- self._std_pce_prior_pred = y_std
-
- # Correct the predictions with Model discrepancy
- if hasattr(self, 'error_model') and self.error_model:
- y_hat_corr, y_std = self.error_MetaModel.eval_model_error(
- self.bias_inputs, self.__mean_pce_prior_pred
- )
- self.__mean_pce_prior_pred = y_hat_corr
- self._std_pce_prior_pred = y_std
-
- # Surrogate model's error using RMSE of test data
- if hasattr(MetaModel, 'rmse'):
- surrError = MetaModel.rmse
- else:
- surrError = None
-
- else:
- # Evaluate the original model
- self.__model_prior_pred = self._eval_model(
- samples=self.samples, key='PriorPred'
- )
- surrError = None
-
- # Start the likelihood-BME computations for the perturbed data
- for itr_idx, data in tqdm(
- enumerate(self.perturbed_data),
- total=self.n_bootstrap_itrs,
- desc="Bootstrapping the BME calculations", ascii=True
- ):
-
- # ---------------- Likelihood calculation ----------------
- if self.emulator:
- model_evals = self.__mean_pce_prior_pred
- else:
- model_evals = self.__model_prior_pred
-
- # Leave one out
- if self.bayes_loocv or self.just_analysis:
- self.selected_indices = np.nonzero(data)[0]
-
- # Prepare data dataframe
- nobs = list(self.measured_data.count().values[1:])
- numbers = list(np.cumsum(nobs))
- indices = list(zip([0] + numbers, numbers))
- data_dict = {
- output_names[i]: data[j:k] for i, (j, k) in
- enumerate(indices)
- }
- #print(output_names)
- #print(indices)
- #print(numbers)
- #print(nobs)
- #print(self.measured_data)
- #for i, (j, k) in enumerate(indices):
- # print(i,j,k)
- #print(data)
- #print(data_dict)
- #stop
-
- # Unknown sigma2
- if opt_sigma == 'C' or hasattr(self, 'sigma2s'):
- logLikelihoods[:, itr_idx] = self.normpdf(
- model_evals, data_dict, total_sigma2,
- sigma2=self.sigma2s, std=surrError
- )
- else:
- # known sigma2
- logLikelihoods[:, itr_idx] = self.normpdf(
- model_evals, data_dict, total_sigma2,
- std=surrError
- )
-
- # ---------------- BME Calculations ----------------
- # BME (log)
- log_BME[itr_idx] = np.log(
- np.nanmean(np.exp(logLikelihoods[:, itr_idx],
- dtype=np.longdouble))#float128))
- )
-
- # BME correction when using Emulator
- if self.emulator:
- BME_Corr[itr_idx] = self.__corr_factor_BME(
- data_dict, total_sigma2, log_BME[itr_idx]
- )
-
- # Rejection Step
- if 'kld' in list(map(str.lower, self.valid_metrics)) and\
- 'inf_entropy' in list(map(str.lower, self.valid_metrics)):
- # Random numbers between 0 and 1
- unif = np.random.rand(1, self.n_samples)[0]
-
- # Reject the poorly performed prior
- Likelihoods = np.exp(logLikelihoods[:, itr_idx],
- dtype=np.float64)
- accepted = (Likelihoods/np.max(Likelihoods)) >= unif
- posterior = self.samples[accepted]
-
- # Posterior-based expectation of likelihoods
- postExpLikelihoods = np.mean(
- logLikelihoods[:, itr_idx][accepted]
- )
-
- # Calculate Kullback-Leibler Divergence
- KLD[itr_idx] = postExpLikelihoods - log_BME[itr_idx]
-
- # Posterior-based expectation of prior densities
- if 'inf_entropy' in list(map(str.lower, self.valid_metrics)):
- n_thread = int(0.875 * multiprocessing.cpu_count())
- with multiprocessing.Pool(n_thread) as p:
- postExpPrior = np.mean(np.concatenate(
- p.map(
- self.engine.ExpDesign.JDist.pdf,
- np.array_split(posterior.T, n_thread, axis=1))
- )
- )
- # Information Entropy based on Entropy paper Eq. 38
- inf_entropy[itr_idx] = log_BME[itr_idx] - postExpPrior - \
- postExpLikelihoods
-
- # Clear memory
- gc.collect(generation=2)
-
- # ---------- Store metrics for perturbed data set ----------------
- # Likelihoods (Size: n_samples, n_bootstrap_itr)
- self.log_likes = logLikelihoods
-
- # BME (log), KLD, infEntropy (Size: 1,n_bootstrap_itr)
- self.log_BME = log_BME
-
- # BMECorrFactor (log) (Size: 1,n_bootstrap_itr)
- if self.emulator:
- self.log_BME_corr_factor = BME_Corr
-
- if 'kld' in list(map(str.lower, self.valid_metrics)):
- self.KLD = KLD
- if 'inf_entropy' in list(map(str.lower, self.valid_metrics)):
- self.inf_entropy = inf_entropy
-
- # BME = BME + BMECorrFactor
- if self.emulator:
- self.log_BME += self.log_BME_corr_factor
-
- # ---------------- Parameter Bayesian inference ----------------
- if self.inference_method.lower() == 'mcmc':
- # Instantiate the MCMC object
- MCMC_Obj = MCMC(self)
- self.posterior_df = MCMC_Obj.run_sampler(
- self.measured_data, total_sigma2
- )
-
- elif self.name.lower() == 'valid':
- # Convert to a dataframe if samples are provided after calibration.
- self.posterior_df = pd.DataFrame(self.samples, columns=par_names)
-
- else:
- # Rejection sampling
- self.posterior_df = self._rejection_sampling()
-
- # Provide posterior's summary
- print('\n')
- print('-'*15 + 'Posterior summary' + '-'*15)
- pd.options.display.max_columns = None
- pd.options.display.max_rows = None
- print(self.posterior_df.describe())
- print('-'*50)
-
- # -------- Model Discrepancy -----------
- if hasattr(self, 'error_model') and self.error_model \
- and self.name.lower() == 'calib':
- if self.inference_method.lower() == 'mcmc':
- self.error_MetaModel = MCMC_Obj.error_MetaModel
- else:
- # Select posterior mean as MAP
- if opt_sigma == "B":
- posterior_df = self.posterior_df.values
- else:
- posterior_df = self.posterior_df.values[:, :-Model.n_outputs]
-
- # Select posterior mean as Maximum a posteriori
- map_theta = posterior_df.mean(axis=0).reshape((1, n_params))
- # map_theta = stats.mode(Posterior_df,axis=0)[0]
-
- # Evaluate the (meta-)model at the MAP
- y_MAP, y_std_MAP = MetaModel.eval_metamodel(samples=map_theta)
-
- # Train a GPR meta-model using MAP
- self.error_MetaModel = MetaModel.create_model_error(
- self.bias_inputs, y_MAP, Name=self.name
- )
-
- # -------- Posterior perdictive -----------
- self._posterior_predictive()
-
- # -----------------------------------------------------
- # ------------------ Visualization --------------------
- # -----------------------------------------------------
- # Create Output directory, if it doesn't exist already.
- out_dir = f'Outputs_Bayes_{Model.name}_{self.name}'
- os.makedirs(out_dir, exist_ok=True)
-
- # -------- Posteior parameters --------
- if opt_sigma != "B":
- par_names.extend(
- [self.Discrepancy.InputDisc.Marginals[i].name for i
- in range(len(self.Discrepancy.InputDisc.Marginals))]
- )
- # Pot with corner
- figPosterior = corner.corner(self.posterior_df.to_numpy(),
- labels=par_names,
- quantiles=[0.15, 0.5, 0.85],
- show_titles=True,
- title_fmt=self.corner_title_fmt,
- labelpad=0.2,
- use_math_text=True,
- title_kwargs={"fontsize": 28},
- plot_datapoints=False,
- plot_density=False,
- fill_contours=True,
- smooth=0.5,
- smooth1d=0.5)
-
- # Loop over axes and set x limits
- if opt_sigma == "B":
- axes = np.array(figPosterior.axes).reshape(
- (len(par_names), len(par_names))
- )
- for yi in range(len(par_names)):
- ax = axes[yi, yi]
- ax.set_xlim(self.engine.ExpDesign.bound_tuples[yi])
- for xi in range(yi):
- ax = axes[yi, xi]
- ax.set_xlim(self.engine.ExpDesign.bound_tuples[xi])
- plt.close()
-
- # Turn off gridlines
- for ax in figPosterior.axes:
- ax.grid(False)
-
- if self.emulator:
- plotname = f'/Posterior_Dist_{Model.name}_emulator'
- else:
- plotname = f'/Posterior_Dist_{Model.name}'
-
- figPosterior.set_size_inches((24, 16))
- figPosterior.savefig(f'./{out_dir}{plotname}.pdf',
- bbox_inches='tight')
-
- # -------- Plot MAP --------
- if self.plot_map_pred:
- self._plot_max_a_posteriori()
-
- # -------- Plot log_BME dist --------
- if self.bootstrap:
-
- # Computing the TOM performance
- self.log_BME_tom = stats.chi2.rvs(
- self.n_tot_measurement, size=self.log_BME.shape[0]
- )
-
- fig, ax = plt.subplots()
- sns.kdeplot(self.log_BME_tom, ax=ax, color="green", shade=True)
- sns.kdeplot(
- self.log_BME, ax=ax, color="blue", shade=True,
- label='Model BME')
-
- ax.set_xlabel('log$_{10}$(BME)')
- ax.set_ylabel('Probability density')
-
- legend_elements = [
- Patch(facecolor='green', edgecolor='green', label='TOM BME'),
- Patch(facecolor='blue', edgecolor='blue', label='Model BME')
- ]
- ax.legend(handles=legend_elements)
-
- if self.emulator:
- plotname = f'/BME_hist_{Model.name}_emulator'
- else:
- plotname = f'/BME_hist_{Model.name}'
-
- plt.savefig(f'./{out_dir}{plotname}.pdf', bbox_inches='tight')
- plt.show()
- plt.close()
-
- # -------- Posteior perdictives --------
- if self.plot_post_pred:
- # Plot the posterior predictive
- self._plot_post_predictive()
-
- return self
-
- # -------------------------------------------------------------------------
- def _perturb_data(self, data, output_names):
- """
- Returns an array with n_bootstrap_itrs rowsof perturbed data.
- The first row includes the original observation data.
- If `self.bayes_loocv` is True, a 2d-array will be returned with
- repeated rows and zero diagonal entries.
-
- Parameters
- ----------
- data : pandas DataFrame
- Observation data.
- output_names : list
- List of the output names.
-
- Returns
- -------
- final_data : array
- Perturbed data set.
-
- """
- noise_level = self.bootstrap_noise
- obs_data = data[output_names].values
- n_measurement, n_outs = obs_data.shape
- self.n_tot_measurement = obs_data[~np.isnan(obs_data)].shape[0]
- # Number of bootstrap iterations
- if self.bayes_loocv:
- self.n_bootstrap_itrs = self.n_tot_measurement
-
- # Pass loocv dataset
- if self.bayes_loocv:
- obs = obs_data.T[~np.isnan(obs_data.T)]
- final_data = np.repeat(np.atleast_2d(obs), self.n_bootstrap_itrs,
- axis=0)
- np.fill_diagonal(final_data, 0)
- return final_data
-
- else:
- final_data = np.zeros(
- (self.n_bootstrap_itrs, self.n_tot_measurement)
- )
- final_data[0] = obs_data.T[~np.isnan(obs_data.T)]
- for itrIdx in range(1, self.n_bootstrap_itrs):
- data = np.zeros((n_measurement, n_outs))
- for idx in range(len(output_names)):
- std = np.nanstd(obs_data[:, idx])
- if std == 0:
- std = 0.001
- noise = std * noise_level
- data[:, idx] = np.add(
- obs_data[:, idx],
- np.random.normal(0, 1, obs_data.shape[0]) * noise,
- )
-
- final_data[itrIdx] = data.T[~np.isnan(data.T)]
-
- return final_data
-
- # -------------------------------------------------------------------------
- def _logpdf(self, x, mean, cov):
- """
- computes the likelihood based on a multivariate normal distribution.
-
- Parameters
- ----------
- x : TYPE
- DESCRIPTION.
- mean : array_like
- Observation data.
- cov : 2d array
- Covariance matrix of the distribution.
-
- Returns
- -------
- log_lik : float
- Log likelihood.
-
- """
- n = len(mean)
- L = spla.cholesky(cov, lower=True)
- beta = np.sum(np.log(np.diag(L)))
- dev = x - mean
- alpha = dev.dot(spla.cho_solve((L, True), dev))
- log_lik = -0.5 * alpha - beta - n / 2. * np.log(2 * np.pi)
- return log_lik
-
- # -------------------------------------------------------------------------
- def _eval_model(self, samples=None, key='MAP'):
- """
- Evaluates Forward Model.
-
- Parameters
- ----------
- samples : array of shape (n_samples, n_params), optional
- Parameter sets. The default is None.
- key : str, optional
- Key string to be passed to the run_model_parallel method.
- The default is 'MAP'.
-
- Returns
- -------
- model_outputs : dict
- Model outputs.
-
- """
- MetaModel = self.MetaModel
- Model = self.engine.Model
-
- if samples is None:
- self.samples = self.engine.ExpDesign.generate_samples(
- self.n_samples, 'random')
- else:
- self.samples = samples
- self.n_samples = len(samples)
-
- model_outputs, _ = Model.run_model_parallel(
- self.samples, key_str=key+self.name)
-
- # Clean up
- # Zip the subdirectories
- try:
- dir_name = f'{Model.name}MAP{self.name}'
- key = dir_name + '_'
- Model.zip_subdirs(dir_name, key)
- except:
- pass
-
- return model_outputs
-
- # -------------------------------------------------------------------------
- def _kernel_rbf(self, X, hyperparameters):
- """
- Isotropic squared exponential kernel.
-
- Higher l values lead to smoother functions and therefore to coarser
- approximations of the training data. Lower l values make functions
- more wiggly with wide uncertainty regions between training data points.
-
- sigma_f controls the marginal variance of b(x)
-
- Parameters
- ----------
- X : ndarray of shape (n_samples_X, n_features)
-
- hyperparameters : Dict
- Lambda characteristic length
- sigma_f controls the marginal variance of b(x)
- sigma_0 unresolvable error nugget term, interpreted as random
- error that cannot be attributed to measurement error.
- Returns
- -------
- var_cov_matrix : ndarray of shape (n_samples_X,n_samples_X)
- Kernel k(X, X).
-
- """
- from sklearn.gaussian_process.kernels import RBF
- min_max_scaler = preprocessing.MinMaxScaler()
- X_minmax = min_max_scaler.fit_transform(X)
-
- nparams = len(hyperparameters)
- # characteristic length (0,1]
- Lambda = hyperparameters[0]
- # sigma_f controls the marginal variance of b(x)
- sigma2_f = hyperparameters[1]
-
- # cov_matrix = sigma2_f*rbf_kernel(X_minmax, gamma = 1/Lambda**2)
-
- rbf = RBF(length_scale=Lambda)
- cov_matrix = sigma2_f * rbf(X_minmax)
- if nparams > 2:
- # (unresolvable error) nugget term that is interpreted as random
- # error that cannot be attributed to measurement error.
- sigma2_0 = hyperparameters[2:]
- for i, j in np.ndindex(cov_matrix.shape):
- cov_matrix[i, j] += np.sum(sigma2_0) if i == j else 0
-
- return cov_matrix
-
- # -------------------------------------------------------------------------
- def normpdf(self, outputs, obs_data, total_sigma2s, sigma2=None, std=None):
- """
- Calculates the likelihood of simulation outputs compared with
- observation data.
-
- Parameters
- ----------
- outputs : dict
- A dictionary containing the simulation outputs as array of shape
- (n_samples, n_measurement) for each model output.
- obs_data : dict
- A dictionary/dataframe containing the observation data.
- total_sigma2s : dict
- A dictionary with known values of the covariance diagonal entries,
- a.k.a sigma^2.
- sigma2 : array, optional
- An array of the sigma^2 samples, when the covariance diagonal
- entries are unknown and are being jointly inferred. The default is
- None.
- std : dict, optional
- A dictionary containing the root mean squared error as array of
- shape (n_samples, n_measurement) for each model output. The default
- is None.
-
- Returns
- -------
- logLik : array of shape (n_samples)
- Likelihoods.
-
- """
- Model = self.engine.Model
- logLik = 0.0
-
- # Extract the requested model outputs for likelihood calulation
- if self.req_outputs is None:
- req_outputs = Model.Output.names
- else:
- req_outputs = list(self.req_outputs)
-
- # Loop over the outputs
- for idx, out in enumerate(req_outputs):
-
- # (Meta)Model Output
- nsamples, nout = outputs[out].shape
-
- # Prepare data and remove NaN
- try:
- data = obs_data[out].values[~np.isnan(obs_data[out])]
- except AttributeError:
- data = obs_data[out][~np.isnan(obs_data[out])]
-
- # Prepare sigma2s
- non_nan_indices = ~np.isnan(total_sigma2s[out])
- tot_sigma2s = total_sigma2s[out][non_nan_indices][:nout]
-
- # Add the std of the PCE is chosen as emulator.
- if self.emulator:
- if std is not None:
- tot_sigma2s += std[out]**2
-
- # Covariance Matrix
- covMatrix = np.diag(tot_sigma2s)
-
- # Select the data points to compare
- try:
- indices = self.selected_indices[out]
- except:
- indices = list(range(nout))
- covMatrix = np.diag(covMatrix[indices, indices])
-
- # If sigma2 is not given, use given total_sigma2s
- if sigma2 is None:
- logLik += stats.multivariate_normal.logpdf(
- outputs[out][:, indices], data[indices], covMatrix)
- continue
-
- # Loop over each run/sample and calculate logLikelihood
- logliks = np.zeros(nsamples)
- for s_idx in range(nsamples):
-
- # Simulation run
- tot_outputs = outputs[out]
-
- # Covariance Matrix
- covMatrix = np.diag(tot_sigma2s)
-
- if sigma2 is not None:
- # Check the type error term
- if hasattr(self, 'bias_inputs') and \
- not hasattr(self, 'error_model'):
- # Infer a Bias model usig Gaussian Process Regression
- bias_inputs = np.hstack(
- (self.bias_inputs[out],
- tot_outputs[s_idx].reshape(-1, 1)))
-
- params = sigma2[s_idx, idx*3:(idx+1)*3]
- covMatrix = self._kernel_rbf(bias_inputs, params)
- else:
- # Infer equal sigma2s
- try:
- sigma_2 = sigma2[s_idx, idx]
- except TypeError:
- sigma_2 = 0.0
-
- covMatrix += sigma_2 * np.eye(nout)
- # covMatrix = np.diag(sigma2 * total_sigma2s)
-
- # Select the data points to compare
- try:
- indices = self.selected_indices[out]
- except:
- indices = list(range(nout))
- covMatrix = np.diag(covMatrix[indices, indices])
-
- # Compute loglikelihood
- logliks[s_idx] = self._logpdf(
- tot_outputs[s_idx, indices], data[indices], covMatrix
- )
-
- logLik += logliks
- return logLik
-
- # -------------------------------------------------------------------------
- def _corr_factor_BME_old(self, Data, total_sigma2s, posterior):
- """
- Calculates the correction factor for BMEs.
- """
- MetaModel = self.MetaModel
- OrigModelOutput = self.engine.ExpDesign.Y
- Model = self.engine.Model
-
- # Posterior with guassian-likelihood
- postDist = stats.gaussian_kde(posterior.T)
-
- # Remove NaN
- Data = Data[~np.isnan(Data)]
- total_sigma2s = total_sigma2s[~np.isnan(total_sigma2s)]
-
- # Covariance Matrix
- covMatrix = np.diag(total_sigma2s[:self.n_tot_measurement])
-
- # Extract the requested model outputs for likelihood calulation
- if self.req_outputs is None:
- OutputType = Model.Output.names
- else:
- OutputType = list(self.req_outputs)
-
- # SampleSize = OrigModelOutput[OutputType[0]].shape[0]
-
-
- # Flatten the OutputType for OrigModel
- TotalOutputs = np.concatenate([OrigModelOutput[x] for x in OutputType], 1)
-
- NrofBayesSamples = self.n_samples
- # Evaluate MetaModel on the experimental design
- Samples = self.engine.ExpDesign.X
- OutputRS, stdOutputRS = MetaModel.eval_metamodel(samples=Samples)
-
- # Reset the NrofSamples to NrofBayesSamples
- self.n_samples = NrofBayesSamples
-
- # Flatten the OutputType for MetaModel
- TotalPCEOutputs = np.concatenate([OutputRS[x] for x in OutputRS], 1)
- TotalPCEstdOutputRS= np.concatenate([stdOutputRS[x] for x in stdOutputRS], 1)
-
- logweight = 0
- for i, sample in enumerate(Samples):
- # Compute likelilhood output vs RS
- covMatrix = np.diag(TotalPCEstdOutputRS[i]**2)
- logLik = self._logpdf(TotalOutputs[i], TotalPCEOutputs[i], covMatrix)
- # Compute posterior likelihood of the collocation points
- logpostLik = np.log(postDist.pdf(sample[:, None]))[0]
- if logpostLik != -np.inf:
- logweight += logLik + logpostLik
- return logweight
-
- # -------------------------------------------------------------------------
- def __corr_factor_BME(self, obs_data, total_sigma2s, logBME):
- """
- Calculates the correction factor for BMEs.
- """
- MetaModel = self.MetaModel
- samples = self.engine.ExpDesign.X
- model_outputs = self.engine.ExpDesign.Y
- Model = self.engine.Model
- n_samples = samples.shape[0]
-
- # Extract the requested model outputs for likelihood calulation
- output_names = Model.Output.names
-
- # Evaluate MetaModel on the experimental design and ValidSet
- OutputRS, stdOutputRS = MetaModel.eval_metamodel(samples=samples)
-
- logLik_data = np.zeros((n_samples))
- logLik_model = np.zeros((n_samples))
- # Loop over the outputs
- for idx, out in enumerate(output_names):
-
- # (Meta)Model Output
- nsamples, nout = model_outputs[out].shape
-
- # Prepare data and remove NaN
- try:
- data = obs_data[out].values[~np.isnan(obs_data[out])]
- except AttributeError:
- data = obs_data[out][~np.isnan(obs_data[out])]
-
- # Prepare sigma2s
- non_nan_indices = ~np.isnan(total_sigma2s[out])
- tot_sigma2s = total_sigma2s[out][non_nan_indices][:nout]
-
- # Covariance Matrix
- covMatrix_data = np.diag(tot_sigma2s)
-
- for i, sample in enumerate(samples):
-
- # Simulation run
- y_m = model_outputs[out][i]
-
- # Surrogate prediction
- y_m_hat = OutputRS[out][i]
-
- # CovMatrix with the surrogate error
- covMatrix = np.eye(len(y_m)) * 1/(2*np.pi)
-
- # Select the data points to compare
- try:
- indices = self.selected_indices[out]
- except:
- indices = list(range(nout))
- covMatrix = np.diag(covMatrix[indices, indices])
- covMatrix_data = np.diag(covMatrix_data[indices, indices])
-
- # Compute likelilhood output vs data
- logLik_data[i] += self._logpdf(
- y_m_hat[indices], data[indices],
- covMatrix_data
- )
-
- # Compute likelilhood output vs surrogate
- logLik_model[i] += self._logpdf(
- y_m_hat[indices], y_m[indices],
- covMatrix
- )
-
- # Weight
- logLik_data -= logBME
- weights = np.mean(np.exp(logLik_model+logLik_data))
-
- return np.log(weights)
-
- # -------------------------------------------------------------------------
- def _rejection_sampling(self):
- """
- Performs rejection sampling to update the prior distribution on the
- input parameters.
-
- Returns
- -------
- posterior : pandas.dataframe
- Posterior samples of the input parameters.
-
- """
-
- MetaModel = self.MetaModel
- try:
- sigma2_prior = self.Discrepancy.sigma2_prior
- except:
- sigma2_prior = None
-
- # Check if the discrepancy is defined as a distribution:
- samples = self.samples
-
- if sigma2_prior is not None:
- samples = np.hstack((samples, sigma2_prior))
-
- # Take the first column of Likelihoods (Observation data without noise)
- if self.just_analysis or self.bayes_loocv:
- index = self.n_tot_measurement-1
- likelihoods = np.exp(self.log_likes[:, index], dtype=np.longdouble)#np.float128)
- else:
- likelihoods = np.exp(self.log_likes[:, 0], dtype=np.longdouble)#np.float128)
-
- n_samples = len(likelihoods)
- norm_ikelihoods = likelihoods / np.max(likelihoods)
-
- # Normalize based on min if all Likelihoods are zero
- if all(likelihoods == 0.0):
- likelihoods = self.log_likes[:, 0]
- norm_ikelihoods = likelihoods / np.min(likelihoods)
-
- # Random numbers between 0 and 1
- unif = np.random.rand(1, n_samples)[0]
-
- # Reject the poorly performed prior
- accepted_samples = samples[norm_ikelihoods >= unif]
-
- # Output the Posterior
- par_names = self.engine.ExpDesign.par_names
- if sigma2_prior is not None:
- for name in self.Discrepancy.name:
- par_names.append(name)
-
- return pd.DataFrame(accepted_samples, columns=sigma2_prior)
-
- # -------------------------------------------------------------------------
- def _posterior_predictive(self):
- """
- Stores the prior- and posterior predictive samples, i.e. model
- evaluations using the samples, into hdf5 files.
-
- priorPredictive.hdf5 : Prior predictive samples.
- postPredictive_wo_noise.hdf5 : Posterior predictive samples without
- the additive noise.
- postPredictive.hdf5 : Posterior predictive samples with the additive
- noise.
-
- Returns
- -------
- None.
-
- """
-
- MetaModel = self.MetaModel
- Model = self.engine.Model
-
- # Make a directory to save the prior/posterior predictive
- out_dir = f'Outputs_Bayes_{Model.name}_{self.name}'
- os.makedirs(out_dir, exist_ok=True)
-
- # Read observation data and perturb it if requested
- if self.measured_data is None:
- self.measured_data = Model.read_observation(case=self.name)
-
- if not isinstance(self.measured_data, pd.DataFrame):
- self.measured_data = pd.DataFrame(self.measured_data)
-
- # X_values
- x_values = self.engine.ExpDesign.x_values
-
- try:
- sigma2_prior = self.Discrepancy.sigma2_prior
- except:
- sigma2_prior = None
-
- # Extract posterior samples
- posterior_df = self.posterior_df
-
- # Take care of the sigma2
- if sigma2_prior is not None:
- try:
- sigma2s = posterior_df[self.Discrepancy.name].values
- posterior_df = posterior_df.drop(
- labels=self.Discrepancy.name, axis=1
- )
- except:
- sigma2s = self.sigma2s
-
- # Posterior predictive
- if self.emulator:
- if self.inference_method == 'rejection':
- prior_pred = self.__mean_pce_prior_pred
- if self.name.lower() != 'calib':
- post_pred = self.__mean_pce_prior_pred
- post_pred_std = self._std_pce_prior_pred
- else:
- post_pred, post_pred_std = MetaModel.eval_metamodel(
- samples=posterior_df.values
- )
-
- else:
- if self.inference_method == 'rejection':
- prior_pred = self.__model_prior_pred
- if self.name.lower() != 'calib':
- post_pred = self.__mean_pce_prior_pred,
- post_pred_std = self._std_pce_prior_pred
- else:
- post_pred = self._eval_model(
- samples=posterior_df.values, key='PostPred'
- )
- # Correct the predictions with Model discrepancy
- if hasattr(self, 'error_model') and self.error_model:
- y_hat, y_std = self.error_MetaModel.eval_model_error(
- self.bias_inputs, post_pred
- )
- post_pred, post_pred_std = y_hat, y_std
-
- # Add discrepancy from likelihood Sample to the current posterior runs
- total_sigma2 = self.Discrepancy.total_sigma2
- post_pred_withnoise = copy.deepcopy(post_pred)
- for varIdx, var in enumerate(Model.Output.names):
- for i in range(len(post_pred[var])):
- pred = post_pred[var][i]
-
- # Known sigma2s
- clean_sigma2 = total_sigma2[var][~np.isnan(total_sigma2[var])]
- tot_sigma2 = clean_sigma2[:len(pred)]
- cov = np.diag(tot_sigma2)
-
- # Check the type error term
- if sigma2_prior is not None:
- # Inferred sigma2s
- if hasattr(self, 'bias_inputs') and \
- not hasattr(self, 'error_model'):
- # TODO: Infer a Bias model usig GPR
- bias_inputs = np.hstack((
- self.bias_inputs[var], pred.reshape(-1, 1)))
- params = sigma2s[i, varIdx*3:(varIdx+1)*3]
- cov = self._kernel_rbf(bias_inputs, params)
- else:
- # Infer equal sigma2s
- try:
- sigma2 = sigma2s[i, varIdx]
- except TypeError:
- sigma2 = 0.0
-
- # Convert biasSigma2s to a covMatrix
- cov += sigma2 * np.eye(len(pred))
-
- if self.emulator:
- if hasattr(MetaModel, 'rmse') and \
- MetaModel.rmse is not None:
- stdPCE = MetaModel.rmse[var]
- else:
- stdPCE = post_pred_std[var][i]
- # Expected value of variance (Assump: i.i.d stds)
- cov += np.diag(stdPCE**2)
-
- # Sample a multivariate normal distribution with mean of
- # prediction and variance of cov
- post_pred_withnoise[var][i] = np.random.multivariate_normal(
- pred, cov, 1
- )
-
- # ----- Prior Predictive -----
- if self.inference_method.lower() == 'rejection':
- # Create hdf5 metadata
- hdf5file = f'{out_dir}/priorPredictive.hdf5'
- hdf5_exist = os.path.exists(hdf5file)
- if hdf5_exist:
- os.remove(hdf5file)
- file = h5py.File(hdf5file, 'a')
-
- # Store x_values
- if type(x_values) is dict:
- grp_x_values = file.create_group("x_values/")
- for varIdx, var in enumerate(Model.Output.names):
- grp_x_values.create_dataset(var, data=x_values[var])
- else:
- file.create_dataset("x_values", data=x_values)
-
- # Store posterior predictive
- grpY = file.create_group("EDY/")
- for varIdx, var in enumerate(Model.Output.names):
- grpY.create_dataset(var, data=prior_pred[var])
-
- # ----- Posterior Predictive only model evaluations -----
- # Create hdf5 metadata
- hdf5file = out_dir+'/postPredictive_wo_noise.hdf5'
- hdf5_exist = os.path.exists(hdf5file)
- if hdf5_exist:
- os.remove(hdf5file)
- file = h5py.File(hdf5file, 'a')
-
- # Store x_values
- if type(x_values) is dict:
- grp_x_values = file.create_group("x_values/")
- for varIdx, var in enumerate(Model.Output.names):
- grp_x_values.create_dataset(var, data=x_values[var])
- else:
- file.create_dataset("x_values", data=x_values)
-
- # Store posterior predictive
- grpY = file.create_group("EDY/")
- for varIdx, var in enumerate(Model.Output.names):
- grpY.create_dataset(var, data=post_pred[var])
-
- # ----- Posterior Predictive with noise -----
- # Create hdf5 metadata
- hdf5file = out_dir+'/postPredictive.hdf5'
- hdf5_exist = os.path.exists(hdf5file)
- if hdf5_exist:
- os.remove(hdf5file)
- file = h5py.File(hdf5file, 'a')
-
- # Store x_values
- if type(x_values) is dict:
- grp_x_values = file.create_group("x_values/")
- for varIdx, var in enumerate(Model.Output.names):
- grp_x_values.create_dataset(var, data=x_values[var])
- else:
- file.create_dataset("x_values", data=x_values)
-
- # Store posterior predictive
- grpY = file.create_group("EDY/")
- for varIdx, var in enumerate(Model.Output.names):
- grpY.create_dataset(var, data=post_pred_withnoise[var])
-
- return
-
- # -------------------------------------------------------------------------
- def _plot_max_a_posteriori(self):
- """
- Plots the response of the model output against that of the metamodel at
- the maximum a posteriori sample (mean or mode of posterior.)
-
- Returns
- -------
- None.
-
- """
-
- MetaModel = self.MetaModel
- Model = self.engine.Model
- out_dir = f'Outputs_Bayes_{Model.name}_{self.name}'
- opt_sigma = self.Discrepancy.opt_sigma
-
- # -------- Find MAP and run MetaModel and origModel --------
- # Compute the MAP
- if self.max_a_posteriori.lower() == 'mean':
- if opt_sigma == "B":
- Posterior_df = self.posterior_df.values
- else:
- Posterior_df = self.posterior_df.values[:, :-Model.n_outputs]
- map_theta = Posterior_df.mean(axis=0).reshape(
- (1, MetaModel.n_params))
- else:
- map_theta = stats.mode(Posterior_df.values, axis=0)[0]
- # Prin report
- print("\nPoint estimator:\n", map_theta[0])
-
- # Run the models for MAP
- # MetaModel
- map_metamodel_mean, map_metamodel_std = MetaModel.eval_metamodel(
- samples=map_theta)
- self.map_metamodel_mean = map_metamodel_mean
- self.map_metamodel_std = map_metamodel_std
-
- # origModel
- map_orig_model = self._eval_model(samples=map_theta)
- self.map_orig_model = map_orig_model
-
- # Extract slicing index
- x_values = map_orig_model['x_values']
-
- # List of markers and colors
- Color = ['k', 'b', 'g', 'r']
- Marker = 'x'
-
- # Create a PdfPages object
- pdf = PdfPages(f'./{out_dir}MAP_PCE_vs_Model_{self.name}.pdf')
- fig = plt.figure()
- for i, key in enumerate(Model.Output.names):
-
- y_val = map_orig_model[key]
- y_pce_val = map_metamodel_mean[key]
- y_pce_val_std = map_metamodel_std[key]
-
- plt.plot(x_values, y_val, color=Color[i], marker=Marker,
- lw=2.0, label='$Y_{MAP}^{M}$')
-
- plt.plot(
- x_values, y_pce_val[i], color=Color[i], lw=2.0,
- marker=Marker, linestyle='--', label='$Y_{MAP}^{PCE}$'
- )
- # plot the confidence interval
- plt.fill_between(
- x_values, y_pce_val[i] - 1.96*y_pce_val_std[i],
- y_pce_val[i] + 1.96*y_pce_val_std[i],
- color=Color[i], alpha=0.15
- )
-
- # Calculate the adjusted R_squared and RMSE
- R2 = r2_score(y_pce_val.reshape(-1, 1), y_val.reshape(-1, 1))
- rmse = np.sqrt(mean_squared_error(y_pce_val, y_val))
-
- plt.ylabel(key)
- plt.xlabel("Time [s]")
- plt.title(f'Model vs MetaModel {key}')
-
- ax = fig.axes[0]
- leg = ax.legend(loc='best', frameon=True)
- fig.canvas.draw()
- p = leg.get_window_extent().inverse_transformed(ax.transAxes)
- ax.text(
- p.p0[1]-0.05, p.p1[1]-0.25,
- f'RMSE = {rmse:.3f}\n$R^2$ = {R2:.3f}',
- transform=ax.transAxes, color='black',
- bbox=dict(facecolor='none', edgecolor='black',
- boxstyle='round,pad=1'))
-
- plt.show()
-
- # save the current figure
- pdf.savefig(fig, bbox_inches='tight')
-
- # Destroy the current plot
- plt.clf()
-
- pdf.close()
-
- # -------------------------------------------------------------------------
- def _plot_post_predictive(self):
- """
- Plots the posterior predictives against the observation data.
-
- Returns
- -------
- None.
-
- """
-
- Model = self.engine.Model
- out_dir = f'Outputs_Bayes_{Model.name}_{self.name}'
- # Plot the posterior predictive
- for out_idx, out_name in enumerate(Model.Output.names):
- fig, ax = plt.subplots()
- with sns.axes_style("ticks"):
- x_key = list(self.measured_data)[0]
-
- # --- Read prior and posterior predictive ---
- if self.inference_method == 'rejection' and \
- self.name.lower() != 'valid':
- # --- Prior ---
- # Load posterior predictive
- f = h5py.File(
- f'{out_dir}/priorPredictive.hdf5', 'r+')
-
- try:
- x_coords = np.array(f[f"x_values/{out_name}"])
- except:
- x_coords = np.array(f["x_values"])
-
- X_values = np.repeat(x_coords, 10000)
-
- prior_pred_df = {}
- prior_pred_df[x_key] = X_values
- prior_pred_df[out_name] = np.array(
- f[f"EDY/{out_name}"])[:10000].flatten('F')
- prior_pred_df = pd.DataFrame(prior_pred_df)
-
- tags_post = ['prior'] * len(prior_pred_df)
- prior_pred_df.insert(
- len(prior_pred_df.columns), "Tags", tags_post,
- True)
- f.close()
-
- # --- Posterior ---
- f = h5py.File(f"{out_dir}/postPredictive.hdf5", 'r+')
-
- X_values = np.repeat(
- x_coords, np.array(f[f"EDY/{out_name}"]).shape[0])
-
- post_pred_df = {}
- post_pred_df[x_key] = X_values
- post_pred_df[out_name] = np.array(
- f[f"EDY/{out_name}"]).flatten('F')
-
- post_pred_df = pd.DataFrame(post_pred_df)
-
- tags_post = ['posterior'] * len(post_pred_df)
- post_pred_df.insert(
- len(post_pred_df.columns), "Tags", tags_post, True)
- f.close()
- # Concatenate two dataframes based on x_values
- frames = [prior_pred_df, post_pred_df]
- all_pred_df = pd.concat(frames)
-
- # --- Plot posterior predictive ---
- sns.violinplot(
- x_key, y=out_name, data=all_pred_df, hue="Tags",
- legend=False, ax=ax, split=True, inner=None,
- color=".8")
-
- # --- Plot Data ---
- # Find the x,y coordinates for each point
- x_coords = np.arange(x_coords.shape[0])
- first_header = list(self.measured_data)[0]
- obs_data = self.measured_data.round({first_header: 6})
- sns.pointplot(
- x=first_header, y=out_name, color='g', markers='x',
- linestyles='', capsize=16, data=obs_data, ax=ax)
-
- ax.errorbar(
- x_coords, obs_data[out_name].values,
- yerr=1.96*self.measurement_error[out_name],
- ecolor='g', fmt=' ', zorder=-1)
-
- # Add labels to the legend
- handles, labels = ax.get_legend_handles_labels()
- labels.append('Data')
-
- data_marker = mlines.Line2D(
- [], [], color='lime', marker='+', linestyle='None',
- markersize=10)
- handles.append(data_marker)
-
- # Add legend
- ax.legend(handles=handles, labels=labels, loc='best',
- fontsize='large', frameon=True)
-
- else:
- # Load posterior predictive
- f = h5py.File(f"{out_dir}/postPredictive.hdf5", 'r+')
-
- try:
- x_coords = np.array(f[f"x_values/{out_name}"])
- except:
- x_coords = np.array(f["x_values"])
-
- mu = np.mean(np.array(f[f"EDY/{out_name}"]), axis=0)
- std = np.std(np.array(f[f"EDY/{out_name}"]), axis=0)
-
- # --- Plot posterior predictive ---
- plt.plot(
- x_coords, mu, marker='o', color='b',
- label='Mean Post. Predictive')
- plt.fill_between(
- x_coords, mu-1.96*std, mu+1.96*std, color='b',
- alpha=0.15)
-
- # --- Plot Data ---
- ax.plot(
- x_coords, self.measured_data[out_name].values,
- 'ko', label='data', markeredgecolor='w')
-
- # --- Plot ExpDesign ---
- orig_ED_Y = self.engine.ExpDesign.Y[out_name]
- for output in orig_ED_Y:
- plt.plot(
- x_coords, output, color='grey', alpha=0.15
- )
-
- # Add labels for axes
- plt.xlabel('Time [s]')
- plt.ylabel(out_name)
-
- # Add labels to the legend
- handles, labels = ax.get_legend_handles_labels()
-
- patch = Patch(color='b', alpha=0.15)
- handles.insert(1, patch)
- labels.insert(1, '95 $\\%$ CI')
-
- # Add legend
- ax.legend(handles=handles, labels=labels, loc='best',
- frameon=True)
-
- # Save figure in pdf format
- if self.emulator:
- plotname = f'/Post_Prior_Perd_{Model.name}_emulator'
- else:
- plotname = f'/Post_Prior_Perd_{Model.name}'
-
- fig.savefig(f'./{out_dir}{plotname}_{out_name}.pdf',
- bbox_inches='tight')
diff --git a/examples/model-comparison/bayesvalidrox/bayes_inference/bayes_model_comparison.py b/examples/model-comparison/bayesvalidrox/bayes_inference/bayes_model_comparison.py
deleted file mode 100644
index 828613556e90ec0c529b91f2592eec148c98136b..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/bayes_inference/bayes_model_comparison.py
+++ /dev/null
@@ -1,654 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-import numpy as np
-import os
-from scipy import stats
-import seaborn as sns
-import matplotlib.patches as patches
-import matplotlib.colors as mcolors
-import matplotlib.pylab as plt
-from .bayes_inference import BayesInference
-
-# Load the mplstyle
-plt.style.use(os.path.join(os.path.split(__file__)[0],
- '../', 'bayesvalidrox.mplstyle'))
-
-
-class BayesModelComparison:
- """
- A class to perform Bayesian Analysis.
-
-
- Attributes
- ----------
- justifiability : bool, optional
- Whether to perform the justifiability analysis. The default is
- `True`.
- perturbed_data : array of shape (n_bootstrap_itrs, n_obs), optional
- User defined perturbed data. The default is `None`.
- n_bootstarp : int
- Number of bootstrap iteration. The default is `1000`.
- data_noise_level : float
- A noise level to perturb the data set. The default is `0.01`.
- just_n_meas : int
- Number of measurements considered for visualization of the
- justifiability results.
-
- """
-
- def __init__(self, justifiability=True, perturbed_data=None,
- n_bootstarp=1000, data_noise_level=0.01, just_n_meas=2):
-
- self.justifiability = justifiability
- self.perturbed_data = perturbed_data
- self.n_bootstarp = n_bootstarp
- self.data_noise_level = data_noise_level
- self.just_n_meas = just_n_meas
-
- # --------------------------------------------------------------------------
- def create_model_comparison(self, model_dict, opts_dict):
- """
- Starts the two-stage model comparison.
- Stage I: Compare models using Bayes factors.
- Stage II: Compare models via justifiability analysis.
-
- Parameters
- ----------
- model_dict : dict
- A dictionary including the metamodels.
- opts_dict : dict
- A dictionary given the `BayesInference` options.
-
- Example:
-
- >>> opts_bootstrap = {
- "bootstrap": True,
- "n_samples": 10000,
- "Discrepancy": DiscrepancyOpts,
- "emulator": True,
- "plot_post_pred": True
- }
-
- Returns
- -------
- output : dict
- A dictionary containing the objects and the model weights for the
- comparison using Bayes factors and justifiability analysis.
-
- """
-
- # Bayes factor
- bayes_dict_bf, model_weights_dict_bf = self.compare_models(
- model_dict, opts_dict
- )
-
- output = {
- 'Bayes objects BF': bayes_dict_bf,
- 'Model weights BF': model_weights_dict_bf
- }
-
- # Justifiability analysis
- if self.justifiability:
- bayes_dict_ja, model_weights_dict_ja = self.compare_models(
- model_dict, opts_dict, justifiability=True
- )
-
- output['Bayes objects JA'] = bayes_dict_ja
- output['Model weights JA'] = model_weights_dict_ja
-
- return output
-
- # --------------------------------------------------------------------------
- def compare_models(self, model_dict, opts_dict, justifiability=False):
- """
- Passes the options to instantiates the BayesInference class for each
- model and passes the options from `opts_dict`. Then, it starts the
- computations.
- It also creates a folder and saves the diagrams, e.g., Bayes factor
- plot, confusion matrix, etc.
-
- Parameters
- ----------
- model_dict : dict
- A dictionary including the metamodels.
- opts_dict : dict
- A dictionary given the `BayesInference` options.
- justifiability : bool, optional
- Whether to perform the justifiability analysis. The default is
- `False`.
-
- Returns
- -------
- bayes_dict : dict
- A dictionary with `BayesInference` objects.
- model_weights_dict : dict
- A dictionary containing the model weights.
-
- """
-
- if not isinstance(model_dict, dict):
- raise Exception("To run model comparsion, you need to pass a "
- "dictionary of models.")
-
- # Extract model names
- self.model_names = [*model_dict]
-
- # Compute total number of the measurement points
- Engine = list(model_dict.items())[0][1]
- Engine.Model.read_observation()
- self.n_meas = Engine.Model.n_obs
-
- # ----- Generate data -----
- # Find n_bootstrap
- if self.perturbed_data is None:
- n_bootstarp = self.n_bootstarp
- else:
- n_bootstarp = self.perturbed_data.shape[0]
-
- # Create dataset
- justData = self.generate_dataset(
- model_dict, justifiability, n_bootstarp=n_bootstarp)
-
- # Run create Interface for each model
- bayes_dict = {}
- for model in model_dict.keys():
- print("-"*20)
- print("Bayesian inference of {}.\n".format(model))
-
- BayesOpts = BayesInference(model_dict[model])
-
- # Set BayesInference options
- for key, value in opts_dict.items():
- if key in BayesOpts.__dict__.keys():
- if key == "Discrepancy" and isinstance(value, dict):
- setattr(BayesOpts, key, value[model])
- else:
- setattr(BayesOpts, key, value)
-
- # Pass justifiability data as perturbed data
- BayesOpts.perturbed_data = justData
- BayesOpts.just_analysis = justifiability
-
- bayes_dict[model] = BayesOpts.create_inference()
- print("-"*20)
-
- # Compute model weights
- BME_Dict = dict()
- for modelName, bayesObj in bayes_dict.items():
- BME_Dict[modelName] = np.exp(bayesObj.log_BME, dtype=np.longdouble)#float128)
-
- # BME correction in BayesInference class
- model_weights = self.cal_model_weight(
- BME_Dict, justifiability, n_bootstarp=n_bootstarp)
-
- # Plot model weights
- if justifiability:
- model_names = self.model_names
- model_names.insert(0, 'Observation')
-
- # Split the model weights and save in a dict
- list_ModelWeights = np.split(
- model_weights, model_weights.shape[1]/self.n_meas, axis=1)
- model_weights_dict = {key: weights for key, weights in
- zip(model_names, list_ModelWeights)}
-
- #self.plot_just_analysis(model_weights_dict)
- else:
- # Create box plot for model weights
- self.plot_model_weights(model_weights, 'model_weights')
-
- # Create kde plot for bayes factors
- self.plot_bayes_factor(BME_Dict, 'kde_plot')
-
- # Store model weights in a dict
- model_weights_dict = {key: weights for key, weights in
- zip(self.model_names, model_weights)}
-
- return bayes_dict, model_weights_dict
-
- # -------------------------------------------------------------------------
- def generate_dataset(self, model_dict, justifiability=False,
- n_bootstarp=1):
- """
- Generates the perturbed data set for the Bayes factor calculations and
- the data set for the justifiability analysis.
-
- Parameters
- ----------
- model_dict : dict
- A dictionary including the metamodels.
- bool, optional
- Whether to perform the justifiability analysis. The default is
- `False`.
- n_bootstarp : int, optional
- Number of bootstrap iterations. The default is `1`.
-
- Returns
- -------
- all_just_data: array
- Created data set.
-
- """
- # Compute some variables
- all_just_data = []
- Engine = list(model_dict.items())[0][1]
- out_names = Engine.Model.Output.names
-
- # Perturb observations for Bayes Factor
- if self.perturbed_data is None:
- self.perturbed_data = self.__perturb_data(
- Engine.Model.observations, out_names, n_bootstarp,
- noise_level=self.data_noise_level)
-
- # Only for Bayes Factor
- if not justifiability:
- return self.perturbed_data
-
- # Evaluate metamodel
- runs = {}
- for key, metaModel in model_dict.items():
- y_hat, _ = metaModel.eval_metamodel(nsamples=n_bootstarp)
- runs[key] = y_hat
-
- # Generate data
- for i in range(n_bootstarp):
- y_data = self.perturbed_data[i].reshape(1, -1)
- justData = np.tril(np.repeat(y_data, y_data.shape[1], axis=0))
- # Use surrogate runs for data-generating process
- for key, metaModel in model_dict.items():
- model_data = np.array(
- [runs[key][out][i] for out in out_names]).reshape(y_data.shape)
- justData = np.vstack((
- justData,
- np.tril(np.repeat(model_data, model_data.shape[1], axis=0))
- ))
- # Save in a list
- all_just_data.append(justData)
-
- # Squeeze the array
- all_just_data = np.array(all_just_data).transpose(1, 0, 2).reshape(
- -1, np.array(all_just_data).shape[2]
- )
-
- return all_just_data
-
- # -------------------------------------------------------------------------
- def __perturb_data(self, data, output_names, n_bootstrap, noise_level):
- """
- Returns an array with n_bootstrap_itrs rowsof perturbed data.
- The first row includes the original observation data.
- If `self.bayes_loocv` is True, a 2d-array will be returned with
- repeated rows and zero diagonal entries.
-
- Parameters
- ----------
- data : pandas DataFrame
- Observation data.
- output_names : list
- List of the output names.
-
- Returns
- -------
- final_data : array
- Perturbed data set.
-
- """
- obs_data = data[output_names].values
- n_measurement, n_outs = obs_data.shape
- n_tot_measurement = obs_data[~np.isnan(obs_data)].shape[0]
- final_data = np.zeros(
- (n_bootstrap, n_tot_measurement)
- )
- final_data[0] = obs_data.T[~np.isnan(obs_data.T)]
- for itrIdx in range(1, n_bootstrap):
- data = np.zeros((n_measurement, n_outs))
- for idx in range(len(output_names)):
- std = np.nanstd(obs_data[:, idx])
- if std == 0:
- std = 0.001
- noise = std * noise_level
- data[:, idx] = np.add(
- obs_data[:, idx],
- np.random.normal(0, 1, obs_data.shape[0]) * noise,
- )
-
- final_data[itrIdx] = data.T[~np.isnan(data.T)]
-
- return final_data
-
- # -------------------------------------------------------------------------
- def cal_model_weight(self, BME_Dict, justifiability=False, n_bootstarp=1):
- """
- Normalize the BME (Asumption: Model Prior weights are equal for models)
-
- Parameters
- ----------
- BME_Dict : dict
- A dictionary containing the BME values.
-
- Returns
- -------
- model_weights : array
- Model weights.
-
- """
- # Stack the BME values for all models
- all_BME = np.vstack(list(BME_Dict.values()))
-
- if justifiability:
- # Compute expected log_BME for justifiabiliy analysis
- all_BME = all_BME.reshape(
- all_BME.shape[0], -1, n_bootstarp).mean(axis=2)
-
- # Model weights
- model_weights = np.divide(all_BME, np.nansum(all_BME, axis=0))
-
- return model_weights
-
- # -------------------------------------------------------------------------
- def plot_just_analysis(self, model_weights_dict):
- """
- Visualizes the confusion matrix and the model wights for the
- justifiability analysis.
-
- Parameters
- ----------
- model_weights_dict : dict
- Model weights.
-
- Returns
- -------
- None.
-
- """
-
- directory = 'Outputs_Comparison/'
- os.makedirs(directory, exist_ok=True)
- Color = [*mcolors.TABLEAU_COLORS]
- names = [*model_weights_dict]
-
- model_names = [model.replace('_', '$-$') for model in self.model_names]
- for name in names:
- fig, ax = plt.subplots()
- for i, model in enumerate(model_names[1:]):
- plt.plot(list(range(1, self.n_meas+1)),
- model_weights_dict[name][i],
- color=Color[i], marker='o',
- ms=10, linewidth=2, label=model
- )
-
- plt.title(f"Data generated by: {name.replace('_', '$-$')}")
- plt.ylabel("Weights")
- plt.xlabel("No. of measurement points")
- ax.set_xticks(list(range(1, self.n_meas+1)))
- plt.legend(loc="best")
- fig.savefig(
- f'{directory}modelWeights_{name}.svg', bbox_inches='tight'
- )
- plt.close()
-
- # Confusion matrix for some measurement points
- epsilon = 1 if self.just_n_meas != 1 else 0
- for index in range(0, self.n_meas+epsilon, self.just_n_meas):
- weights = np.array(
- [model_weights_dict[key][:, index] for key in model_weights_dict]
- )
- g = sns.heatmap(
- weights.T, annot=True, cmap='Blues', xticklabels=model_names,
- yticklabels=model_names[1:], annot_kws={"size": 24}
- )
-
- # x axis on top
- g.xaxis.tick_top()
- g.xaxis.set_label_position('top')
- g.set_xlabel(r"\textbf{Data generated by:}", labelpad=15)
- g.set_ylabel(r"\textbf{Model weight for:}", labelpad=15)
- g.figure.savefig(
- f"{directory}confusionMatrix_ND_{index+1}.pdf",
- bbox_inches='tight'
- )
- plt.close()
-
- # -------------------------------------------------------------------------
- def plot_model_weights(self, model_weights, plot_name):
- """
- Visualizes the model weights resulting from BMS via the observation
- data.
-
- Parameters
- ----------
- model_weights : array
- Model weights.
- plot_name : str
- Plot name.
-
- Returns
- -------
- None.
-
- """
- font_size = 40
- # mkdir for plots
- directory = 'Outputs_Comparison/'
- os.makedirs(directory, exist_ok=True)
-
- # Create figure
- fig, ax = plt.subplots()
-
- # Filter data using np.isnan
- mask = ~np.isnan(model_weights.T)
- filtered_data = [d[m] for d, m in zip(model_weights, mask.T)]
-
- # Create the boxplot
- bp = ax.boxplot(filtered_data, patch_artist=True, showfliers=False)
-
- # change outline color, fill color and linewidth of the boxes
- for box in bp['boxes']:
- # change outline color
- box.set(color='#7570b3', linewidth=4)
- # change fill color
- box.set(facecolor='#1b9e77')
-
- # change color and linewidth of the whiskers
- for whisker in bp['whiskers']:
- whisker.set(color='#7570b3', linewidth=2)
-
- # change color and linewidth of the caps
- for cap in bp['caps']:
- cap.set(color='#7570b3', linewidth=2)
-
- # change color and linewidth of the medians
- for median in bp['medians']:
- median.set(color='#b2df8a', linewidth=2)
-
- # change the style of fliers and their fill
- # for flier in bp['fliers']:
- # flier.set(marker='o', color='#e7298a', alpha=0.75)
-
- # Custom x-axis labels
- model_names = [model.replace('_', '$-$') for model in self.model_names]
- ax.set_xticklabels(model_names)
-
- ax.set_ylabel('Weight', fontsize=font_size)
-
- # Title
- plt.title('Posterior Model Weights')
-
- # Set y lim
- ax.set_ylim((-0.05, 1.05))
-
- # Set size of the ticks
- for t in ax.get_xticklabels():
- t.set_fontsize(font_size)
- for t in ax.get_yticklabels():
- t.set_fontsize(font_size)
-
- # Save the figure
- fig.savefig(
- f'./{directory}{plot_name}.pdf', bbox_inches='tight'
- )
-
- plt.close()
-
- # -------------------------------------------------------------------------
- def plot_bayes_factor(self, BME_Dict, plot_name=''):
- """
- Plots the Bayes factor distibutions in a :math:`N_m \\times N_m`
- matrix, where :math:`N_m` is the number of the models.
-
- Parameters
- ----------
- BME_Dict : dict
- A dictionary containing the BME values of the models.
- plot_name : str, optional
- Plot name. The default is ''.
-
- Returns
- -------
- None.
-
- """
-
- font_size = 40
-
- # mkdir for plots
- directory = 'Outputs_Comparison/'
- os.makedirs(directory, exist_ok=True)
-
- Colors = ["blue", "green", "gray", "brown"]
-
- model_names = list(BME_Dict.keys())
- nModels = len(model_names)
-
- # Plots
- fig, axes = plt.subplots(
- nrows=nModels, ncols=nModels, sharex=True, sharey=True
- )
-
- for i, key_i in enumerate(model_names):
-
- for j, key_j in enumerate(model_names):
- ax = axes[i, j]
- # Set size of the ticks
- for t in ax.get_xticklabels():
- t.set_fontsize(font_size)
- for t in ax.get_yticklabels():
- t.set_fontsize(font_size)
-
- if j != i:
-
- # Null hypothesis: key_j is the better model
- BayesFactor = np.log10(
- np.divide(BME_Dict[key_i], BME_Dict[key_j])
- )
-
- # sns.kdeplot(BayesFactor, ax=ax, color=Colors[i], shade=True)
- # sns.histplot(BayesFactor, ax=ax, stat="probability",
- # kde=True, element='step',
- # color=Colors[j])
-
- # taken from seaborn's source code (utils.py and
- # distributions.py)
- def seaborn_kde_support(data, bw, gridsize, cut, clip):
- if clip is None:
- clip = (-np.inf, np.inf)
- support_min = max(data.min() - bw * cut, clip[0])
- support_max = min(data.max() + bw * cut, clip[1])
- return np.linspace(support_min, support_max, gridsize)
-
- kde_estim = stats.gaussian_kde(
- BayesFactor, bw_method='scott'
- )
-
- # manual linearization of data
- # linearized = np.linspace(
- # quotient.min(), quotient.max(), num=500)
-
- # or better: mimic seaborn's internal stuff
- bw = kde_estim.scotts_factor() * np.std(BayesFactor)
- linearized = seaborn_kde_support(
- BayesFactor, bw, 100, 3, None)
-
- # computes values of the estimated function on the
- # estimated linearized inputs
- Z = kde_estim.evaluate(linearized)
-
- # https://stackoverflow.com/questions/29661574/normalize-
- # numpy-array-columns-in-python
- def normalize(x):
- return (x - x.min(0)) / x.ptp(0)
-
- # normalize so it is between 0;1
- Z2 = normalize(Z)
- ax.plot(linearized, Z2, "-", color=Colors[i], linewidth=4)
- ax.fill_between(
- linearized, 0, Z2, color=Colors[i], alpha=0.25
- )
-
- # Draw BF significant levels according to Jeffreys 1961
- # Strong evidence for both models
- ax.axvline(
- x=np.log10(3), ymin=0, linewidth=4, color='dimgrey'
- )
- # Strong evidence for one model
- ax.axvline(
- x=np.log10(10), ymin=0, linewidth=4, color='orange'
- )
- # Decisive evidence for one model
- ax.axvline(
- x=np.log10(100), ymin=0, linewidth=4, color='r'
- )
-
- # legend
- BF_label = key_i.replace('_', '$-$') + \
- '/' + key_j.replace('_', '$-$')
- legend_elements = [
- patches.Patch(facecolor=Colors[i], edgecolor=Colors[i],
- label=f'BF({BF_label})')
- ]
- ax.legend(
- loc='upper left', handles=legend_elements,
- fontsize=font_size-(nModels+1)*5
- )
-
- elif j == i:
- # build a rectangle in axes coords
- left, width = 0, 1
- bottom, height = 0, 1
-
- # axes coordinates are 0,0 is bottom left and 1,1 is upper
- # right
- p = patches.Rectangle(
- (left, bottom), width, height, color='white',
- fill=True, transform=ax.transAxes, clip_on=False
- )
- ax.grid(False)
- ax.add_patch(p)
- # ax.text(0.5*(left+right), 0.5*(bottom+top), key_i,
- fsize = font_size+20 if nModels < 4 else font_size
- ax.text(0.5, 0.5, key_i.replace('_', '$-$'),
- horizontalalignment='center',
- verticalalignment='center',
- fontsize=fsize, color=Colors[i],
- transform=ax.transAxes)
-
- # Defining custom 'ylim' values.
- custom_ylim = (0, 1.05)
-
- # Setting the values for all axes.
- plt.setp(axes, ylim=custom_ylim)
-
- # set labels
- for i in range(nModels):
- axes[-1, i].set_xlabel('log$_{10}$(BF)', fontsize=font_size)
- axes[i, 0].set_ylabel('Probability', fontsize=font_size)
-
- # Adjust subplots
- plt.subplots_adjust(wspace=0.2, hspace=0.1)
-
- plt.savefig(
- f'./{directory}Bayes_Factor{plot_name}.pdf', bbox_inches='tight'
- )
-
- plt.close()
diff --git a/examples/model-comparison/bayesvalidrox/bayes_inference/discrepancy.py b/examples/model-comparison/bayesvalidrox/bayes_inference/discrepancy.py
deleted file mode 100644
index fff32a2500ae20b3667c7b0ec2cc85c1da614688..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/bayes_inference/discrepancy.py
+++ /dev/null
@@ -1,106 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-import scipy.stats as stats
-from bayesvalidrox.surrogate_models.exp_designs import ExpDesigns
-
-
-class Discrepancy:
- """
- Discrepancy class for Bayesian inference method.
- We define the reference or reality to be equal to what we can model and a
- descripancy term \\( \\epsilon \\). We consider the followin format:
-
- $$\\textbf{y}_{\\text{reality}} = \\mathcal{M}(\\theta) + \\epsilon,$$
-
- where \\( \\epsilon \\in R^{N_{out}} \\) represents the the effects of
- measurement error and model inaccuracy. For simplicity, it can be defined
- as an additive Gaussian disrepancy with zeromean and given covariance
- matrix \\( \\Sigma \\):
-
- $$\\epsilon \\sim \\mathcal{N}(\\epsilon|0, \\Sigma). $$
-
- In the context of model inversion or calibration, an observation point
- \\( \\textbf{y}_i \\in \\mathcal{y} \\) is a realization of a Gaussian
- distribution with mean value of \\(\\mathcal{M}(\\theta) \\) and covariance
- matrix of \\( \\Sigma \\).
-
- $$ p(\\textbf{y}|\\theta) = \\mathcal{N}(\\textbf{y}|\\mathcal{M}
- (\\theta))$$
-
- The following options are available:
-
- * Option A: With known redidual covariance matrix \\(\\Sigma\\) for
- independent measurements.
-
- * Option B: With unknown redidual covariance matrix \\(\\Sigma\\),
- paramethrized as \\(\\Sigma(\\theta_{\\epsilon})=\\sigma^2 \\textbf{I}_
- {N_{out}}\\) with unknown residual variances \\(\\sigma^2\\).
- This term will be jointly infer with the uncertain input parameters. For
- the inversion, you need to define a prior marginal via `Input` class. Note
- that \\(\\sigma^2\\) is only a single scalar multiplier for the diagonal
- entries of the covariance matrix \\(\\Sigma\\).
-
- Attributes
- ----------
- InputDisc : obj
- Input object. When the \\(\\sigma^2\\) is expected to be inferred
- jointly with the parameters (`Option B`).If multiple output groups are
- defined by `Model.Output.names`, each model output needs to have.
- a prior marginal using the `Input` class. The default is `''`.
- disc_type : str
- Type of the noise definition. `'Gaussian'` is only supported so far.
- parameters : dict or pandas.DataFrame
- Known residual variance \\(\\sigma^2\\), i.e. diagonal entry of the
- covariance matrix of the multivariate normal likelihood in case of
- `Option A`.
-
- """
-
- def __init__(self, InputDisc='', disc_type='Gaussian', parameters=None):
- self.InputDisc = InputDisc
- self.disc_type = disc_type
- self.parameters = parameters
-
- # -------------------------------------------------------------------------
- def get_sample(self, n_samples):
- """
- Generate samples for the \\(\\sigma^2\\), i.e. the diagonal entries of
- the variance-covariance matrix in the multivariate normal distribution.
-
- Parameters
- ----------
- n_samples : int
- Number of samples (parameter sets).
-
- Returns
- -------
- sigma2_prior: array of shape (n_samples, n_params)
- \\(\\sigma^2\\) samples.
-
- """
- self.n_samples = n_samples # TODO: not used again in here - needed from the outside?
-
- if self.InputDisc == '':
- raise AttributeError('Cannot create new samples, please provide input distributions')
-
- # Create and store BoundTuples
- self.ExpDesign = ExpDesigns(self.InputDisc)
- self.ExpDesign.sampling_method = 'random'
- self.ExpDesign.generate_ED(
- n_samples, max_pce_deg=1
- )
- # TODO: need to recheck the following line
- # This used to simply be the return from the call above
- self.sigma2_prior = self.ExpDesign.X
-
- # Naive approach: Fit a gaussian kernel to the provided data
- self.ExpDesign.JDist = stats.gaussian_kde(self.ExpDesign.raw_data)
-
- # Save the names of sigmas
- if len(self.InputDisc.Marginals) != 0:
- self.name = []
- for Marginalidx in range(len(self.InputDisc.Marginals)):
- self.name.append(self.InputDisc.Marginals[Marginalidx].name)
-
- return self.sigma2_prior
diff --git a/examples/model-comparison/bayesvalidrox/bayes_inference/mcmc.py b/examples/model-comparison/bayesvalidrox/bayes_inference/mcmc.py
deleted file mode 100644
index fe22a152f117aab7023bfe6592ce3a48bb0b3aec..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/bayes_inference/mcmc.py
+++ /dev/null
@@ -1,909 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-import os
-import numpy as np
-import emcee
-import pandas as pd
-import matplotlib.pyplot as plt
-from matplotlib.backends.backend_pdf import PdfPages
-import multiprocessing
-import scipy.stats as st
-from scipy.linalg import cholesky as chol
-import warnings
-import shutil
-os.environ["OMP_NUM_THREADS"] = "1"
-
-
-class MCMC:
- """
- A class for bayesian inference via a Markov-Chain Monte-Carlo (MCMC)
- Sampler to approximate the posterior distribution of the Bayes theorem:
- $$p(\\theta|\\mathcal{y}) = \\frac{p(\\mathcal{y}|\\theta) p(\\theta)}
- {p(\\mathcal{y})}.$$
-
- This class make inference with emcee package [1] using an Affine Invariant
- Ensemble sampler (AIES) [2].
-
- [1] Foreman-Mackey, D., Hogg, D.W., Lang, D. and Goodman, J., 2013.emcee:
- the MCMC hammer. Publications of the Astronomical Society of the
- Pacific, 125(925), p.306. https://emcee.readthedocs.io/en/stable/
-
- [2] Goodman, J. and Weare, J., 2010. Ensemble samplers with affine
- invariance. Communications in applied mathematics and computational
- science, 5(1), pp.65-80.
-
-
- Attributes
- ----------
- BayesOpts : obj
- Bayes object.
- """
-
- def __init__(self, BayesOpts):
-
- self.BayesOpts = BayesOpts
-
- def run_sampler(self, observation, total_sigma2):
-
- BayesObj = self.BayesOpts
- MetaModel = BayesObj.engine.MetaModel
- Model = BayesObj.engine.Model
- Discrepancy = self.BayesOpts.Discrepancy
- n_cpus = Model.n_cpus
- priorDist = BayesObj.engine.ExpDesign.JDist
- ndim = MetaModel.n_params
- self.counter = 0
- output_dir = f'Outputs_Bayes_{Model.name}_{self.BayesOpts.name}'
- if not os.path.exists(output_dir):
- os.makedirs(output_dir)
-
- self.observation = observation
- self.total_sigma2 = total_sigma2
-
- # Unpack mcmc parameters given to BayesObj.mcmc_params
- self.initsamples = None
- self.nwalkers = 100
- self.nburn = 200
- self.nsteps = 100000
- self.moves = None
- self.mp = False
- self.verbose = False
-
- # Extract initial samples
- if 'init_samples' in BayesObj.mcmc_params:
- self.initsamples = BayesObj.mcmc_params['init_samples']
- if isinstance(self.initsamples, pd.DataFrame):
- self.initsamples = self.initsamples.values
-
- # Extract number of steps per walker
- if 'n_steps' in BayesObj.mcmc_params:
- self.nsteps = int(BayesObj.mcmc_params['n_steps'])
- # Extract number of walkers (chains)
- if 'n_walkers' in BayesObj.mcmc_params:
- self.nwalkers = int(BayesObj.mcmc_params['n_walkers'])
- # Extract moves
- if 'moves' in BayesObj.mcmc_params:
- self.moves = BayesObj.mcmc_params['moves']
- # Extract multiprocessing
- if 'multiprocessing' in BayesObj.mcmc_params:
- self.mp = BayesObj.mcmc_params['multiprocessing']
- # Extract verbose
- if 'verbose' in BayesObj.mcmc_params:
- self.verbose = BayesObj.mcmc_params['verbose']
-
- # Set initial samples
- np.random.seed(0)
- if self.initsamples is None:
- try:
- initsamples = priorDist.sample(self.nwalkers).T
- except:
- # when aPCE selected - gaussian kernel distribution
- inputSamples = MetaModel.ExpDesign.raw_data.T
- random_indices = np.random.choice(
- len(inputSamples), size=self.nwalkers, replace=False
- )
- initsamples = inputSamples[random_indices]
-
- else:
- if self.initsamples.ndim == 1:
- # When MAL is given.
- theta = self.initsamples
- initsamples = [theta + 1e-1*np.multiply(
- np.random.randn(ndim), theta) for i in
- range(self.nwalkers)]
- else:
- # Pick samples based on a uniform dist between min and max of
- # each dim
- initsamples = np.zeros((self.nwalkers, ndim))
- bound_tuples = []
- for idx_dim in range(ndim):
- lower = np.min(self.initsamples[:, idx_dim])
- upper = np.max(self.initsamples[:, idx_dim])
- bound_tuples.append((lower, upper))
- dist = st.uniform(loc=lower, scale=upper-lower)
- initsamples[:, idx_dim] = dist.rvs(size=self.nwalkers)
-
- # Update lower and upper
- MetaModel.ExpDesign.bound_tuples = bound_tuples
-
- # Check if sigma^2 needs to be inferred
- if Discrepancy.opt_sigma != 'B':
- sigma2_samples = Discrepancy.get_sample(self.nwalkers)
-
- # Update initsamples
- initsamples = np.hstack((initsamples, sigma2_samples))
-
- # Update ndim
- ndim = initsamples.shape[1]
-
- # Discrepancy bound
- disc_bound_tuple = Discrepancy.ExpDesign.bound_tuples
-
- # Update bound_tuples
- BayesObj.engine.ExpDesign.bound_tuples += disc_bound_tuple
-
- print("\n>>>> Bayesian inference with MCMC for "
- f"{self.BayesOpts.name} started. <<<<<<")
-
- # Set up the backend
- filename = f"{output_dir}/emcee_sampler.h5"
- backend = emcee.backends.HDFBackend(filename)
- # Clear the backend in case the file already exists
- backend.reset(self.nwalkers, ndim)
-
- # Define emcee sampler
- # Here we'll set up the computation. emcee combines multiple "walkers",
- # each of which is its own MCMC chain. The number of trace results will
- # be nwalkers * nsteps.
- if self.mp:
- # Run in parallel
- if n_cpus is None:
- n_cpus = multiprocessing.cpu_count()
-
- with multiprocessing.Pool(n_cpus) as pool:
- sampler = emcee.EnsembleSampler(
- self.nwalkers, ndim, self.log_posterior, moves=self.moves,
- pool=pool, backend=backend
- )
-
- # Check if a burn-in phase is needed!
- if self.initsamples is None:
- # Burn-in
- print("\n Burn-in period is starting:")
- pos = sampler.run_mcmc(
- initsamples, self.nburn, progress=True
- )
-
- # Reset sampler
- sampler.reset()
- pos = pos.coords
- else:
- pos = initsamples
-
- # Production run
- print("\n Production run is starting:")
- pos, prob, state = sampler.run_mcmc(
- pos, self.nsteps, progress=True
- )
-
- else:
- # Run in series and monitor the convergence
- sampler = emcee.EnsembleSampler(
- self.nwalkers, ndim, self.log_posterior, moves=self.moves,
- backend=backend, vectorize=True
- )
-
- # Check if a burn-in phase is needed!
- if self.initsamples is None:
- # Burn-in
- print("\n Burn-in period is starting:")
- pos = sampler.run_mcmc(
- initsamples, self.nburn, progress=True
- )
-
- # Reset sampler
- sampler.reset()
- pos = pos.coords
- else:
- pos = initsamples
-
- # Production run
- print("\n Production run is starting:")
-
- # Track how the average autocorrelation time estimate changes
- autocorrIdx = 0
- autocorr = np.empty(self.nsteps)
- tauold = np.inf
- autocorreverynsteps = 50
-
- # sample step by step using the generator sampler.sample
- for sample in sampler.sample(pos,
- iterations=self.nsteps,
- tune=True,
- progress=True):
-
- # only check convergence every autocorreverynsteps steps
- if sampler.iteration % autocorreverynsteps:
- continue
-
- # Train model discrepancy/error
- if hasattr(BayesObj, 'errorModel') and BayesObj.errorModel \
- and not sampler.iteration % 3 * autocorreverynsteps:
- try:
- self.error_MetaModel = self.train_error_model(sampler)
- except:
- pass
-
- # Print the current mean acceptance fraction
- if self.verbose:
- print("\nStep: {}".format(sampler.iteration))
- acc_fr = np.mean(sampler.acceptance_fraction)
- print(f"Mean acceptance fraction: {acc_fr:.3f}")
-
- # compute the autocorrelation time so far
- # using tol=0 means that we'll always get an estimate even if
- # it isn't trustworthy
- tau = sampler.get_autocorr_time(tol=0)
- # average over walkers
- autocorr[autocorrIdx] = np.nanmean(tau)
- autocorrIdx += 1
-
- # output current autocorrelation estimate
- if self.verbose:
- print(f"Mean autocorr. time estimate: {np.nanmean(tau):.3f}")
- list_gr = np.round(self.gelman_rubin(sampler.chain), 3)
- print("Gelman-Rubin Test*: ", list_gr)
-
- # check convergence
- converged = np.all(tau*autocorreverynsteps < sampler.iteration)
- converged &= np.all(np.abs(tauold - tau) / tau < 0.01)
- converged &= np.all(self.gelman_rubin(sampler.chain) < 1.1)
-
- if converged:
- break
- tauold = tau
-
- # Posterior diagnostics
- try:
- tau = sampler.get_autocorr_time(tol=0)
- except emcee.autocorr.AutocorrError:
- tau = 5
-
- if all(np.isnan(tau)):
- tau = 5
-
- burnin = int(2*np.nanmax(tau))
- thin = int(0.5*np.nanmin(tau)) if int(0.5*np.nanmin(tau)) != 0 else 1
- finalsamples = sampler.get_chain(discard=burnin, flat=True, thin=thin)
- acc_fr = np.nanmean(sampler.acceptance_fraction)
- list_gr = np.round(self.gelman_rubin(sampler.chain[:, burnin:]), 3)
-
- # Print summary
- print('\n')
- print('-'*15 + 'Posterior diagnostics' + '-'*15)
- print(f"Mean auto-correlation time: {np.nanmean(tau):.3f}")
- print(f"Thin: {thin}")
- print(f"Burn-in: {burnin}")
- print(f"Flat chain shape: {finalsamples.shape}")
- print(f"Mean acceptance fraction*: {acc_fr:.3f}")
- print("Gelman-Rubin Test**: ", list_gr)
-
- print("\n* This value must lay between 0.234 and 0.5.")
- print("** These values must be smaller than 1.1.")
- print('-'*50)
-
- print(f"\n>>>> Bayesian inference with MCMC for {self.BayesOpts.name} "
- "successfully completed. <<<<<<\n")
-
- # Extract parameter names and their prior ranges
- par_names = self.BayesOpts.engine.ExpDesign.par_names
-
- if Discrepancy.opt_sigma != 'B':
- for i in range(len(Discrepancy.InputDisc.Marginals)):
- par_names.append(Discrepancy.InputDisc.Marginals[i].name)
-
- params_range = self.BayesOpts.engine.ExpDesign.bound_tuples
-
- # Plot traces
- if self.verbose and self.nsteps < 10000:
- pdf = PdfPages(output_dir+'/traceplots.pdf')
- fig = plt.figure()
- for parIdx in range(ndim):
- # Set up the axes with gridspec
- fig = plt.figure()
- grid = plt.GridSpec(4, 4, hspace=0.2, wspace=0.2)
- main_ax = fig.add_subplot(grid[:-1, :3])
- y_hist = fig.add_subplot(grid[:-1, -1], xticklabels=[],
- sharey=main_ax)
-
- for i in range(self.nwalkers):
- samples = sampler.chain[i, :, parIdx]
- main_ax.plot(samples, '-')
-
- # histogram on the attached axes
- y_hist.hist(samples[burnin:], 40, histtype='stepfilled',
- orientation='horizontal', color='gray')
-
- main_ax.set_ylim(params_range[parIdx])
- main_ax.set_title('traceplot for ' + par_names[parIdx])
- main_ax.set_xlabel('step number')
-
- # save the current figure
- pdf.savefig(fig, bbox_inches='tight')
-
- # Destroy the current plot
- plt.clf()
-
- pdf.close()
-
- # plot development of autocorrelation estimate
- if not self.mp:
- fig1 = plt.figure()
- steps = autocorreverynsteps*np.arange(1, autocorrIdx+1)
- taus = autocorr[:autocorrIdx]
- plt.plot(steps, steps / autocorreverynsteps, "--k")
- plt.plot(steps, taus)
- plt.xlim(0, steps.max())
- plt.ylim(0, np.nanmax(taus)+0.1*(np.nanmax(taus)-np.nanmin(taus)))
- plt.xlabel("number of steps")
- plt.ylabel(r"mean $\hat{\tau}$")
- fig1.savefig(f"{output_dir}/autocorrelation_time.pdf",
- bbox_inches='tight')
-
- # logml_dict = self.marginal_llk_emcee(sampler, self.nburn, logp=None,
- # maxiter=5000)
- # print('\nThe Bridge Sampling Estimation is "
- # f"{logml_dict['logml']:.5f}.')
-
- # # Posterior-based expectation of posterior probablity
- # postExpPostLikelihoods = np.mean(sampler.get_log_prob(flat=True)
- # [self.nburn*self.nwalkers:])
-
- # # Posterior-based expectation of prior densities
- # postExpPrior = np.mean(self.log_prior(emcee_trace.T))
-
- # # Posterior-based expectation of likelihoods
- # postExpLikelihoods_emcee = postExpPostLikelihoods - postExpPrior
-
- # # Calculate Kullback-Leibler Divergence
- # KLD_emcee = postExpLikelihoods_emcee - logml_dict['logml']
- # print("Kullback-Leibler divergence: %.5f"%KLD_emcee)
-
- # # Information Entropy based on Entropy paper Eq. 38
- # infEntropy_emcee = logml_dict['logml'] - postExpPrior -
- # postExpLikelihoods_emcee
- # print("Information Entropy: %.5f" %infEntropy_emcee)
-
- Posterior_df = pd.DataFrame(finalsamples, columns=par_names)
-
- return Posterior_df
-
- # -------------------------------------------------------------------------
- def log_prior(self, theta):
- """
- Calculates the log prior likelihood \\( p(\\theta)\\) for the given
- parameter set(s) \\( \\theta \\).
-
- Parameters
- ----------
- theta : array of shape (n_samples, n_params)
- Parameter sets, i.e. proposals of MCMC chains.
-
- Returns
- -------
- logprior: float or array of shape n_samples
- Log prior likelihood. If theta has only one row, a single value is
- returned otherwise an array.
-
- """
-
- MetaModel = self.BayesOpts.MetaModel
- Discrepancy = self.BayesOpts.Discrepancy
-
- # Find the number of sigma2 parameters
- if Discrepancy.opt_sigma != 'B':
- disc_bound_tuples = Discrepancy.ExpDesign.bound_tuples
- disc_marginals = Discrepancy.ExpDesign.InputObj.Marginals
- disc_prior_space = Discrepancy.ExpDesign.prior_space
- n_sigma2 = len(disc_bound_tuples)
- else:
- n_sigma2 = -len(theta)
- prior_dist = self.BayesOpts.engine.ExpDesign.prior_space
- params_range = self.BayesOpts.engine.ExpDesign.bound_tuples
- theta = theta if theta.ndim != 1 else theta.reshape((1, -1))
- nsamples = theta.shape[0]
- logprior = -np.inf*np.ones(nsamples)
-
- for i in range(nsamples):
- # Check if the sample is within the parameters' range
- if self._check_ranges(theta[i], params_range):
- # Check if all dists are uniform, if yes priors are equal.
- if all(MetaModel.input_obj.Marginals[i].dist_type == 'uniform'
- for i in range(MetaModel.n_params)):
- logprior[i] = 0.0
- else:
- logprior[i] = np.log(
- prior_dist.pdf(theta[i, :-n_sigma2].T)
- )
-
- # Check if bias term needs to be inferred
- if Discrepancy.opt_sigma != 'B':
- if self._check_ranges(theta[i, -n_sigma2:],
- disc_bound_tuples):
- if all('unif' in disc_marginals[i].dist_type for i in
- range(Discrepancy.ExpDesign.ndim)):
- logprior[i] = 0.0
- else:
- logprior[i] += np.log(
- disc_prior_space.pdf(theta[i, -n_sigma2:])
- )
-
- if nsamples == 1:
- return logprior[0]
- else:
- return logprior
-
- # -------------------------------------------------------------------------
- def log_likelihood(self, theta):
- """
- Computes likelihood \\( p(\\mathcal{Y}|\\theta)\\) of the performance
- of the (meta-)model in reproducing the observation data.
-
- Parameters
- ----------
- theta : array of shape (n_samples, n_params)
- Parameter set, i.e. proposals of the MCMC chains.
-
- Returns
- -------
- log_like : array of shape (n_samples)
- Log likelihood.
-
- """
-
- BayesOpts = self.BayesOpts
- MetaModel = BayesOpts.MetaModel
- Discrepancy = self.BayesOpts.Discrepancy
-
- # Find the number of sigma2 parameters
- if Discrepancy.opt_sigma != 'B':
- disc_bound_tuples = Discrepancy.ExpDesign.bound_tuples
- n_sigma2 = len(disc_bound_tuples)
- else:
- n_sigma2 = -len(theta)
- # Check if bias term needs to be inferred
- if Discrepancy.opt_sigma != 'B':
- sigma2 = theta[:, -n_sigma2:]
- theta = theta[:, :-n_sigma2]
- else:
- sigma2 = None
- theta = theta if theta.ndim != 1 else theta.reshape((1, -1))
-
- # Evaluate Model/MetaModel at theta
- mean_pred, BayesOpts._std_pce_prior_pred = self.eval_model(theta)
-
- # Surrogate model's error using RMSE of test data
- surrError = MetaModel.rmse if hasattr(MetaModel, 'rmse') else None
-
- # Likelihood
- log_like = BayesOpts.normpdf(
- mean_pred, self.observation, self.total_sigma2, sigma2,
- std=surrError
- )
- return log_like
-
- # -------------------------------------------------------------------------
- def log_posterior(self, theta):
- """
- Computes the posterior likelihood \\(p(\\theta| \\mathcal{Y})\\) for
- the given parameterset.
-
- Parameters
- ----------
- theta : array of shape (n_samples, n_params)
- Parameter set, i.e. proposals of the MCMC chains.
-
- Returns
- -------
- log_like : array of shape (n_samples)
- Log posterior likelihood.
-
- """
-
- nsamples = 1 if theta.ndim == 1 else theta.shape[0]
-
- if nsamples == 1:
- if self.log_prior(theta) == -np.inf:
- return -np.inf
- else:
- # Compute log prior
- log_prior = self.log_prior(theta)
- # Compute log Likelihood
- log_likelihood = self.log_likelihood(theta)
-
- return log_prior + log_likelihood
- else:
- # Compute log prior
- log_prior = self.log_prior(theta)
-
- # Initialize log_likelihood
- log_likelihood = -np.inf*np.ones(nsamples)
-
- # find the indices for -inf sets
- non_inf_idx = np.where(log_prior != -np.inf)[0]
-
- # Compute loLikelihoods
- if non_inf_idx.size != 0:
- log_likelihood[non_inf_idx] = self.log_likelihood(
- theta[non_inf_idx]
- )
-
- return log_prior + log_likelihood
-
- # -------------------------------------------------------------------------
- def eval_model(self, theta):
- """
- Evaluates the (meta-) model at the given theta.
-
- Parameters
- ----------
- theta : array of shape (n_samples, n_params)
- Parameter set, i.e. proposals of the MCMC chains.
-
- Returns
- -------
- mean_pred : dict
- Mean model prediction.
- std_pred : dict
- Std of model prediction.
-
- """
-
- BayesObj = self.BayesOpts
- MetaModel = BayesObj.MetaModel
- Model = BayesObj.engine.Model
-
- if BayesObj.emulator:
- # Evaluate the MetaModel
- mean_pred, std_pred = MetaModel.eval_metamodel(samples=theta)
- else:
- # Evaluate the origModel
- mean_pred, std_pred = dict(), dict()
-
- model_outs, _ = Model.run_model_parallel(
- theta, prevRun_No=self.counter,
- key_str='_MCMC', mp=False, verbose=False)
-
- # Save outputs in respective dicts
- for varIdx, var in enumerate(Model.Output.names):
- mean_pred[var] = model_outs[var]
- std_pred[var] = np.zeros((mean_pred[var].shape))
-
- # Remove the folder
- if Model.link_type.lower() != 'function':
- shutil.rmtree(f"{Model.name}_MCMC_{self.counter+1}")
-
- # Add one to the counter
- self.counter += 1
-
- if hasattr(self, 'error_MetaModel') and BayesObj.error_model:
- meanPred, stdPred = self.error_MetaModel.eval_model_error(
- BayesObj.BiasInputs, mean_pred
- )
-
- return mean_pred, std_pred
-
- # -------------------------------------------------------------------------
- def train_error_model(self, sampler):
- """
- Trains an error model using a Gaussian Process Regression.
-
- Parameters
- ----------
- sampler : obj
- emcee sampler.
-
- Returns
- -------
- error_MetaModel : obj
- A error model.
-
- """
- BayesObj = self.BayesOpts
- MetaModel = BayesObj.MetaModel
-
- # Prepare the poster samples
- try:
- tau = sampler.get_autocorr_time(tol=0)
- except emcee.autocorr.AutocorrError:
- tau = 5
-
- if all(np.isnan(tau)):
- tau = 5
-
- burnin = int(2*np.nanmax(tau))
- thin = int(0.5*np.nanmin(tau)) if int(0.5*np.nanmin(tau)) != 0 else 1
- finalsamples = sampler.get_chain(discard=burnin, flat=True, thin=thin)
- posterior = finalsamples[:, :MetaModel.n_params]
-
- # Select posterior mean as MAP
- map_theta = posterior.mean(axis=0).reshape((1, MetaModel.n_params))
- # MAP_theta = st.mode(Posterior_df,axis=0)[0]
-
- # Evaluate the (meta-)model at the MAP
- y_map, y_std_map = MetaModel.eval_metamodel(samples=map_theta)
-
- # Train a GPR meta-model using MAP
- error_MetaModel = MetaModel.create_model_error(
- BayesObj.BiasInputs, y_map, name='Calib')
-
- return error_MetaModel
-
- # -------------------------------------------------------------------------
- def gelman_rubin(self, chain, return_var=False):
- """
- The potential scale reduction factor (PSRF) defined by the variance
- within one chain, W, with the variance between chains B.
- Both variances are combined in a weighted sum to obtain an estimate of
- the variance of a parameter \\( \\theta \\).The square root of the
- ratio of this estimates variance to the within chain variance is called
- the potential scale reduction.
- For a well converged chain it should approach 1. Values greater than
- 1.1 typically indicate that the chains have not yet fully converged.
-
- Source: http://joergdietrich.github.io/emcee-convergence.html
-
- https://github.com/jwalton3141/jwalton3141.github.io/blob/master/assets/posts/ESS/rwmh.py
-
- Parameters
- ----------
- chain : array (n_walkers, n_steps, n_params)
- The emcee ensamples.
-
- Returns
- -------
- R_hat : float
- The Gelman-Robin values.
-
- """
- m_chains, n_iters = chain.shape[:2]
-
- # Calculate between-chain variance
- θb = np.mean(chain, axis=1)
- θbb = np.mean(θb, axis=0)
- B_over_n = ((θbb - θb)**2).sum(axis=0)
- B_over_n /= (m_chains - 1)
-
- # Calculate within-chain variances
- ssq = np.var(chain, axis=1, ddof=1)
- W = np.mean(ssq, axis=0)
-
- # (over) estimate of variance
- var_θ = W * (n_iters - 1) / n_iters + B_over_n
-
- if return_var:
- return var_θ
- else:
- # The square root of the ratio of this estimates variance to the
- # within chain variance
- R_hat = np.sqrt(var_θ / W)
- return R_hat
-
- # -------------------------------------------------------------------------
- def marginal_llk_emcee(self, sampler, nburn=None, logp=None, maxiter=1000):
- """
- The Bridge Sampling Estimator of the Marginal Likelihood based on
- https://gist.github.com/junpenglao/4d2669d69ddfe1d788318264cdcf0583
-
- Parameters
- ----------
- sampler : TYPE
- MultiTrace, result of MCMC run.
- nburn : int, optional
- Number of burn-in step. The default is None.
- logp : TYPE, optional
- Model Log-probability function. The default is None.
- maxiter : int, optional
- Maximum number of iterations. The default is 1000.
-
- Returns
- -------
- marg_llk : dict
- Estimated Marginal log-Likelihood.
-
- """
- r0, tol1, tol2 = 0.5, 1e-10, 1e-4
-
- if logp is None:
- logp = sampler.log_prob_fn
-
- # Split the samples into two parts
- # Use the first 50% for fiting the proposal distribution
- # and the second 50% in the iterative scheme.
- if nburn is None:
- mtrace = sampler.chain
- else:
- mtrace = sampler.chain[:, nburn:, :]
-
- nchain, len_trace, nrofVars = mtrace.shape
-
- N1_ = len_trace // 2
- N1 = N1_*nchain
- N2 = len_trace*nchain - N1
-
- samples_4_fit = np.zeros((nrofVars, N1))
- samples_4_iter = np.zeros((nrofVars, N2))
- effective_n = np.zeros((nrofVars))
-
- # matrix with already transformed samples
- for var in range(nrofVars):
-
- # for fitting the proposal
- x = mtrace[:, :N1_, var]
-
- samples_4_fit[var, :] = x.flatten()
- # for the iterative scheme
- x2 = mtrace[:, N1_:, var]
- samples_4_iter[var, :] = x2.flatten()
-
- # effective sample size of samples_4_iter, scalar
- effective_n[var] = self._my_ESS(x2)
-
- # median effective sample size (scalar)
- neff = np.median(effective_n)
-
- # get mean & covariance matrix and generate samples from proposal
- m = np.mean(samples_4_fit, axis=1)
- V = np.cov(samples_4_fit)
- L = chol(V, lower=True)
-
- # Draw N2 samples from the proposal distribution
- gen_samples = m[:, None] + np.dot(
- L, st.norm.rvs(0, 1, size=samples_4_iter.shape)
- )
-
- # Evaluate proposal distribution for posterior & generated samples
- q12 = st.multivariate_normal.logpdf(samples_4_iter.T, m, V)
- q22 = st.multivariate_normal.logpdf(gen_samples.T, m, V)
-
- # Evaluate unnormalized posterior for posterior & generated samples
- q11 = logp(samples_4_iter.T)
- q21 = logp(gen_samples.T)
-
- # Run iterative scheme:
- tmp = self._iterative_scheme(
- N1, N2, q11, q12, q21, q22, r0, neff, tol1, maxiter, 'r'
- )
- if ~np.isfinite(tmp['logml']):
- warnings.warn(
- "Logml could not be estimated within maxiter, rerunning with "
- "adjusted starting value. Estimate might be more variable than"
- " usual.")
- # use geometric mean as starting value
- r0_2 = np.sqrt(tmp['r_vals'][-2]*tmp['r_vals'][-1])
- tmp = self._iterative_scheme(
- q11, q12, q21, q22, r0_2, neff, tol2, maxiter, 'logml'
- )
-
- marg_llk = dict(
- logml=tmp['logml'], niter=tmp['niter'], method="normal",
- q11=q11, q12=q12, q21=q21, q22=q22
- )
- return marg_llk
-
- # -------------------------------------------------------------------------
- def _iterative_scheme(self, N1, N2, q11, q12, q21, q22, r0, neff, tol,
- maxiter, criterion):
- """
- Iterative scheme as proposed in Meng and Wong (1996) to estimate the
- marginal likelihood
-
- """
- l1 = q11 - q12
- l2 = q21 - q22
- # To increase numerical stability,
- # subtracting the median of l1 from l1 & l2 later
- lstar = np.median(l1)
- s1 = neff/(neff + N2)
- s2 = N2/(neff + N2)
- r = r0
- r_vals = [r]
- logml = np.log(r) + lstar
- criterion_val = 1 + tol
-
- i = 0
- while (i <= maxiter) & (criterion_val > tol):
- rold = r
- logmlold = logml
- numi = np.exp(l2 - lstar)/(s1 * np.exp(l2 - lstar) + s2 * r)
- deni = 1/(s1 * np.exp(l1 - lstar) + s2 * r)
- if np.sum(~np.isfinite(numi))+np.sum(~np.isfinite(deni)) > 0:
- warnings.warn(
- """Infinite value in iterative scheme, returning NaN.
- Try rerunning with more samples.""")
- r = (N1/N2) * np.sum(numi)/np.sum(deni)
- r_vals.append(r)
- logml = np.log(r) + lstar
- i += 1
- if criterion == 'r':
- criterion_val = np.abs((r - rold)/r)
- elif criterion == 'logml':
- criterion_val = np.abs((logml - logmlold)/logml)
-
- if i >= maxiter:
- return dict(logml=np.NaN, niter=i, r_vals=np.asarray(r_vals))
- else:
- return dict(logml=logml, niter=i)
-
- # -------------------------------------------------------------------------
- def _my_ESS(self, x):
- """
- Compute the effective sample size of estimand of interest.
- Vectorised implementation.
- https://github.com/jwalton3141/jwalton3141.github.io/blob/master/assets/posts/ESS/rwmh.py
-
-
- Parameters
- ----------
- x : array of shape (n_walkers, n_steps)
- MCMC Samples.
-
- Returns
- -------
- int
- Effective sample size.
-
- """
- m_chains, n_iters = x.shape
-
- def variogram(t):
- variogram = ((x[:, t:] - x[:, :(n_iters - t)])**2).sum()
- variogram /= (m_chains * (n_iters - t))
- return variogram
-
- post_var = self.gelman_rubin(x, return_var=True)
-
- t = 1
- rho = np.ones(n_iters)
- negative_autocorr = False
-
- # Iterate until the sum of consecutive estimates of autocorrelation is
- # negative
- while not negative_autocorr and (t < n_iters):
- rho[t] = 1 - variogram(t) / (2 * post_var)
-
- if not t % 2:
- negative_autocorr = sum(rho[t-1:t+1]) < 0
-
- t += 1
-
- return int(m_chains*n_iters / (1 + 2*rho[1:t].sum()))
-
- # -------------------------------------------------------------------------
- def _check_ranges(self, theta, ranges):
- """
- This function checks if theta lies in the given ranges.
-
- Parameters
- ----------
- theta : array
- Proposed parameter set.
- ranges : nested list
- List of the praremeter ranges.
-
- Returns
- -------
- c : bool
- If it lies in the given range, it return True else False.
-
- """
- c = True
- # traverse in the list1
- for i, bounds in enumerate(ranges):
- x = theta[i]
- # condition check
- if x < bounds[0] or x > bounds[1]:
- c = False
- return c
- return c
diff --git a/examples/model-comparison/bayesvalidrox/bayesvalidrox.mplstyle b/examples/model-comparison/bayesvalidrox/bayesvalidrox.mplstyle
deleted file mode 100644
index 1f31c01f24597de0e0be741be4d3a706c4213a6c..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/bayesvalidrox.mplstyle
+++ /dev/null
@@ -1,16 +0,0 @@
-figure.titlesize : 30
-axes.titlesize : 30
-axes.labelsize : 30
-axes.linewidth : 3
-axes.grid : True
-lines.linewidth : 3
-lines.markersize : 10
-xtick.labelsize : 30
-ytick.labelsize : 30
-legend.fontsize : 30
-font.family : serif
-font.serif : Arial
-font.size : 30
-text.usetex : True
-grid.linestyle : -
-figure.figsize : 24, 16
diff --git a/examples/model-comparison/bayesvalidrox/post_processing/__init__.py b/examples/model-comparison/bayesvalidrox/post_processing/__init__.py
deleted file mode 100644
index 81c9825420b6ed3f027fb3c141be8af05a89f695..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/post_processing/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-# -*- coding: utf-8 -*-
-
-from .post_processing import PostProcessing
-
-__all__ = [
- "PostProcessing"
- ]
diff --git a/examples/model-comparison/bayesvalidrox/post_processing/__pycache__/__init__.cpython-310.pyc b/examples/model-comparison/bayesvalidrox/post_processing/__pycache__/__init__.cpython-310.pyc
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diff --git a/examples/model-comparison/bayesvalidrox/post_processing/post_processing.py b/examples/model-comparison/bayesvalidrox/post_processing/post_processing.py
deleted file mode 100644
index 6520a40f9f2393798f6b8abac026b9ed38fe33ca..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/post_processing/post_processing.py
+++ /dev/null
@@ -1,1338 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-import numpy as np
-import math
-import os
-from itertools import combinations, cycle
-import pandas as pd
-import scipy.stats as stats
-from sklearn.linear_model import LinearRegression
-from sklearn.metrics import mean_squared_error, r2_score
-import matplotlib.pyplot as plt
-import matplotlib.ticker as ticker
-from matplotlib.offsetbox import AnchoredText
-from matplotlib.patches import Patch
-# Load the mplstyle
-plt.style.use(os.path.join(os.path.split(__file__)[0],
- '../', 'bayesvalidrox.mplstyle'))
-
-
-class PostProcessing:
- """
- This class provides many helper functions to post-process the trained
- meta-model.
-
- Attributes
- ----------
- MetaModel : obj
- MetaModel object to do postprocessing on.
- name : str
- Type of the anaylsis. The default is `'calib'`. If a validation is
- expected to be performed change this to `'valid'`.
- """
-
- def __init__(self, engine, name='calib'):
- self.engine = engine
- self.MetaModel = engine.MetaModel
- self.ExpDesign = engine.ExpDesign
- self.ModelObj = engine.Model
- self.name = name
-
- # -------------------------------------------------------------------------
- def plot_moments(self, xlabel='Time [s]', plot_type=None):
- """
- Plots the moments in a pdf format in the directory
- `Outputs_PostProcessing`.
-
- Parameters
- ----------
- xlabel : str, optional
- String to be displayed as x-label. The default is `'Time [s]'`.
- plot_type : str, optional
- Options: bar or line. The default is `None`.
-
- Returns
- -------
- pce_means: dict
- Mean of the model outputs.
- pce_means: dict
- Standard deviation of the model outputs.
-
- """
-
- bar_plot = True if plot_type == 'bar' else False
- meta_model_type = self.MetaModel.meta_model_type
- Model = self.ModelObj
-
- # Read Monte-Carlo reference
- self.mc_reference = Model.read_observation('mc_ref')
-
- # Set the x values
- x_values_orig = self.engine.ExpDesign.x_values
-
- # Compute the moments with the PCEModel object
- self.pce_means, self.pce_stds = self.compute_pce_moments()
-
- # Get the variables
- out_names = Model.Output.names
-
- # Open a pdf for the plots
- newpath = (f'Outputs_PostProcessing_{self.name}/')
- if not os.path.exists(newpath):
- os.makedirs(newpath)
-
- # Plot the best fit line, set the linewidth (lw), color and
- # transparency (alpha) of the line
- for key in out_names:
- fig, ax = plt.subplots(nrows=1, ncols=2)
-
- # Extract mean and std
- mean_data = self.pce_means[key]
- std_data = self.pce_stds[key]
-
- # Extract a list of x values
- if type(x_values_orig) is dict:
- x = x_values_orig[key]
- else:
- x = x_values_orig
-
- # Plot: bar plot or line plot
- if bar_plot:
- ax[0].bar(list(map(str, x)), mean_data, color='b',
- width=0.25)
- ax[1].bar(list(map(str, x)), std_data, color='b',
- width=0.25)
- ax[0].legend(labels=[meta_model_type])
- ax[1].legend(labels=[meta_model_type])
- else:
- ax[0].plot(x, mean_data, lw=3, color='k', marker='x',
- label=meta_model_type)
- ax[1].plot(x, std_data, lw=3, color='k', marker='x',
- label=meta_model_type)
-
- if self.mc_reference is not None:
- if bar_plot:
- ax[0].bar(list(map(str, x)), self.mc_reference['mean'],
- color='r', width=0.25)
- ax[1].bar(list(map(str, x)), self.mc_reference['std'],
- color='r', width=0.25)
- ax[0].legend(labels=[meta_model_type])
- ax[1].legend(labels=[meta_model_type])
- else:
- ax[0].plot(x, self.mc_reference['mean'], lw=3, marker='x',
- color='r', label='Ref.')
- ax[1].plot(x, self.mc_reference['std'], lw=3, marker='x',
- color='r', label='Ref.')
-
- # Label the axes and provide a title
- ax[0].set_xlabel(xlabel)
- ax[1].set_xlabel(xlabel)
- ax[0].set_ylabel(key)
- ax[1].set_ylabel(key)
-
- # Provide a title
- ax[0].set_title('Mean of ' + key)
- ax[1].set_title('Std of ' + key)
-
- if not bar_plot:
- ax[0].legend(loc='best')
- ax[1].legend(loc='best')
-
- plt.tight_layout()
-
- # save the current figure
- fig.savefig(
- f'./{newpath}Mean_Std_PCE_{key}.pdf',
- bbox_inches='tight'
- )
-
- return self.pce_means, self.pce_stds
-
- # -------------------------------------------------------------------------
- def valid_metamodel(self, n_samples=1, samples=None, model_out_dict=None,
- x_axis='Time [s]'):
- """
- Evaluates and plots the meta model and the PCEModel outputs for the
- given number of samples or the given samples.
-
- Parameters
- ----------
- n_samples : int, optional
- Number of samples to be evaluated. The default is 1.
- samples : array of shape (n_samples, n_params), optional
- Samples to be evaluated. The default is None.
- model_out_dict: dict
- The model runs using the samples provided.
- x_axis : str, optional
- Label of x axis. The default is `'Time [s]'`.
-
- Returns
- -------
- None.
-
- """
- MetaModel = self.MetaModel
- Model = self.ModelObj
-
- if samples is None:
- self.n_samples = n_samples
- samples = self._get_sample()
- else:
- self.n_samples = samples.shape[0]
-
- # Extract x_values
- x_values = self.engine.ExpDesign.x_values
-
- if model_out_dict is not None:
- self.model_out_dict = model_out_dict
- else:
- self.model_out_dict = self._eval_model(samples, key_str='valid')
- self.pce_out_mean, self.pce_out_std = MetaModel.eval_metamodel(samples)
-
- try:
- key = Model.Output.names[1]
- except IndexError:
- key = Model.Output.names[0]
-
- n_obs = self.model_out_dict[key].shape[1]
-
- if n_obs == 1:
- self._plot_validation()
- else:
- self._plot_validation_multi(x_values=x_values, x_axis=x_axis)
-
- # -------------------------------------------------------------------------
- def check_accuracy(self, n_samples=None, samples=None, outputs=None):
- """
- Checks accuracy of the metamodel by computing the root mean square
- error and validation error for all outputs.
-
- Parameters
- ----------
- n_samples : int, optional
- Number of samples. The default is None.
- samples : array of shape (n_samples, n_params), optional
- Parameter sets to be checked. The default is None.
- outputs : dict, optional
- Output dictionary with model outputs for all given output types in
- `Model.Output.names`. The default is None.
-
- Raises
- ------
- Exception
- When neither n_samples nor samples are provided.
-
- Returns
- -------
- rmse: dict
- Root mean squared error for each output.
- valid_error : dict
- Validation error for each output.
-
- """
- MetaModel = self.MetaModel
- Model = self.ModelObj
-
- # Set the number of samples
- if n_samples:
- self.n_samples = n_samples
- elif samples is not None:
- self.n_samples = samples.shape[0]
- else:
- raise Exception("Please provide either samples or pass the number"
- " of samples!")
-
- # Generate random samples if necessary
- Samples = self._get_sample() if samples is None else samples
-
- # Run the original model with the generated samples
- if outputs is None:
- outputs = self._eval_model(Samples, key_str='validSet')
-
- # Run the PCE model with the generated samples
- pce_outputs, _ = MetaModel.eval_metamodel(samples=Samples)
-
- self.rmse = {}
- self.valid_error = {}
- # Loop over the keys and compute RMSE error.
- for key in Model.Output.names:
- # Root mena square
- self.rmse[key] = mean_squared_error(outputs[key], pce_outputs[key],
- squared=False,
- multioutput='raw_values')
- # Validation error
- self.valid_error[key] = (self.rmse[key]**2) / \
- np.var(outputs[key], ddof=1, axis=0)
-
- # Print a report table
- print("\n>>>>> Errors of {} <<<<<".format(key))
- print("\nIndex | RMSE | Validation Error")
- print('-'*35)
- print('\n'.join(f'{i+1} | {k:.3e} | {j:.3e}' for i, (k, j)
- in enumerate(zip(self.rmse[key],
- self.valid_error[key]))))
- # Save error dicts in PCEModel object
- self.MetaModel.rmse = self.rmse
- self.MetaModel.valid_error = self.valid_error
-
- return
-
- # -------------------------------------------------------------------------
- def plot_seq_design_diagnostics(self, ref_BME_KLD=None):
- """
- Plots the Bayesian Model Evidence (BME) and Kullback-Leibler divergence
- (KLD) for the sequential design.
-
- Parameters
- ----------
- ref_BME_KLD : array, optional
- Reference BME and KLD . The default is `None`.
-
- Returns
- -------
- None.
-
- """
- engine = self.engine
- PCEModel = self.MetaModel
- n_init_samples = engine.ExpDesign.n_init_samples
- n_total_samples = engine.ExpDesign.X.shape[0]
-
- newpath = f'Outputs_PostProcessing_{self.name}/seq_design_diagnostics/'
- if not os.path.exists(newpath):
- os.makedirs(newpath)
-
- plotList = ['Modified LOO error', 'Validation error', 'KLD', 'BME',
- 'RMSEMean', 'RMSEStd', 'Hellinger distance']
- seqList = [engine.SeqModifiedLOO, engine.seqValidError,
- engine.SeqKLD, engine.SeqBME, engine.seqRMSEMean,
- engine.seqRMSEStd, engine.SeqDistHellinger]
-
- markers = ('x', 'o', 'd', '*', '+')
- colors = ('k', 'darkgreen', 'b', 'navy', 'darkred')
-
- # Plot the evolution of the diagnostic criteria of the
- # Sequential Experimental Design.
- for plotidx, plot in enumerate(plotList):
- fig, ax = plt.subplots()
- seq_dict = seqList[plotidx]
- name_util = list(seq_dict.keys())
-
- if len(name_util) == 0:
- continue
-
- # Box plot when Replications have been detected.
- if any(int(name.split("rep_", 1)[1]) > 1 for name in name_util):
- # Extract the values from dict
- sorted_seq_opt = {}
- # Number of replications
- n_reps = engine.ExpDesign.n_replication
-
- # Get the list of utility function names
- # Handle if only one UtilityFunction is provided
- if not isinstance(engine.ExpDesign.util_func, list):
- util_funcs = [engine.ExpDesign.util_func]
- else:
- util_funcs = engine.ExpDesign.util_func
-
- for util in util_funcs:
- sortedSeq = {}
- # min number of runs available from reps
- n_runs = min([seq_dict[f'{util}_rep_{i+1}'].shape[0]
- for i in range(n_reps)])
-
- for runIdx in range(n_runs):
- values = []
- for key in seq_dict.keys():
- if util in key:
- values.append(seq_dict[key][runIdx].mean())
- sortedSeq['SeqItr_'+str(runIdx)] = np.array(values)
- sorted_seq_opt[util] = sortedSeq
-
- # BoxPlot
- def draw_plot(data, labels, edge_color, fill_color, idx):
- pos = labels - (idx-1)
- bp = plt.boxplot(data, positions=pos, labels=labels,
- patch_artist=True, sym='', widths=0.75)
- elements = ['boxes', 'whiskers', 'fliers', 'means',
- 'medians', 'caps']
- for element in elements:
- plt.setp(bp[element], color=edge_color[idx])
-
- for patch in bp['boxes']:
- patch.set(facecolor=fill_color[idx])
-
- if engine.ExpDesign.n_new_samples != 1:
- step1 = engine.ExpDesign.n_new_samples
- step2 = 1
- else:
- step1 = 5
- step2 = 5
- edge_color = ['red', 'blue', 'green']
- fill_color = ['tan', 'cyan', 'lightgreen']
- plot_label = plot
- # Plot for different Utility Functions
- for idx, util in enumerate(util_funcs):
- all_errors = np.empty((n_reps, 0))
-
- for key in list(sorted_seq_opt[util].keys()):
- errors = sorted_seq_opt.get(util, {}).get(key)[:, None]
- all_errors = np.hstack((all_errors, errors))
-
- # Special cases for BME and KLD
- if plot == 'KLD' or plot == 'BME':
- # BME convergence if refBME is provided
- if ref_BME_KLD is not None:
- if plot == 'BME':
- refValue = ref_BME_KLD[0]
- plot_label = r'BME/BME$^{Ref.}$'
- if plot == 'KLD':
- refValue = ref_BME_KLD[1]
- plot_label = '$D_{KL}[p(\\theta|y_*),p(\\theta)]'\
- ' / D_{KL}^{Ref.}[p(\\theta|y_*), '\
- 'p(\\theta)]$'
-
- # Difference between BME/KLD and the ref. values
- all_errors = np.divide(all_errors,
- np.full((all_errors.shape),
- refValue))
-
- # Plot baseline for zero, i.e. no difference
- plt.axhline(y=1.0, xmin=0, xmax=1, c='green',
- ls='--', lw=2)
-
- # Plot each UtilFuncs
- labels = np.arange(n_init_samples, n_total_samples+1, step1)
- draw_plot(all_errors[:, ::step2], labels, edge_color,
- fill_color, idx)
-
- plt.xticks(labels, labels)
- # Set the major and minor locators
- ax.xaxis.set_major_locator(ticker.AutoLocator())
- ax.xaxis.set_minor_locator(ticker.AutoMinorLocator())
- ax.xaxis.grid(True, which='major', linestyle='-')
- ax.xaxis.grid(True, which='minor', linestyle='--')
-
- # Legend
- legend_elements = []
- for idx, util in enumerate(util_funcs):
- legend_elements.append(Patch(facecolor=fill_color[idx],
- edgecolor=edge_color[idx],
- label=util))
- plt.legend(handles=legend_elements[::-1], loc='best')
-
- if plot != 'BME' and plot != 'KLD':
- plt.yscale('log')
- plt.autoscale(True)
- plt.xlabel('\\# of training samples')
- plt.ylabel(plot_label)
- plt.title(plot)
-
- # save the current figure
- plot_name = plot.replace(' ', '_')
- fig.savefig(
- f'./{newpath}/seq_{plot_name}.pdf',
- bbox_inches='tight'
- )
- # Destroy the current plot
- plt.clf()
- # Save arrays into files
- f = open(f'./{newpath}/seq_{plot_name}.txt', 'w')
- f.write(str(sorted_seq_opt))
- f.close()
- else:
- for idx, name in enumerate(name_util):
- seq_values = seq_dict[name]
- if engine.ExpDesign.n_new_samples != 1:
- step = engine.ExpDesign.n_new_samples
- else:
- step = 1
- x_idx = np.arange(n_init_samples, n_total_samples+1, step)
- if n_total_samples not in x_idx:
- x_idx = np.hstack((x_idx, n_total_samples))
-
- if plot == 'KLD' or plot == 'BME':
- # BME convergence if refBME is provided
- if ref_BME_KLD is not None:
- if plot == 'BME':
- refValue = ref_BME_KLD[0]
- plot_label = r'BME/BME$^{Ref.}$'
- if plot == 'KLD':
- refValue = ref_BME_KLD[1]
- plot_label = '$D_{KL}[p(\\theta|y_*),p(\\theta)]'\
- ' / D_{KL}^{Ref.}[p(\\theta|y_*), '\
- 'p(\\theta)]$'
-
- # Difference between BME/KLD and the ref. values
- values = np.divide(seq_values,
- np.full((seq_values.shape),
- refValue))
-
- # Plot baseline for zero, i.e. no difference
- plt.axhline(y=1.0, xmin=0, xmax=1, c='green',
- ls='--', lw=2)
-
- # Set the limits
- plt.ylim([1e-1, 1e1])
-
- # Create the plots
- plt.semilogy(x_idx, values, marker=markers[idx],
- color=colors[idx], ls='--', lw=2,
- label=name.split("_rep", 1)[0])
- else:
- plot_label = plot
-
- # Create the plots
- plt.plot(x_idx, seq_values, marker=markers[idx],
- color=colors[idx], ls='--', lw=2,
- label=name.split("_rep", 1)[0])
-
- else:
- plot_label = plot
- seq_values = np.nan_to_num(seq_values)
-
- # Plot the error evolution for each output
- plt.semilogy(x_idx, seq_values.mean(axis=1),
- marker=markers[idx], ls='--', lw=2,
- color=colors[idx],
- label=name.split("_rep", 1)[0])
-
- # Set the major and minor locators
- ax.xaxis.set_major_locator(ticker.AutoLocator())
- ax.xaxis.set_minor_locator(ticker.AutoMinorLocator())
- ax.xaxis.grid(True, which='major', linestyle='-')
- ax.xaxis.grid(True, which='minor', linestyle='--')
-
- ax.tick_params(axis='both', which='major', direction='in',
- width=3, length=10)
- ax.tick_params(axis='both', which='minor', direction='in',
- width=2, length=8)
- plt.xlabel('Number of runs')
- plt.ylabel(plot_label)
- plt.title(plot)
- plt.legend(frameon=True)
-
- # save the current figure
- plot_name = plot.replace(' ', '_')
- fig.savefig(
- f'./{newpath}/seq_{plot_name}.pdf',
- bbox_inches='tight'
- )
- # Destroy the current plot
- plt.clf()
-
- # ---------------- Saving arrays into files ---------------
- np.save(f'./{newpath}/seq_{plot_name}.npy', seq_values)
-
- return
-
- # -------------------------------------------------------------------------
- def sobol_indices(self, xlabel='Time [s]', plot_type=None):
- """
- Provides Sobol indices as a sensitivity measure to infer the importance
- of the input parameters. See Eq. 27 in [1] for more details. For the
- case with Principal component analysis refer to [2].
-
- [1] Global sensitivity analysis: A flexible and efficient framework
- with an example from stochastic hydrogeology S. Oladyshkin, F.P.
- de Barros, W. Nowak https://doi.org/10.1016/j.advwatres.2011.11.001
-
- [2] Nagel, J.B., Rieckermann, J. and Sudret, B., 2020. Principal
- component analysis and sparse polynomial chaos expansions for global
- sensitivity analysis and model calibration: Application to urban
- drainage simulation. Reliability Engineering & System Safety, 195,
- p.106737.
-
- Parameters
- ----------
- xlabel : str, optional
- Label of the x-axis. The default is `'Time [s]'`.
- plot_type : str, optional
- Plot type. The default is `None`. This corresponds to line plot.
- Bar chart can be selected by `bar`.
-
- Returns
- -------
- sobol_cell: dict
- Sobol indices.
- total_sobol: dict
- Total Sobol indices.
-
- """
- # Extract the necessary variables
- PCEModel = self.MetaModel
- basis_dict = PCEModel.basis_dict
- coeffs_dict = PCEModel.coeffs_dict
- n_params = PCEModel.n_params
- max_order = np.max(PCEModel.pce_deg)
- sobol_cell_b = {}
- total_sobol_b = {}
- cov_Z_p_q = np.zeros((n_params))
-
- for b_i in range(PCEModel.n_bootstrap_itrs):
-
- sobol_cell_, total_sobol_ = {}, {}
-
- for output in self.ModelObj.Output.names:
-
- n_meas_points = len(coeffs_dict[f'b_{b_i+1}'][output])
-
- # Initialize the (cell) array containing the (total) Sobol indices.
- sobol_array = dict.fromkeys(range(1, max_order+1), [])
- sobol_cell_array = dict.fromkeys(range(1, max_order+1), [])
-
- for i_order in range(1, max_order+1):
- n_comb = math.comb(n_params, i_order)
-
- sobol_cell_array[i_order] = np.zeros((n_comb, n_meas_points))
-
- total_sobol_array = np.zeros((n_params, n_meas_points))
-
- # Initialize the cell to store the names of the variables
- TotalVariance = np.zeros((n_meas_points))
- # Loop over all measurement points and calculate sobol indices
- for pIdx in range(n_meas_points):
-
- # Extract the basis indices (alpha) and coefficients
- Basis = basis_dict[f'b_{b_i+1}'][output][f'y_{pIdx+1}']
-
- try:
- clf_poly = PCEModel.clf_poly[f'b_{b_i+1}'][output][f'y_{pIdx+1}']
- PCECoeffs = clf_poly.coef_
- except:
- PCECoeffs = coeffs_dict[f'b_{b_i+1}'][output][f'y_{pIdx+1}']
-
- # Compute total variance
- TotalVariance[pIdx] = np.sum(np.square(PCECoeffs[1:]))
-
- nzidx = np.where(PCECoeffs != 0)[0]
- # Set all the Sobol indices equal to zero in the presence of a
- # null output.
- if len(nzidx) == 0:
- # This is buggy.
- for i_order in range(1, max_order+1):
- sobol_cell_array[i_order][:, pIdx] = 0
-
- # Otherwise compute them by summing well-chosen coefficients
- else:
- nz_basis = Basis[nzidx]
- for i_order in range(1, max_order+1):
- idx = np.where(np.sum(nz_basis > 0, axis=1) == i_order)
- subbasis = nz_basis[idx]
- Z = np.array(list(combinations(range(n_params), i_order)))
-
- for q in range(Z.shape[0]):
- Zq = Z[q]
- subsubbasis = subbasis[:, Zq]
- subidx = np.prod(subsubbasis, axis=1) > 0
- sum_ind = nzidx[idx[0][subidx]]
- if TotalVariance[pIdx] == 0.0:
- sobol_cell_array[i_order][q, pIdx] = 0.0
- else:
- sobol = np.sum(np.square(PCECoeffs[sum_ind]))
- sobol /= TotalVariance[pIdx]
- sobol_cell_array[i_order][q, pIdx] = sobol
-
- # Compute the TOTAL Sobol indices.
- for ParIdx in range(n_params):
- idx = nz_basis[:, ParIdx] > 0
- sum_ind = nzidx[idx]
-
- if TotalVariance[pIdx] == 0.0:
- total_sobol_array[ParIdx, pIdx] = 0.0
- else:
- sobol = np.sum(np.square(PCECoeffs[sum_ind]))
- sobol /= TotalVariance[pIdx]
- total_sobol_array[ParIdx, pIdx] = sobol
-
- # ----- if PCA selected: Compute covariance -----
- if PCEModel.dim_red_method.lower() == 'pca':
- # Extract the basis indices (alpha) and coefficients for
- # next component
- if pIdx < n_meas_points-1:
- nextBasis = basis_dict[f'b_{b_i+1}'][output][f'y_{pIdx+2}']
- if PCEModel.bootstrap_method != 'fast' or b_i == 0:
- clf_poly = PCEModel.clf_poly[f'b_{b_i+1}'][output][f'y_{pIdx+2}']
- nextPCECoeffs = clf_poly.coef_
- else:
- nextPCECoeffs = coeffs_dict[f'b_{b_i+1}'][output][f'y_{pIdx+2}']
-
- # Choose the common non-zero basis
- mask = (Basis[:, None] == nextBasis).all(-1).any(-1)
- n_mask = (nextBasis[:, None] == Basis).all(-1).any(-1)
-
- # Compute the covariance in Eq 17.
- for ParIdx in range(n_params):
- idx = (mask) & (Basis[:, ParIdx] > 0)
- n_idx = (n_mask) & (nextBasis[:, ParIdx] > 0)
- try:
- cov_Z_p_q[ParIdx] += np.sum(np.dot(
- PCECoeffs[idx], nextPCECoeffs[n_idx])
- )
- except:
- pass
-
- # Compute the sobol indices according to Ref. 2
- if PCEModel.dim_red_method.lower() == 'pca':
- n_c_points = self.engine.ExpDesign.Y[output].shape[1]
- PCA = PCEModel.pca[f'b_{b_i+1}'][output]
- compPCA = PCA.components_
- nComp = compPCA.shape[0]
- var_Z_p = PCA.explained_variance_
-
- # Extract the sobol index of the components
- for i_order in range(1, max_order+1):
- n_comb = math.comb(n_params, i_order)
- sobol_array[i_order] = np.zeros((n_comb, n_c_points))
- Z = np.array(list(combinations(range(n_params), i_order)))
-
- # Loop over parameters
- for q in range(Z.shape[0]):
- S_Z_i = sobol_cell_array[i_order][q]
-
- for tIdx in range(n_c_points):
- var_Y_t = np.var(
- self.engine.ExpDesign.Y[output][:, tIdx])
- if var_Y_t == 0.0:
- term1, term2 = 0.0, 0.0
- else:
- # Eq. 17
- term1 = 0.0
- for i in range(nComp):
- a = S_Z_i[i] * var_Z_p[i]
- a *= compPCA[i, tIdx]**2
- term1 += a
-
- # TODO: Term 2
- # term2 = 0.0
- # for i in range(nComp-1):
- # term2 += cov_Z_p_q[q] * compPCA[i, tIdx]
- # term2 *= compPCA[i+1, tIdx]
- # term2 *= 2
-
- sobol_array[i_order][q, tIdx] = term1 #+ term2
-
- # Devide over total output variance Eq. 18
- sobol_array[i_order][q, tIdx] /= var_Y_t
-
- # Compute the TOTAL Sobol indices.
- total_sobol = np.zeros((n_params, n_c_points))
- for ParIdx in range(n_params):
- S_Z_i = total_sobol_array[ParIdx]
-
- for tIdx in range(n_c_points):
- var_Y_t = np.var(self.engine.ExpDesign.Y[output][:, tIdx])
- if var_Y_t == 0.0:
- term1, term2 = 0.0, 0.0
- else:
- term1 = 0
- for i in range(nComp):
- term1 += S_Z_i[i] * var_Z_p[i] * \
- (compPCA[i, tIdx]**2)
-
- # Term 2
- term2 = 0
- for i in range(nComp-1):
- term2 += cov_Z_p_q[ParIdx] * compPCA[i, tIdx] \
- * compPCA[i+1, tIdx]
- term2 *= 2
-
- total_sobol[ParIdx, tIdx] = term1 #+ term2
-
- # Devide over total output variance Eq. 18
- total_sobol[ParIdx, tIdx] /= var_Y_t
-
- sobol_cell_[output] = sobol_array
- total_sobol_[output] = total_sobol
- else:
- sobol_cell_[output] = sobol_cell_array
- total_sobol_[output] = total_sobol_array
-
- # Save for each bootsrtap iteration
- sobol_cell_b[b_i] = sobol_cell_
- total_sobol_b[b_i] = total_sobol_
-
- # Average total sobol indices
- total_sobol_all = {}
- for i in sorted(total_sobol_b):
- for k, v in total_sobol_b[i].items():
- if k not in total_sobol_all:
- total_sobol_all[k] = [None] * len(total_sobol_b)
- total_sobol_all[k][i] = v
-
- self.total_sobol = {}
- for output in self.ModelObj.Output.names:
- self.total_sobol[output] = np.mean(total_sobol_all[output], axis=0)
-
- # ---------------- Plot -----------------------
- par_names = self.engine.ExpDesign.par_names
- x_values_orig = self.engine.ExpDesign.x_values
-
- newpath = (f'Outputs_PostProcessing_{self.name}/')
- if not os.path.exists(newpath):
- os.makedirs(newpath)
-
- fig = plt.figure()
-
- for outIdx, output in enumerate(self.ModelObj.Output.names):
-
- # Extract total Sobol indices
- total_sobol = self.total_sobol[output]
-
- # Compute quantiles
- q_5 = np.quantile(total_sobol_all[output], q=0.05, axis=0)
- q_97_5 = np.quantile(total_sobol_all[output], q=0.975, axis=0)
-
- # Extract a list of x values
- if type(x_values_orig) is dict:
- x = x_values_orig[output]
- else:
- x = x_values_orig
-
- if plot_type == 'bar':
- ax = fig.add_axes([0, 0, 1, 1])
- dict1 = {xlabel: x}
- dict2 = {param: sobolIndices for param, sobolIndices
- in zip(par_names, total_sobol)}
-
- df = pd.DataFrame({**dict1, **dict2})
- df.plot(x=xlabel, y=par_names, kind="bar", ax=ax, rot=0,
- colormap='Dark2', yerr=q_97_5-q_5)
- ax.set_ylabel('Total Sobol indices, $S^T$')
-
- else:
- for i, sobolIndices in enumerate(total_sobol):
- plt.plot(x, sobolIndices, label=par_names[i],
- marker='x', lw=2.5)
- plt.fill_between(x, q_5[i], q_97_5[i], alpha=0.15)
-
- plt.ylabel('Total Sobol indices, $S^T$')
- plt.xlabel(xlabel)
-
- plt.title(f'Sensitivity analysis of {output}')
- if plot_type != 'bar':
- plt.legend(loc='best', frameon=True)
-
- # Save indices
- np.savetxt(f'./{newpath}totalsobol_' +
- output.replace('/', '_') + '.csv',
- total_sobol.T, delimiter=',',
- header=','.join(par_names), comments='')
-
- # save the current figure
- fig.savefig(
- f'./{newpath}Sobol_indices_{output}.pdf',
- bbox_inches='tight'
- )
-
- # Destroy the current plot
- plt.clf()
-
- return self.total_sobol
-
- # -------------------------------------------------------------------------
- def check_reg_quality(self, n_samples=1000, samples=None):
- """
- Checks the quality of the metamodel for single output models based on:
- https://towardsdatascience.com/how-do-you-check-the-quality-of-your-regression-model-in-python-fa61759ff685
-
-
- Parameters
- ----------
- n_samples : int, optional
- Number of parameter sets to use for the check. The default is 1000.
- samples : array of shape (n_samples, n_params), optional
- Parameter sets to use for the check. The default is None.
-
- Returns
- -------
- None.
-
- """
- MetaModel = self.MetaModel
-
- if samples is None:
- self.n_samples = n_samples
- samples = self._get_sample()
- else:
- self.n_samples = samples.shape[0]
-
- # Evaluate the original and the surrogate model
- y_val = self._eval_model(samples, key_str='valid')
- y_pce_val, _ = MetaModel.eval_metamodel(samples=samples)
-
- # Open a pdf for the plots
- newpath = f'Outputs_PostProcessing_{self.name}/'
- if not os.path.exists(newpath):
- os.makedirs(newpath)
-
- # Fit the data(train the model)
- for key in y_pce_val.keys():
-
- y_pce_val_ = y_pce_val[key]
- y_val_ = y_val[key]
- residuals = y_val_ - y_pce_val_
-
- # ------ Residuals vs. predicting variables ------
- # Check the assumptions of linearity and independence
- fig1 = plt.figure()
- for i, par in enumerate(self.engine.ExpDesign.par_names):
- plt.title(f"{key}: Residuals vs. {par}")
- plt.scatter(
- x=samples[:, i], y=residuals, color='blue', edgecolor='k')
- plt.grid(True)
- xmin, xmax = min(samples[:, i]), max(samples[:, i])
- plt.hlines(y=0, xmin=xmin*0.9, xmax=xmax*1.1, color='red',
- lw=3, linestyle='--')
- plt.xlabel(par)
- plt.ylabel('Residuals')
- plt.show()
-
- # save the current figure
- fig1.savefig(f'./{newpath}/Residuals_vs_Par_{i+1}.pdf',
- bbox_inches='tight')
- # Destroy the current plot
- plt.clf()
-
- # ------ Fitted vs. residuals ------
- # Check the assumptions of linearity and independence
- fig2 = plt.figure()
- plt.title(f"{key}: Residuals vs. fitted values")
- plt.scatter(x=y_pce_val_, y=residuals, color='blue', edgecolor='k')
- plt.grid(True)
- xmin, xmax = min(y_val_), max(y_val_)
- plt.hlines(y=0, xmin=xmin*0.9, xmax=xmax*1.1, color='red', lw=3,
- linestyle='--')
- plt.xlabel(key)
- plt.ylabel('Residuals')
- plt.show()
-
- # save the current figure
- fig2.savefig(f'./{newpath}/Fitted_vs_Residuals.pdf',
- bbox_inches='tight')
- # Destroy the current plot
- plt.clf()
-
- # ------ Histogram of normalized residuals ------
- fig3 = plt.figure()
- resid_pearson = residuals / (max(residuals)-min(residuals))
- plt.hist(resid_pearson, bins=20, edgecolor='k')
- plt.ylabel('Count')
- plt.xlabel('Normalized residuals')
- plt.title(f"{key}: Histogram of normalized residuals")
-
- # Normality (Shapiro-Wilk) test of the residuals
- ax = plt.gca()
- _, p = stats.shapiro(residuals)
- if p < 0.01:
- annText = "The residuals seem to come from a Gaussian Process."
- else:
- annText = "The normality assumption may not hold."
- at = AnchoredText(annText, prop=dict(size=30), frameon=True,
- loc='upper left')
- at.patch.set_boxstyle("round,pad=0.,rounding_size=0.2")
- ax.add_artist(at)
-
- plt.show()
-
- # save the current figure
- fig3.savefig(f'./{newpath}/Hist_NormResiduals.pdf',
- bbox_inches='tight')
- # Destroy the current plot
- plt.clf()
-
- # ------ Q-Q plot of the normalized residuals ------
- plt.figure()
- stats.probplot(residuals[:, 0], plot=plt)
- plt.xticks()
- plt.yticks()
- plt.xlabel("Theoretical quantiles")
- plt.ylabel("Sample quantiles")
- plt.title(f"{key}: Q-Q plot of normalized residuals")
- plt.grid(True)
- plt.show()
-
- # save the current figure
- plt.savefig(f'./{newpath}/QQPlot_NormResiduals.pdf',
- bbox_inches='tight')
- # Destroy the current plot
- plt.clf()
-
- # -------------------------------------------------------------------------
- def eval_pce_model_3d(self):
-
- self.n_samples = 1000
-
- PCEModel = self.MetaModel
- Model = self.ModelObj
- n_samples = self.n_samples
-
- # Create 3D-Grid
- # TODO: Make it general
- x = np.linspace(-5, 10, n_samples)
- y = np.linspace(0, 15, n_samples)
-
- X, Y = np.meshgrid(x, y)
- PCE_Z = np.zeros((self.n_samples, self.n_samples))
- Model_Z = np.zeros((self.n_samples, self.n_samples))
-
- for idxMesh in range(self.n_samples):
- sample_mesh = np.vstack((X[:, idxMesh], Y[:, idxMesh])).T
-
- univ_p_val = PCEModel.univ_basis_vals(sample_mesh)
-
- for Outkey, ValuesDict in PCEModel.coeffs_dict.items():
-
- pce_out_mean = np.zeros((len(sample_mesh), len(ValuesDict)))
- pce_out_std = np.zeros((len(sample_mesh), len(ValuesDict)))
- model_outs = np.zeros((len(sample_mesh), len(ValuesDict)))
-
- for Inkey, InIdxValues in ValuesDict.items():
- idx = int(Inkey.split('_')[1]) - 1
- basis_deg_ind = PCEModel.basis_dict[Outkey][Inkey]
- clf_poly = PCEModel.clf_poly[Outkey][Inkey]
-
- PSI_Val = PCEModel.create_psi(basis_deg_ind, univ_p_val)
-
- # Perdiction with error bar
- y_mean, y_std = clf_poly.predict(PSI_Val, return_std=True)
-
- pce_out_mean[:, idx] = y_mean
- pce_out_std[:, idx] = y_std
-
- # Model evaluation
- model_out_dict, _ = Model.run_model_parallel(sample_mesh,
- key_str='Valid3D')
- model_outs[:, idx] = model_out_dict[Outkey].T
-
- PCE_Z[:, idxMesh] = y_mean
- Model_Z[:, idxMesh] = model_outs[:, 0]
-
- # ---------------- 3D plot for PCEModel -----------------------
- fig_PCE = plt.figure()
- ax = plt.axes(projection='3d')
- ax.plot_surface(X, Y, PCE_Z, rstride=1, cstride=1,
- cmap='viridis', edgecolor='none')
- ax.set_title('PCEModel')
- ax.set_xlabel('$x_1$')
- ax.set_ylabel('$x_2$')
- ax.set_zlabel('$f(x_1,x_2)$')
-
- plt.grid()
- plt.show()
-
- # Saving the figure
- newpath = f'Outputs_PostProcessing_{self.name}/'
- if not os.path.exists(newpath):
- os.makedirs(newpath)
-
- # save the figure to file
- fig_PCE.savefig(f'./{newpath}/3DPlot_PCEModel.pdf',
- bbox_inches='tight')
- plt.close(fig_PCE)
-
- # ---------------- 3D plot for Model -----------------------
- fig_Model = plt.figure()
- ax = plt.axes(projection='3d')
- ax.plot_surface(X, Y, PCE_Z, rstride=1, cstride=1,
- cmap='viridis', edgecolor='none')
- ax.set_title('Model')
- ax.set_xlabel('$x_1$')
- ax.set_ylabel('$x_2$')
- ax.set_zlabel('$f(x_1,x_2)$')
-
- plt.grid()
- plt.show()
-
- # Save the figure
- fig_Model.savefig(f'./{newpath}/3DPlot_Model.pdf',
- bbox_inches='tight')
- plt.close(fig_Model)
-
- return
-
- # -------------------------------------------------------------------------
- def compute_pce_moments(self):
- """
- Computes the first two moments using the PCE-based meta-model.
-
- Returns
- -------
- pce_means: dict
- The first moments (mean) of outpust.
- pce_means: dict
- The first moments (mean) of outpust.
-
- """
-
- MetaModel = self.MetaModel
- outputs = self.ModelObj.Output.names
- pce_means_b = {}
- pce_stds_b = {}
-
- # Loop over bootstrap iterations
- for b_i in range(MetaModel.n_bootstrap_itrs):
- # Loop over the metamodels
- coeffs_dicts = MetaModel.coeffs_dict[f'b_{b_i+1}'].items()
- means = {}
- stds = {}
- for output, coef_dict in coeffs_dicts:
-
- pce_mean = np.zeros((len(coef_dict)))
- pce_var = np.zeros((len(coef_dict)))
-
- for index, values in coef_dict.items():
- idx = int(index.split('_')[1]) - 1
- coeffs = MetaModel.coeffs_dict[f'b_{b_i+1}'][output][index]
-
- # Mean = c_0
- if coeffs[0] != 0:
- pce_mean[idx] = coeffs[0]
- else:
- clf_poly = MetaModel.clf_poly[f'b_{b_i+1}'][output]
- pce_mean[idx] = clf_poly[index].intercept_
- # Var = sum(coeffs[1:]**2)
- pce_var[idx] = np.sum(np.square(coeffs[1:]))
-
- # Save predictions for each output
- if MetaModel.dim_red_method.lower() == 'pca':
- PCA = MetaModel.pca[f'b_{b_i+1}'][output]
- means[output] = PCA.inverse_transform(pce_mean)
- stds[output] = np.sqrt(np.dot(pce_var,
- PCA.components_**2))
- else:
- means[output] = pce_mean
- stds[output] = np.sqrt(pce_var)
-
- # Save predictions for each bootstrap iteration
- pce_means_b[b_i] = means
- pce_stds_b[b_i] = stds
-
- # Change the order of nesting
- mean_all = {}
- for i in sorted(pce_means_b):
- for k, v in pce_means_b[i].items():
- if k not in mean_all:
- mean_all[k] = [None] * len(pce_means_b)
- mean_all[k][i] = v
- std_all = {}
- for i in sorted(pce_stds_b):
- for k, v in pce_stds_b[i].items():
- if k not in std_all:
- std_all[k] = [None] * len(pce_stds_b)
- std_all[k][i] = v
-
- # Back transformation if PCA is selected.
- pce_means, pce_stds = {}, {}
- for output in outputs:
- pce_means[output] = np.mean(mean_all[output], axis=0)
- pce_stds[output] = np.mean(std_all[output], axis=0)
-
- # Print a report table
- print("\n>>>>> Moments of {} <<<<<".format(output))
- print("\nIndex | Mean | Std. deviation")
- print('-'*35)
- print('\n'.join(f'{i+1} | {k:.3e} | {j:.3e}' for i, (k, j)
- in enumerate(zip(pce_means[output],
- pce_stds[output]))))
- print('-'*40)
-
- return pce_means, pce_stds
-
- # -------------------------------------------------------------------------
- def _get_sample(self, n_samples=None):
- """
- Generates random samples taken from the input parameter space.
-
- Returns
- -------
- samples : array of shape (n_samples, n_params)
- Generated samples.
-
- """
- if n_samples is None:
- n_samples = self.n_samples
- self.samples = self.ExpDesign.generate_samples(
- n_samples,
- sampling_method='random')
- return self.samples
-
- # -------------------------------------------------------------------------
- def _eval_model(self, samples=None, key_str='Valid'):
- """
- Evaluates Forward Model for the given number of self.samples or given
- samples.
-
- Parameters
- ----------
- samples : array of shape (n_samples, n_params), optional
- Samples to evaluate the model at. The default is None.
- key_str : str, optional
- Key string pass to the model. The default is 'Valid'.
-
- Returns
- -------
- model_outs : dict
- Dictionary of results.
-
- """
- Model = self.ModelObj
-
- if samples is None:
- samples = self._get_sample()
- self.samples = samples
- else:
- self.n_samples = len(samples)
-
- model_outs, _ = Model.run_model_parallel(samples, key_str=key_str)
-
- return model_outs
-
- # -------------------------------------------------------------------------
- def _plot_validation(self):
- """
- Plots outputs for visual comparison of metamodel outputs with that of
- the (full) original model.
-
- Returns
- -------
- None.
-
- """
- PCEModel = self.MetaModel
-
- # get the samples
- x_val = self.samples
- y_pce_val = self.pce_out_mean
- y_val = self.model_out_dict
-
- # Open a pdf for the plots
- newpath = f'Outputs_PostProcessing_{self.name}/'
- if not os.path.exists(newpath):
- os.makedirs(newpath)
-
- fig = plt.figure()
- # Fit the data(train the model)
- for key in y_pce_val.keys():
-
- y_pce_val_ = y_pce_val[key]
- y_val_ = y_val[key]
-
- regression_model = LinearRegression()
- regression_model.fit(y_pce_val_, y_val_)
-
- # Predict
- x_new = np.linspace(np.min(y_pce_val_), np.max(y_val_), 100)
- y_predicted = regression_model.predict(x_new[:, np.newaxis])
-
- plt.scatter(y_pce_val_, y_val_, color='gold', linewidth=2)
- plt.plot(x_new, y_predicted, color='k')
-
- # Calculate the adjusted R_squared and RMSE
- # the total number of explanatory variables in the model
- # (not including the constant term)
- length_list = []
- for key, value in PCEModel.coeffs_dict['b_1'][key].items():
- length_list.append(len(value))
- n_predictors = min(length_list)
- n_samples = x_val.shape[0]
-
- R2 = r2_score(y_pce_val_, y_val_)
- AdjR2 = 1 - (1 - R2) * (n_samples - 1) / \
- (n_samples - n_predictors - 1)
- rmse = mean_squared_error(y_pce_val_, y_val_, squared=False)
-
- plt.annotate(f'RMSE = {rmse:.3f}\n Adjusted $R^2$ = {AdjR2:.3f}',
- xy=(0.05, 0.85), xycoords='axes fraction')
-
- plt.ylabel("Original Model")
- plt.xlabel("PCE Model")
- plt.grid()
- plt.show()
-
- # save the current figure
- plot_name = key.replace(' ', '_')
- fig.savefig(f'./{newpath}/Model_vs_PCEModel_{plot_name}.pdf',
- bbox_inches='tight')
-
- # Destroy the current plot
- plt.clf()
-
- # -------------------------------------------------------------------------
- def _plot_validation_multi(self, x_values=[], x_axis="x [m]"):
- """
- Plots outputs for visual comparison of metamodel outputs with that of
- the (full) multioutput original model
-
- Parameters
- ----------
- x_values : list or array, optional
- List of x values. The default is [].
- x_axis : str, optional
- Label of the x axis. The default is "x [m]".
-
- Returns
- -------
- None.
-
- """
- Model = self.ModelObj
-
- newpath = f'Outputs_PostProcessing_{self.name}/'
- if not os.path.exists(newpath):
- os.makedirs(newpath)
-
- # List of markers and colors
- color = cycle((['b', 'g', 'r', 'y', 'k']))
- marker = cycle(('x', 'd', '+', 'o', '*'))
-
- fig = plt.figure()
- # Plot the model vs PCE model
- for keyIdx, key in enumerate(Model.Output.names):
-
- y_pce_val = self.pce_out_mean[key]
- y_pce_val_std = self.pce_out_std[key]
- y_val = self.model_out_dict[key]
- try:
- x = self.model_out_dict['x_values'][key]
- except (TypeError, IndexError):
- x = x_values
-
- for idx in range(y_val.shape[0]):
- Color = next(color)
- Marker = next(marker)
-
- plt.plot(x, y_val[idx], color=Color, marker=Marker,
- label='$Y_{%s}^M$'%(idx+1))
-
- plt.plot(x, y_pce_val[idx], color=Color, marker=Marker,
- linestyle='--',
- label='$Y_{%s}^{PCE}$'%(idx+1))
- plt.fill_between(x, y_pce_val[idx]-1.96*y_pce_val_std[idx],
- y_pce_val[idx]+1.96*y_pce_val_std[idx],
- color=Color, alpha=0.15)
-
- # Calculate the RMSE
- rmse = mean_squared_error(y_pce_val, y_val, squared=False)
- R2 = r2_score(y_pce_val[idx].reshape(-1, 1),
- y_val[idx].reshape(-1, 1))
-
- plt.annotate(f'RMSE = {rmse:.3f}\n $R^2$ = {R2:.3f}',
- xy=(0.85, 0.1), xycoords='axes fraction')
-
- plt.ylabel(key)
- plt.xlabel(x_axis)
- plt.legend(loc='best')
- plt.grid()
-
- # save the current figure
- plot_name = key.replace(' ', '_')
- fig.savefig(f'./{newpath}/Model_vs_PCEModel_{plot_name}.pdf',
- bbox_inches='tight')
-
- # Destroy the current plot
- plt.clf()
-
- # Zip the subdirectories
- Model.zip_subdirs(f'{Model.name}valid', f'{Model.name}valid_')
diff --git a/examples/model-comparison/bayesvalidrox/pylink/__init__.py b/examples/model-comparison/bayesvalidrox/pylink/__init__.py
deleted file mode 100644
index 4bd81739faf43956324b30f6d8e5365b29d55677..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/pylink/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-# -*- coding: utf-8 -*-
-
-from .pylink import PyLinkForwardModel
-
-__all__ = [
- "PyLinkForwardModel"
- ]
diff --git a/examples/model-comparison/bayesvalidrox/pylink/__pycache__/__init__.cpython-310.pyc b/examples/model-comparison/bayesvalidrox/pylink/__pycache__/__init__.cpython-310.pyc
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diff --git a/examples/model-comparison/bayesvalidrox/pylink/pylink.py b/examples/model-comparison/bayesvalidrox/pylink/pylink.py
deleted file mode 100644
index 227a51ab38cd834e7e85f6193d83563c7ed3437a..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/pylink/pylink.py
+++ /dev/null
@@ -1,803 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Calls to the model and evaluations
-"""
-
-from dataclasses import dataclass
-
-import os
-import shutil
-import h5py
-import numpy as np
-import time
-import zipfile
-import pandas as pd
-import multiprocessing
-from functools import partial
-import tqdm
-
-#from multiprocessing import get_context
-from multiprocess import get_context
-
-
-
-def within_range(out, minout, maxout):
- """
- Checks if all the values in out lie between minout and maxout
-
- Parameters
- ----------
- out : array or list
- Data to check against range
- minout : int
- Lower bound of the range
- maxout : int
- Upper bound of the range
-
- Returns
- -------
- inside : bool
- True if all values in out are in the specified range
-
- """
- try:
- out = np.array(out)
- except:
- raise AttributeError('The given values should be a 1D array, but are not')
- if out.ndim != 1:
- raise AttributeError('The given values should be a 1D array, but are not')
-
- if minout > maxout:
- raise ValueError('The lower and upper bounds do not form a valid range, they might be switched')
-
- inside = False
- if (out > minout).all() and (out < maxout).all():
- inside = True
- return inside
-
-
-class PyLinkForwardModel(object):
- """
- A forward model binder
-
- This calss serves as a code wrapper. This wrapper allows the execution of
- a third-party software/solver within the scope of BayesValidRox.
-
- Attributes
- ----------
- link_type : str
- The type of the wrapper. The default is `'pylink'`. This runs the
- third-party software or an executable using a shell command with given
- input files.
- Second option is `'function'` which assumed that model can be run using
- a function written separately in a Python script.
- name : str
- Name of the model.
- py_file : str
- Python file name without `.py` extension to be run for the `'function'`
- wrapper. Note that the name of the python file and that of the function
- must be simillar. This function must recieve the parameters in an array
- of shape `(n_samples, n_params)` and returns a dictionary with the
- x_values and output arrays for given output names.
- func_args : dict
- Additional arguments for the python file. The default is `{}`.
- shell_command : str
- Shell command to be executed for the `'pylink'` wrapper.
- input_file : str or list
- The input file to be passed to the `'pylink'` wrapper.
- input_template : str or list
- A template input file to be passed to the `'pylink'` wrapper. This file
- must be a copy of `input_file` with `<Xi>` place holder for the input
- parameters defined using `inputs` class, with i being the number of
- parameter. The file name ending should include `.tpl` before the actual
- extension of the input file, for example, `params.tpl.input`.
- aux_file : str or list
- The list of auxiliary files needed for the `'pylink'` wrapper.
- exe_path : str
- Execution path if you wish to run the model for the `'pylink'` wrapper
- in another directory. The default is `None`, which corresponds to the
- currecnt working directory.
- output_file_names : list of str
- List of the name of the model output text files for the `'pylink'`
- wrapper.
- output_names : list of str
- List of the model outputs to be used for the analysis.
- output_parser : str
- Name of the model parser file (without `.py` extension) that recieves
- the `output_file_names` and returns a 2d-array with the first row being
- the x_values, e.g. x coordinates or time and the rest of raws pass the
- simulation output for each model output defined in `output_names`. Note
- that again here the name of the file and that of the function must be
- the same.
- multi_process: bool
- Whether the model runs to be executed in parallel for the `'pylink'`
- wrapper. The default is `True`.
- n_cpus: int
- The number of cpus to be used for the parallel model execution for the
- `'pylink'` wrapper. The default is `None`, which corresponds to all
- available cpus.
- meas_file : str
- The name of the measurement text-based file. This file must contain
- x_values as the first column and one column for each model output. The
- default is `None`. Only needed for the Bayesian Inference.
- meas_file_valid : str
- The name of the measurement text-based file for the validation. The
- default is `None`. Only needed for the validation with Bayesian
- Inference.
- mc_ref_file : str
- The name of the text file for the Monte-Carlo reference (mean and
- standard deviation) values. It must contain `x_values` as the first
- column, `mean` as the second column and `std` as the third. It can be
- used to compare the estimated moments using meta-model in the post-
- processing step. This is only available for one output.
- obs_dict : dict
- A dictionary containing the measurement text-based file. It must
- contain `x_values` as the first item and one item for each model output
- . The default is `{}`. Only needed for the Bayesian Inference.
- obs_dict_valid : dict
- A dictionary containing the validation measurement text-based file. It
- must contain `x_values` as the first item and one item for each model
- output. The default is `{}`.
- mc_ref_dict : dict
- A dictionary containing the Monte-Carlo reference (mean and standard
- deviation) values. It must contain `x_values` as the first item and
- `mean` as the second item and `std` as the third. The default is `{}`.
- This is only available for one output.
- """
-
- # Nested class
- @dataclass
- class OutputData(object):
- parser: str = ""
- names: list = None
- file_names: list = None
-
- def __init__(self, link_type='pylink', name=None, py_file=None,
- func_args={}, shell_command='', input_file=None,
- input_template=None, aux_file=None, exe_path='',
- output_file_names=[], output_names=[], output_parser='',
- multi_process=True, n_cpus=None, meas_file=None,
- meas_file_valid=None, mc_ref_file=None, obs_dict={},
- obs_dict_valid={}, mc_ref_dict={}):
- self.link_type = link_type
- self.name = name
- self.shell_command = shell_command
- self.py_file = py_file
- self.func_args = func_args
- self.input_file = input_file
- self.input_template = input_template
- self.aux_file = aux_file
- self.exe_path = exe_path
- self.multi_process = multi_process
- self.n_cpus = n_cpus
- self.Output = self.OutputData(
- parser=output_parser,
- names=output_names,
- file_names=output_file_names,
- )
- self.n_outputs = len(self.Output.names)
- self.meas_file = meas_file
- self.meas_file_valid = meas_file_valid
- self.mc_ref_file = mc_ref_file
- self.observations = obs_dict
- self.observations_valid = obs_dict_valid
- self.mc_reference = mc_ref_dict
-
- # -------------------------------------------------------------------------
- def read_observation(self, case='calib'):
- """
- Reads/prepare the observation/measurement data for
- calibration.
-
- Parameters
- ----------
- case : str
- The type of observation to read in. Can be either 'calib',
- 'valid' or 'mc_ref'
-
- Returns
- -------
- DataFrame
- A dataframe with the calibration data.
-
- """
- # TOOD: check that what is read in/transformed matches the expected form of data/reference
- if case.lower() == 'calib':
- if isinstance(self.observations, dict) and bool(self.observations):
- self.observations = pd.DataFrame.from_dict(self.observations)
- elif self.meas_file is not None:
- file_path = os.path.join(os.getcwd(), self.meas_file)
- self.observations = pd.read_csv(file_path, delimiter=',')
- elif isinstance(self.observations, pd.DataFrame):
- self.observations = self.observations
- else:
- raise Exception("Please provide the observation data as a "
- "dictionary via observations attribute or pass"
- " the csv-file path to MeasurementFile "
- "attribute")
- # Compute the number of observation
- self.n_obs = self.observations[self.Output.names].notnull().sum().values.sum()
- return self.observations
-
- elif case.lower() == 'valid':
- if isinstance(self.observations_valid, dict) and \
- bool(self.observations_valid):
- self.observations_valid = pd.DataFrame.from_dict(self.observations_valid)
- elif self.meas_file_valid is not None:
- file_path = os.path.join(os.getcwd(), self.meas_file_valid)
- self.observations_valid = pd.read_csv(file_path, delimiter=',')
- elif isinstance(self.observations_valid, pd.DataFrame):
- self.observations_valid = self.observations_valid
- else:
- raise Exception("Please provide the observation data as a "
- "dictionary via observations attribute or pass"
- " the csv-file path to MeasurementFile "
- "attribute")
- # Compute the number of observation
- self.n_obs_valid = self.observations_valid[self.Output.names].notnull().sum().values.sum()
- return self.observations_valid
-
- elif case.lower() == 'mc_ref':
- if self.mc_ref_file is None and \
- isinstance(self.mc_reference, pd.DataFrame):
- return self.mc_reference
- elif isinstance(self.mc_reference, dict) and bool(self.mc_reference):
- self.mc_reference = pd.DataFrame.from_dict(self.mc_reference)
- elif self.mc_ref_file is not None:
- file_path = os.path.join(os.getcwd(), self.mc_ref_file)
- self.mc_reference = pd.read_csv(file_path, delimiter=',')
- else:
- self.mc_reference = None
- return self.mc_reference
-
-
- # -------------------------------------------------------------------------
- def read_output(self):
- """
- Reads the the parser output file and returns it as an
- executable function. It is required when the models returns the
- simulation outputs in csv files.
-
- Returns
- -------
- Output : func
- Output parser function.
-
- """
- output_func_name = self.Output.parser
-
- output_func = getattr(__import__(output_func_name), output_func_name)
-
- file_names = []
- for File in self.Output.file_names:
- file_names.append(os.path.join(self.exe_path, File))
- try:
- output = output_func(self.name, file_names)
- except TypeError:
- output = output_func(file_names)
- return output
-
- # -------------------------------------------------------------------------
- def update_input_params(self, new_input_file, param_set):
- """
- Finds this pattern with <X1> in the new_input_file and replace it with
- the new value from the array param_sets.
-
- Parameters
- ----------
- new_input_file : list
- List of the input files with the adapted names.
- param_set : array of shape (n_params)
- Parameter set.
-
- Returns
- -------
- None.
-
- """
- NofPa = param_set.shape[0]
- text_to_search_list = [f'<X{i+1}>' for i in range(NofPa)]
-
- for filename in new_input_file:
- # Read in the file
- with open(filename, 'r') as file:
- filedata = file.read()
-
- # Replace the target string
- for text_to_search, params in zip(text_to_search_list, param_set):
- filedata = filedata.replace(text_to_search, f'{params:0.4e}')
-
- # Write the file out again
- with open(filename, 'w') as file:
- file.write(filedata)
-
- # -------------------------------------------------------------------------
- def run_command(self, command, output_file_names):
- """
- Runs the execution command given by the user to run the given model.
- It checks if the output files have been generated. If yes, the jobe is
- done and it extracts and returns the requested output(s). Otherwise,
- it executes the command again.
-
- Parameters
- ----------
- command : str
- The shell command to be executed.
- output_file_names : list
- Name of the output file names.
-
- Returns
- -------
- simulation_outputs : array of shape (n_obs, n_outputs)
- Simulation outputs.
-
- """
-
- # Check if simulation is finished
- while True:
- time.sleep(3)
- files = os.listdir(".")
- if all(elem in files for elem in output_file_names):
- break
- else:
- # Run command
- Process = os.system(f'./../{command}')
- if Process != 0:
- print('\nMessage 1:')
- print(f'\tIf the value of \'{Process}\' is a non-zero value'
- ', then compilation problems occur \n' % Process)
- os.chdir("..")
-
- # Read the output
- simulation_outputs = self.read_output()
-
- return simulation_outputs
-
- # -------------------------------------------------------------------------
- def run_forwardmodel(self, xx):
- """
- This function creates subdirectory for the current run and copies the
- necessary files to this directory and renames them. Next, it executes
- the given command.
-
- Parameters
- ----------
- xx : tuple
- A tuple including parameter set, simulation number and key string.
-
- Returns
- -------
- output : array of shape (n_outputs+1, n_obs)
- An array passed by the output paraser containing the x_values as
- the first row and the simulations results stored in the the rest of
- the array.
-
- """
- c_points, run_no, key_str = xx
-
- # Handle if only one imput file is provided
- if not isinstance(self.input_template, list):
- self.input_template = [self.input_template]
- if not isinstance(self.input_file, list):
- self.input_file = [self.input_file]
-
- new_input_file = []
- # Loop over the InputTemplates:
- for in_temp in self.input_template:
- if '/' in in_temp:
- in_temp = in_temp.split('/')[-1]
- new_input_file.append(in_temp.split('.tpl')[0] + key_str +
- f"_{run_no+1}" + in_temp.split('.tpl')[1])
-
- # Create directories
- newpath = self.name + key_str + f'_{run_no+1}'
- if not os.path.exists(newpath):
- os.makedirs(newpath)
-
- # Copy the necessary files to the directories
- print(self.input_template)
- for in_temp in self.input_template:
- # Input file(s) of the model
- shutil.copy2(in_temp, newpath)
- # Auxiliary file
- if self.aux_file is not None:
- shutil.copy2(self.aux_file, newpath) # Auxiliary file
-
- # Rename the Inputfile and/or auxiliary file
- os.chdir(newpath)
- for input_tem, input_file in zip(self.input_template, new_input_file):
- if '/' in input_tem:
- input_tem = input_tem.split('/')[-1]
- os.rename(input_tem, input_file)
-
- # Update the parametrs in Input file
- self.update_input_params(new_input_file, c_points)
-
- # Update the user defined command and the execution path
- try:
- new_command = self.shell_command.replace(self.input_file[0],
- new_input_file[0])
- new_command = new_command.replace(self.input_file[1],
- new_input_file[1])
- except:
- new_command = self.shell_command.replace(self.input_file[0],
- new_input_file[0])
- # Set the exe path if not provided
- if not bool(self.exe_path):
- self.exe_path = os.getcwd()
-
- # Run the model
- print(new_command)
- output = self.run_command(new_command, self.Output.file_names)
-
- return output
-
- # -------------------------------------------------------------------------
- def run_model_parallel(self, c_points, prevRun_No=0, key_str='',
- mp=True, verbose=True):
- """
- Runs model simulations. If mp is true (default), then the simulations
- are started in parallel.
-
- Parameters
- ----------
- c_points : array of shape (n_samples, n_params)
- Collocation points (training set).
- prevRun_No : int, optional
- Previous run number, in case the sequential design is selected.
- The default is `0`.
- key_str : str, optional
- A descriptive string for validation runs. The default is `''`.
- mp : bool, optional
- Multiprocessing. The default is `True`.
- verbose: bool, optional
- Verbosity. The default is `True`.
-
- Returns
- -------
- all_outputs : dict
- A dictionary with x values (time step or point id) and all outputs.
- Each key contains an array of the shape `(n_samples, n_obs)`.
- new_c_points : array
- Updated collocation points (training set). If a simulation does not
- executed successfully, the parameter set is removed.
-
- """
-
- # Initilization
- n_c_points = len(c_points)
- all_outputs = {}
-
- # If the link type is UM-Bridge, then no parallel needs to be started from here
- if self.link_type.lower() == 'umbridge':
- import umbridge
- if not hasattr(self, 'x_values'):
- raise AttributeError('For model type `umbridge` the attribute `x_values` needs to be set for the model!')
- # Init model
- #model = umbridge.HTTPModel('http://localhost:4242', 'forward')
- self.model = umbridge.HTTPModel(self.host, 'forward') # TODO: is this always forward?
- Function = self.uMBridge_model
-
- # Extract the function
- if self.link_type.lower() == 'function':
- # Prepare the function
- Function = getattr(__import__(self.py_file), self.py_file)
- # ---------------------------------------------------------------
- # -------------- Multiprocessing with Pool Class ----------------
- # ---------------------------------------------------------------
- # Start a pool with the number of CPUs
- if self.n_cpus is None:
- n_cpus = multiprocessing.cpu_count()
- else:
- n_cpus = self.n_cpus
-
- # Run forward model
- if n_c_points == 1 or not mp:
- if n_c_points== 1:
- if self.link_type.lower() == 'function' or self.link_type.lower() == 'umbridge':
- group_results = Function(c_points, **self.func_args)
- else:
- group_results = self.run_forwardmodel(
- (c_points[0], prevRun_No, key_str)
- )
- else:
- for i in range(c_points.shape[0]):
- if i == 0:
- if self.link_type.lower() == 'function' or self.link_type.lower() == 'umbridge':
- group_results = Function(np.array([c_points[0]]), **self.func_args)
- else:
- group_results = self.run_forwardmodel(
- (c_points[0], prevRun_No, key_str)
- )
- for key in group_results:
- if key != 'x_values':
- group_results[key] = [group_results[key]]
- else:
- if self.link_type.lower() == 'function' or self.link_type.lower() == 'umbridge':
- res = Function(np.array([c_points[i]]), **self.func_args)
- else:
- res = self.run_forwardmodel(
- (c_points[i], prevRun_No, key_str)
- )
- for key in res:
- if key != 'x_values':
- group_results[key].append(res[key])
-
- for key in group_results:
- if key != 'x_values':
- group_results[key]= np.array(group_results[key])
-
- elif self.multi_process or mp:
- with get_context('spawn').Pool(n_cpus) as p:
- #with multiprocessing.Pool(n_cpus) as p:
-
- if self.link_type.lower() == 'function' or self.link_type.lower() == 'umbridge':
- imap_var = p.imap(partial(Function, **self.func_args),
- c_points[:, np.newaxis])
- else:
- args = zip(c_points,
- [prevRun_No+i for i in range(n_c_points)],
- [key_str]*n_c_points)
- imap_var = p.imap(self.run_forwardmodel, args)
-
- if verbose:
- desc = f'Running forward model {key_str}'
- group_results = list(tqdm.tqdm(imap_var, total=n_c_points,
- desc=desc))
- else:
- group_results = list(imap_var)
-
- # Check for NaN
- for var_i, var in enumerate(self.Output.names):
- # If results are given as one dictionary
- if isinstance(group_results, dict):
- Outputs = np.asarray(group_results[var])
- # If results are given as list of dictionaries
- elif isinstance(group_results, list):
- Outputs = np.asarray([item[var] for item in group_results],
- dtype=np.float64)
- NaN_idx = np.unique(np.argwhere(np.isnan(Outputs))[:, 0])
- new_c_points = np.delete(c_points, NaN_idx, axis=0)
- all_outputs[var] = np.atleast_2d(
- np.delete(Outputs, NaN_idx, axis=0)
- )
-
- # Print the collocation points whose simulations crashed
- if len(NaN_idx) != 0:
- print('\n')
- print('*'*20)
- print("\nThe following parameter sets have been removed:\n",
- c_points[NaN_idx])
- print("\n")
- print('*'*20)
-
- # Save time steps or x-values
- if isinstance(group_results, dict):
- all_outputs["x_values"] = group_results["x_values"]
- elif any(isinstance(i, dict) for i in group_results):
- all_outputs["x_values"] = group_results[0]["x_values"]
-
- # Store simulations in a hdf5 file
- self._store_simulations(
- c_points, all_outputs, NaN_idx, key_str, prevRun_No
- )
-
- return all_outputs, new_c_points
-
- def uMBridge_model(self, params):
- """
- Function that calls a UMBridge model and transforms its output into the
- shape expected for the surrogate.
-
- Parameters
- ----------
- params : 2d np.array, shape (#samples, #params)
- The parameter values for which the model is run.
-
- Returns
- -------
- dict
- The transformed model outputs.
-
- """
- # Run the model
- #out = np.array(model(np.ndarray.tolist(params), {'level':0}))
- out = np.array(self.model(np.ndarray.tolist(params), self.modelparams))
-
- # Sort into dict
- out_dict = {}
- cnt = 0
- for key in self.Output.names:
- # # If needed resort into single-value outputs
- # if self.output_type == 'single-valued':
- # if out.shape[1]>1: # TODO: this doesn't fully seem correct??
- # for i in range(out[:,key]): # TODO: this doesn't fully seem correct??
- # new_key = key+str(i)
- # if new_key not in self.Output.names:
- # self.Output.names.append(new_key)
- # if i == 0:
- # self.Ouptut.names.remove(key)
- # out_dict[new_key] = out[:,cnt,i] # TODO: not sure about this, need to test
- # else:
- # out_dict[key] = out[:,cnt]
- #
- #
- # else:
- out_dict[key] = out[:,cnt]
- cnt += 1
-
-
- ## TODO: how to deal with the x-values?
- #if self.output_type == 'single-valued':
- # out_dict['x_values'] = [0]
- #else:
- # out_dict['x_values'] = np.arange(0,out[:,0].shape[0],1)
- out_dict['x_values'] = self.x_values
-
- #return {'T1':out[:,0], 'T2':out[:,1], 'H1':out[:,2], 'H2':out[:,3],
- # 'x_values':[0]}
- return out_dict
-
- # -------------------------------------------------------------------------
- def _store_simulations(self, c_points, all_outputs, NaN_idx, key_str,
- prevRun_No):
- """
-
-
- Parameters
- ----------
- c_points : TYPE
- DESCRIPTION.
- all_outputs : TYPE
- DESCRIPTION.
- NaN_idx : TYPE
- DESCRIPTION.
- key_str : TYPE
- DESCRIPTION.
- prevRun_No : TYPE
- DESCRIPTION.
-
- Returns
- -------
- None.
-
- """
-
- # Create hdf5 metadata
- if key_str == '':
- hdf5file = f'ExpDesign_{self.name}.hdf5'
- else:
- hdf5file = f'ValidSet_{self.name}.hdf5'
- hdf5_exist = os.path.exists(hdf5file)
- file = h5py.File(hdf5file, 'a')
-
- # ---------- Save time steps or x-values ----------
- if not hdf5_exist:
- if type(all_outputs["x_values"]) is dict:
- grp_x_values = file.create_group("x_values/")
- for varIdx, var in enumerate(self.Output.names):
- grp_x_values.create_dataset(
- var, data=all_outputs["x_values"][var]
- )
- else:
- file.create_dataset("x_values", data=all_outputs["x_values"])
-
- # ---------- Save outputs ----------
- for varIdx, var in enumerate(self.Output.names):
- if not hdf5_exist:
- grpY = file.create_group("EDY/"+var)
- else:
- grpY = file.get("EDY/"+var)
-
- if prevRun_No == 0 and key_str == '':
- grpY.create_dataset(f'init_{key_str}', data=all_outputs[var])
- else:
- try:
- oldEDY = np.array(file[f'EDY/{var}/adaptive_{key_str}'])
- del file[f'EDY/{var}/adaptive_{key_str}']
- data = np.vstack((oldEDY, all_outputs[var]))
- except KeyError:
- data = all_outputs[var]
- grpY.create_dataset('adaptive_'+key_str, data=data)
-
- if prevRun_No == 0 and key_str == '':
- grpY.create_dataset(f"New_init_{key_str}",
- data=all_outputs[var])
- else:
- try:
- name = f'EDY/{var}/New_adaptive_{key_str}'
- oldEDY = np.array(file[name])
- del file[f'EDY/{var}/New_adaptive_{key_str}']
- data = np.vstack((oldEDY, all_outputs[var]))
- except KeyError:
- data = all_outputs[var]
- grpY.create_dataset(f'New_adaptive_{key_str}', data=data)
-
- # ---------- Save CollocationPoints ----------
- new_c_points = np.delete(c_points, NaN_idx, axis=0)
- grpX = file.create_group("EDX") if not hdf5_exist else file.get("EDX")
- if prevRun_No == 0 and key_str == '':
- grpX.create_dataset("init_"+key_str, data=c_points)
- if len(NaN_idx) != 0:
- grpX.create_dataset("New_init_"+key_str, data=new_c_points)
-
- else:
- try:
- name = f'EDX/adaptive_{key_str}'
- oldCollocationPoints = np.array(file[name])
- del file[f'EDX/adaptive_{key_str}']
- data = np.vstack((oldCollocationPoints, new_c_points))
- except KeyError:
- data = new_c_points
- grpX.create_dataset('adaptive_'+key_str, data=data)
-
- if len(NaN_idx) != 0:
- try:
- name = f'EDX/New_adaptive_{key_str}'
- oldCollocationPoints = np.array(file[name])
- del file[f'EDX/New_adaptive_{key_str}']
- data = np.vstack((oldCollocationPoints, new_c_points))
- except KeyError:
- data = new_c_points
- grpX.create_dataset('New_adaptive_'+key_str, data=data)
-
- # Close h5py file
- file.close()
-
- # -------------------------------------------------------------------------
- def zip_subdirs(self, dir_name, key):
- """
- Zips all the files containing the key(word).
-
- Parameters
- ----------
- dir_name : str
- Directory name.
- key : str
- Keyword to search for.
-
- Returns
- -------
- None.
-
- """
- # setup file paths variable
- dir_list = []
- file_paths = []
-
- # Read all directory, subdirectories and file lists
- dir_path = os.getcwd()
-
- for root, directories, files in os.walk(dir_path):
- for directory in directories:
- # Create the full filepath by using os module.
- if key in directory:
- folderPath = os.path.join(dir_path, directory)
- dir_list.append(folderPath)
-
- # Loop over the identified directories to store the file paths
- for direct_name in dir_list:
- for root, directories, files in os.walk(direct_name):
- for filename in files:
- # Create the full filepath by using os module.
- filePath = os.path.join(root, filename)
- file_paths.append('.'+filePath.split(dir_path)[1])
-
- # writing files to a zipfile
- if len(file_paths) != 0:
- zip_file = zipfile.ZipFile(dir_name+'.zip', 'w')
- with zip_file:
- # writing each file one by one
- for file in file_paths:
- zip_file.write(file)
-
- file_paths = [path for path in os.listdir('.') if key in path]
-
- for path in file_paths:
- shutil.rmtree(path)
-
- print("\n")
- print(f'{dir_name}.zip has been created successfully!\n')
-
- return
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/__init__.py b/examples/model-comparison/bayesvalidrox/surrogate_models/__init__.py
deleted file mode 100644
index 70bfb20f570464c2907a0a4128f4ed99b6c13736..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-# -*- coding: utf-8 -*-
-
-from .surrogate_models import MetaModel
-
-__all__ = [
- "MetaModel"
- ]
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diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/adaptPlot.py b/examples/model-comparison/bayesvalidrox/surrogate_models/adaptPlot.py
deleted file mode 100644
index 102f0373c1086ba4420ada2fb2fc723b78bbd53f..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/adaptPlot.py
+++ /dev/null
@@ -1,109 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Aug 13 13:46:24 2020
-
-@author: farid
-"""
-import os
-from sklearn.metrics import mean_squared_error, r2_score
-from itertools import cycle
-from matplotlib.backends.backend_pdf import PdfPages
-import matplotlib.pyplot as plt
-
-
-def adaptPlot(PCEModel, Y_Val, Y_PC_Val, Y_PC_Val_std, x_values=[],
- plotED=False, SaveFig=True):
-
- NrofSamples = PCEModel.ExpDesign.n_new_samples
- initNSamples = PCEModel.ExpDesign.n_init_samples
- itrNr = 1 + (PCEModel.ExpDesign.X.shape[0] - initNSamples)//NrofSamples
-
- oldEDY = PCEModel.ExpDesign.Y
-
- if SaveFig:
- newpath = 'adaptivePlots'
- os.makedirs(newpath, exist_ok=True)
-
- # create a PdfPages object
- pdf = PdfPages(f'./{newpath}/Model_vs_PCEModel_itr_{itrNr}.pdf')
-
- # List of markers and colors
- color = cycle((['b', 'g', 'r', 'y', 'k']))
- marker = cycle(('x', 'd', '+', 'o', '*'))
-
- OutNames = list(Y_Val.keys())
- x_axis = 'Time [s]'
-
- if len(OutNames) == 1:
- OutNames.insert(0, x_axis)
- try:
- x_values = Y_Val['x_values']
- except KeyError:
- x_values = x_values
-
- fig = plt.figure(figsize=(24, 16))
-
- # Plot the model vs PCE model
- for keyIdx, key in enumerate(PCEModel.ModelObj.Output.names):
- Y_PC_Val_ = Y_PC_Val[key]
- Y_PC_Val_std_ = Y_PC_Val_std[key]
- Y_Val_ = Y_Val[key]
- if Y_Val_.ndim == 1:
- Y_Val_ = Y_Val_.reshape(1, -1)
- old_EDY = oldEDY[key]
- if isinstance(x_values, dict):
- x = x_values[key]
- else:
- x = x_values
-
- for idx, y in enumerate(Y_Val_):
- Color = next(color)
- Marker = next(marker)
-
- plt.plot(
- x, y, color=Color, marker=Marker,
- lw=2.0, label='$Y_{%s}^{M}$'%(idx+itrNr)
- )
-
- plt.plot(
- x, Y_PC_Val_[idx], color=Color, marker=Marker,
- lw=2.0, linestyle='--', label='$Y_{%s}^{PCE}$'%(idx+itrNr)
- )
- plt.fill_between(
- x, Y_PC_Val_[idx]-1.96*Y_PC_Val_std_[idx],
- Y_PC_Val_[idx]+1.96*Y_PC_Val_std_[idx], color=Color,
- alpha=0.15
- )
-
- if plotED:
- for output in old_EDY:
- plt.plot(x, output, color='grey', alpha=0.1)
-
- # Calculate the RMSE
- RMSE = mean_squared_error(Y_PC_Val_, Y_Val_, squared=False)
- R2 = r2_score(Y_PC_Val_.reshape(-1, 1), Y_Val_.reshape(-1, 1))
-
- plt.ylabel(key)
- plt.xlabel(x_axis)
- plt.title(key)
-
- ax = fig.axes[0]
- ax.legend(loc='best', frameon=True)
- fig.canvas.draw()
- ax.text(0.65, 0.85,
- f'RMSE = {round(RMSE, 3)}\n$R^2$ = {round(R2, 3)}',
- transform=ax.transAxes, color='black',
- bbox=dict(facecolor='none',
- edgecolor='black',
- boxstyle='round,pad=1')
- )
- plt.grid()
-
- if SaveFig:
- # save the current figure
- pdf.savefig(fig, bbox_inches='tight')
-
- # Destroy the current plot
- plt.clf()
- pdf.close()
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/apoly_construction.py b/examples/model-comparison/bayesvalidrox/surrogate_models/apoly_construction.py
deleted file mode 100644
index 40830fe8aaa94248df4828c0c49bd4d23e755abd..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/apoly_construction.py
+++ /dev/null
@@ -1,124 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-import numpy as np
-
-
-def apoly_construction(Data, degree):
- """
- Construction of Data-driven Orthonormal Polynomial Basis
- Author: Dr.-Ing. habil. Sergey Oladyshkin
- Department of Stochastic Simulation and Safety Research for Hydrosystems
- Institute for Modelling Hydraulic and Environmental Systems
- Universitaet Stuttgart, Pfaffenwaldring 5a, 70569 Stuttgart
- E-mail: Sergey.Oladyshkin@iws.uni-stuttgart.de
- http://www.iws-ls3.uni-stuttgart.de
- The current script is based on definition of arbitrary polynomial chaos
- expansion (aPC), which is presented in the following manuscript:
- Oladyshkin, S. and W. Nowak. Data-driven uncertainty quantification using
- the arbitrary polynomial chaos expansion. Reliability Engineering & System
- Safety, Elsevier, V. 106, P. 179-190, 2012.
- DOI: 10.1016/j.ress.2012.05.002.
-
- Parameters
- ----------
- Data : array
- Raw data.
- degree : int
- Maximum polynomial degree.
-
- Returns
- -------
- Polynomial : array
- The coefficients of the univariate orthonormal polynomials.
-
- """
- if Data.ndim !=1:
- raise AttributeError('Data should be a 1D array')
-
- # Initialization
- dd = degree + 1
- nsamples = len(Data)
-
- # Forward linear transformation (Avoiding numerical issues)
- MeanOfData = np.mean(Data)
- Data = Data/MeanOfData
-
- # Compute raw moments of input data
- raw_moments = [np.sum(np.power(Data, p))/nsamples for p in range(2*dd+2)]
-
- # Main Loop for Polynomial with degree up to dd
- PolyCoeff_NonNorm = np.empty((0, 1))
- Polynomial = np.zeros((dd+1, dd+1))
-
- for degree in range(dd+1):
- Mm = np.zeros((degree+1, degree+1))
- Vc = np.zeros((degree+1))
-
- # Define Moments Matrix Mm
- for i in range(degree+1):
- for j in range(degree+1):
- if (i < degree):
- Mm[i, j] = raw_moments[i+j]
-
- elif (i == degree) and (j == degree):
- Mm[i, j] = 1
-
- # Numerical Optimization for Matrix Solver
- Mm[i] = Mm[i] / max(abs(Mm[i]))
-
- # Defenition of Right Hand side ortogonality conditions: Vc
- for i in range(degree+1):
- Vc[i] = 1 if i == degree else 0
-
- # Solution: Coefficients of Non-Normal Orthogonal Polynomial: Vp Eq.(4)
- try:
- Vp = np.linalg.solve(Mm, Vc)
- except:
- inv_Mm = np.linalg.pinv(Mm)
- Vp = np.dot(inv_Mm, Vc.T)
-
- if degree == 0:
- PolyCoeff_NonNorm = np.append(PolyCoeff_NonNorm, Vp)
-
- if degree != 0:
- if degree == 1:
- zero = [0]
- else:
- zero = np.zeros((degree, 1))
- PolyCoeff_NonNorm = np.hstack((PolyCoeff_NonNorm, zero))
-
- PolyCoeff_NonNorm = np.vstack((PolyCoeff_NonNorm, Vp))
-
- if 100*abs(sum(abs(np.dot(Mm, Vp)) - abs(Vc))) > 0.5:
- print('\n---> Attention: Computational Error too high !')
- print('\n---> Problem: Convergence of Linear Solver')
-
- # Original Numerical Normalization of Coefficients with Norm and
- # orthonormal Basis computation Matrix Storrage
- # Note: Polynomial(i,j) correspont to coefficient number "j-1"
- # of polynomial degree "i-1"
- P_norm = 0
- for i in range(nsamples):
- Poly = 0
- for k in range(degree+1):
- if degree == 0:
- Poly += PolyCoeff_NonNorm[k] * (Data[i]**k)
- else:
- Poly += PolyCoeff_NonNorm[degree, k] * (Data[i]**k)
-
- P_norm += Poly**2 / nsamples
-
- P_norm = np.sqrt(P_norm)
-
- for k in range(degree+1):
- if degree == 0:
- Polynomial[degree, k] = PolyCoeff_NonNorm[k]/P_norm
- else:
- Polynomial[degree, k] = PolyCoeff_NonNorm[degree, k]/P_norm
-
- # Backward linear transformation to the real data space
- Data *= MeanOfData
- for k in range(len(Polynomial)):
- Polynomial[:, k] = Polynomial[:, k] / (MeanOfData**(k))
-
- return Polynomial
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/bayes_linear.py b/examples/model-comparison/bayesvalidrox/surrogate_models/bayes_linear.py
deleted file mode 100644
index 3bd827ac0ecc5b3a38116b21767e8a8799593b24..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/bayes_linear.py
+++ /dev/null
@@ -1,523 +0,0 @@
-import numpy as np
-from sklearn.base import RegressorMixin
-from sklearn.linear_model._base import LinearModel
-from sklearn.utils import check_X_y, check_array, as_float_array
-from sklearn.utils.validation import check_is_fitted
-from scipy.linalg import svd
-import warnings
-from sklearn.preprocessing import normalize as f_normalize
-
-
-
-class BayesianLinearRegression(RegressorMixin,LinearModel):
- '''
- Superclass for Empirical Bayes and Variational Bayes implementations of
- Bayesian Linear Regression Model
- '''
- def __init__(self, n_iter, tol, fit_intercept,copy_X, verbose):
- self.n_iter = n_iter
- self.fit_intercept = fit_intercept
- self.copy_X = copy_X
- self.verbose = verbose
- self.tol = tol
-
-
- def _check_convergence(self, mu, mu_old):
- '''
- Checks convergence of algorithm using changes in mean of posterior
- distribution of weights
- '''
- return np.sum(abs(mu-mu_old)>self.tol) == 0
-
-
- def _center_data(self,X,y):
- ''' Centers data'''
- X = as_float_array(X,copy = self.copy_X)
- # normalisation should be done in preprocessing!
- X_std = np.ones(X.shape[1], dtype = X.dtype)
- if self.fit_intercept:
- X_mean = np.average(X,axis = 0)
- y_mean = np.average(y,axis = 0)
- X -= X_mean
- y = y - y_mean
- else:
- X_mean = np.zeros(X.shape[1],dtype = X.dtype)
- y_mean = 0. if y.ndim == 1 else np.zeros(y.shape[1], dtype=X.dtype)
- return X,y, X_mean, y_mean, X_std
-
-
- def predict_dist(self,X):
- '''
- Calculates mean and variance of predictive distribution for each data
- point of test set.(Note predictive distribution for each data point is
- Gaussian, therefore it is uniquely determined by mean and variance)
-
- Parameters
- ----------
- x: array-like of size (n_test_samples, n_features)
- Set of features for which corresponding responses should be predicted
-
- Returns
- -------
- :list of two numpy arrays [mu_pred, var_pred]
-
- mu_pred : numpy array of size (n_test_samples,)
- Mean of predictive distribution
-
- var_pred: numpy array of size (n_test_samples,)
- Variance of predictive distribution
- '''
- # Note check_array and check_is_fitted are done within self._decision_function(X)
- mu_pred = self._decision_function(X)
- data_noise = 1./self.beta_
- model_noise = np.sum(np.dot(X,self.eigvecs_)**2 * self.eigvals_,1)
- var_pred = data_noise + model_noise
- return [mu_pred,var_pred]
-
-
-
-
-class EBLinearRegression(BayesianLinearRegression):
- '''
- Bayesian Regression with type II maximum likelihood (Empirical Bayes)
-
- Parameters:
- -----------
- n_iter: int, optional (DEFAULT = 300)
- Maximum number of iterations
-
- tol: float, optional (DEFAULT = 1e-3)
- Threshold for convergence
-
- optimizer: str, optional (DEFAULT = 'fp')
- Method for optimization , either Expectation Maximization or
- Fixed Point Gull-MacKay {'em','fp'}. Fixed point iterations are
- faster, but can be numerically unstable (especially in case of near perfect fit).
-
- fit_intercept: bool, optional (DEFAULT = True)
- If True includes bias term in model
-
- perfect_fit_tol: float (DEAFAULT = 1e-5)
- Prevents overflow of precision parameters (this is smallest value RSS can have).
- ( !!! Note if using EM instead of fixed-point, try smaller values
- of perfect_fit_tol, for better estimates of variance of predictive distribution )
-
- alpha: float (DEFAULT = 1)
- Initial value of precision paramter for coefficients ( by default we define
- very broad distribution )
-
- copy_X : boolean, optional (DEFAULT = True)
- If True, X will be copied, otherwise will be
-
- verbose: bool, optional (Default = False)
- If True at each iteration progress report is printed out
-
- Attributes
- ----------
- coef_ : array, shape = (n_features)
- Coefficients of the regression model (mean of posterior distribution)
-
- intercept_: float
- Value of bias term (if fit_intercept is False, then intercept_ = 0)
-
- alpha_ : float
- Estimated precision of coefficients
-
- beta_ : float
- Estimated precision of noise
-
- eigvals_ : array, shape = (n_features, )
- Eigenvalues of covariance matrix (from posterior distribution of weights)
-
- eigvecs_ : array, shape = (n_features, n_featues)
- Eigenvectors of covariance matrix (from posterior distribution of weights)
-
- '''
-
- def __init__(self,n_iter = 300, tol = 1e-3, optimizer = 'fp', fit_intercept = True,
- normalize=True, perfect_fit_tol = 1e-6, alpha = 1, copy_X = True, verbose = False):
- super(EBLinearRegression,self).__init__(n_iter, tol, fit_intercept, copy_X, verbose)
- if optimizer not in ['em','fp']:
- raise ValueError('Optimizer can be either "em" or "fp" ')
- self.optimizer = optimizer
- self.alpha = alpha
- self.perfect_fit = False
- self.normalize = True
- self.scores_ = [np.NINF]
- self.perfect_fit_tol = perfect_fit_tol
-
- def _check_convergence(self, mu, mu_old):
- '''
- Checks convergence of algorithm using changes in mean of posterior
- distribution of weights
- '''
- return np.sum(abs(mu-mu_old)>self.tol) == 0
-
-
- def _center_data(self,X,y):
- ''' Centers data'''
- X = as_float_array(X,copy = self.copy_X)
- # normalisation should be done in preprocessing!
- X_std = np.ones(X.shape[1], dtype = X.dtype)
- if self.fit_intercept:
- X_mean = np.average(X, axis=0)
- X -= X_mean
- if self.normalize:
- X, X_std = f_normalize(X, axis=0, copy=False,
- return_norm=True)
- else:
- X_std = np.ones(X.shape[1], dtype=X.dtype)
- y_mean = np.average(y, axis=0)
- y = y - y_mean
- else:
- X_mean = np.zeros(X.shape[1],dtype = X.dtype)
- y_mean = 0. if y.ndim == 1 else np.zeros(y.shape[1], dtype=X.dtype)
- return X,y, X_mean, y_mean, X_std
-
- def fit(self, X, y):
- '''
- Fits Bayesian Linear Regression using Empirical Bayes
-
- Parameters
- ----------
- X: array-like of size [n_samples,n_features]
- Matrix of explanatory variables (should not include bias term)
-
- y: array-like of size [n_features]
- Vector of dependent variables.
-
- Returns
- -------
- object: self
- self
-
- '''
- # preprocess data
- X, y = check_X_y(X, y, dtype=np.float64, y_numeric=True)
- n_samples, n_features = X.shape
- X, y, X_mean, y_mean, X_std = self._center_data(X, y)
- self._x_mean_ = X_mean
- self._y_mean = y_mean
- self._x_std = X_std
-
- # precision of noise & and coefficients
- alpha = self.alpha
- var_y = np.var(y)
- # check that variance is non zero !!!
- if var_y == 0 :
- beta = 1e-2
- else:
- beta = 1. / np.var(y)
-
- # to speed all further computations save svd decomposition and reuse it later
- u,d,vt = svd(X, full_matrices = False)
- Uy = np.dot(u.T,y)
- dsq = d**2
- mu = 0
-
- for i in range(self.n_iter):
-
- # find mean for posterior of w ( for EM this is E-step)
- mu_old = mu
- if n_samples > n_features:
- mu = vt.T * d/(dsq+alpha/beta)
- else:
- # clever use of SVD here , faster for large n_features
- mu = u * 1./(dsq + alpha/beta)
- mu = np.dot(X.T,mu)
- mu = np.dot(mu,Uy)
-
- # precompute errors, since both methods use it in estimation
- error = y - np.dot(X,mu)
- sqdErr = np.sum(error**2)
-
- if sqdErr / n_samples < self.perfect_fit_tol:
- self.perfect_fit = True
- warnings.warn( ('Almost perfect fit!!! Estimated values of variance '
- 'for predictive distribution are computed using only RSS'))
- break
-
- if self.optimizer == "fp":
- gamma = np.sum(beta*dsq/(beta*dsq + alpha))
- # use updated mu and gamma parameters to update alpha and beta
- # !!! made computation numerically stable for perfect fit case
- alpha = gamma / (np.sum(mu**2) + np.finfo(np.float32).eps )
- beta = ( n_samples - gamma ) / (sqdErr + np.finfo(np.float32).eps )
- else:
- # M-step, update parameters alpha and beta to maximize ML TYPE II
- eigvals = 1. / (beta * dsq + alpha)
- alpha = n_features / ( np.sum(mu**2) + np.sum(1/eigvals) )
- beta = n_samples / ( sqdErr + np.sum(dsq/eigvals) )
-
- # if converged or exceeded maximum number of iterations => terminate
- converged = self._check_convergence(mu_old,mu)
- if self.verbose:
- print( "Iteration {0} completed".format(i) )
- if converged is True:
- print("Algorithm converged after {0} iterations".format(i))
- if converged or i==self.n_iter -1:
- break
- eigvals = 1./(beta * dsq + alpha)
- self.coef_ = beta*np.dot(vt.T*d*eigvals ,Uy)
- self._set_intercept(X_mean,y_mean,X_std)
- self.beta_ = beta
- self.alpha_ = alpha
- self.eigvals_ = eigvals
- self.eigvecs_ = vt.T
-
- # set intercept_
- if self.fit_intercept:
- self.coef_ = self.coef_ / X_std
- self.intercept_ = y_mean - np.dot(X_mean, self.coef_.T)
- else:
- self.intercept_ = 0.
-
- return self
-
- def predict(self,X, return_std=False):
- '''
- Computes predictive distribution for test set.
- Predictive distribution for each data point is one dimensional
- Gaussian and therefore is characterised by mean and variance.
-
- Parameters
- -----------
- X: {array-like, sparse} (n_samples_test, n_features)
- Test data, matrix of explanatory variables
-
- Returns
- -------
- : list of length two [y_hat, var_hat]
-
- y_hat: numpy array of size (n_samples_test,)
- Estimated values of targets on test set (i.e. mean of predictive
- distribution)
-
- var_hat: numpy array of size (n_samples_test,)
- Variance of predictive distribution
- '''
- y_hat = np.dot(X,self.coef_) + self.intercept_
-
- if return_std:
- if self.normalize:
- X = (X - self._x_mean_) / self._x_std
- data_noise = 1./self.beta_
- model_noise = np.sum(np.dot(X,self.eigvecs_)**2 * self.eigvals_,1)
- var_pred = data_noise + model_noise
- std_hat = np.sqrt(var_pred)
- return y_hat, std_hat
- else:
- return y_hat
-
-
-# ============================== VBLR =========================================
-
-def gamma_mean(a,b):
- '''
- Computes mean of gamma distribution
-
- Parameters
- ----------
- a: float
- Shape parameter of Gamma distribution
-
- b: float
- Rate parameter of Gamma distribution
-
- Returns
- -------
- : float
- Mean of Gamma distribution
- '''
- return float(a) / b
-
-
-
-class VBLinearRegression(BayesianLinearRegression):
- '''
- Implements Bayesian Linear Regression using mean-field approximation.
- Assumes gamma prior on precision parameters of coefficients and noise.
-
- Parameters:
- -----------
- n_iter: int, optional (DEFAULT = 100)
- Maximum number of iterations for KL minimization
-
- tol: float, optional (DEFAULT = 1e-3)
- Convergence threshold
-
- fit_intercept: bool, optional (DEFAULT = True)
- If True will use bias term in model fitting
-
- a: float, optional (Default = 1e-4)
- Shape parameter of Gamma prior for precision of coefficients
-
- b: float, optional (Default = 1e-4)
- Rate parameter of Gamma prior for precision coefficients
-
- c: float, optional (Default = 1e-4)
- Shape parameter of Gamma prior for precision of noise
-
- d: float, optional (Default = 1e-4)
- Rate parameter of Gamma prior for precision of noise
-
- verbose: bool, optional (Default = False)
- If True at each iteration progress report is printed out
-
- Attributes
- ----------
- coef_ : array, shape = (n_features)
- Coefficients of the regression model (mean of posterior distribution)
-
- intercept_: float
- Value of bias term (if fit_intercept is False, then intercept_ = 0)
-
- alpha_ : float
- Mean of precision of coefficients
-
- beta_ : float
- Mean of precision of noise
-
- eigvals_ : array, shape = (n_features, )
- Eigenvalues of covariance matrix (from posterior distribution of weights)
-
- eigvecs_ : array, shape = (n_features, n_featues)
- Eigenvectors of covariance matrix (from posterior distribution of weights)
-
- '''
-
- def __init__(self, n_iter = 100, tol =1e-4, fit_intercept = True,
- a = 1e-4, b = 1e-4, c = 1e-4, d = 1e-4, copy_X = True,
- verbose = False):
- super(VBLinearRegression,self).__init__(n_iter, tol, fit_intercept, copy_X,
- verbose)
- self.a,self.b = a, b
- self.c,self.d = c, d
-
-
- def fit(self,X,y):
- '''
- Fits Variational Bayesian Linear Regression Model
-
- Parameters
- ----------
- X: array-like of size [n_samples,n_features]
- Matrix of explanatory variables (should not include bias term)
-
- Y: array-like of size [n_features]
- Vector of dependent variables.
-
- Returns
- -------
- object: self
- self
- '''
- # preprocess data
- X, y = check_X_y(X, y, dtype=np.float64, y_numeric=True)
- n_samples, n_features = X.shape
- X, y, X_mean, y_mean, X_std = self._center_data(X, y)
- self._x_mean_ = X_mean
- self._y_mean = y_mean
- self._x_std = X_std
-
- # SVD decomposition, done once , reused at each iteration
- u,D,vt = svd(X, full_matrices = False)
- dsq = D**2
- UY = np.dot(u.T,y)
-
- # some parameters of Gamma distribution have closed form solution
- a = self.a + 0.5 * n_features
- c = self.c + 0.5 * n_samples
- b,d = self.b, self.d
-
- # initial mean of posterior for coefficients
- mu = 0
-
- for i in range(self.n_iter):
-
- # update parameters of distribution Q(weights)
- e_beta = gamma_mean(c,d)
- e_alpha = gamma_mean(a,b)
- mu_old = np.copy(mu)
- mu,eigvals = self._posterior_weights(e_beta,e_alpha,UY,dsq,u,vt,D,X)
-
- # update parameters of distribution Q(precision of weights)
- b = self.b + 0.5*( np.sum(mu**2) + np.sum(eigvals))
-
- # update parameters of distribution Q(precision of likelihood)
- sqderr = np.sum((y - np.dot(X,mu))**2)
- xsx = np.sum(dsq*eigvals)
- d = self.d + 0.5*(sqderr + xsx)
-
- # check convergence
- converged = self._check_convergence(mu,mu_old)
- if self.verbose is True:
- print("Iteration {0} is completed".format(i))
- if converged is True:
- print("Algorithm converged after {0} iterations".format(i))
-
- # terminate if convergence or maximum number of iterations are achieved
- if converged or i==(self.n_iter-1):
- break
-
- # save necessary parameters
- self.beta_ = gamma_mean(c,d)
- self.alpha_ = gamma_mean(a,b)
- self.coef_, self.eigvals_ = self._posterior_weights(self.beta_, self.alpha_, UY,
- dsq, u, vt, D, X)
- self._set_intercept(X_mean,y_mean,X_std)
- self.eigvecs_ = vt.T
- return self
-
-
- def _posterior_weights(self, e_beta, e_alpha, UY, dsq, u, vt, d, X):
- '''
- Calculates parameters of approximate posterior distribution
- of weights
- '''
- # eigenvalues of covariance matrix
- sigma = 1./ (e_beta*dsq + e_alpha)
-
- # mean of approximate posterior distribution
- n_samples, n_features = X.shape
- if n_samples > n_features:
- mu = vt.T * d/(dsq + e_alpha/e_beta)# + np.finfo(np.float64).eps)
- else:
- mu = u * 1./(dsq + e_alpha/e_beta)# + np.finfo(np.float64).eps)
- mu = np.dot(X.T,mu)
- mu = np.dot(mu,UY)
- return mu,sigma
-
- def predict(self,X, return_std=False):
- '''
- Computes predictive distribution for test set.
- Predictive distribution for each data point is one dimensional
- Gaussian and therefore is characterised by mean and variance.
-
- Parameters
- -----------
- X: {array-like, sparse} (n_samples_test, n_features)
- Test data, matrix of explanatory variables
-
- Returns
- -------
- : list of length two [y_hat, var_hat]
-
- y_hat: numpy array of size (n_samples_test,)
- Estimated values of targets on test set (i.e. mean of predictive
- distribution)
-
- var_hat: numpy array of size (n_samples_test,)
- Variance of predictive distribution
- '''
- x = (X - self._x_mean_) / self._x_std
- y_hat = np.dot(x,self.coef_) + self._y_mean
-
- if return_std:
- data_noise = 1./self.beta_
- model_noise = np.sum(np.dot(X,self.eigvecs_)**2 * self.eigvals_,1)
- var_pred = data_noise + model_noise
- std_hat = np.sqrt(var_pred)
- return y_hat, std_hat
- else:
- return y_hat
\ No newline at end of file
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/engine.py b/examples/model-comparison/bayesvalidrox/surrogate_models/engine.py
deleted file mode 100644
index 42307d4770d4ae23a40107dfea64057aac682c23..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/engine.py
+++ /dev/null
@@ -1,2225 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Engine to train the surrogate
-
-"""
-import copy
-from copy import deepcopy, copy
-import h5py
-import joblib
-import numpy as np
-import os
-
-from scipy import stats, signal, linalg, sparse
-from scipy.spatial import distance
-from tqdm import tqdm
-import scipy.optimize as opt
-from sklearn.metrics import mean_squared_error
-import multiprocessing
-import matplotlib.pyplot as plt
-import pandas as pd
-import sys
-import seaborn as sns
-from joblib import Parallel, delayed
-
-
-from bayesvalidrox.bayes_inference.bayes_inference import BayesInference
-from bayesvalidrox.bayes_inference.discrepancy import Discrepancy
-from .exploration import Exploration
-import pathlib
-
-#from .inputs import Input
-#from .exp_designs import ExpDesigns
-#from .surrogate_models import MetaModel
-#from bayesvalidrox.post_processing.post_processing import PostProcessing
-
-def hellinger_distance(P, Q):
- """
- Hellinger distance between two continuous distributions.
-
- The maximum distance 1 is achieved when P assigns probability zero to
- every set to which Q assigns a positive probability, and vice versa.
- 0 (identical) and 1 (maximally different)
-
- Parameters
- ----------
- P : array
- Reference likelihood.
- Q : array
- Estimated likelihood.
-
- Returns
- -------
- float
- Hellinger distance of two distributions.
-
- """
- P = np.array(P)
- Q= np.array(Q)
-
- mu1 = P.mean()
- Sigma1 = np.std(P)
-
- mu2 = Q.mean()
- Sigma2 = np.std(Q)
-
- term1 = np.sqrt(2*Sigma1*Sigma2 / (Sigma1**2 + Sigma2**2))
-
- term2 = np.exp(-.25 * (mu1 - mu2)**2 / (Sigma1**2 + Sigma2**2))
-
- H_squared = 1 - term1 * term2
-
- return np.sqrt(H_squared)
-
-
-def logpdf(x, mean, cov):
- """
- Computes the likelihood based on a multivariate normal distribution.
-
- Parameters
- ----------
- x : TYPE
- DESCRIPTION.
- mean : array_like
- Observation data.
- cov : 2d array
- Covariance matrix of the distribution.
-
- Returns
- -------
- log_lik : float
- Log likelihood.
-
- """
- n = len(mean)
- L = linalg.cholesky(cov, lower=True)
- beta = np.sum(np.log(np.diag(L)))
- dev = x - mean
- alpha = dev.dot(linalg.cho_solve((L, True), dev))
- log_lik = -0.5 * alpha - beta - n / 2. * np.log(2 * np.pi)
-
- return log_lik
-
-def subdomain(Bounds, n_new_samples):
- """
- Divides a domain defined by Bounds into sub domains.
-
- Parameters
- ----------
- Bounds : list of tuples
- List of lower and upper bounds.
- n_new_samples : int
- Number of samples to divide the domain for.
- n_params : int
- The number of params to build the subdomains for
-
- Returns
- -------
- Subdomains : List of tuples of tuples
- Each tuple of tuples divides one set of bounds into n_new_samples parts.
-
- """
- n_params = len(Bounds)
- n_subdomains = n_new_samples + 1
- LinSpace = np.zeros((n_params, n_subdomains))
-
- for i in range(n_params):
- LinSpace[i] = np.linspace(start=Bounds[i][0], stop=Bounds[i][1],
- num=n_subdomains)
- Subdomains = []
- for k in range(n_subdomains-1):
- mylist = []
- for i in range(n_params):
- mylist.append((LinSpace[i, k+0], LinSpace[i, k+1]))
- Subdomains.append(tuple(mylist))
-
- return Subdomains
-
-class Engine():
-
-
- def __init__(self, MetaMod, Model, ExpDes):
- self.MetaModel = MetaMod
- self.Model = Model
- self.ExpDesign = ExpDes
- self.parallel = False
-
- def start_engine(self) -> None:
- """
- Do all the preparations that need to be run before the actual training
-
- Returns
- -------
- None
-
- """
- self.out_names = self.Model.Output.names
- self.MetaModel.out_names = self.out_names
-
-
- def train_normal(self, parallel = False, verbose = False, save = False) -> None:
- """
- Trains surrogate on static samples only.
- Samples are taken from the experimental design and the specified
- model is run on them.
- Alternatively the samples can be read in from a provided hdf5 file.
-
-
- Returns
- -------
- None
-
- """
-
- ExpDesign = self.ExpDesign
- MetaModel = self.MetaModel
-
- # Read ExpDesign (training and targets) from the provided hdf5
- if ExpDesign.hdf5_file is not None:
- # TODO: need to run 'generate_ED' as well after this or not?
- ExpDesign.read_from_file(self.out_names)
- else:
- # Check if an old hdf5 file exists: if yes, rename it
- hdf5file = f'ExpDesign_{self.Model.name}.hdf5'
- if os.path.exists(hdf5file):
- # os.rename(hdf5file, 'old_'+hdf5file)
- file = pathlib.Path(hdf5file)
- file.unlink()
-
- # Prepare X samples
- # For training the surrogate use ExpDesign.X_tr, ExpDesign.X is for the model to run on
- ExpDesign.generate_ED(ExpDesign.n_init_samples,
- transform=True,
- max_pce_deg=np.max(MetaModel.pce_deg))
-
- # Run simulations at X
- if not hasattr(ExpDesign, 'Y') or ExpDesign.Y is None:
- print('\n Now the forward model needs to be run!\n')
- ED_Y, up_ED_X = self.Model.run_model_parallel(ExpDesign.X, mp = parallel)
- ExpDesign.Y = ED_Y
- else:
- # Check if a dict has been passed.
- if not type(ExpDesign.Y) is dict:
- raise Exception('Please provide either a dictionary or a hdf5'
- 'file to ExpDesign.hdf5_file argument.')
-
- # Separate output dict and x-values
- if 'x_values' in ExpDesign.Y:
- ExpDesign.x_values = ExpDesign.Y['x_values']
- del ExpDesign.Y['x_values']
- else:
- print('No x_values are given, this might lead to issues during PostProcessing')
-
-
- # Fit the surrogate
- MetaModel.fit(ExpDesign.X, ExpDesign.Y, parallel, verbose)
-
- # Save what there is to save
- if save:
- # Save surrogate
- with open(f'surrogates/surrogate_{self.Model.name}.pk1', 'wb') as output:
- joblib.dump(MetaModel, output, 2)
-
- # Zip the model run directories
- if self.Model.link_type.lower() == 'pylink' and\
- self.ExpDesign.sampling_method.lower() != 'user':
- self.Model.zip_subdirs(self.Model.name, f'{self.Model.name}_')
-
-
- def train_sequential(self, parallel = False, verbose = False) -> None:
- """
- Train the surrogate in a sequential manner.
- First build and train evereything on the static samples, then iterate
- choosing more samples and refitting the surrogate on them.
-
- Returns
- -------
- None
-
- """
- #self.train_normal(parallel, verbose)
- self.parallel = parallel
- self.train_seq_design(parallel, verbose)
-
-
- # -------------------------------------------------------------------------
- def eval_metamodel(self, samples=None, nsamples=None,
- sampling_method='random', return_samples=False):
- """
- Evaluates meta-model at the requested samples. One can also generate
- nsamples.
-
- Parameters
- ----------
- samples : array of shape (n_samples, n_params), optional
- Samples to evaluate meta-model at. The default is None.
- nsamples : int, optional
- Number of samples to generate, if no `samples` is provided. The
- default is None.
- sampling_method : str, optional
- Type of sampling, if no `samples` is provided. The default is
- 'random'.
- return_samples : bool, optional
- Retun samples, if no `samples` is provided. The default is False.
-
- Returns
- -------
- mean_pred : dict
- Mean of the predictions.
- std_pred : dict
- Standard deviatioon of the predictions.
- """
- # Generate or transform (if need be) samples
- if samples is None:
- # Generate
- samples = self.ExpDesign.generate_samples(
- nsamples,
- sampling_method
- )
-
- # Transformation to other space is to be done in the MetaModel
- # TODO: sort the transformations better
- mean_pred, std_pred = self.MetaModel.eval_metamodel(samples)
-
- if return_samples:
- return mean_pred, std_pred, samples
- else:
- return mean_pred, std_pred
-
-
- # -------------------------------------------------------------------------
- def train_seq_design(self, parallel = False, verbose = False):
- """
- Starts the adaptive sequential design for refining the surrogate model
- by selecting training points in a sequential manner.
-
- Returns
- -------
- MetaModel : object
- Meta model object.
-
- """
- self.parallel = parallel
-
- # Initialization
- self.SeqModifiedLOO = {}
- self.seqValidError = {}
- self.SeqBME = {}
- self.SeqKLD = {}
- self.SeqDistHellinger = {}
- self.seqRMSEMean = {}
- self.seqRMSEStd = {}
- self.seqMinDist = []
-
- if not hasattr(self.MetaModel, 'valid_samples'):
- self.ExpDesign.valid_samples = []
- self.ExpDesign.valid_model_runs = []
- self.valid_likelihoods = []
-
- validError = None
-
-
- # Determine the metamodel type
- if self.MetaModel.meta_model_type.lower() != 'gpe':
- pce = True
- else:
- pce = False
- mc_ref = True if bool(self.Model.mc_reference) else False
- if mc_ref:
- self.Model.read_observation('mc_ref')
-
- # Get the parameters
- max_n_samples = self.ExpDesign.n_max_samples
- mod_LOO_threshold = self.ExpDesign.mod_LOO_threshold
- n_canddidate = self.ExpDesign.n_canddidate
- post_snapshot = self.ExpDesign.post_snapshot
- n_replication = self.ExpDesign.n_replication
- util_func = self.ExpDesign.util_func
- output_name = self.out_names
-
- # Handle if only one UtilityFunctions is provided
- if not isinstance(util_func, list):
- util_func = [self.ExpDesign.util_func]
-
- # Read observations or MCReference
- # TODO: recheck the logic in this if statement
- if (len(self.Model.observations) != 0 or self.Model.meas_file is not None) and hasattr(self.MetaModel, 'Discrepancy'):
- self.observations = self.Model.read_observation()
- obs_data = self.observations
- else:
- obs_data = []
- # TODO: TotalSigma2 not defined if not in this else???
- # TODO: no self.observations if in here
- TotalSigma2 = {}
-
- # ---------- Initial self.MetaModel ----------
- self.train_normal(parallel = parallel, verbose=verbose)
-
- initMetaModel = deepcopy(self.MetaModel)
-
- # Validation error if validation set is provided.
- if self.ExpDesign.valid_model_runs:
- init_rmse, init_valid_error = self._validError(initMetaModel)
- init_valid_error = list(init_valid_error.values())
- else:
- init_rmse = None
-
- # Check if discrepancy is provided
- if len(obs_data) != 0 and hasattr(self.MetaModel, 'Discrepancy'):
- TotalSigma2 = self.MetaModel.Discrepancy.parameters
-
- # Calculate the initial BME
- out = self._BME_Calculator(
- obs_data, TotalSigma2, init_rmse)
- init_BME, init_KLD, init_post, init_likes, init_dist_hellinger = out
- print(f"\nInitial BME: {init_BME:.2f}")
- print(f"Initial KLD: {init_KLD:.2f}")
-
- # Posterior snapshot (initial)
- if post_snapshot:
- parNames = self.ExpDesign.par_names
- print('Posterior snapshot (initial) is being plotted...')
- self.__posteriorPlot(init_post, parNames, 'SeqPosterior_init')
-
- # Check the convergence of the Mean & Std
- if mc_ref and pce:
- init_rmse_mean, init_rmse_std = self._error_Mean_Std()
- print(f"Initial Mean and Std error: {init_rmse_mean:.2f},"
- f" {init_rmse_std:.2f}")
-
- # Read the initial experimental design
- Xinit = self.ExpDesign.X
- init_n_samples = len(self.ExpDesign.X)
- initYprev = self.ExpDesign.Y#initMetaModel.ModelOutputDict
- #self.MetaModel.ModelOutputDict = self.ExpDesign.Y
- initLCerror = initMetaModel.LCerror
- n_itrs = max_n_samples - init_n_samples
-
- ## Get some initial statistics
- # Read the initial ModifiedLOO
- if pce:
- Scores_all, varExpDesignY = [], []
- for out_name in output_name:
- y = self.ExpDesign.Y[out_name]
- Scores_all.append(list(
- self.MetaModel.score_dict['b_1'][out_name].values()))
- if self.MetaModel.dim_red_method.lower() == 'pca':
- pca = self.MetaModel.pca['b_1'][out_name]
- components = pca.transform(y)
- varExpDesignY.append(np.var(components, axis=0))
- else:
- varExpDesignY.append(np.var(y, axis=0))
-
- Scores = [item for sublist in Scores_all for item in sublist]
- weights = [item for sublist in varExpDesignY for item in sublist]
- init_mod_LOO = [np.average([1-score for score in Scores],
- weights=weights)]
-
- prevMetaModel_dict = {}
- #prevExpDesign_dict = {}
- # Can run sequential design multiple times for comparison
- for repIdx in range(n_replication):
- print(f'\n>>>> Replication: {repIdx+1}<<<<')
-
- # util_func: the function to use inside the type of exploitation
- for util_f in util_func:
- print(f'\n>>>> Utility Function: {util_f} <<<<')
- # To avoid changes ub original aPCE object
- self.ExpDesign.X = Xinit
- self.ExpDesign.Y = initYprev
- self.ExpDesign.LCerror = initLCerror
-
- # Set the experimental design
- Xprev = Xinit
- total_n_samples = init_n_samples
- Yprev = initYprev
-
- Xfull = []
- Yfull = []
-
- # Store the initial ModifiedLOO
- if pce:
- print("\nInitial ModifiedLOO:", init_mod_LOO)
- SeqModifiedLOO = np.array(init_mod_LOO)
-
- if len(self.ExpDesign.valid_model_runs) != 0:
- SeqValidError = np.array(init_valid_error)
-
- # Check if data is provided
- if len(obs_data) != 0 and hasattr(self.MetaModel, 'Discrepancy'):
- SeqBME = np.array([init_BME])
- SeqKLD = np.array([init_KLD])
- SeqDistHellinger = np.array([init_dist_hellinger])
-
- if mc_ref and pce:
- seqRMSEMean = np.array([init_rmse_mean])
- seqRMSEStd = np.array([init_rmse_std])
-
- # ------- Start Sequential Experimental Design -------
- postcnt = 1
- for itr_no in range(1, n_itrs+1):
- print(f'\n>>>> Iteration number {itr_no} <<<<')
-
- # Save the metamodel prediction before updating
- prevMetaModel_dict[itr_no] = deepcopy(self.MetaModel)
- #prevExpDesign_dict[itr_no] = deepcopy(self.ExpDesign)
- if itr_no > 1:
- pc_model = prevMetaModel_dict[itr_no-1]
- self._y_hat_prev, _ = pc_model.eval_metamodel(
- samples=Xfull[-1].reshape(1, -1))
- del prevMetaModel_dict[itr_no-1]
-
- # Optimal Bayesian Design
- #self.MetaModel.ExpDesignFlag = 'sequential'
- Xnew, updatedPrior = self.choose_next_sample(TotalSigma2,
- n_canddidate,
- util_f)
- S = np.min(distance.cdist(Xinit, Xnew, 'euclidean'))
- self.seqMinDist.append(S)
- print(f"\nmin Dist from OldExpDesign: {S:2f}")
- print("\n")
-
- # Evaluate the full model response at the new sample
- Ynew, _ = self.Model.run_model_parallel(
- Xnew, prevRun_No=total_n_samples
- )
- total_n_samples += Xnew.shape[0]
-
- # ------ Plot the surrogate model vs Origninal Model ------
- if hasattr(self.ExpDesign, 'adapt_verbose') and \
- self.ExpDesign.adapt_verbose:
- from .adaptPlot import adaptPlot
- y_hat, std_hat = self.MetaModel.eval_metamodel(
- samples=Xnew
- )
- adaptPlot(
- self.MetaModel, Ynew, y_hat, std_hat,
- plotED=False
- )
-
- # -------- Retrain the surrogate model -------
- # Extend new experimental design
- Xfull = np.vstack((Xprev, Xnew))
-
- # Updating experimental design Y
- for out_name in output_name:
- Yfull = np.vstack((Yprev[out_name], Ynew[out_name]))
- self.ExpDesign.Y[out_name] = Yfull
-
- # Pass new design to the metamodel object
- self.ExpDesign.sampling_method = 'user'
- self.ExpDesign.X = Xfull
- #self.ExpDesign.Y = self.MetaModel.ModelOutputDict
-
- # Save the Experimental Design for next iteration
- Xprev = Xfull
- Yprev = self.ExpDesign.Y
-
- # Pass the new prior as the input
- # TODO: another look at this - no difference apc to pce to gpe?
- self.MetaModel.input_obj.poly_coeffs_flag = False
- if updatedPrior is not None:
- self.MetaModel.input_obj.poly_coeffs_flag = True
- print("updatedPrior:", updatedPrior.shape)
- # Arbitrary polynomial chaos
- for i in range(updatedPrior.shape[1]):
- self.MetaModel.input_obj.Marginals[i].dist_type = None
- x = updatedPrior[:, i]
- self.MetaModel.input_obj.Marginals[i].raw_data = x
-
- # Train the surrogate model for new ExpDesign
- self.train_normal(parallel=False)
-
- # -------- Evaluate the retrained surrogate model -------
- # Extract Modified LOO from Output
- if pce:
- Scores_all, varExpDesignY = [], []
- for out_name in output_name:
- y = self.ExpDesign.Y[out_name]
- Scores_all.append(list(
- self.MetaModel.score_dict['b_1'][out_name].values()))
- if self.MetaModel.dim_red_method.lower() == 'pca':
- pca = self.MetaModel.pca['b_1'][out_name]
- components = pca.transform(y)
- varExpDesignY.append(np.var(components,
- axis=0))
- else:
- varExpDesignY.append(np.var(y, axis=0))
- Scores = [item for sublist in Scores_all for item
- in sublist]
- weights = [item for sublist in varExpDesignY for item
- in sublist]
- ModifiedLOO = [np.average(
- [1-score for score in Scores], weights=weights)]
-
- print('\n')
- print(f"Updated ModifiedLOO {util_f}:\n", ModifiedLOO)
- print('\n')
-
- # Compute the validation error
- if self.ExpDesign.valid_model_runs:
- rmse, validError = self._validError(self.MetaModel)
- ValidError = list(validError.values())
- else:
- rmse = None
-
- # Store updated ModifiedLOO
- if pce:
- SeqModifiedLOO = np.vstack(
- (SeqModifiedLOO, ModifiedLOO))
- if len(self.ExpDesign.valid_model_runs) != 0:
- SeqValidError = np.vstack(
- (SeqValidError, ValidError))
- # -------- Caclulation of BME as accuracy metric -------
- # Check if data is provided
- if len(obs_data) != 0:
- # Calculate the initial BME
- out = self._BME_Calculator(obs_data, TotalSigma2, rmse)
- BME, KLD, Posterior, likes, DistHellinger = out
- print('\n')
- print(f"Updated BME: {BME:.2f}")
- print(f"Updated KLD: {KLD:.2f}")
- print('\n')
-
- # Plot some snapshots of the posterior
- step_snapshot = self.ExpDesign.step_snapshot
- if post_snapshot and postcnt % step_snapshot == 0:
- parNames = self.ExpDesign.par_names
- print('Posterior snapshot is being plotted...')
- self.__posteriorPlot(Posterior, parNames,
- f'SeqPosterior_{postcnt}')
- postcnt += 1
-
- # Check the convergence of the Mean&Std
- if mc_ref and pce:
- print('\n')
- RMSE_Mean, RMSE_std = self._error_Mean_Std()
- print(f"Updated Mean and Std error: {RMSE_Mean:.2f}, "
- f"{RMSE_std:.2f}")
- print('\n')
-
- # Store the updated BME & KLD
- # Check if data is provided
- if len(obs_data) != 0:
- SeqBME = np.vstack((SeqBME, BME))
- SeqKLD = np.vstack((SeqKLD, KLD))
- SeqDistHellinger = np.vstack((SeqDistHellinger,
- DistHellinger))
- if mc_ref and pce:
- seqRMSEMean = np.vstack((seqRMSEMean, RMSE_Mean))
- seqRMSEStd = np.vstack((seqRMSEStd, RMSE_std))
-
- if pce and any(LOO < mod_LOO_threshold
- for LOO in ModifiedLOO):
- break
-
- # Clean up
- if len(obs_data) != 0:
- del out
- print()
- print('-'*50)
- print()
-
- # Store updated ModifiedLOO and BME in dictonary
- strKey = f'{util_f}_rep_{repIdx+1}'
- if pce:
- self.SeqModifiedLOO[strKey] = SeqModifiedLOO
- if len(self.ExpDesign.valid_model_runs) != 0:
- self.seqValidError[strKey] = SeqValidError
-
- # Check if data is provided
- if len(obs_data) != 0:
- self.SeqBME[strKey] = SeqBME
- self.SeqKLD[strKey] = SeqKLD
- if hasattr(self.MetaModel, 'valid_likelihoods') and \
- self.valid_likelihoods:
- self.SeqDistHellinger[strKey] = SeqDistHellinger
- if mc_ref and pce:
- self.seqRMSEMean[strKey] = seqRMSEMean
- self.seqRMSEStd[strKey] = seqRMSEStd
-
- # return self.MetaModel
-
- # -------------------------------------------------------------------------
- def util_VarBasedDesign(self, X_can, index, util_func='Entropy'):
- """
- Computes the exploitation scores based on:
- active learning MacKay(ALM) and active learning Cohn (ALC)
- Paper: Sequential Design with Mutual Information for Computer
- Experiments (MICE): Emulation of a Tsunami Model by Beck and Guillas
- (2016)
-
- Parameters
- ----------
- X_can : array of shape (n_samples, n_params)
- Candidate samples.
- index : int
- Model output index.
- UtilMethod : string, optional
- Exploitation utility function. The default is 'Entropy'.
-
- Returns
- -------
- float
- Score.
-
- """
- MetaModel = self.MetaModel
- ED_X = self.ExpDesign.X
- out_dict_y = self.ExpDesign.Y
- out_names = self.out_names
-
- # Run the Metamodel for the candidate
- X_can = X_can.reshape(1, -1)
- Y_PC_can, std_PC_can = MetaModel.eval_metamodel(samples=X_can)
-
- if util_func.lower() == 'alm':
- # ----- Entropy/MMSE/active learning MacKay(ALM) -----
- # Compute perdiction variance of the old model
- canPredVar = {key: std_PC_can[key]**2 for key in out_names}
-
- varPCE = np.zeros((len(out_names), X_can.shape[0]))
- for KeyIdx, key in enumerate(out_names):
- varPCE[KeyIdx] = np.max(canPredVar[key], axis=1)
- score = np.max(varPCE, axis=0)
-
- elif util_func.lower() == 'eigf':
- # ----- Expected Improvement for Global fit -----
- # Find closest EDX to the candidate
- distances = distance.cdist(ED_X, X_can, 'euclidean')
- index = np.argmin(distances)
-
- # Compute perdiction error and variance of the old model
- predError = {key: Y_PC_can[key] for key in out_names}
- canPredVar = {key: std_PC_can[key]**2 for key in out_names}
-
- # Compute perdiction error and variance of the old model
- # Eq (5) from Liu et al.(2018)
- EIGF_PCE = np.zeros((len(out_names), X_can.shape[0]))
- for KeyIdx, key in enumerate(out_names):
- residual = predError[key] - out_dict_y[key][int(index)]
- var = canPredVar[key]
- EIGF_PCE[KeyIdx] = np.max(residual**2 + var, axis=1)
- score = np.max(EIGF_PCE, axis=0)
-
- return -1 * score # -1 is for minimization instead of maximization
-
- # -------------------------------------------------------------------------
- def util_BayesianActiveDesign(self, y_hat, std, sigma2Dict, var='DKL'):
- """
- Computes scores based on Bayesian active design criterion (var).
-
- It is based on the following paper:
- Oladyshkin, Sergey, Farid Mohammadi, Ilja Kroeker, and Wolfgang Nowak.
- "Bayesian3 active learning for the gaussian process emulator using
- information theory." Entropy 22, no. 8 (2020): 890.
-
- Parameters
- ----------
- X_can : array of shape (n_samples, n_params)
- Candidate samples.
- sigma2Dict : dict
- A dictionary containing the measurement errors (sigma^2).
- var : string, optional
- BAL design criterion. The default is 'DKL'.
-
- Returns
- -------
- float
- Score.
-
- """
-
- # Get the data
- obs_data = self.observations
- # TODO: this should be optimizable to be calculated explicitly
- if hasattr(self.Model, 'n_obs'):
- n_obs = self.Model.n_obs
- else:
- n_obs = self.n_obs
- mc_size = 10000
-
- # Sample a distribution for a normal dist
- # with Y_mean_can as the mean and Y_std_can as std.
- Y_MC, std_MC = {}, {}
- logPriorLikelihoods = np.zeros((mc_size))
- # print(y_hat)
- # print(list[y_hat])
- for key in list(y_hat):
- cov = np.diag(std[key]**2)
- # print(y_hat[key], cov)
- # TODO: added the allow_singular = True here
- rv = stats.multivariate_normal(mean=y_hat[key], cov=cov,)
- Y_MC[key] = rv.rvs(size=mc_size)
- logPriorLikelihoods += rv.logpdf(Y_MC[key])
- std_MC[key] = np.zeros((mc_size, y_hat[key].shape[0]))
-
- # Likelihood computation (Comparison of data and simulation
- # results via PCE with candidate design)
- likelihoods = self._normpdf(Y_MC, std_MC, obs_data, sigma2Dict)
-
- # Rejection Step
- # Random numbers between 0 and 1
- unif = np.random.rand(1, mc_size)[0]
-
- # Reject the poorly performed prior
- accepted = (likelihoods/np.max(likelihoods)) >= unif
-
- # Prior-based estimation of BME
- logBME = np.log(np.nanmean(likelihoods), dtype=np.longdouble)#float128)
-
- # Posterior-based expectation of likelihoods
- postLikelihoods = likelihoods[accepted]
- postExpLikelihoods = np.mean(np.log(postLikelihoods))
-
- # Posterior-based expectation of prior densities
- postExpPrior = np.mean(logPriorLikelihoods[accepted])
-
- # Utility function Eq.2 in Ref. (2)
- # Posterior covariance matrix after observing data y
- # Kullback-Leibler Divergence (Sergey's paper)
- if var == 'DKL':
-
- # TODO: Calculate the correction factor for BME
- # BMECorrFactor = self.BME_Corr_Weight(PCE_SparseBayes_can,
- # ObservationData, sigma2Dict)
- # BME += BMECorrFactor
- # Haun et al implementation
- # U_J_d = np.mean(np.log(Likelihoods[Likelihoods!=0])- logBME)
- U_J_d = postExpLikelihoods - logBME
-
- # Marginal log likelihood
- elif var == 'BME':
- U_J_d = np.nanmean(likelihoods)
-
- # Entropy-based information gain
- elif var == 'infEntropy':
- logBME = np.log(np.nanmean(likelihoods))
- infEntropy = logBME - postExpPrior - postExpLikelihoods
- U_J_d = infEntropy * -1 # -1 for minimization
-
- # Bayesian information criterion
- elif var == 'BIC':
- coeffs = self.MetaModel.coeffs_dict.values()
- nModelParams = max(len(v) for val in coeffs for v in val.values())
- maxL = np.nanmax(likelihoods)
- U_J_d = -2 * np.log(maxL) + np.log(n_obs) * nModelParams
-
- # Akaike information criterion
- elif var == 'AIC':
- coeffs = self.MetaModel.coeffs_dict.values()
- nModelParams = max(len(v) for val in coeffs for v in val.values())
- maxlogL = np.log(np.nanmax(likelihoods))
- AIC = -2 * maxlogL + 2 * nModelParams
- # 2 * nModelParams * (nModelParams+1) / (n_obs-nModelParams-1)
- penTerm = 0
- U_J_d = 1*(AIC + penTerm)
-
- # Deviance information criterion
- elif var == 'DIC':
- # D_theta_bar = np.mean(-2 * Likelihoods)
- N_star_p = 0.5 * np.var(np.log(likelihoods[likelihoods != 0]))
- Likelihoods_theta_mean = self._normpdf(
- y_hat, std, obs_data, sigma2Dict
- )
- DIC = -2 * np.log(Likelihoods_theta_mean) + 2 * N_star_p
-
- U_J_d = DIC
-
- else:
- print('The algorithm you requested has not been implemented yet!')
-
- # Handle inf and NaN (replace by zero)
- if np.isnan(U_J_d) or U_J_d == -np.inf or U_J_d == np.inf:
- U_J_d = 0.0
-
- # Clear memory
- del likelihoods
- del Y_MC
- del std_MC
-
- return -1 * U_J_d # -1 is for minimization instead of maximization
-
- # -------------------------------------------------------------------------
- def util_BayesianDesign(self, X_can, X_MC, sigma2Dict, var='DKL'):
- """
- Computes scores based on Bayesian sequential design criterion (var).
-
- Parameters
- ----------
- X_can : array of shape (n_samples, n_params)
- Candidate samples.
- sigma2Dict : dict
- A dictionary containing the measurement errors (sigma^2).
- var : string, optional
- Bayesian design criterion. The default is 'DKL'.
-
- Returns
- -------
- float
- Score.
-
- """
-
- # To avoid changes ub original aPCE object
- MetaModel = self.MetaModel
- out_names = self.out_names
- if X_can.ndim == 1:
- X_can = X_can.reshape(1, -1)
-
- # Compute the mean and std based on the MetaModel
- # pce_means, pce_stds = self._compute_pce_moments(MetaModel)
- if var == 'ALC':
- Y_MC, Y_MC_std = MetaModel.eval_metamodel(samples=X_MC)
-
- # Old Experimental design
- oldExpDesignX = self.ExpDesign.X
- oldExpDesignY = self.ExpDesign.Y
-
- # Evaluate the PCE metamodels at that location ???
- Y_PC_can, Y_std_can = MetaModel.eval_metamodel(samples=X_can)
- PCE_Model_can = deepcopy(MetaModel)
- engine_can = deepcopy(self)
- # Add the candidate to the ExpDesign
- NewExpDesignX = np.vstack((oldExpDesignX, X_can))
-
- NewExpDesignY = {}
- for key in oldExpDesignY.keys():
- NewExpDesignY[key] = np.vstack(
- (oldExpDesignY[key], Y_PC_can[key])
- )
-
- engine_can.ExpDesign.sampling_method = 'user'
- engine_can.ExpDesign.X = NewExpDesignX
- #engine_can.ModelOutputDict = NewExpDesignY
- engine_can.ExpDesign.Y = NewExpDesignY
-
- # Train the model for the observed data using x_can
- engine_can.MetaModel.input_obj.poly_coeffs_flag = False
- engine_can.start_engine()
- engine_can.train_normal(parallel=False)
- engine_can.MetaModel.fit(NewExpDesignX, NewExpDesignY)
-# engine_can.train_norm_design(parallel=False)
-
- # Set the ExpDesign to its original values
- engine_can.ExpDesign.X = oldExpDesignX
- engine_can.ModelOutputDict = oldExpDesignY
- engine_can.ExpDesign.Y = oldExpDesignY
-
- if var.lower() == 'mi':
- # Mutual information based on Krause et al
- # Adapted from Beck & Guillas (MICE) paper
- _, std_PC_can = engine_can.MetaModel.eval_metamodel(samples=X_can)
- std_can = {key: std_PC_can[key] for key in out_names}
-
- std_old = {key: Y_std_can[key] for key in out_names}
-
- varPCE = np.zeros((len(out_names)))
- for i, key in enumerate(out_names):
- varPCE[i] = np.mean(std_old[key]**2/std_can[key]**2)
- score = np.mean(varPCE)
-
- return -1 * score
-
- elif var.lower() == 'alc':
- # Active learning based on Gramyc and Lee
- # Adaptive design and analysis of supercomputer experiments Techno-
- # metrics, 51 (2009), pp. 130–145.
-
- # Evaluate the MetaModel at the given samples
- Y_MC_can, Y_MC_std_can = engine_can.MetaModel.eval_metamodel(samples=X_MC)
-
- # Compute the score
- score = []
- for i, key in enumerate(out_names):
- pce_var = Y_MC_std_can[key]**2
- pce_var_can = Y_MC_std[key]**2
- score.append(np.mean(pce_var-pce_var_can, axis=0))
- score = np.mean(score)
-
- return -1 * score
-
- # ---------- Inner MC simulation for computing Utility Value ----------
- # Estimation of the integral via Monte Varlo integration
- MCsize = X_MC.shape[0]
- ESS = 0
-
- while ((ESS > MCsize) or (ESS < 1)):
-
- # Enriching Monte Carlo samples if need be
- if ESS != 0:
- X_MC = self.ExpDesign.generate_samples(
- MCsize, 'random'
- )
-
- # Evaluate the MetaModel at the given samples
- Y_MC, std_MC = PCE_Model_can.eval_metamodel(samples=X_MC)
-
- # Likelihood computation (Comparison of data and simulation
- # results via PCE with candidate design)
- likelihoods = self._normpdf(
- Y_MC, std_MC, self.observations, sigma2Dict
- )
-
- # Check the Effective Sample Size (1<ESS<MCsize)
- ESS = 1 / np.sum(np.square(likelihoods/np.sum(likelihoods)))
-
- # Enlarge sample size if it doesn't fulfill the criteria
- if ((ESS > MCsize) or (ESS < 1)):
- print("--- increasing MC size---")
- MCsize *= 10
- ESS = 0
-
- # Rejection Step
- # Random numbers between 0 and 1
- unif = np.random.rand(1, MCsize)[0]
-
- # Reject the poorly performed prior
- accepted = (likelihoods/np.max(likelihoods)) >= unif
-
- # -------------------- Utility functions --------------------
- # Utility function Eq.2 in Ref. (2)
- # Kullback-Leibler Divergence (Sergey's paper)
- if var == 'DKL':
-
- # Prior-based estimation of BME
- logBME = np.log(np.nanmean(likelihoods, dtype=np.longdouble))#float128))
-
- # Posterior-based expectation of likelihoods
- postLikelihoods = likelihoods[accepted]
- postExpLikelihoods = np.mean(np.log(postLikelihoods))
-
- # Haun et al implementation
- U_J_d = np.mean(np.log(likelihoods[likelihoods != 0]) - logBME)
-
- # U_J_d = np.sum(G_n_m_all)
- # Ryan et al (2014) implementation
- # importanceWeights = Likelihoods[Likelihoods!=0]/np.sum(Likelihoods[Likelihoods!=0])
- # U_J_d = np.mean(importanceWeights*np.log(Likelihoods[Likelihoods!=0])) - logBME
-
- # U_J_d = postExpLikelihoods - logBME
-
- # Marginal likelihood
- elif var == 'BME':
-
- # Prior-based estimation of BME
- logBME = np.log(np.nanmean(likelihoods))
- U_J_d = logBME
-
- # Bayes risk likelihood
- elif var == 'BayesRisk':
-
- U_J_d = -1 * np.var(likelihoods)
-
- # Entropy-based information gain
- elif var == 'infEntropy':
- # Prior-based estimation of BME
- logBME = np.log(np.nanmean(likelihoods))
-
- # Posterior-based expectation of likelihoods
- postLikelihoods = likelihoods[accepted]
- postLikelihoods /= np.nansum(likelihoods[accepted])
- postExpLikelihoods = np.mean(np.log(postLikelihoods))
-
- # Posterior-based expectation of prior densities
- postExpPrior = np.mean(logPriorLikelihoods[accepted])
-
- infEntropy = logBME - postExpPrior - postExpLikelihoods
-
- U_J_d = infEntropy * -1 # -1 for minimization
-
- # D-Posterior-precision
- elif var == 'DPP':
- X_Posterior = X_MC[accepted]
- # covariance of the posterior parameters
- U_J_d = -np.log(np.linalg.det(np.cov(X_Posterior)))
-
- # A-Posterior-precision
- elif var == 'APP':
- X_Posterior = X_MC[accepted]
- # trace of the posterior parameters
- U_J_d = -np.log(np.trace(np.cov(X_Posterior)))
-
- else:
- print('The algorithm you requested has not been implemented yet!')
-
- # Clear memory
- del likelihoods
- del Y_MC
- del std_MC
-
- return -1 * U_J_d # -1 is for minimization instead of maximization
-
-
- # -------------------------------------------------------------------------
- def run_util_func(self, method, candidates, index, sigma2Dict=None,
- var=None, X_MC=None):
- """
- Runs the utility function based on the given method.
-
- Parameters
- ----------
- method : string
- Exploitation method: `VarOptDesign`, `BayesActDesign` and
- `BayesOptDesign`.
- candidates : array of shape (n_samples, n_params)
- All candidate parameter sets.
- index : int
- ExpDesign index.
- sigma2Dict : dict, optional
- A dictionary containing the measurement errors (sigma^2). The
- default is None.
- var : string, optional
- Utility function. The default is None.
- X_MC : TYPE, optional
- DESCRIPTION. The default is None.
-
- Returns
- -------
- index : TYPE
- DESCRIPTION.
- List
- Scores.
-
- """
-
- if method.lower() == 'varoptdesign':
- # U_J_d = self.util_VarBasedDesign(candidates, index, var)
- U_J_d = np.zeros((candidates.shape[0]))
- for idx, X_can in tqdm(enumerate(candidates), ascii=True,
- desc="varoptdesign"):
- U_J_d[idx] = self.util_VarBasedDesign(X_can, index, var)
-
- elif method.lower() == 'bayesactdesign':
- NCandidate = candidates.shape[0]
- U_J_d = np.zeros((NCandidate))
- # Evaluate all candidates
- y_can, std_can = self.MetaModel.eval_metamodel(samples=candidates)
- # loop through candidates
- for idx, X_can in tqdm(enumerate(candidates), ascii=True,
- desc="BAL Design"):
- y_hat = {key: items[idx] for key, items in y_can.items()}
- std = {key: items[idx] for key, items in std_can.items()}
-
- # print(y_hat)
- # print(std)
- U_J_d[idx] = self.util_BayesianActiveDesign(
- y_hat, std, sigma2Dict, var)
-
- elif method.lower() == 'bayesoptdesign':
- NCandidate = candidates.shape[0]
- U_J_d = np.zeros((NCandidate))
- for idx, X_can in tqdm(enumerate(candidates), ascii=True,
- desc="OptBayesianDesign"):
- U_J_d[idx] = self.util_BayesianDesign(X_can, X_MC, sigma2Dict,
- var)
- return (index, -1 * U_J_d)
-
- # -------------------------------------------------------------------------
- def dual_annealing(self, method, Bounds, sigma2Dict, var, Run_No,
- verbose=False):
- """
- Exploration algorithm to find the optimum parameter space.
-
- Parameters
- ----------
- method : string
- Exploitation method: `VarOptDesign`, `BayesActDesign` and
- `BayesOptDesign`.
- Bounds : list of tuples
- List of lower and upper boundaries of parameters.
- sigma2Dict : dict
- A dictionary containing the measurement errors (sigma^2).
- Run_No : int
- Run number.
- verbose : bool, optional
- Print out a summary. The default is False.
-
- Returns
- -------
- Run_No : int
- Run number.
- array
- Optimial candidate.
-
- """
-
- Model = self.Model
- max_func_itr = self.ExpDesign.max_func_itr
-
- if method == 'VarOptDesign':
- Res_Global = opt.dual_annealing(self.util_VarBasedDesign,
- bounds=Bounds,
- args=(Model, var),
- maxfun=max_func_itr)
-
- elif method == 'BayesOptDesign':
- Res_Global = opt.dual_annealing(self.util_BayesianDesign,
- bounds=Bounds,
- args=(Model, sigma2Dict, var),
- maxfun=max_func_itr)
-
- if verbose:
- print(f"Global minimum: xmin = {Res_Global.x}, "
- f"f(xmin) = {Res_Global.fun:.6f}, nfev = {Res_Global.nfev}")
-
- return (Run_No, Res_Global.x)
-
- # -------------------------------------------------------------------------
- def tradeoff_weights(self, tradeoff_scheme, old_EDX, old_EDY):
- """
- Calculates weights for exploration scores based on the requested
- scheme: `None`, `equal`, `epsilon-decreasing` and `adaptive`.
-
- `None`: No exploration.
- `equal`: Same weights for exploration and exploitation scores.
- `epsilon-decreasing`: Start with more exploration and increase the
- influence of exploitation along the way with a exponential decay
- function
- `adaptive`: An adaptive method based on:
- Liu, Haitao, Jianfei Cai, and Yew-Soon Ong. "An adaptive sampling
- approach for Kriging metamodeling by maximizing expected prediction
- error." Computers & Chemical Engineering 106 (2017): 171-182.
-
- Parameters
- ----------
- tradeoff_scheme : string
- Trade-off scheme for exloration and exploitation scores.
- old_EDX : array (n_samples, n_params)
- Old experimental design (training points).
- old_EDY : dict
- Old model responses (targets).
-
- Returns
- -------
- exploration_weight : float
- Exploration weight.
- exploitation_weight: float
- Exploitation weight.
-
- """
- if tradeoff_scheme is None:
- exploration_weight = 0
-
- elif tradeoff_scheme == 'equal':
- exploration_weight = 0.5
-
- elif tradeoff_scheme == 'epsilon-decreasing':
- # epsilon-decreasing scheme
- # Start with more exploration and increase the influence of
- # exploitation along the way with a exponential decay function
- initNSamples = self.ExpDesign.n_init_samples
- n_max_samples = self.ExpDesign.n_max_samples
-
- itrNumber = (self.ExpDesign.X.shape[0] - initNSamples)
- itrNumber //= self.ExpDesign.n_new_samples
-
- tau2 = -(n_max_samples-initNSamples-1) / np.log(1e-8)
- exploration_weight = signal.exponential(n_max_samples-initNSamples,
- 0, tau2, False)[itrNumber]
-
- elif tradeoff_scheme == 'adaptive':
-
- # Extract itrNumber
- initNSamples = self.ExpDesign.n_init_samples
- n_max_samples = self.ExpDesign.n_max_samples
- itrNumber = (self.ExpDesign.X.shape[0] - initNSamples)
- itrNumber //= self.ExpDesign.n_new_samples
-
- if itrNumber == 0:
- exploration_weight = 0.5
- else:
- # New adaptive trade-off according to Liu et al. (2017)
- # Mean squared error for last design point
- last_EDX = old_EDX[-1].reshape(1, -1)
- lastPCEY, _ = self.MetaModel.eval_metamodel(samples=last_EDX)
- pce_y = np.array(list(lastPCEY.values()))[:, 0]
- y = np.array(list(old_EDY.values()))[:, -1, :]
- mseError = mean_squared_error(pce_y, y)
-
- # Mean squared CV - error for last design point
- pce_y_prev = np.array(list(self._y_hat_prev.values()))[:, 0]
- mseCVError = mean_squared_error(pce_y_prev, y)
-
- exploration_weight = min([0.5*mseError/mseCVError, 1])
-
- # Exploitation weight
- exploitation_weight = 1 - exploration_weight
-
- return exploration_weight, exploitation_weight
-
- # -------------------------------------------------------------------------
- def choose_next_sample(self, sigma2=None, n_candidates=5, var='DKL'):
- """
- Runs optimal sequential design.
-
- Parameters
- ----------
- sigma2 : dict, optional
- A dictionary containing the measurement errors (sigma^2). The
- default is None.
- n_candidates : int, optional
- Number of candidate samples. The default is 5.
- var : string, optional
- Utility function. The default is None. # TODO: default is set to DKL, not none
-
- Raises
- ------
- NameError
- Wrong utility function.
-
- Returns
- -------
- Xnew : array (n_samples, n_params)
- Selected new training point(s).
- """
-
- # Initialization
- Bounds = self.ExpDesign.bound_tuples
- n_new_samples = self.ExpDesign.n_new_samples
- explore_method = self.ExpDesign.explore_method
- exploit_method = self.ExpDesign.exploit_method
- n_cand_groups = self.ExpDesign.n_cand_groups
- tradeoff_scheme = self.ExpDesign.tradeoff_scheme
-
- old_EDX = self.ExpDesign.X
- old_EDY = self.ExpDesign.Y.copy()
- ndim = self.ExpDesign.X.shape[1]
- OutputNames = self.out_names
-
- # -----------------------------------------
- # ----------- CUSTOMIZED METHODS ----------
- # -----------------------------------------
- # Utility function exploit_method provided by user
- if exploit_method.lower() == 'user':
- if not hasattr(self.ExpDesign, 'ExploitFunction'):
- raise AttributeError('Function `ExploitFunction` not given to the ExpDesign, thus cannor run user-defined sequential scheme')
- # TODO: syntax does not fully match the rest - can test this??
- Xnew, filteredSamples = self.ExpDesign.ExploitFunction(self)
-
- print("\n")
- print("\nXnew:\n", Xnew)
-
- return Xnew, filteredSamples
-
-
- # Dual-Annealing works differently from the rest, so deal with this first
- # Here exploration and exploitation are performed simulataneously
- if explore_method == 'dual annealing':
- # ------- EXPLORATION: OPTIMIZATION -------
- import time
- start_time = time.time()
-
- # Divide the domain to subdomains
- subdomains = subdomain(Bounds, n_new_samples)
-
- # Multiprocessing
- if self.parallel:
- args = []
- for i in range(n_new_samples):
- args.append((exploit_method, subdomains[i], sigma2, var, i))
- pool = multiprocessing.Pool(multiprocessing.cpu_count())
-
- # With Pool.starmap_async()
- results = pool.starmap_async(self.dual_annealing, args).get()
-
- # Close the pool
- pool.close()
- # Without multiprocessing
- else:
- results = []
- for i in range(n_new_samples):
- results.append(self.dual_annealing(exploit_method, subdomains[i], sigma2, var, i))
-
- # New sample
- Xnew = np.array([results[i][1] for i in range(n_new_samples)])
- print("\nXnew:\n", Xnew)
-
- # Computational cost
- elapsed_time = time.time() - start_time
- print("\n")
- print(f"Elapsed_time: {round(elapsed_time,2)} sec.")
- print('-'*20)
-
- return Xnew, None
-
- # Generate needed Exploration class
- explore = Exploration(self.ExpDesign, n_candidates)
- explore.w = 100 # * ndim #500 # TODO: where does this value come from?
-
- # Select criterion (mc-intersite-proj-th, mc-intersite-proj)
- explore.mc_criterion = 'mc-intersite-proj'
-
- # Generate the candidate samples
- # TODO: here use the sampling method provided by the expdesign?
- sampling_method = self.ExpDesign.sampling_method
-
- # TODO: changed this from 'random' for LOOCV
- if explore_method == 'LOOCV':
- allCandidates = self.ExpDesign.generate_samples(n_candidates,
- sampling_method)
- else:
- allCandidates, scoreExploration = explore.get_exploration_samples()
-
- # -----------------------------------------
- # ---------- EXPLORATION METHODS ----------
- # -----------------------------------------
- if explore_method == 'LOOCV':
- # -----------------------------------------------------------------
- # TODO: LOOCV model construnction based on Feng et al. (2020)
- # 'LOOCV':
- # Initilize the ExploitScore array
-
- # Generate random samples
- allCandidates = self.ExpDesign.generate_samples(n_candidates,
- 'random')
-
- # Construct error model based on LCerror
- errorModel = self.MetaModel.create_ModelError(old_EDX, self.LCerror)
- self.errorModel.append(copy(errorModel))
-
- # Evaluate the error models for allCandidates
- eLCAllCands, _ = errorModel.eval_errormodel(allCandidates)
- # Select the maximum as the representative error
- eLCAllCands = np.dstack(eLCAllCands.values())
- eLCAllCandidates = np.max(eLCAllCands, axis=1)[:, 0]
-
- # Normalize the error w.r.t the maximum error
- scoreExploration = eLCAllCandidates / np.sum(eLCAllCandidates)
-
- else:
- # ------- EXPLORATION: SPACE-FILLING DESIGN -------
- # Generate candidate samples from Exploration class
- explore = Exploration(self.ExpDesign, n_candidates)
- explore.w = 100 # * ndim #500
- # Select criterion (mc-intersite-proj-th, mc-intersite-proj)
- explore.mc_criterion = 'mc-intersite-proj'
- allCandidates, scoreExploration = explore.get_exploration_samples()
-
- # Temp: ---- Plot all candidates -----
- if ndim == 2:
- def plotter(points, allCandidates, Method,
- scoreExploration=None):
- if Method == 'Voronoi':
- from scipy.spatial import Voronoi, voronoi_plot_2d
- vor = Voronoi(points)
- fig = voronoi_plot_2d(vor)
- ax1 = fig.axes[0]
- else:
- fig = plt.figure()
- ax1 = fig.add_subplot(111)
- ax1.scatter(points[:, 0], points[:, 1], s=10, c='r',
- marker="s", label='Old Design Points')
- ax1.scatter(allCandidates[:, 0], allCandidates[:, 1], s=10,
- c='b', marker="o", label='Design candidates')
- for i in range(points.shape[0]):
- txt = 'p'+str(i+1)
- ax1.annotate(txt, (points[i, 0], points[i, 1]))
- if scoreExploration is not None:
- for i in range(allCandidates.shape[0]):
- txt = str(round(scoreExploration[i], 5))
- ax1.annotate(txt, (allCandidates[i, 0],
- allCandidates[i, 1]))
-
- plt.xlim(self.bound_tuples[0])
- plt.ylim(self.bound_tuples[1])
- # plt.show()
- plt.legend(loc='upper left')
-
- # -----------------------------------------
- # --------- EXPLOITATION METHODS ----------
- # -----------------------------------------
- if exploit_method == 'BayesOptDesign' or\
- exploit_method == 'BayesActDesign':
-
- # ------- Calculate Exoploration weight -------
- # Compute exploration weight based on trade off scheme
- explore_w, exploit_w = self.tradeoff_weights(tradeoff_scheme,
- old_EDX,
- old_EDY)
- print(f"\n Exploration weight={explore_w:0.3f} "
- f"Exploitation weight={exploit_w:0.3f}\n")
-
- # ------- EXPLOITATION: BayesOptDesign & ActiveLearning -------
- if explore_w != 1.0:
- # Check if all needed properties are set
- if not hasattr(self.ExpDesign, 'max_func_itr'):
- raise AttributeError('max_func_itr not given to the experimental design')
-
- # Create a sample pool for rejection sampling
- MCsize = 15000
- X_MC = self.ExpDesign.generate_samples(MCsize, 'random')
- candidates = self.ExpDesign.generate_samples(
- n_candidates, 'latin_hypercube')
-
- # Split the candidates in groups for multiprocessing
- split_cand = np.array_split(
- candidates, n_cand_groups, axis=0
- )
- # print(candidates)
- # print(split_cand)
- if self.parallel:
- results = Parallel(n_jobs=-1, backend='multiprocessing')(
- delayed(self.run_util_func)(
- exploit_method, split_cand[i], i, sigma2, var, X_MC)
- for i in range(n_cand_groups))
- else:
- results = []
- for i in range(n_cand_groups):
- results.append(self.run_util_func(exploit_method, split_cand[i], i, sigma2, var, X_MC))
-
- # Retrieve the results and append them
- U_J_d = np.concatenate([results[NofE][1] for NofE in
- range(n_cand_groups)])
-
- # Check if all scores are inf
- if np.isinf(U_J_d).all() or np.isnan(U_J_d).all():
- U_J_d = np.ones(len(U_J_d))
-
- # Get the expected value (mean) of the Utility score
- # for each cell
- if explore_method == 'Voronoi':
- U_J_d = np.mean(U_J_d.reshape(-1, n_candidates), axis=1)
-
- # Normalize U_J_d
- norm_U_J_d = U_J_d / np.sum(U_J_d)
- else:
- norm_U_J_d = np.zeros((len(scoreExploration)))
-
- # ------- Calculate Total score -------
- # ------- Trade off between EXPLORATION & EXPLOITATION -------
- # Accumulate the samples
- finalCandidates = np.concatenate((allCandidates, candidates), axis = 0)
- finalCandidates = np.unique(finalCandidates, axis = 0)
-
- # Calculations take into account both exploration and exploitation
- # samples without duplicates
- totalScore = np.zeros(finalCandidates.shape[0])
- #self.totalScore = totalScore
-
- for cand_idx in range(finalCandidates.shape[0]):
- # find candidate indices
- idx1 = np.where(allCandidates == finalCandidates[cand_idx])[0]
- idx2 = np.where(candidates == finalCandidates[cand_idx])[0]
-
- # exploration
- if idx1 != []:
- idx1 = idx1[0]
- totalScore[cand_idx] += explore_w * scoreExploration[idx1]
-
- # exploitation
- if idx2 != []:
- idx2 = idx2[0]
- totalScore[cand_idx] += exploit_w * norm_U_J_d[idx2]
-
-
- # Total score
- totalScore = exploit_w * norm_U_J_d
- totalScore += explore_w * scoreExploration
-
- # temp: Plot
- # dim = self.ExpDesign.X.shape[1]
- # if dim == 2:
- # plotter(self.ExpDesign.X, allCandidates, explore_method)
-
- # ------- Select the best candidate -------
- # find an optimal point subset to add to the initial design by
- # maximization of the utility score and taking care of NaN values
- temp = totalScore.copy()
- temp[np.isnan(totalScore)] = -np.inf
- sorted_idxtotalScore = np.argsort(temp)[::-1]
- bestIdx = sorted_idxtotalScore[:n_new_samples]
-
- # select the requested number of samples
- if explore_method == 'Voronoi':
- Xnew = np.zeros((n_new_samples, ndim))
- for i, idx in enumerate(bestIdx):
- X_can = explore.closestPoints[idx]
-
- # Calculate the maxmin score for the region of interest
- newSamples, maxminScore = explore.get_mc_samples(X_can)
-
- # select the requested number of samples
- Xnew[i] = newSamples[np.argmax(maxminScore)]
- else:
- # Changed this from allCandiates to full set of candidates
- # TODO: still not changed for e.g. 'Voronoi'
- Xnew = finalCandidates[sorted_idxtotalScore[:n_new_samples]]
-
-
- elif exploit_method == 'VarOptDesign':
- # ------- EXPLOITATION: VarOptDesign -------
- UtilMethod = var
-
- # ------- Calculate Exoploration weight -------
- # Compute exploration weight based on trade off scheme
- explore_w, exploit_w = self.tradeoff_weights(tradeoff_scheme,
- old_EDX,
- old_EDY)
- print(f"\nweightExploration={explore_w:0.3f} "
- f"weightExploitation={exploit_w:0.3f}")
-
- # Generate candidate samples from Exploration class
- nMeasurement = old_EDY[OutputNames[0]].shape[1]
-
- # print(UtilMethod)
-
- # Find sensitive region
- if UtilMethod == 'LOOCV':
- LCerror = self.MetaModel.LCerror
- allModifiedLOO = np.zeros((len(old_EDX), len(OutputNames),
- nMeasurement))
- for y_idx, y_key in enumerate(OutputNames):
- for idx, key in enumerate(LCerror[y_key].keys()):
- allModifiedLOO[:, y_idx, idx] = abs(
- LCerror[y_key][key])
-
- ExploitScore = np.max(np.max(allModifiedLOO, axis=1), axis=1)
- # print(allModifiedLOO.shape)
-
- elif UtilMethod in ['EIGF', 'ALM']:
- # ----- All other in ['EIGF', 'ALM'] -----
- # Initilize the ExploitScore array
- ExploitScore = np.zeros((len(old_EDX), len(OutputNames)))
-
- # Split the candidates in groups for multiprocessing
- if explore_method != 'Voronoi':
- split_cand = np.array_split(allCandidates,
- n_cand_groups,
- axis=0)
- goodSampleIdx = range(n_cand_groups)
- else:
- # Find indices of the Vornoi cells with samples
- goodSampleIdx = []
- for idx in range(len(explore.closest_points)):
- if len(explore.closest_points[idx]) != 0:
- goodSampleIdx.append(idx)
- split_cand = explore.closest_points
-
- # Split the candidates in groups for multiprocessing
- args = []
- for index in goodSampleIdx:
- args.append((exploit_method, split_cand[index], index,
- sigma2, var))
-
- # Multiprocessing
- pool = multiprocessing.Pool(multiprocessing.cpu_count())
- # With Pool.starmap_async()
- results = pool.starmap_async(self.run_util_func, args).get()
-
- # Close the pool
- pool.close()
-
- # Retrieve the results and append them
- if explore_method == 'Voronoi':
- ExploitScore = [np.mean(results[k][1]) for k in
- range(len(goodSampleIdx))]
- else:
- ExploitScore = np.concatenate(
- [results[k][1] for k in range(len(goodSampleIdx))])
-
- else:
- raise NameError('The requested utility function is not '
- 'available.')
-
- # print("ExploitScore:\n", ExploitScore)
-
- # find an optimal point subset to add to the initial design by
- # maximization of the utility score and taking care of NaN values
- # Total score
- # Normalize U_J_d
- ExploitScore = ExploitScore / np.sum(ExploitScore)
- totalScore = exploit_w * ExploitScore
- # print(totalScore.shape)
- # print(explore_w)
- # print(scoreExploration.shape)
- totalScore += explore_w * scoreExploration
-
- temp = totalScore.copy()
- sorted_idxtotalScore = np.argsort(temp, axis=0)[::-1]
- bestIdx = sorted_idxtotalScore[:n_new_samples]
-
- Xnew = np.zeros((n_new_samples, ndim))
- if explore_method != 'Voronoi':
- Xnew = allCandidates[bestIdx]
- else:
- for i, idx in enumerate(bestIdx.flatten()):
- X_can = explore.closest_points[idx]
- # plotter(self.ExpDesign.X, X_can, explore_method,
- # scoreExploration=None)
-
- # Calculate the maxmin score for the region of interest
- newSamples, maxminScore = explore.get_mc_samples(X_can)
-
- # select the requested number of samples
- Xnew[i] = newSamples[np.argmax(maxminScore)]
-
- elif exploit_method == 'alphabetic':
- # ------- EXPLOITATION: ALPHABETIC -------
- Xnew = self.util_AlphOptDesign(allCandidates, var)
-
- elif exploit_method == 'Space-filling':
- # ------- EXPLOITATION: SPACE-FILLING -------
- totalScore = scoreExploration
-
- # ------- Select the best candidate -------
- # find an optimal point subset to add to the initial design by
- # maximization of the utility score and taking care of NaN values
- temp = totalScore.copy()
- temp[np.isnan(totalScore)] = -np.inf
- sorted_idxtotalScore = np.argsort(temp)[::-1]
-
- # select the requested number of samples
- Xnew = allCandidates[sorted_idxtotalScore[:n_new_samples]]
-
- else:
- raise NameError('The requested design method is not available.')
-
- print("\n")
- print("\nRun No. {}:".format(old_EDX.shape[0]+1))
- print("Xnew:\n", Xnew)
-
- # TODO: why does it also return None?
- return Xnew, None
-
- # -------------------------------------------------------------------------
- def util_AlphOptDesign(self, candidates, var='D-Opt'):
- """
- Enriches the Experimental design with the requested alphabetic
- criterion based on exploring the space with number of sampling points.
-
- Ref: Hadigol, M., & Doostan, A. (2018). Least squares polynomial chaos
- expansion: A review of sampling strategies., Computer Methods in
- Applied Mechanics and Engineering, 332, 382-407.
-
- Arguments
- ---------
- NCandidate : int
- Number of candidate points to be searched
-
- var : string
- Alphabetic optimality criterion
-
- Returns
- -------
- X_new : array of shape (1, n_params)
- The new sampling location in the input space.
- """
- MetaModelOrig = self # TODO: this doesn't fully seem correct?
- n_new_samples = MetaModelOrig.ExpDesign.n_new_samples
- NCandidate = candidates.shape[0]
-
- # TODO: Loop over outputs
- OutputName = self.out_names[0]
-
- # To avoid changes ub original aPCE object
- MetaModel = deepcopy(MetaModelOrig)
-
- # Old Experimental design
- oldExpDesignX = self.ExpDesign.X
-
- # TODO: Only one psi can be selected.
- # Suggestion: Go for the one with the highest LOO error
- # TODO: this is just a patch, need to look at again!
- Scores = list(self.MetaModel.score_dict['b_1'][OutputName].values())
- #print(Scores)
- #print(self.MetaModel.score_dict)
- #print(self.MetaModel.score_dict.values())
- #print(self.MetaModel.score_dict['b_1'].values())
- #print(self.MetaModel.score_dict['b_1'][OutputName].values())
- ModifiedLOO = [1-score for score in Scores]
- outIdx = np.argmax(ModifiedLOO)
-
- # Initialize Phi to save the criterion's values
- Phi = np.zeros((NCandidate))
-
- # TODO: also patched here
- BasisIndices = self.MetaModel.basis_dict['b_1'][OutputName]["y_"+str(outIdx+1)]
- P = len(BasisIndices)
-
- # ------ Old Psi ------------
- univ_p_val = self.MetaModel.univ_basis_vals(oldExpDesignX)
- Psi = self.MetaModel.create_psi(BasisIndices, univ_p_val)
-
- # ------ New candidates (Psi_c) ------------
- # Assemble Psi_c
- univ_p_val_c = self.MetaModel.univ_basis_vals(candidates)
- Psi_c = self.MetaModel.create_psi(BasisIndices, univ_p_val_c)
-
- for idx in range(NCandidate):
-
- # Include the new row to the original Psi
- Psi_cand = np.vstack((Psi, Psi_c[idx]))
-
- # Information matrix
- PsiTPsi = np.dot(Psi_cand.T, Psi_cand)
- M = PsiTPsi / (len(oldExpDesignX)+1)
-
- if np.linalg.cond(PsiTPsi) > 1e-12 \
- and np.linalg.cond(PsiTPsi) < 1 / sys.float_info.epsilon:
- # faster
- invM = linalg.solve(M, sparse.eye(PsiTPsi.shape[0]).toarray())
- else:
- # stabler
- invM = np.linalg.pinv(M)
-
- # ---------- Calculate optimality criterion ----------
- # Optimality criteria according to Section 4.5.1 in Ref.
-
- # D-Opt
- if var.lower() == 'd-opt':
- Phi[idx] = (np.linalg.det(invM)) ** (1/P)
-
- # A-Opt
- elif var.lower() == 'a-opt':
- Phi[idx] = np.trace(invM)
-
- # K-Opt
- elif var.lower() == 'k-opt':
- Phi[idx] = np.linalg.cond(M)
-
- else:
- # print(var.lower())
- raise Exception('The optimality criterion you requested has '
- 'not been implemented yet!')
-
- # find an optimal point subset to add to the initial design
- # by minimization of the Phi
- sorted_idxtotalScore = np.argsort(Phi)
-
- # select the requested number of samples
- Xnew = candidates[sorted_idxtotalScore[:n_new_samples]]
-
- return Xnew
-
- # -------------------------------------------------------------------------
- def _normpdf(self, y_hat_pce, std_pce, obs_data, total_sigma2s,
- rmse=None):
- """
- Calculated gaussian likelihood for given y+std based on given obs+sigma
- # TODO: is this understanding correct?
-
- Parameters
- ----------
- y_hat_pce : dict of 2d np arrays
- Mean output of the surrogate.
- std_pce : dict of 2d np arrays
- Standard deviation output of the surrogate.
- obs_data : dict of 1d np arrays
- Observed data.
- total_sigma2s : pandas dataframe, matches obs_data
- Estimated uncertainty for the observed data.
- rmse : dict, optional
- RMSE values from validation of the surrogate. The default is None.
-
- Returns
- -------
- likelihoods : dict of float
- The likelihood for each surrogate eval in y_hat_pce compared to the
- observations (?).
-
- """
-
- likelihoods = 1.0
-
- # Loop over the outputs
- for idx, out in enumerate(self.out_names):
-
- # (Meta)Model Output
- # print(y_hat_pce[out])
- nsamples, nout = y_hat_pce[out].shape
-
- # Prepare data and remove NaN
- try:
- data = obs_data[out].values[~np.isnan(obs_data[out])]
- except AttributeError:
- data = obs_data[out][~np.isnan(obs_data[out])]
-
- # Prepare sigma2s
- non_nan_indices = ~np.isnan(total_sigma2s[out])
- tot_sigma2s = total_sigma2s[out][non_nan_indices][:nout].values
-
- # Surrogate error if valid dataset is given.
- if rmse is not None:
- tot_sigma2s += rmse[out]**2
- else:
- tot_sigma2s += np.mean(std_pce[out])**2
-
- likelihoods *= stats.multivariate_normal.pdf(
- y_hat_pce[out], data, np.diag(tot_sigma2s),
- allow_singular=True)
-
- # TODO: remove this here
- self.Likelihoods = likelihoods
-
- return likelihoods
-
- # -------------------------------------------------------------------------
- def _corr_factor_BME(self, obs_data, total_sigma2s, logBME):
- """
- Calculates the correction factor for BMEs.
- """
- MetaModel = self.MetaModel
- samples = self.ExpDesign.X # valid_samples
- model_outputs = self.ExpDesign.Y # valid_model_runs
- n_samples = samples.shape[0]
-
- # Extract the requested model outputs for likelihood calulation
- output_names = self.out_names
-
- # TODO: Evaluate MetaModel on the experimental design and ValidSet
- OutputRS, stdOutputRS = MetaModel.eval_metamodel(samples=samples)
-
- logLik_data = np.zeros((n_samples))
- logLik_model = np.zeros((n_samples))
- # Loop over the outputs
- for idx, out in enumerate(output_names):
-
- # (Meta)Model Output
- nsamples, nout = model_outputs[out].shape
-
- # Prepare data and remove NaN
- try:
- data = obs_data[out].values[~np.isnan(obs_data[out])]
- except AttributeError:
- data = obs_data[out][~np.isnan(obs_data[out])]
-
- # Prepare sigma2s
- non_nan_indices = ~np.isnan(total_sigma2s[out])
- tot_sigma2s = total_sigma2s[out][non_nan_indices][:nout]
-
- # Covariance Matrix
- covMatrix_data = np.diag(tot_sigma2s)
-
- for i, sample in enumerate(samples):
-
- # Simulation run
- y_m = model_outputs[out][i]
-
- # Surrogate prediction
- y_m_hat = OutputRS[out][i]
-
- # CovMatrix with the surrogate error
- # covMatrix = np.diag(stdOutputRS[out][i]**2)
- covMatrix = np.diag((y_m-y_m_hat)**2)
- covMatrix = np.diag(
- np.mean((model_outputs[out]-OutputRS[out]), axis=0)**2
- )
-
- # Compute likelilhood output vs data
- logLik_data[i] += logpdf(
- y_m_hat, data, covMatrix_data
- )
-
- # Compute likelilhood output vs surrogate
- logLik_model[i] += logpdf(y_m_hat, y_m, covMatrix)
-
- # Weight
- logLik_data -= logBME
- weights = np.exp(logLik_model+logLik_data)
-
- return np.log(np.mean(weights))
-
- # -------------------------------------------------------------------------
- def _posteriorPlot(self, posterior, par_names, key):
- """
- Plot the posterior of a specific key as a corner plot
-
- Parameters
- ----------
- posterior : 2d np.array
- Samples of the posterior.
- par_names : list of strings
- List of the parameter names.
- key : string
- Output key that this posterior belongs to.
-
- Returns
- -------
- figPosterior : corner.corner
- Plot of the posterior.
-
- """
-
- # Initialization
- newpath = (r'Outputs_SeqPosteriorComparison/posterior')
- os.makedirs(newpath, exist_ok=True)
-
- bound_tuples = self.ExpDesign.bound_tuples
- n_params = len(par_names)
- font_size = 40
- if n_params == 2:
-
- figPosterior, ax = plt.subplots(figsize=(15, 15))
-
- sns.kdeplot(x=posterior[:, 0], y=posterior[:, 1],
- fill=True, ax=ax, cmap=plt.cm.jet,
- clip=bound_tuples)
- # Axis labels
- plt.xlabel(par_names[0], fontsize=font_size)
- plt.ylabel(par_names[1], fontsize=font_size)
-
- # Set axis limit
- plt.xlim(bound_tuples[0])
- plt.ylim(bound_tuples[1])
-
- # Increase font size
- plt.xticks(fontsize=font_size)
- plt.yticks(fontsize=font_size)
-
- # Switch off the grids
- plt.grid(False)
-
- else:
- import corner
- figPosterior = corner.corner(posterior, labels=par_names,
- title_fmt='.2e', show_titles=True,
- title_kwargs={"fontsize": 12})
-
- figPosterior.savefig(f'./{newpath}/{key}.pdf', bbox_inches='tight')
- plt.close()
-
- # Save the posterior as .npy
- np.save(f'./{newpath}/{key}.npy', posterior)
-
- return figPosterior
-
-
- # -------------------------------------------------------------------------
- def _BME_Calculator(self, obs_data, sigma2Dict, rmse=None):
- """
- This function computes the Bayesian model evidence (BME) via Monte
- Carlo integration.
-
- Parameters
- ----------
- obs_data : dict of 1d np arrays
- Observed data.
- sigma2Dict : pandas dataframe, matches obs_data
- Estimated uncertainty for the observed data.
- rmse : dict of floats, optional
- RMSE values for each output-key. The dafault is None.
-
- Returns
- -------
- (logBME, KLD, X_Posterior, Likelihoods, distHellinger)
-
- """
- # Initializations
- if hasattr(self, 'valid_likelihoods'):
- valid_likelihoods = self.valid_likelihoods
- else:
- valid_likelihoods = []
- valid_likelihoods = np.array(valid_likelihoods)
-
- post_snapshot = self.ExpDesign.post_snapshot
- if post_snapshot or valid_likelihoods.shape[0] != 0:
- newpath = (r'Outputs_SeqPosteriorComparison/likelihood_vs_ref')
- os.makedirs(newpath, exist_ok=True)
-
- SamplingMethod = 'random'
- MCsize = 10000
- ESS = 0
-
- # Estimation of the integral via Monte Varlo integration
- while (ESS > MCsize) or (ESS < 1):
-
- # Generate samples for Monte Carlo simulation
- X_MC = self.ExpDesign.generate_samples(
- MCsize, SamplingMethod
- )
-
- # Monte Carlo simulation for the candidate design
- Y_MC, std_MC = self.MetaModel.eval_metamodel(samples=X_MC)
-
- # Likelihood computation (Comparison of data and
- # simulation results via PCE with candidate design)
- Likelihoods = self._normpdf(
- Y_MC, std_MC, obs_data, sigma2Dict, rmse
- )
-
- # Check the Effective Sample Size (1000<ESS<MCsize)
- ESS = 1 / np.sum(np.square(Likelihoods/np.sum(Likelihoods)))
-
- # Enlarge sample size if it doesn't fulfill the criteria
- if (ESS > MCsize) or (ESS < 1):
- print(f'ESS={ESS} MC size should be larger.')
- MCsize *= 10
- ESS = 0
-
- # Rejection Step
- # Random numbers between 0 and 1
- unif = np.random.rand(1, MCsize)[0]
-
- # Reject the poorly performed prior
- accepted = (Likelihoods/np.max(Likelihoods)) >= unif
- X_Posterior = X_MC[accepted]
-
- # ------------------------------------------------------------
- # --- Kullback-Leibler Divergence & Information Entropy ------
- # ------------------------------------------------------------
- # Prior-based estimation of BME
- logBME = np.log(np.nanmean(Likelihoods))
-
- # TODO: Correction factor
- # log_weight = self.__corr_factor_BME(obs_data, sigma2Dict, logBME)
-
- # Posterior-based expectation of likelihoods
- postExpLikelihoods = np.mean(np.log(Likelihoods[accepted]))
-
- # Posterior-based expectation of prior densities
- postExpPrior = np.mean(
- np.log(self.ExpDesign.JDist.pdf(X_Posterior.T))
- )
-
- # Calculate Kullback-Leibler Divergence
- # KLD = np.mean(np.log(Likelihoods[Likelihoods!=0])- logBME)
- KLD = postExpLikelihoods - logBME
-
- # Information Entropy based on Entropy paper Eq. 38
- infEntropy = logBME - postExpPrior - postExpLikelihoods
-
- # If post_snapshot is True, plot likelihood vs refrence
- if post_snapshot or valid_likelihoods:
- # Hellinger distance
- valid_likelihoods = np.array(valid_likelihoods)
- ref_like = np.log(valid_likelihoods[(valid_likelihoods > 0)])
- est_like = np.log(Likelihoods[Likelihoods > 0])
- distHellinger = hellinger_distance(ref_like, est_like)
-
- idx = len([name for name in os.listdir(newpath) if 'Likelihoods_'
- in name and os.path.isfile(os.path.join(newpath, name))])
-
- fig, ax = plt.subplots()
- try:
- sns.kdeplot(np.log(valid_likelihoods[valid_likelihoods > 0]),
- shade=True, color="g", label='Ref. Likelihood')
- sns.kdeplot(np.log(Likelihoods[Likelihoods > 0]), shade=True,
- color="b", label='Likelihood with PCE')
- except:
- pass
-
- text = f"Hellinger Dist.={distHellinger:.3f}\n logBME={logBME:.3f}"
- "\n DKL={KLD:.3f}"
-
- plt.text(0.05, 0.75, text, bbox=dict(facecolor='wheat',
- edgecolor='black',
- boxstyle='round,pad=1'),
- transform=ax.transAxes)
-
- fig.savefig(f'./{newpath}/Likelihoods_{idx}.pdf',
- bbox_inches='tight')
- plt.close()
-
- else:
- distHellinger = 0.0
-
- # Bayesian inference with Emulator only for 2D problem
- if post_snapshot and self.MetaModel.n_params == 2 and not idx % 5:
- BayesOpts = BayesInference(self)
-
- BayesOpts.emulator = True
- BayesOpts.plot_post_pred = False
-
- # Select the inference method
- import emcee
- BayesOpts.inference_method = "MCMC"
- # Set the MCMC parameters passed to self.mcmc_params
- BayesOpts.mcmc_params = {
- 'n_steps': 1e5,
- 'n_walkers': 30,
- 'moves': emcee.moves.KDEMove(),
- 'verbose': False
- }
-
- # ----- Define the discrepancy model -------
- # TODO: check with Farid if this first line is how it should be
- BayesOpts.measured_data = obs_data
- obs_data = pd.DataFrame(obs_data, columns=self.out_names)
- BayesOpts.measurement_error = obs_data
- # TODO: shouldn't the uncertainty be sigma2Dict instead of obs_data?
-
- # # -- (Option B) --
- DiscrepancyOpts = Discrepancy('')
- DiscrepancyOpts.type = 'Gaussian'
- DiscrepancyOpts.parameters = obs_data**2
- BayesOpts.Discrepancy = DiscrepancyOpts
- # Start the calibration/inference
- Bayes_PCE = BayesOpts.create_inference()
- X_Posterior = Bayes_PCE.posterior_df.values
-
- return (logBME, KLD, X_Posterior, Likelihoods, distHellinger)
-
- # -------------------------------------------------------------------------
- def _validError(self):
- """
- Evaluate the metamodel on the validation samples and calculate the
- error against the corresponding model runs
-
- Returns
- -------
- rms_error : dict
- RMSE for each validation run.
- valid_error : dict
- Normed (?)RMSE for each validation run.
-
- """
- # Extract the original model with the generated samples
- valid_model_runs = self.ExpDesign.valid_model_runs
-
- # Run the PCE model with the generated samples
- valid_PCE_runs, _ = self.MetaModel.eval_metamodel(samples=self.ExpDesign.valid_samples)
-
- rms_error = {}
- valid_error = {}
- # Loop over the keys and compute RMSE error.
- for key in self.out_names:
- rms_error[key] = mean_squared_error(
- valid_model_runs[key], valid_PCE_runs[key],
- multioutput='raw_values',
- sample_weight=None,
- squared=False)
- # Validation error
- valid_error[key] = (rms_error[key]**2)
- valid_error[key] /= np.var(valid_model_runs[key], ddof=1, axis=0)
-
- # Print a report table
- print("\n>>>>> Updated Errors of {} <<<<<".format(key))
- print("\nIndex | RMSE | Validation Error")
- print('-'*35)
- print('\n'.join(f'{i+1} | {k:.3e} | {j:.3e}' for i, (k, j)
- in enumerate(zip(rms_error[key],
- valid_error[key]))))
-
- return rms_error, valid_error
-
- # -------------------------------------------------------------------------
- def _error_Mean_Std(self):
- """
- Calculates the error in the overall mean and std approximation of the
- surrogate against the mc-reference provided to the model.
- This can only be applied to metamodels of polynomial type
-
- Returns
- -------
- RMSE_Mean : float
- RMSE of the means
- RMSE_std : float
- RMSE of the standard deviations
-
- """
- # Compute the mean and std based on the MetaModel
- pce_means, pce_stds = self.MetaModel._compute_pce_moments()
-
- # Compute the root mean squared error
- for output in self.out_names:
-
- # Compute the error between mean and std of MetaModel and OrigModel
- RMSE_Mean = mean_squared_error(
- self.Model.mc_reference['mean'], pce_means[output], squared=False
- )
- RMSE_std = mean_squared_error(
- self.Model.mc_reference['std'], pce_stds[output], squared=False
- )
-
- return RMSE_Mean, RMSE_std
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/eval_rec_rule.py b/examples/model-comparison/bayesvalidrox/surrogate_models/eval_rec_rule.py
deleted file mode 100644
index b583c7eb2ec58d55d19b34130812730d21a12368..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/eval_rec_rule.py
+++ /dev/null
@@ -1,197 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-
-
-Based on the implementation in UQLab [1].
-
-References:
-1. S. Marelli, and B. Sudret, UQLab: A framework for uncertainty quantification
-in Matlab, Proc. 2nd Int. Conf. on Vulnerability, Risk Analysis and Management
-(ICVRAM2014), Liverpool, United Kingdom, 2014, 2554-2563.
-
-2. S. Marelli, N. Lüthen, B. Sudret, UQLab user manual – Polynomial chaos
-expansions, Report # UQLab-V1.4-104, Chair of Risk, Safety and Uncertainty
-Quantification, ETH Zurich, Switzerland, 2021.
-
-Author: Farid Mohammadi, M.Sc.
-E-Mail: farid.mohammadi@iws.uni-stuttgart.de
-Department of Hydromechanics and Modelling of Hydrosystems (LH2)
-Institute for Modelling Hydraulic and Environmental Systems (IWS), University
-of Stuttgart, www.iws.uni-stuttgart.de/lh2/
-Pfaffenwaldring 61
-70569 Stuttgart
-
-Created on Fri Jan 14 2022
-"""
-import numpy as np
-from numpy.polynomial.polynomial import polyval
-
-
-def poly_rec_coeffs(n_max, poly_type, params=None):
- """
- Computes the recurrence coefficients for classical Wiener-Askey orthogonal
- polynomials.
-
- Parameters
- ----------
- n_max : int
- Maximum polynomial degree.
- poly_type : string
- Polynomial type.
- params : list, optional
- Parameters required for `laguerre` poly type. The default is None.
-
- Returns
- -------
- AB : dict
- The 3 term recursive coefficients and the applicable ranges.
-
- """
-
- if poly_type == 'legendre':
-
- def an(n):
- return np.zeros((n+1, 1))
-
- def sqrt_bn(n):
- sq_bn = np.zeros((n+1, 1))
- sq_bn[0, 0] = 1
- for i in range(1, n+1):
- sq_bn[i, 0] = np.sqrt(1./(4-i**-2))
- return sq_bn
-
- bounds = [-1, 1]
-
- elif poly_type == 'hermite':
-
- def an(n):
- return np.zeros((n+1, 1))
-
- def sqrt_bn(n):
- sq_bn = np.zeros((n+1, 1))
- sq_bn[0, 0] = 1
- for i in range(1, n+1):
- sq_bn[i, 0] = np.sqrt(i)
- return sq_bn
-
- bounds = [-np.inf, np.inf]
-
- elif poly_type == 'laguerre':
-
- def an(n):
- a = np.zeros((n+1, 1))
- for i in range(1, n+1):
- a[i] = 2*n + params[1]
- return a
-
- def sqrt_bn(n):
- sq_bn = np.zeros((n+1, 1))
- sq_bn[0, 0] = 1
- for i in range(1, n+1):
- sq_bn[i, 0] = -np.sqrt(i * (i+params[1]-1))
- return sq_bn
-
- bounds = [0, np.inf]
-
- AB = {'alpha_beta': np.concatenate((an(n_max), sqrt_bn(n_max)), axis=1),
- 'bounds': bounds}
-
- return AB
-
-
-def eval_rec_rule(x, max_deg, poly_type):
- """
- Evaluates the polynomial that corresponds to the Jacobi matrix defined
- from the AB.
-
- Parameters
- ----------
- x : array (n_samples)
- Points where the polynomials are evaluated.
- max_deg : int
- Maximum degree.
- poly_type : string
- Polynomial type.
-
- Returns
- -------
- values : array of shape (n_samples, max_deg+1)
- Polynomials corresponding to the Jacobi matrix.
-
- """
- AB = poly_rec_coeffs(max_deg, poly_type)
- AB = AB['alpha_beta']
-
- values = np.zeros((len(x), AB.shape[0]+1))
- values[:, 1] = 1 / AB[0, 1]
-
- for k in range(AB.shape[0]-1):
- values[:, k+2] = np.multiply((x - AB[k, 0]), values[:, k+1]) - \
- np.multiply(values[:, k], AB[k, 1])
- values[:, k+2] = np.divide(values[:, k+2], AB[k+1, 1])
- return values[:, 1:]
-
-
-def eval_rec_rule_arbitrary(x, max_deg, poly_coeffs):
- """
- Evaluates the polynomial at sample array x.
-
- Parameters
- ----------
- x : array (n_samples)
- Points where the polynomials are evaluated.
- max_deg : int
- Maximum degree.
- poly_coeffs : dict
- Polynomial coefficients computed based on moments.
-
- Returns
- -------
- values : array of shape (n_samples, max_deg+1)
- Univariate Polynomials evaluated at samples.
-
- """
- values = np.zeros((len(x), max_deg+1))
-
- for deg in range(max_deg+1):
- values[:, deg] = polyval(x, poly_coeffs[deg]).T
-
- return values
-
-
-def eval_univ_basis(x, max_deg, poly_types, apoly_coeffs=None):
- """
- Evaluates univariate regressors along input directions.
-
- Parameters
- ----------
- x : array of shape (n_samples, n_params)
- Training samples.
- max_deg : int
- Maximum polynomial degree.
- poly_types : list of strings
- List of polynomial types for all parameters.
- apoly_coeffs : dict , optional
- Polynomial coefficients computed based on moments. The default is None.
-
- Returns
- -------
- univ_vals : array of shape (n_samples, n_params, max_deg+1)
- Univariate polynomials for all degrees and parameters evaluated at x.
-
- """
- # Initilize the output array
- n_samples, n_params = x.shape
- univ_vals = np.zeros((n_samples, n_params, max_deg+1))
-
- for i in range(n_params):
-
- if poly_types[i] == 'arbitrary':
- polycoeffs = apoly_coeffs[f'p_{i+1}']
- univ_vals[:, i] = eval_rec_rule_arbitrary(x[:, i], max_deg,
- polycoeffs)
- else:
- univ_vals[:, i] = eval_rec_rule(x[:, i], max_deg, poly_types[i])
-
- return univ_vals
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/exp_designs.py b/examples/model-comparison/bayesvalidrox/surrogate_models/exp_designs.py
deleted file mode 100644
index fa03fe17d96fb2c1f19546b7b72fb2fd6dd1c13a..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/exp_designs.py
+++ /dev/null
@@ -1,479 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Experimental design with associated sampling methods
-"""
-
-import numpy as np
-import math
-import itertools
-import chaospy
-import scipy.stats as st
-from tqdm import tqdm
-import h5py
-import os
-
-from .apoly_construction import apoly_construction
-from .input_space import InputSpace
-
-# -------------------------------------------------------------------------
-def check_ranges(theta, ranges):
- """
- This function checks if theta lies in the given ranges.
-
- Parameters
- ----------
- theta : array
- Proposed parameter set.
- ranges : nested list
- List of the praremeter ranges.
-
- Returns
- -------
- c : bool
- If it lies in the given range, it return True else False.
-
- """
- c = True
- # traverse in the list1
- for i, bounds in enumerate(ranges):
- x = theta[i]
- # condition check
- if x < bounds[0] or x > bounds[1]:
- c = False
- return c
- return c
-
-
-class ExpDesigns(InputSpace):
- """
- This class generates samples from the prescribed marginals for the model
- parameters using the `Input` object.
-
- Attributes
- ----------
- Input : obj
- Input object containing the parameter marginals, i.e. name,
- distribution type and distribution parameters or available raw data.
- meta_Model_type : str
- Type of the meta_Model_type.
- sampling_method : str
- Name of the sampling method for the experimental design. The following
- sampling method are supported:
-
- * random
- * latin_hypercube
- * sobol
- * halton
- * hammersley
- * chebyshev(FT)
- * grid(FT)
- * user
- hdf5_file : str
- Name of the hdf5 file that contains the experimental design.
- n_new_samples : int
- Number of (initial) training points.
- n_max_samples : int
- Number of maximum training points.
- mod_LOO_threshold : float
- The modified leave-one-out cross validation threshold where the
- sequential design stops.
- tradeoff_scheme : str
- Trade-off scheme to assign weights to the exploration and exploitation
- scores in the sequential design.
- n_canddidate : int
- Number of candidate training sets to calculate the scores for.
- explore_method : str
- Type of the exploration method for the sequential design. The following
- methods are supported:
-
- * Voronoi
- * random
- * latin_hypercube
- * LOOCV
- * dual annealing
- exploit_method : str
- Type of the exploitation method for the sequential design. The
- following methods are supported:
-
- * BayesOptDesign
- * BayesActDesign
- * VarOptDesign
- * alphabetic
- * Space-filling
- util_func : str or list
- The utility function to be specified for the `exploit_method`. For the
- available utility functions see Note section.
- n_cand_groups : int
- Number of candidate groups. Each group of candidate training sets will
- be evaulated separately in parallel.
- n_replication : int
- Number of replications. Only for comparison. The default is 1.
- post_snapshot : int
- Whether to plot the posterior in the sequential design. The default is
- `True`.
- step_snapshot : int
- The number of steps to plot the posterior in the sequential design. The
- default is 1.
- max_a_post : list or array
- Maximum a posteriori of the posterior distribution, if known. The
- default is `[]`.
- adapt_verbose : bool
- Whether to plot the model response vs that of metamodel for the new
- trining point in the sequential design.
-
- Note
- ----------
- The following utiliy functions for the **exploitation** methods are
- supported:
-
- #### BayesOptDesign (when data is available)
- - DKL (Kullback-Leibler Divergence)
- - DPP (D-Posterior-percision)
- - APP (A-Posterior-percision)
-
- #### VarBasedOptDesign -> when data is not available
- - Entropy (Entropy/MMSE/active learning)
- - EIGF (Expected Improvement for Global fit)
- - LOOCV (Leave-one-out Cross Validation)
-
- #### alphabetic
- - D-Opt (D-Optimality)
- - A-Opt (A-Optimality)
- - K-Opt (K-Optimality)
- """
-
- def __init__(self, Input, meta_Model_type='pce',
- sampling_method='random', hdf5_file=None,
- n_new_samples=1, n_max_samples=None, mod_LOO_threshold=1e-16,
- tradeoff_scheme=None, n_canddidate=1, explore_method='random',
- exploit_method='Space-filling', util_func='Space-filling',
- n_cand_groups=4, n_replication=1, post_snapshot=False,
- step_snapshot=1, max_a_post=[], adapt_verbose=False, max_func_itr=1):
-
- self.InputObj = Input
- self.meta_Model_type = meta_Model_type
- self.sampling_method = sampling_method
- self.hdf5_file = hdf5_file
- self.n_new_samples = n_new_samples
- self.n_max_samples = n_max_samples
- self.mod_LOO_threshold = mod_LOO_threshold
- self.explore_method = explore_method
- self.exploit_method = exploit_method
- self.util_func = util_func
- self.tradeoff_scheme = tradeoff_scheme
- self.n_canddidate = n_canddidate
- self.n_cand_groups = n_cand_groups
- self.n_replication = n_replication
- self.post_snapshot = post_snapshot
- self.step_snapshot = step_snapshot
- self.max_a_post = max_a_post
- self.adapt_verbose = adapt_verbose
- self.max_func_itr = max_func_itr
-
- # Other
- self.apce = None
- self.ndim = None
-
- # Init
- self.check_valid_inputs()
-
- # -------------------------------------------------------------------------
- def generate_samples(self, n_samples, sampling_method='random',
- transform=False):
- """
- Generates samples with given sampling method
-
- Parameters
- ----------
- n_samples : int
- Number of requested samples.
- sampling_method : str, optional
- Sampling method. The default is `'random'`.
- transform : bool, optional
- Transformation via an isoprobabilistic transformation method. The
- default is `False`.
-
- Returns
- -------
- samples: array of shape (n_samples, n_params)
- Generated samples from defined model input object.
-
- """
- try:
- samples = chaospy.generate_samples(
- int(n_samples), domain=self.origJDist, rule=sampling_method
- )
- except:
- samples = self.random_sampler(int(n_samples)).T
-
- return samples.T
-
-
-
- # -------------------------------------------------------------------------
- def generate_ED(self, n_samples, transform=False,
- max_pce_deg=None):
- """
- Generates experimental designs (training set) with the given method.
-
- Parameters
- ----------
- n_samples : int
- Number of requested training points.
- sampling_method : str, optional
- Sampling method. The default is `'random'`.
- transform : bool, optional
- Isoprobabilistic transformation. The default is `False`.
- max_pce_deg : int, optional
- Maximum PCE polynomial degree. The default is `None`.
-
- Returns
- -------
- None
-
- """
- if n_samples <0:
- raise ValueError('A negative number of samples cannot be created. Please provide positive n_samples')
- n_samples = int(n_samples)
-
- if not hasattr(self, 'n_init_samples'):
- self.n_init_samples = n_samples
-
- # Generate the samples based on requested method
- self.init_param_space(max_pce_deg)
-
- sampling_method = self.sampling_method
- # Pass user-defined samples as ED
- if sampling_method == 'user':
- if not hasattr(self, 'X'):
- raise AttributeError('User-defined sampling cannot proceed as no samples provided. Please add them to this class as attribute X')
- if not self.X.ndim == 2:
- raise AttributeError('The provided samples shuld have 2 dimensions')
- samples = self.X
- self.n_samples = len(samples)
-
- # Sample the distribution of parameters
- elif self.input_data_given:
- # Case II: Input values are directly given by the user.
-
- if sampling_method == 'random':
- samples = self.random_sampler(n_samples)
-
- elif sampling_method == 'PCM' or \
- sampling_method == 'LSCM':
- samples = self.pcm_sampler(n_samples, max_pce_deg)
-
- else:
- # Create ExpDesign in the actual space using chaospy
- try:
- samples = chaospy.generate_samples(n_samples,
- domain=self.JDist,
- rule=sampling_method).T
- except:
- samples = self.JDist.resample(n_samples).T
-
- elif not self.input_data_given:
- # Case I = User passed known distributions
- samples = chaospy.generate_samples(n_samples, domain=self.JDist,
- rule=sampling_method).T
-
- self.X = samples
-
- def read_from_file(self, out_names):
- """
- Reads in the ExpDesign from a provided h5py file and saves the results.
-
- Parameters
- ----------
- out_names : list of strings
- The keys that are in the outputs (y) saved in the provided file.
-
- Returns
- -------
- None.
-
- """
- if self.hdf5_file == None:
- raise AttributeError('ExpDesign cannot be read in, please provide hdf5 file first')
-
- # Read hdf5 file
- f = h5py.File(self.hdf5_file, 'r+')
-
- # Read EDX and pass it to ExpDesign object
- try:
- self.X = np.array(f["EDX/New_init_"])
- except KeyError:
- self.X = np.array(f["EDX/init_"])
-
- # Update number of initial samples
- self.n_init_samples = self.X.shape[0]
-
- # Read EDX and pass it to ExpDesign object
- self.Y = {}
-
- # Extract x values
- try:
- self.Y["x_values"] = dict()
- for varIdx, var in enumerate(out_names):
- x = np.array(f[f"x_values/{var}"])
- self.Y["x_values"][var] = x
- except KeyError:
- self.Y["x_values"] = np.array(f["x_values"])
-
- # Store the output
- for varIdx, var in enumerate(out_names):
- try:
- y = np.array(f[f"EDY/{var}/New_init_"])
- except KeyError:
- y = np.array(f[f"EDY/{var}/init_"])
- self.Y[var] = y
- f.close()
- print(f'Experimental Design is read in from file {self.hdf5_file}')
- print('')
-
-
-
- # -------------------------------------------------------------------------
- def random_sampler(self, n_samples, max_deg = None):
- """
- Samples the given raw data randomly.
-
- Parameters
- ----------
- n_samples : int
- Number of requested samples.
-
- max_deg : int, optional
- Maximum degree. The default is `None`.
- This will be used to run init_param_space, if it has not been done
- until now.
-
- Returns
- -------
- samples: array of shape (n_samples, n_params)
- The sampling locations in the input space.
-
- """
- if not hasattr(self, 'raw_data'):
- self.init_param_space(max_deg)
- else:
- if np.array(self.raw_data).ndim !=2:
- raise AttributeError('The given raw data for sampling should have two dimensions')
- samples = np.zeros((n_samples, self.ndim))
- sample_size = self.raw_data.shape[1]
-
- # Use a combination of raw data
- if n_samples < sample_size:
- for pa_idx in range(self.ndim):
- # draw random indices
- rand_idx = np.random.randint(0, sample_size, n_samples)
- # store the raw data with given random indices
- samples[:, pa_idx] = self.raw_data[pa_idx, rand_idx]
- else:
- try:
- samples = self.JDist.resample(int(n_samples)).T
- except AttributeError:
- samples = self.JDist.sample(int(n_samples)).T
- # Check if all samples are in the bound_tuples
- for idx, param_set in enumerate(samples):
- if not check_ranges(param_set, self.bound_tuples):
- try:
- proposed_sample = chaospy.generate_samples(
- 1, domain=self.JDist, rule='random').T[0]
- except:
- proposed_sample = self.JDist.resample(1).T[0]
- while not check_ranges(proposed_sample,
- self.bound_tuples):
- try:
- proposed_sample = chaospy.generate_samples(
- 1, domain=self.JDist, rule='random').T[0]
- except:
- proposed_sample = self.JDist.resample(1).T[0]
- samples[idx] = proposed_sample
-
- return samples
-
- # -------------------------------------------------------------------------
- def pcm_sampler(self, n_samples, max_deg):
- """
- Generates collocation points based on the root of the polynomial
- degrees.
-
- Parameters
- ----------
- n_samples : int
- Number of requested samples.
- max_deg : int
- Maximum degree defined by user. Will also be used to run
- init_param_space if that has not been done beforehand.
-
- Returns
- -------
- opt_col_points: array of shape (n_samples, n_params)
- Collocation points.
-
- """
-
- if not hasattr(self, 'raw_data'):
- self.init_param_space(max_deg)
-
- raw_data = self.raw_data
-
- # Guess the closest degree to self.n_samples
- def M_uptoMax(deg):
- result = []
- for d in range(1, deg+1):
- result.append(math.factorial(self.ndim+d) //
- (math.factorial(self.ndim) * math.factorial(d)))
- return np.array(result)
- #print(M_uptoMax(max_deg))
- #print(np.where(M_uptoMax(max_deg) > n_samples)[0])
-
- guess_Deg = np.where(M_uptoMax(max_deg) > n_samples)[0][0]
-
- c_points = np.zeros((guess_Deg+1, self.ndim))
-
- def PolynomialPa(parIdx):
- return apoly_construction(self.raw_data[parIdx], max_deg)
-
- for i in range(self.ndim):
- poly_coeffs = PolynomialPa(i)[guess_Deg+1][::-1]
- c_points[:, i] = np.trim_zeros(np.roots(poly_coeffs))
-
- # Construction of optimal integration points
- Prod = itertools.product(np.arange(1, guess_Deg+2), repeat=self.ndim)
- sort_dig_unique_combos = np.array(list(filter(lambda x: x, Prod)))
-
- # Ranking relatively mean
- Temp = np.empty(shape=[0, guess_Deg+1])
- for j in range(self.ndim):
- s = abs(c_points[:, j]-np.mean(raw_data[j]))
- Temp = np.append(Temp, [s], axis=0)
- temp = Temp.T
-
- index_CP = np.sort(temp, axis=0)
- sort_cpoints = np.empty((0, guess_Deg+1))
-
- for j in range(self.ndim):
- #print(index_CP[:, j])
- sort_cp = c_points[index_CP[:, j], j]
- sort_cpoints = np.vstack((sort_cpoints, sort_cp))
-
- # Mapping of Combination to Cpoint Combination
- sort_unique_combos = np.empty(shape=[0, self.ndim])
- for i in range(len(sort_dig_unique_combos)):
- sort_un_comb = []
- for j in range(self.ndim):
- SortUC = sort_cpoints[j, sort_dig_unique_combos[i, j]-1]
- sort_un_comb.append(SortUC)
- sort_uni_comb = np.asarray(sort_un_comb)
- sort_unique_combos = np.vstack((sort_unique_combos, sort_uni_comb))
-
- # Output the collocation points
- if self.sampling_method.lower() == 'lscm':
- opt_col_points = sort_unique_combos
- else:
- opt_col_points = sort_unique_combos[0:self.n_samples]
-
- return opt_col_points
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/exploration.py b/examples/model-comparison/bayesvalidrox/surrogate_models/exploration.py
deleted file mode 100644
index 6abb652f145fadb410ecf8f987142e8ceb544a41..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/exploration.py
+++ /dev/null
@@ -1,367 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Exploration for sequential training of metamodels
-"""
-
-import numpy as np
-from scipy.spatial import distance
-
-
-class Exploration:
- """
- Created based on the Surrogate Modeling Toolbox (SUMO) [1].
-
- [1] Gorissen, D., Couckuyt, I., Demeester, P., Dhaene, T. and Crombecq, K.,
- 2010. A surrogate modeling and adaptive sampling toolbox for computer
- based design. Journal of machine learning research.-Cambridge, Mass.,
- 11, pp.2051-2055. sumo@sumo.intec.ugent.be - http://sumo.intec.ugent.be
-
- Attributes
- ----------
- ExpDesign : obj
- ExpDesign object.
- n_candidate : int
- Number of candidate samples.
- mc_criterion : str
- Selection crieterion. The default is `'mc-intersite-proj-th'`. Another
- option is `'mc-intersite-proj'`.
- w : int
- Number of random points in the domain for each sample of the
- training set.
- """
-
- def __init__(self, ExpDesign, n_candidate,
- mc_criterion='mc-intersite-proj-th'):
- self.ExpDesign = ExpDesign
- self.n_candidate = n_candidate
- self.mc_criterion = mc_criterion
- self.w = 100
-
- def get_exploration_samples(self):
- """
- This function generates candidates to be selected as new design and
- their associated exploration scores.
-
- Returns
- -------
- all_candidates : array of shape (n_candidate, n_params)
- A list of samples.
- exploration_scores: arrays of shape (n_candidate)
- Exploration scores.
- """
- explore_method = self.ExpDesign.explore_method
-
- print("\n")
- print(f' The {explore_method}-Method is selected as the exploration '
- 'method.')
- print("\n")
-
- if explore_method == 'Voronoi':
- # Generate samples using the Voronoi method
- all_candidates, exploration_scores = self.get_vornoi_samples()
- else:
- # Generate samples using the MC method
- all_candidates, exploration_scores = self.get_mc_samples()
-
- return all_candidates, exploration_scores
-
- # -------------------------------------------------------------------------
- def get_vornoi_samples(self):
- """
- This function generates samples based on voronoi cells and their
- corresponding scores
-
- Returns
- -------
- new_samples : array of shape (n_candidate, n_params)
- A list of samples.
- exploration_scores: arrays of shape (n_candidate)
- Exploration scores.
- """
-
- mc_criterion = self.mc_criterion
- n_candidate = self.n_candidate
- # Get the Old ExpDesign #samples
- old_ED_X = self.ExpDesign.X
- ndim = old_ED_X.shape[1]
-
- # calculate error #averageErrors
- error_voronoi, all_candidates = self.approximate_voronoi(
- self.w, old_ED_X
- )
-
- # Pick the best candidate point in the voronoi cell
- # for each best sample
- selected_samples = np.empty((0, ndim))
- bad_samples = []
-
- for index in range(len(error_voronoi)):
-
- # get candidate new samples from voronoi tesselation
- candidates = self.closest_points[index]
-
- # get total number of candidates
- n_new_samples = candidates.shape[0]
-
- # still no candidate samples around this one, skip it!
- if n_new_samples == 0:
- print('The following sample has been skipped because there '
- 'were no candidate samples around it...')
- print(old_ED_X[index])
- bad_samples.append(index)
- continue
-
- # find candidate that is farthest away from any existing sample
- max_min_distance = 0
- best_candidate = 0
- min_intersite_dist = np.zeros((n_new_samples))
- min_projected_dist = np.zeros((n_new_samples))
-
- for j in range(n_new_samples):
-
- new_samples = np.vstack((old_ED_X, selected_samples))
-
- # find min distorted distance from all other samples
- euclidean_dist = self._build_dist_matrix_point(
- new_samples, candidates[j], do_sqrt=True)
- min_euclidean_dist = np.min(euclidean_dist)
- min_intersite_dist[j] = min_euclidean_dist
-
- # Check if this is the maximum minimum distance from all other
- # samples
- if min_euclidean_dist >= max_min_distance:
- max_min_distance = min_euclidean_dist
- best_candidate = j
-
- # Projected distance
- projected_dist = distance.cdist(
- new_samples, [candidates[j]], 'chebyshev')
- min_projected_dist[j] = np.min(projected_dist)
-
- if mc_criterion == 'mc-intersite-proj':
- weight_euclidean_dist = 0.5 * ((n_new_samples+1)**(1/ndim) - 1)
- weight_projected_dist = 0.5 * (n_new_samples+1)
- total_dist_scores = weight_euclidean_dist * min_intersite_dist
- total_dist_scores += weight_projected_dist * min_projected_dist
-
- elif mc_criterion == 'mc-intersite-proj-th':
- alpha = 0.5 # chosen (tradeoff)
- d_min = 2 * alpha / n_new_samples
- if any(min_projected_dist < d_min):
- candidates = np.delete(
- candidates, [min_projected_dist < d_min], axis=0
- )
- total_dist_scores = np.delete(
- min_intersite_dist, [min_projected_dist < d_min],
- axis=0
- )
- else:
- total_dist_scores = min_intersite_dist
- else:
- raise NameError(
- 'The MC-Criterion you requested is not available.'
- )
-
- # Add the best candidate to the list of new samples
- best_candidate = np.argsort(total_dist_scores)[::-1][:n_candidate]
- selected_samples = np.vstack(
- (selected_samples, candidates[best_candidate])
- )
-
- self.new_samples = selected_samples
- self.exploration_scores = np.delete(error_voronoi, bad_samples, axis=0)
-
- return self.new_samples, self.exploration_scores
-
- # -------------------------------------------------------------------------
- def get_mc_samples(self, all_candidates=None):
- """
- This function generates random samples based on Global Monte Carlo
- methods and their corresponding scores, based on [1].
-
- [1] Crombecq, K., Laermans, E. and Dhaene, T., 2011. Efficient
- space-filling and non-collapsing sequential design strategies for
- simulation-based modeling. European Journal of Operational Research
- , 214(3), pp.683-696.
- DOI: https://doi.org/10.1016/j.ejor.2011.05.032
-
- Implemented methods to compute scores:
- 1) mc-intersite-proj
- 2) mc-intersite-proj-th
-
- Arguments
- ---------
- all_candidates : array, optional
- Samples to compute the scores for. The default is `None`. In this
- case, samples will be generated by defined model input marginals.
-
- Returns
- -------
- new_samples : array of shape (n_candidate, n_params)
- A list of samples.
- exploration_scores: arrays of shape (n_candidate)
- Exploration scores.
- """
- explore_method = self.ExpDesign.explore_method
- mc_criterion = self.mc_criterion
- if all_candidates is None:
- n_candidate = self.n_candidate
- else:
- n_candidate = all_candidates.shape[0]
-
- # Get the Old ExpDesign #samples
- old_ED_X = self.ExpDesign.X
- ndim = old_ED_X.shape[1]
-
- # ----- Compute the number of random points -----
- if all_candidates is None:
- # Generate MC Samples
- all_candidates = self.ExpDesign.generate_samples(
- self.n_candidate, explore_method
- )
- self.all_candidates = all_candidates
-
- # initialization
- min_intersite_dist = np.zeros((n_candidate))
- min_projected_dist = np.zeros((n_candidate))
-
- for i, candidate in enumerate(all_candidates):
-
- # find candidate that is farthest away from any existing sample
- maxMinDistance = 0
-
- # find min distorted distance from all other samples
- euclidean_dist = self._build_dist_matrix_point(
- old_ED_X, candidate, do_sqrt=True
- )
- min_euclidean_dist = np.min(euclidean_dist)
- min_intersite_dist[i] = min_euclidean_dist
-
- # Check if this is the maximum minimum distance from all other
- # samples
- if min_euclidean_dist >= maxMinDistance:
- maxMinDistance = min_euclidean_dist
-
- # Projected distance
- projected_dist = self._build_dist_matrix_point(
- old_ED_X, candidate, 'chebyshev'
- )
- min_projected_dist[i] = np.min(projected_dist)
-
- if mc_criterion == 'mc-intersite-proj':
- weight_euclidean_dist = ((n_candidate+1)**(1/ndim) - 1) * 0.5
- weight_projected_dist = (n_candidate+1) * 0.5
- total_dist_scores = weight_euclidean_dist * min_intersite_dist
- total_dist_scores += weight_projected_dist * min_projected_dist
-
- elif mc_criterion == 'mc-intersite-proj-th':
- alpha = 0.5 # chosen (tradeoff)
- d_min = 2 * alpha / n_candidate
- if any(min_projected_dist < d_min):
- all_candidates = np.delete(
- all_candidates, [min_projected_dist < d_min], axis=0
- )
- total_dist_scores = np.delete(
- min_intersite_dist, [min_projected_dist < d_min], axis=0
- )
- else:
- total_dist_scores = min_intersite_dist
- else:
- raise NameError('The MC-Criterion you requested is not available.')
-
- self.new_samples = all_candidates
- self.exploration_scores = total_dist_scores
- self.exploration_scores /= np.nansum(total_dist_scores)
-
- return self.new_samples, self.exploration_scores
-
- # -------------------------------------------------------------------------
- def approximate_voronoi(self, w, samples):
- """
- An approximate (monte carlo) version of Matlab's voronoi command.
-
- Arguments
- ---------
- samples : array
- Old experimental design to be used as center points for voronoi
- cells.
-
- Returns
- -------
- areas : array
- An approximation of the voronoi cells' areas.
- all_candidates: list of arrays
- A list of samples in each voronoi cell.
- """
- n_samples = samples.shape[0]
- ndim = samples.shape[1]
-
- # Compute the number of random points
- n_points = w * samples.shape[0]
- # Generate w random points in the domain for each sample
- points = self.ExpDesign.generate_samples(n_points, 'random')
- self.all_candidates = points
-
- # Calculate the nearest sample to each point
- self.areas = np.zeros((n_samples))
- self.closest_points = [np.empty((0, ndim)) for i in range(n_samples)]
-
- # Compute the minimum distance from all the samples of old_ED_X for
- # each test point
- for idx in range(n_points):
- # calculate the minimum distance
- distances = self._build_dist_matrix_point(
- samples, points[idx], do_sqrt=True
- )
- closest_sample = np.argmin(distances)
-
- # Add to the voronoi list of the closest sample
- self.areas[closest_sample] = self.areas[closest_sample] + 1
- prev_closest_points = self.closest_points[closest_sample]
- self.closest_points[closest_sample] = np.vstack(
- (prev_closest_points, points[idx])
- )
-
- # Divide by the amount of points to get the estimated volume of each
- # voronoi cell
- self.areas /= n_points
-
- self.perc = np.max(self.areas * 100)
-
- self.errors = self.areas
-
- return self.areas, self.all_candidates
-
- # -------------------------------------------------------------------------
- def _build_dist_matrix_point(self, samples, point, method='euclidean',
- do_sqrt=False):
- """
- Calculates the intersite distance of all points in samples from point.
-
- Parameters
- ----------
- samples : array of shape (n_samples, n_params)
- The old experimental design.
- point : array
- A candidate point.
- method : str
- Distance method.
- do_sqrt : bool, optional
- Whether to return distances or squared distances. The default is
- `False`.
-
- Returns
- -------
- distances : array
- Distances.
-
- """
- distances = distance.cdist(samples, np.array([point]), method)
-
- # do square root?
- if do_sqrt:
- return distances
- else:
- return distances**2
-
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/glexindex.py b/examples/model-comparison/bayesvalidrox/surrogate_models/glexindex.py
deleted file mode 100644
index 90877331ec121750e7f81e32a4b69edbc9a110ba..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/glexindex.py
+++ /dev/null
@@ -1,161 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Multi indices for monomial exponents.
-Credit: Jonathan Feinberg
-https://github.com/jonathf/numpoly/blob/master/numpoly/utils/glexindex.py
-"""
-
-import numpy
-import numpy.typing
-
-
-def glexindex(start, stop=None, dimensions=1, cross_truncation=1.,
- graded=False, reverse=False):
- """
- Generate graded lexicographical multi-indices for the monomial exponents.
- Args:
- start (Union[int, numpy.ndarray]):
- The lower order of the indices. If array of int, counts as lower
- bound for each axis.
- stop (Union[int, numpy.ndarray, None]):
- The maximum shape included. If omitted: stop <- start; start <- 0
- If int is provided, set as largest total order. If array of int,
- set as upper bound for each axis.
- dimensions (int):
- The number of dimensions in the expansion.
- cross_truncation (float, Tuple[float, float]):
- Use hyperbolic cross truncation scheme to reduce the number of
- terms in expansion. If two values are provided, first is low bound
- truncation, while the latter upper bound. If only one value, upper
- bound is assumed.
- graded (bool):
- Graded sorting, meaning the indices are always sorted by the index
- sum. E.g. ``(2, 2, 2)`` has a sum of 6, and will therefore be
- consider larger than both ``(3, 1, 1)`` and ``(1, 1, 3)``.
- reverse (bool):
- Reversed lexicographical sorting meaning that ``(1, 3)`` is
- considered smaller than ``(3, 1)``, instead of the opposite.
- Returns:
- list:
- Order list of indices.
- Examples:
- >>> numpoly.glexindex(4).tolist()
- [[0], [1], [2], [3]]
- >>> numpoly.glexindex(2, dimensions=2).tolist()
- [[0, 0], [1, 0], [0, 1]]
- >>> numpoly.glexindex(start=2, stop=3, dimensions=2).tolist()
- [[2, 0], [1, 1], [0, 2]]
- >>> numpoly.glexindex([1, 2, 3]).tolist()
- [[0, 0, 0], [0, 1, 0], [0, 0, 1], [0, 0, 2]]
- >>> numpoly.glexindex([1, 2, 3], cross_truncation=numpy.inf).tolist()
- [[0, 0, 0], [0, 1, 0], [0, 0, 1], [0, 1, 1], [0, 0, 2], [0, 1, 2]]
- """
- if stop is None:
- start, stop = 0, start
- start = numpy.array(start, dtype=int).flatten()
- stop = numpy.array(stop, dtype=int).flatten()
- start, stop, _ = numpy.broadcast_arrays(start, stop, numpy.empty(dimensions))
-
- cross_truncation = cross_truncation*numpy.ones(2)
-
- # Moved here from _glexindex
- bound = stop.max()
- dimensions = len(start)
- start = numpy.clip(start, a_min=0, a_max=None)
- dtype = numpy.uint8 if bound < 256 else numpy.uint16
- range_ = numpy.arange(bound, dtype=dtype)
- indices = range_[:, numpy.newaxis]
-
- for idx in range(dimensions-1):
-
- # Truncate at each step to keep memory usage low
- if idx:
- indices = indices[cross_truncate(indices, bound-1, cross_truncation[1])]
-
- # Repeats the current set of indices.
- # e.g. [0,1,2] -> [0,1,2,0,1,2,...,0,1,2]
- indices = numpy.tile(indices, (bound, 1))
-
- # Stretches ranges over the new dimension.
- # e.g. [0,1,2] -> [0,0,...,0,1,1,...,1,2,2,...,2]
- front = range_.repeat(len(indices)//bound)[:, numpy.newaxis]
-
- # Puts them two together.
- indices = numpy.column_stack((front, indices))
-
- # Complete the truncation scheme
- if dimensions == 1:
- indices = indices[(indices >= start) & (indices < bound)]
- else:
- lower = cross_truncate(indices, start-1, cross_truncation[0])
- upper = cross_truncate(indices, stop-1, cross_truncation[1])
- indices = indices[lower ^ upper]
-
- indices = numpy.array(indices, dtype=int).reshape(-1, dimensions)
- if indices.size:
- # moved here from glexsort
- keys = indices.T
- keys_ = numpy.atleast_2d(keys)
- if reverse:
- keys_ = keys_[::-1]
-
- indices_sort = numpy.array(numpy.lexsort(keys_))
- if graded:
- indices_sort = indices_sort[numpy.argsort(
- numpy.sum(keys_[:, indices_sort], axis=0))].T
-
- indices = indices[indices_sort]
- return indices
-
-def cross_truncate(indices, bound, norm):
- r"""
- Truncate of indices using L_p norm.
- .. math:
- L_p(x) = \sum_i |x_i/b_i|^p ^{1/p} \leq 1
- where :math:`b_i` are bounds that each :math:`x_i` should follow.
- Args:
- indices (Sequence[int]):
- Indices to be truncated.
- bound (int, Sequence[int]):
- The bound function for witch the indices can not be larger than.
- norm (float, Sequence[float]):
- The `p` in the `L_p`-norm. Support includes both `L_0` and `L_inf`.
- Returns:
- Boolean indices to ``indices`` with True for each index where the
- truncation criteria holds.
- Examples:
- >>> indices = numpy.array(numpy.mgrid[:10, :10]).reshape(2, -1).T
- >>> indices[cross_truncate(indices, 2, norm=0)].T
- array([[0, 0, 0, 1, 2],
- [0, 1, 2, 0, 0]])
- >>> indices[cross_truncate(indices, 2, norm=1)].T
- array([[0, 0, 0, 1, 1, 2],
- [0, 1, 2, 0, 1, 0]])
- >>> indices[cross_truncate(indices, [0, 1], norm=1)].T
- array([[0, 0],
- [0, 1]])
- """
- assert norm >= 0, "negative L_p norm not allowed"
- bound = numpy.asfarray(bound).flatten()*numpy.ones(indices.shape[1])
-
- if numpy.any(bound < 0):
- return numpy.zeros((len(indices),), dtype=bool)
-
- if numpy.any(bound == 0):
- out = numpy.all(indices[:, bound == 0] == 0, axis=-1)
- if numpy.any(bound):
- out &= cross_truncate(indices[:, bound != 0], bound[bound != 0], norm=norm)
- return out
-
- if norm == 0:
- out = numpy.sum(indices > 0, axis=-1) <= 1
- out[numpy.any(indices > bound, axis=-1)] = False
- elif norm == numpy.inf:
- out = numpy.max(indices/bound, axis=-1) <= 1
- else:
- out = numpy.sum((indices/bound)**norm, axis=-1)**(1./norm) <= 1
-
- assert numpy.all(out[numpy.all(indices == 0, axis=-1)])
-
- return out
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/input_space.py b/examples/model-comparison/bayesvalidrox/surrogate_models/input_space.py
deleted file mode 100644
index 4e010d66f2933ec243bad756d8f2c5454808d802..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/input_space.py
+++ /dev/null
@@ -1,398 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Input space built from set prior distributions
-"""
-
-import numpy as np
-import chaospy
-import scipy.stats as st
-
-
-class InputSpace:
- """
- This class generates the input space for the metamodel from the
- distributions provided using the `Input` object.
-
- Attributes
- ----------
- Input : obj
- Input object containing the parameter marginals, i.e. name,
- distribution type and distribution parameters or available raw data.
- meta_Model_type : str
- Type of the meta_Model_type.
-
- """
-
- def __init__(self, Input, meta_Model_type='pce'):
- self.InputObj = Input
- self.meta_Model_type = meta_Model_type
-
- # Other
- self.apce = None
- self.ndim = None
-
- # Init
- self.check_valid_inputs()
-
-
- def check_valid_inputs(self)-> None:
- """
- Check if the given InputObj is valid to use for further calculations:
- Has some Marginals
- Marginals have valid priors
- All Marginals given as the same type (samples vs dist)
-
- Returns
- -------
- None
-
- """
- Inputs = self.InputObj
- self.ndim = len(Inputs.Marginals)
-
- # Check if PCE or aPCE metamodel is selected.
- # TODO: test also for 'pce'??
- if self.meta_Model_type.lower() == 'apce':
- self.apce = True
- else:
- self.apce = False
-
- # check if marginals given
- if not self.ndim >=1:
- raise AssertionError('Cannot build distributions if no marginals are given')
-
- # check that each marginal is valid
- for marginals in Inputs.Marginals:
- if len(marginals.input_data) == 0:
- if marginals.dist_type == None:
- raise AssertionError('Not all marginals were provided priors')
- break
- if np.array(marginals.input_data).shape[0] and (marginals.dist_type != None):
- raise AssertionError('Both samples and distribution type are given. Please choose only one.')
- break
-
- # Check if input is given as dist or input_data.
- self.input_data_given = -1
- for marg in Inputs.Marginals:
- #print(self.input_data_given)
- size = np.array(marg.input_data).shape[0]
- #print(f'Size: {size}')
- if size and abs(self.input_data_given) !=1:
- self.input_data_given = 2
- break
- if (not size) and self.input_data_given > 0:
- self.input_data_given = 2
- break
- if not size:
- self.input_data_given = 0
- if size:
- self.input_data_given = 1
-
- if self.input_data_given == 2:
- raise AssertionError('Distributions cannot be built as the priors have different types')
-
-
- # Get the bounds if input_data are directly defined by user:
- if self.input_data_given:
- for i in range(self.ndim):
- low_bound = np.min(Inputs.Marginals[i].input_data)
- up_bound = np.max(Inputs.Marginals[i].input_data)
- Inputs.Marginals[i].parameters = [low_bound, up_bound]
-
-
-
- # -------------------------------------------------------------------------
- def init_param_space(self, max_deg=None):
- """
- Initializes parameter space.
-
- Parameters
- ----------
- max_deg : int, optional
- Maximum degree. The default is `None`.
-
- Creates
- -------
- raw_data : array of shape (n_params, n_samples)
- Raw data.
- bound_tuples : list of tuples
- A list containing lower and upper bounds of parameters.
-
- """
- # Recheck all before running!
- self.check_valid_inputs()
-
- Inputs = self.InputObj
- ndim = self.ndim
- rosenblatt_flag = Inputs.Rosenblatt
- mc_size = 50000
-
- # Save parameter names
- self.par_names = []
- for parIdx in range(ndim):
- self.par_names.append(Inputs.Marginals[parIdx].name)
-
- # Create a multivariate probability distribution
- # TODO: change this to make max_deg obligatory? at least in some specific cases?
- if max_deg is not None:
- JDist, poly_types = self.build_polytypes(rosenblatt=rosenblatt_flag)
- self.JDist, self.poly_types = JDist, poly_types
-
- if self.input_data_given:
- self.MCSize = len(Inputs.Marginals[0].input_data)
- self.raw_data = np.zeros((ndim, self.MCSize))
-
- for parIdx in range(ndim):
- # Save parameter names
- try:
- self.raw_data[parIdx] = np.array(
- Inputs.Marginals[parIdx].input_data)
- except:
- self.raw_data[parIdx] = self.JDist[parIdx].sample(mc_size)
-
- else:
- # Generate random samples based on parameter distributions
- self.raw_data = chaospy.generate_samples(mc_size,
- domain=self.JDist)
-
- # Extract moments
- for parIdx in range(ndim):
- mu = np.mean(self.raw_data[parIdx])
- std = np.std(self.raw_data[parIdx])
- self.InputObj.Marginals[parIdx].moments = [mu, std]
-
- # Generate the bounds based on given inputs for marginals
- bound_tuples = []
- for i in range(ndim):
- if Inputs.Marginals[i].dist_type == 'unif':
- low_bound = Inputs.Marginals[i].parameters[0]
- up_bound = Inputs.Marginals[i].parameters[1]
- else:
- low_bound = np.min(self.raw_data[i])
- up_bound = np.max(self.raw_data[i])
-
- bound_tuples.append((low_bound, up_bound))
-
- self.bound_tuples = tuple(bound_tuples)
-
- # -------------------------------------------------------------------------
- def build_polytypes(self, rosenblatt):
- """
- Creates the polynomial types to be passed to univ_basis_vals method of
- the MetaModel object.
-
- Parameters
- ----------
- rosenblatt : bool
- Rosenblatt transformation flag.
-
- Returns
- -------
- orig_space_dist : object
- A chaospy JDist object or a gaussian_kde object.
- poly_types : list
- List of polynomial types for the parameters.
-
- """
- Inputs = self.InputObj
-
- all_data = []
- all_dist_types = []
- orig_joints = []
- poly_types = []
-
- for parIdx in range(self.ndim):
-
- if Inputs.Marginals[parIdx].dist_type is None:
- data = Inputs.Marginals[parIdx].input_data
- all_data.append(data)
- dist_type = None
- else:
- dist_type = Inputs.Marginals[parIdx].dist_type
- params = Inputs.Marginals[parIdx].parameters
-
- if rosenblatt:
- polytype = 'hermite'
- dist = chaospy.Normal()
-
- elif dist_type is None:
- polytype = 'arbitrary'
- dist = None
-
- elif 'unif' in dist_type.lower():
- polytype = 'legendre'
- if not np.array(params).shape[0]>=2:
- raise AssertionError('Distribution has too few parameters!')
- dist = chaospy.Uniform(lower=params[0], upper=params[1])
-
- elif 'norm' in dist_type.lower() and \
- 'log' not in dist_type.lower():
- if not np.array(params).shape[0]>=2:
- raise AssertionError('Distribution has too few parameters!')
- polytype = 'hermite'
- dist = chaospy.Normal(mu=params[0], sigma=params[1])
-
- elif 'gamma' in dist_type.lower():
- polytype = 'laguerre'
- if not np.array(params).shape[0]>=3:
- raise AssertionError('Distribution has too few parameters!')
- dist = chaospy.Gamma(shape=params[0],
- scale=params[1],
- shift=params[2])
-
- elif 'beta' in dist_type.lower():
- if not np.array(params).shape[0]>=4:
- raise AssertionError('Distribution has too few parameters!')
- polytype = 'jacobi'
- dist = chaospy.Beta(alpha=params[0], beta=params[1],
- lower=params[2], upper=params[3])
-
- elif 'lognorm' in dist_type.lower():
- polytype = 'hermite'
- if not np.array(params).shape[0]>=2:
- raise AssertionError('Distribution has too few parameters!')
- mu = np.log(params[0]**2/np.sqrt(params[0]**2 + params[1]**2))
- sigma = np.sqrt(np.log(1 + params[1]**2 / params[0]**2))
- dist = chaospy.LogNormal(mu, sigma)
- # dist = chaospy.LogNormal(mu=params[0], sigma=params[1])
-
- elif 'expon' in dist_type.lower():
- polytype = 'exponential'
- if not np.array(params).shape[0]>=2:
- raise AssertionError('Distribution has too few parameters!')
- dist = chaospy.Exponential(scale=params[0], shift=params[1])
-
- elif 'weibull' in dist_type.lower():
- polytype = 'weibull'
- if not np.array(params).shape[0]>=3:
- raise AssertionError('Distribution has too few parameters!')
- dist = chaospy.Weibull(shape=params[0], scale=params[1],
- shift=params[2])
-
- else:
- message = (f"DistType {dist_type} for parameter"
- f"{parIdx+1} is not available.")
- raise ValueError(message)
-
- if self.input_data_given or self.apce:
- polytype = 'arbitrary'
-
- # Store dists and poly_types
- orig_joints.append(dist)
- poly_types.append(polytype)
- all_dist_types.append(dist_type)
-
- # Prepare final output to return
- if None in all_dist_types:
- # Naive approach: Fit a gaussian kernel to the provided data
- Data = np.asarray(all_data)
- try:
- orig_space_dist = st.gaussian_kde(Data)
- except:
- raise ValueError('The samples provided to the Marginals should be 1D only')
- self.prior_space = orig_space_dist
- else:
- orig_space_dist = chaospy.J(*orig_joints)
- try:
- self.prior_space = st.gaussian_kde(orig_space_dist.sample(10000))
- except:
- raise ValueError('Parameter values are not valid, please set differently')
-
- return orig_space_dist, poly_types
-
- # -------------------------------------------------------------------------
- def transform(self, X, params=None, method=None):
- """
- Transforms the samples via either a Rosenblatt or an isoprobabilistic
- transformation.
-
- Parameters
- ----------
- X : array of shape (n_samples,n_params)
- Samples to be transformed.
- method : string
- If transformation method is 'user' transform X, else just pass X.
-
- Returns
- -------
- tr_X: array of shape (n_samples,n_params)
- Transformed samples.
-
- """
- # Check for built JDist
- if not hasattr(self, 'JDist'):
- raise AttributeError('Call function init_param_space first to create JDist')
-
- # Check if X is 2d
- if X.ndim != 2:
- raise AttributeError('X should have two dimensions')
-
- # Check if size of X matches Marginals
- if X.shape[1]!= self.ndim:
- raise AttributeError('The second dimension of X should be the same size as the number of marginals in the InputObj')
-
- if self.InputObj.Rosenblatt:
- self.origJDist, _ = self.build_polytypes(False)
- if method == 'user':
- tr_X = self.JDist.inv(self.origJDist.fwd(X.T)).T
- else:
- # Inverse to original spcace -- generate sample ED
- tr_X = self.origJDist.inv(self.JDist.fwd(X.T)).T
- else:
- # Transform samples via an isoprobabilistic transformation
- n_samples, n_params = X.shape
- Inputs = self.InputObj
- origJDist = self.JDist
- poly_types = self.poly_types
-
- disttypes = []
- for par_i in range(n_params):
- disttypes.append(Inputs.Marginals[par_i].dist_type)
-
- # Pass non-transformed X, if arbitrary PCE is selected.
- if None in disttypes or self.input_data_given or self.apce:
- return X
-
- cdfx = np.zeros((X.shape))
- tr_X = np.zeros((X.shape))
-
- for par_i in range(n_params):
-
- # Extract the parameters of the original space
- disttype = disttypes[par_i]
- if disttype is not None:
- dist = origJDist[par_i]
- else:
- dist = None
- polytype = poly_types[par_i]
- cdf = np.vectorize(lambda x: dist.cdf(x))
-
- # Extract the parameters of the transformation space based on
- # polyType
- if polytype == 'legendre' or disttype == 'uniform':
- # Generate Y_Dists based
- params_Y = [-1, 1]
- dist_Y = st.uniform(loc=params_Y[0],
- scale=params_Y[1]-params_Y[0])
- inv_cdf = np.vectorize(lambda x: dist_Y.ppf(x))
-
- elif polytype == 'hermite' or disttype == 'norm':
- params_Y = [0, 1]
- dist_Y = st.norm(loc=params_Y[0], scale=params_Y[1])
- inv_cdf = np.vectorize(lambda x: dist_Y.ppf(x))
-
- elif polytype == 'laguerre' or disttype == 'gamma':
- if params == None:
- raise AttributeError('Additional parameters have to be set for the gamma distribution!')
- params_Y = [1, params[1]]
- dist_Y = st.gamma(loc=params_Y[0], scale=params_Y[1])
- inv_cdf = np.vectorize(lambda x: dist_Y.ppf(x))
-
- # Compute CDF_x(X)
- cdfx[:, par_i] = cdf(X[:, par_i])
-
- # Compute invCDF_y(cdfx)
- tr_X[:, par_i] = inv_cdf(cdfx[:, par_i])
-
- return tr_X
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/inputs.py b/examples/model-comparison/bayesvalidrox/surrogate_models/inputs.py
deleted file mode 100644
index 094e1066fe008e37288e44750524c5a1370bd7a2..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/inputs.py
+++ /dev/null
@@ -1,79 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Inputs and related marginal distributions
-"""
-
-class Input:
- """
- A class to define the uncertain input parameters.
-
- Attributes
- ----------
- Marginals : obj
- Marginal objects. See `inputs.Marginal`.
- Rosenblatt : bool
- If Rossenblatt transformation is required for the dependent input
- parameters.
-
- Examples
- -------
- Marginals can be defined as following:
-
- >>> Inputs.add_marginals()
- >>> Inputs.Marginals[0].name = 'X_1'
- >>> Inputs.Marginals[0].dist_type = 'uniform'
- >>> Inputs.Marginals[0].parameters = [-5, 5]
-
- If there is no common data is avaliable, the input data can be given
- as following:
-
- >>> Inputs.add_marginals()
- >>> Inputs.Marginals[0].name = 'X_1'
- >>> Inputs.Marginals[0].input_data = input_data
- """
- poly_coeffs_flag = True
-
- def __init__(self):
- self.Marginals = []
- self.Rosenblatt = False
-
- def add_marginals(self):
- """
- Adds a new Marginal object to the input object.
-
- Returns
- -------
- None.
-
- """
- self.Marginals.append(Marginal())
-
-
-# Nested class
-class Marginal:
- """
- An object containing the specifications of the marginals for each uncertain
- parameter.
-
- Attributes
- ----------
- name : string
- Name of the parameter. The default is `'$x_1$'`.
- dist_type : string
- Name of the distribution. The default is `None`.
- parameters : list
- List of the parameters corresponding to the distribution type. The
- default is `None`.
- input_data : array
- Available input data. The default is `[]`.
- moments : list
- List of the moments.
- """
-
- def __init__(self):
- self.name = '$x_1$'
- self.dist_type = None
- self.parameters = None
- self.input_data = []
- self.moments = None
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/orthogonal_matching_pursuit.py b/examples/model-comparison/bayesvalidrox/surrogate_models/orthogonal_matching_pursuit.py
deleted file mode 100644
index 96ef9c1d50b10b587ad0846d41733fc7f1cedfe8..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/orthogonal_matching_pursuit.py
+++ /dev/null
@@ -1,366 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Jul 15 14:08:59 2022
-
-@author: farid
-"""
-import numpy as np
-from sklearn.base import RegressorMixin
-from sklearn.linear_model._base import LinearModel
-from sklearn.utils import check_X_y
-
-
-def corr(x, y):
- return abs(x.dot(y))/np.sqrt((x**2).sum())
-
-
-class OrthogonalMatchingPursuit(LinearModel, RegressorMixin):
- '''
- Regression with Orthogonal Matching Pursuit [1].
-
- Parameters
- ----------
- fit_intercept : boolean, optional (DEFAULT = True)
- whether to calculate the intercept for this model. If set
- to false, no intercept will be used in calculations
- (e.g. data is expected to be already centered).
-
- copy_X : boolean, optional (DEFAULT = True)
- If True, X will be copied; else, it may be overwritten.
-
- verbose : boolean, optional (DEFAULT = FALSE)
- Verbose mode when fitting the model
-
- Attributes
- ----------
- coef_ : array, shape = (n_features)
- Coefficients of the regression model (mean of posterior distribution)
-
- active_ : array, dtype = np.bool, shape = (n_features)
- True for non-zero coefficients, False otherwise
-
- References
- ----------
- [1] Pati, Y., Rezaiifar, R., Krishnaprasad, P. (1993). Orthogonal matching
- pursuit: recursive function approximation with application to wavelet
- decomposition. Proceedings of 27th Asilomar Conference on Signals,
- Systems and Computers, 40-44.
- '''
-
- def __init__(self, fit_intercept=True, normalize=False, copy_X=True,
- verbose=False):
- self.fit_intercept = fit_intercept
- self.normalize = normalize
- self.copy_X = copy_X
- self.verbose = verbose
-
- def _preprocess_data(self, X, y):
- """Center and scale data.
- Centers data to have mean zero along axis 0. If fit_intercept=False or
- if the X is a sparse matrix, no centering is done, but normalization
- can still be applied. The function returns the statistics necessary to
- reconstruct the input data, which are X_offset, y_offset, X_scale, such
- that the output
- X = (X - X_offset) / X_scale
- X_scale is the L2 norm of X - X_offset.
- """
-
- if self.copy_X:
- X = X.copy(order='K')
-
- y = np.asarray(y, dtype=X.dtype)
-
- if self.fit_intercept:
- X_offset = np.average(X, axis=0)
- X -= X_offset
- if self.normalize:
- X_scale = np.ones(X.shape[1], dtype=X.dtype)
- std = np.sqrt(np.sum(X**2, axis=0)/(len(X)-1))
- X_scale[std != 0] = std[std != 0]
- X /= X_scale
- else:
- X_scale = np.ones(X.shape[1], dtype=X.dtype)
- y_offset = np.mean(y)
- y = y - y_offset
- else:
- X_offset = np.zeros(X.shape[1], dtype=X.dtype)
- X_scale = np.ones(X.shape[1], dtype=X.dtype)
- if y.ndim == 1:
- y_offset = X.dtype.type(0)
- else:
- y_offset = np.zeros(y.shape[1], dtype=X.dtype)
-
- return X, y, X_offset, y_offset, X_scale
-
- def fit(self, X, y):
- '''
- Fits Regression with Orthogonal Matching Pursuit Algorithm.
-
- Parameters
- -----------
- X: {array-like, sparse matrix} of size (n_samples, n_features)
- Training data, matrix of explanatory variables
-
- y: array-like of size [n_samples, n_features]
- Target values
-
- Returns
- -------
- self : object
- Returns self.
- '''
- X, y = check_X_y(X, y, dtype=np.float64, y_numeric=True)
- n_samples, n_features = X.shape
-
- X, y, X_mean, y_mean, X_std = self._preprocess_data(X, y)
- self._x_mean_ = X_mean
- self._y_mean = y_mean
- self._x_std = X_std
-
- # Normalize columns of Psi, so that each column has norm = 1
- norm_X = np.linalg.norm(X, axis=0)
- X_norm = X/norm_X
-
- # Initialize residual vector to full model response and normalize
- R = y
- norm_y = np.sqrt(np.dot(y, y))
- r = y/norm_y
-
- # Check for constant regressors
- const_indices = np.where(~np.diff(X, axis=0).any(axis=0))[0]
- bool_const = not const_indices
-
- # Start regression using OPM algorithm
- precision = 0 # Set precision criterion to precision of program
- early_stop = True
- cond_early = True # Initialize condition for early stop
- ind = []
- iindx = [] # index of selected columns
- indtot = np.arange(n_features) # Full index set for remaining columns
- kmax = min(n_samples, n_features) # Maximum number of iterations
- LOO = np.PINF * np.ones(kmax) # Store LOO error at each iteration
- LOOmin = np.PINF # Initialize minimum value of LOO
- coeff = np.zeros((n_features, kmax))
- count = 0
- k = 0.1 # Percentage of iteration history for early stop
-
- # Begin iteration over regressors set (Matrix X)
- while (np.linalg.norm(R) > precision) and (count <= kmax-1) and \
- ((cond_early or early_stop) ^ ~cond_early):
-
- # Update index set of columns yet to select
- if count != 0:
- indtot = np.delete(indtot, iindx)
-
- # Find column of X that is most correlated with residual
- h = abs(np.dot(r, X_norm))
- iindx = np.argmax(h[indtot])
- indx = indtot[iindx]
-
- # initialize with the constant regressor, if it exists in the basis
- if (count == 0) and bool_const:
- # overwrite values for iindx and indx
- iindx = const_indices[0]
- indx = indtot[iindx]
-
- # Invert the information matrix at the first iteration, later only
- # update its value on the basis of the previously inverted one,
- if count == 0:
- M = 1 / np.dot(X[:, indx], X[:, indx])
- else:
- x = np.dot(X[:, ind].T, X[:, indx])
- r = np.dot(X[:, indx], X[:, indx])
- M = self.blockwise_inverse(M, x, x.T, r)
-
- # Add newly found index to the selected indexes set
- ind.append(indx)
-
- # Select regressors subset (Projection subspace)
- Xpro = X[:, ind]
-
- # Obtain coefficient by performing OLS
- TT = np.dot(y, Xpro)
- beta = np.dot(M, TT)
- coeff[ind, count] = beta
-
- # Compute LOO error
- LOO[count] = self.loo_error(Xpro, M, y, beta)
-
- # Compute new residual due to new projection
- R = y - np.dot(Xpro, beta)
-
- # Normalize residual
- norm_R = np.sqrt(np.dot(R, R))
- r = R / norm_R
-
- # Update counters and early-stop criterions
- countinf = max(0, int(count-k*kmax))
- LOOmin = min(LOOmin, LOO[count])
-
- if count == 0:
- cond_early = (LOO[0] <= LOOmin)
- else:
- cond_early = (min(LOO[countinf:count+1]) <= LOOmin)
-
- if self.verbose:
- print(f'Iteration: {count+1}, mod. LOOCV error : '
- f'{LOO[count]:.2e}')
-
- # Update counter
- count += 1
-
- # Select projection with smallest cross-validation error
- countmin = np.argmin(LOO[:-1])
- self.coef_ = coeff[:, countmin]
- self.active = coeff[:, countmin] != 0.0
-
- # set intercept_
- if self.fit_intercept:
- self.coef_ = self.coef_ / X_std
- self.intercept_ = y_mean - np.dot(X_mean, self.coef_.T)
- else:
- self.intercept_ = 0.
-
- return self
-
- def predict(self, X):
- '''
- Computes predictive distribution for test set.
-
- Parameters
- -----------
- X: {array-like, sparse} (n_samples_test, n_features)
- Test data, matrix of explanatory variables
-
- Returns
- -------
- y_hat: numpy array of size (n_samples_test,)
- Estimated values of targets on test set (i.e. mean of
- predictive distribution)
- '''
-
- y_hat = np.dot(X, self.coef_) + self.intercept_
-
- return y_hat
-
- def loo_error(self, psi, inv_inf_matrix, y, coeffs):
- """
- Calculates the corrected LOO error for regression on regressor
- matrix `psi` that generated the coefficients based on [1] and [2].
-
- [1] Blatman, G., 2009. Adaptive sparse polynomial chaos expansions for
- uncertainty propagation and sensitivity analysis (Doctoral
- dissertation, Clermont-Ferrand 2).
-
- [2] Blatman, G. and Sudret, B., 2011. Adaptive sparse polynomial chaos
- expansion based on least angle regression. Journal of computational
- Physics, 230(6), pp.2345-2367.
-
- Parameters
- ----------
- psi : array of shape (n_samples, n_feature)
- Orthogonal bases evaluated at the samples.
- inv_inf_matrix : array
- Inverse of the information matrix.
- y : array of shape (n_samples, )
- Targets.
- coeffs : array
- Computed regresssor cofficients.
-
- Returns
- -------
- loo_error : float
- Modified LOOCV error.
-
- """
-
- # NrEvaluation (Size of experimental design)
- N, P = psi.shape
-
- # h factor (the full matrix is not calculated explicitly,
- # only the trace is, to save memory)
- PsiM = np.dot(psi, inv_inf_matrix)
-
- h = np.sum(np.multiply(PsiM, psi), axis=1, dtype=np.longdouble)
-
- # ------ Calculate Error Loocv for each measurement point ----
- # Residuals
- residual = np.dot(psi, coeffs) - y
-
- # Variance
- varY = np.var(y)
-
- if varY == 0:
- norm_emp_error = 0
- loo_error = 0
- else:
- norm_emp_error = np.mean(residual**2)/varY
-
- loo_error = np.mean(np.square(residual / (1-h))) / varY
-
- # if there are NaNs, just return an infinite LOO error (this
- # happens, e.g., when a strongly underdetermined problem is solved)
- if np.isnan(loo_error):
- loo_error = np.inf
-
- # Corrected Error for over-determined system
- tr_M = np.trace(np.atleast_2d(inv_inf_matrix))
- if tr_M < 0 or abs(tr_M) > 1e6:
- tr_M = np.trace(np.linalg.pinv(np.dot(psi.T, psi)))
-
- # Over-determined system of Equation
- if N > P:
- T_factor = N/(N-P) * (1 + tr_M)
-
- # Under-determined system of Equation
- else:
- T_factor = np.inf
-
- loo_error *= T_factor
-
- return loo_error
-
- def blockwise_inverse(self, Ainv, B, C, D):
- """
- non-singular square matrix M defined as M = [[A B]; [C D]] .
- B, C and D can have any dimension, provided their combination defines
- a square matrix M.
-
- Parameters
- ----------
- Ainv : float or array
- inverse of the square-submatrix A.
- B : float or array
- Information matrix with all new regressor.
- C : float or array
- Transpose of B.
- D : float or array
- Information matrix with all selected regressors.
-
- Returns
- -------
- M : array
- Inverse of the information matrix.
-
- """
- if np.isscalar(D):
- # Inverse of D
- Dinv = 1/D
- # Schur complement
- SCinv = 1/(D - np.dot(C, np.dot(Ainv, B[:, None])))[0]
- else:
- # Inverse of D
- Dinv = np.linalg.solve(D, np.eye(D.shape))
- # Schur complement
- SCinv = np.linalg.solve((D - C*Ainv*B), np.eye(D.shape))
-
- T1 = np.dot(Ainv, np.dot(B[:, None], SCinv))
- T2 = np.dot(C, Ainv)
-
- # Assemble the inverse matrix
- M = np.vstack((
- np.hstack((Ainv+T1*T2, -T1)),
- np.hstack((-(SCinv)*T2, SCinv))
- ))
- return M
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/reg_fast_ard.py b/examples/model-comparison/bayesvalidrox/surrogate_models/reg_fast_ard.py
deleted file mode 100644
index e6883a3edd6d247c219b8be328f5206b75780fbb..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/reg_fast_ard.py
+++ /dev/null
@@ -1,475 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Created on Tue Mar 24 19:41:45 2020
-
-@author: farid
-"""
-import numpy as np
-from scipy.linalg import solve_triangular
-from numpy.linalg import LinAlgError
-from sklearn.base import RegressorMixin
-from sklearn.linear_model._base import LinearModel
-import warnings
-from sklearn.utils import check_X_y
-from scipy.linalg import pinvh
-
-
-def update_precisions(Q,S,q,s,A,active,tol,n_samples,clf_bias):
- '''
- Selects one feature to be added/recomputed/deleted to model based on
- effect it will have on value of log marginal likelihood.
- '''
- # initialise vector holding changes in log marginal likelihood
- deltaL = np.zeros(Q.shape[0])
-
- # identify features that can be added , recomputed and deleted in model
- theta = q**2 - s
- add = (theta > 0) * (active == False)
- recompute = (theta > 0) * (active == True)
- delete = ~(add + recompute)
-
- # compute sparsity & quality parameters corresponding to features in
- # three groups identified above
- Qadd,Sadd = Q[add], S[add]
- Qrec,Srec,Arec = Q[recompute], S[recompute], A[recompute]
- Qdel,Sdel,Adel = Q[delete], S[delete], A[delete]
-
- # compute new alpha's (precision parameters) for features that are
- # currently in model and will be recomputed
- Anew = s[recompute]**2/ ( theta[recompute] + np.finfo(np.float32).eps)
- delta_alpha = (1./Anew - 1./Arec)
-
- # compute change in log marginal likelihood
- deltaL[add] = ( Qadd**2 - Sadd ) / Sadd + np.log(Sadd/Qadd**2 )
- deltaL[recompute] = Qrec**2 / (Srec + 1. / delta_alpha) - np.log(1 + Srec*delta_alpha)
- deltaL[delete] = Qdel**2 / (Sdel - Adel) - np.log(1 - Sdel / Adel)
- deltaL = deltaL / n_samples
-
- # find feature which caused largest change in likelihood
- feature_index = np.argmax(deltaL)
-
- # no deletions or additions
- same_features = np.sum( theta[~recompute] > 0) == 0
-
- # changes in precision for features already in model is below threshold
- no_delta = np.sum( abs( Anew - Arec ) > tol ) == 0
- # if same_features: print(abs( Anew - Arec ))
- # print("same_features = {} no_delta = {}".format(same_features,no_delta))
- # check convergence: if no features to add or delete and small change in
- # precision for current features then terminate
- converged = False
- if same_features and no_delta:
- converged = True
- return [A,converged]
-
- # if not converged update precision parameter of weights and return
- if theta[feature_index] > 0:
- A[feature_index] = s[feature_index]**2 / theta[feature_index]
- if active[feature_index] == False:
- active[feature_index] = True
- else:
- # at least two active features
- if active[feature_index] == True and np.sum(active) >= 2:
- # do not remove bias term in classification
- # (in regression it is factored in through centering)
- if not (feature_index == 0 and clf_bias):
- active[feature_index] = False
- A[feature_index] = np.PINF
-
- return [A,converged]
-
-
-class RegressionFastARD(LinearModel, RegressorMixin):
- '''
- Regression with Automatic Relevance Determination (Fast Version uses
- Sparse Bayesian Learning)
- https://github.com/AmazaspShumik/sklearn-bayes/blob/master/skbayes/rvm_ard_models/fast_rvm.py
-
- Parameters
- ----------
- n_iter: int, optional (DEFAULT = 100)
- Maximum number of iterations
-
- start: list, optional (DEFAULT = None)
- Initial selected features.
-
- tol: float, optional (DEFAULT = 1e-3)
- If absolute change in precision parameter for weights is below threshold
- algorithm terminates.
-
- fit_intercept : boolean, optional (DEFAULT = True)
- whether to calculate the intercept for this model. If set
- to false, no intercept will be used in calculations
- (e.g. data is expected to be already centered).
-
- copy_X : boolean, optional (DEFAULT = True)
- If True, X will be copied; else, it may be overwritten.
-
- compute_score : bool, default=False
- If True, compute the log marginal likelihood at each iteration of the
- optimization.
-
- verbose : boolean, optional (DEFAULT = FALSE)
- Verbose mode when fitting the model
-
- Attributes
- ----------
- coef_ : array, shape = (n_features)
- Coefficients of the regression model (mean of posterior distribution)
-
- alpha_ : float
- estimated precision of the noise
-
- active_ : array, dtype = np.bool, shape = (n_features)
- True for non-zero coefficients, False otherwise
-
- lambda_ : array, shape = (n_features)
- estimated precisions of the coefficients
-
- sigma_ : array, shape = (n_features, n_features)
- estimated covariance matrix of the weights, computed only
- for non-zero coefficients
-
- scores_ : array-like of shape (n_iter_+1,)
- If computed_score is True, value of the log marginal likelihood (to be
- maximized) at each iteration of the optimization.
-
- References
- ----------
- [1] Fast marginal likelihood maximisation for sparse Bayesian models
- (Tipping & Faul 2003) (http://www.miketipping.com/papers/met-fastsbl.pdf)
- [2] Analysis of sparse Bayesian learning (Tipping & Faul 2001)
- (http://www.miketipping.com/abstracts.htm#Faul:NIPS01)
- '''
-
- def __init__(self, n_iter=300, start=None, tol=1e-3, fit_intercept=True,
- normalize=False, copy_X=True, compute_score=False, verbose=False):
- self.n_iter = n_iter
- self.start = start
- self.tol = tol
- self.scores_ = list()
- self.fit_intercept = fit_intercept
- self.normalize = normalize
- self.copy_X = copy_X
- self.compute_score = compute_score
- self.verbose = verbose
-
- def _preprocess_data(self, X, y):
- """Center and scale data.
- Centers data to have mean zero along axis 0. If fit_intercept=False or
- if the X is a sparse matrix, no centering is done, but normalization
- can still be applied. The function returns the statistics necessary to
- reconstruct the input data, which are X_offset, y_offset, X_scale, such
- that the output
- X = (X - X_offset) / X_scale
- X_scale is the L2 norm of X - X_offset.
- """
-
- if self.copy_X:
- X = X.copy(order='K')
-
- y = np.asarray(y, dtype=X.dtype)
-
- if self.fit_intercept:
- X_offset = np.average(X, axis=0)
- X -= X_offset
- if self.normalize:
- X_scale = np.ones(X.shape[1], dtype=X.dtype)
- std = np.sqrt(np.sum(X**2, axis=0)/(len(X)-1))
- X_scale[std != 0] = std[std != 0]
- X /= X_scale
- else:
- X_scale = np.ones(X.shape[1], dtype=X.dtype)
- y_offset = np.mean(y)
- y = y - y_offset
- else:
- X_offset = np.zeros(X.shape[1], dtype=X.dtype)
- X_scale = np.ones(X.shape[1], dtype=X.dtype)
- if y.ndim == 1:
- y_offset = X.dtype.type(0)
- else:
- y_offset = np.zeros(y.shape[1], dtype=X.dtype)
-
- return X, y, X_offset, y_offset, X_scale
-
- def fit(self, X, y):
- '''
- Fits ARD Regression with Sequential Sparse Bayes Algorithm.
-
- Parameters
- -----------
- X: {array-like, sparse matrix} of size (n_samples, n_features)
- Training data, matrix of explanatory variables
-
- y: array-like of size [n_samples, n_features]
- Target values
-
- Returns
- -------
- self : object
- Returns self.
- '''
- X, y = check_X_y(X, y, dtype=np.float64, y_numeric=True)
- n_samples, n_features = X.shape
-
- X, y, X_mean, y_mean, X_std = self._preprocess_data(X, y)
- self._x_mean_ = X_mean
- self._y_mean = y_mean
- self._x_std = X_std
-
- # precompute X'*Y , X'*X for faster iterations & allocate memory for
- # sparsity & quality vectors
- XY = np.dot(X.T, y)
- XX = np.dot(X.T, X)
- XXd = np.diag(XX)
-
- # initialise precision of noise & and coefficients
- var_y = np.var(y)
-
- # check that variance is non zero !!!
- if var_y == 0:
- beta = 1e-2
- self.var_y = True
- else:
- beta = 1. / np.var(y)
- self.var_y = False
-
- A = np.PINF * np.ones(n_features)
- active = np.zeros(n_features, dtype=np.bool)
-
- if self.start is not None and not hasattr(self, 'active_'):
- start = self.start
- # start from a given start basis vector
- proj = XY**2 / XXd
- active[start] = True
- A[start] = XXd[start]/(proj[start] - var_y)
-
- else:
- # in case of almost perfect multicollinearity between some features
- # start from feature 0
- if np.sum(XXd - X_mean**2 < np.finfo(np.float32).eps) > 0:
- A[0] = np.finfo(np.float16).eps
- active[0] = True
-
- else:
- # start from a single basis vector with largest projection on
- # targets
- proj = XY**2 / XXd
- start = np.argmax(proj)
- active[start] = True
- A[start] = XXd[start]/(proj[start] - var_y +
- np.finfo(np.float32).eps)
-
- warning_flag = 0
- scores_ = []
- for i in range(self.n_iter):
- # Handle variance zero
- if self.var_y:
- A[0] = y_mean
- active[0] = True
- converged = True
- break
-
- XXa = XX[active, :][:, active]
- XYa = XY[active]
- Aa = A[active]
-
- # mean & covariance of posterior distribution
- Mn, Ri, cholesky = self._posterior_dist(Aa, beta, XXa, XYa)
- if cholesky:
- Sdiag = np.sum(Ri**2, 0)
- else:
- Sdiag = np.copy(np.diag(Ri))
- warning_flag += 1
-
- # raise warning in case cholesky fails
- if warning_flag == 1:
- warnings.warn(("Cholesky decomposition failed! Algorithm uses "
- "pinvh, which is significantly slower. If you "
- "use RVR it is advised to change parameters of "
- "the kernel!"))
-
- # compute quality & sparsity parameters
- s, q, S, Q = self._sparsity_quality(XX, XXd, XY, XYa, Aa, Ri,
- active, beta, cholesky)
-
- # update precision parameter for noise distribution
- rss = np.sum((y - np.dot(X[:, active], Mn))**2)
-
- # if near perfect fit , then terminate
- if (rss / n_samples/var_y) < self.tol:
- warnings.warn('Early termination due to near perfect fit')
- converged = True
- break
- beta = n_samples - np.sum(active) + np.sum(Aa * Sdiag)
- beta /= rss
- # beta /= (rss + np.finfo(np.float32).eps)
-
- # update precision parameters of coefficients
- A, converged = update_precisions(Q, S, q, s, A, active, self.tol,
- n_samples, False)
-
- if self.compute_score:
- scores_.append(self.log_marginal_like(XXa, XYa, Aa, beta))
-
- if self.verbose:
- print(('Iteration: {0}, number of features '
- 'in the model: {1}').format(i, np.sum(active)))
-
- if converged or i == self.n_iter - 1:
- if converged and self.verbose:
- print('Algorithm converged!')
- break
-
- # after last update of alpha & beta update parameters
- # of posterior distribution
- XXa, XYa, Aa = XX[active, :][:, active], XY[active], A[active]
- Mn, Sn, cholesky = self._posterior_dist(Aa, beta, XXa, XYa, True)
- self.coef_ = np.zeros(n_features)
- self.coef_[active] = Mn
- self.sigma_ = Sn
- self.active_ = active
- self.lambda_ = A
- self.alpha_ = beta
- self.converged = converged
- if self.compute_score:
- self.scores_ = np.array(scores_)
-
- # set intercept_
- if self.fit_intercept:
- self.coef_ = self.coef_ / X_std
- self.intercept_ = y_mean - np.dot(X_mean, self.coef_.T)
- else:
- self.intercept_ = 0.
- return self
-
- def log_marginal_like(self, XXa, XYa, Aa, beta):
- """Computes the log of the marginal likelihood."""
- N, M = XXa.shape
- A = np.diag(Aa)
-
- Mn, sigma_, cholesky = self._posterior_dist(Aa, beta, XXa, XYa,
- full_covar=True)
-
- C = sigma_ + np.dot(np.dot(XXa.T, np.linalg.pinv(A)), XXa)
-
- score = np.dot(np.dot(XYa.T, np.linalg.pinv(C)), XYa) +\
- np.log(np.linalg.det(C)) + N * np.log(2 * np.pi)
-
- return -0.5 * score
-
- def predict(self, X, return_std=False):
- '''
- Computes predictive distribution for test set.
- Predictive distribution for each data point is one dimensional
- Gaussian and therefore is characterised by mean and variance based on
- Ref.[1] Section 3.3.2.
-
- Parameters
- -----------
- X: {array-like, sparse} (n_samples_test, n_features)
- Test data, matrix of explanatory variables
-
- Returns
- -------
- : list of length two [y_hat, var_hat]
-
- y_hat: numpy array of size (n_samples_test,)
- Estimated values of targets on test set (i.e. mean of
- predictive distribution)
-
- var_hat: numpy array of size (n_samples_test,)
- Variance of predictive distribution
- References
- ----------
- [1] Bishop, C. M. (2006). Pattern recognition and machine learning.
- springer.
- '''
-
- y_hat = np.dot(X, self.coef_) + self.intercept_
-
- if return_std:
- # Handle the zero variance case
- if self.var_y:
- return y_hat, np.zeros_like(y_hat)
-
- if self.normalize:
- X -= self._x_mean_[self.active_]
- X /= self._x_std[self.active_]
- var_hat = 1./self.alpha_
- var_hat += np.sum(X.dot(self.sigma_) * X, axis=1)
- std_hat = np.sqrt(var_hat)
- return y_hat, std_hat
- else:
- return y_hat
-
- def _posterior_dist(self, A, beta, XX, XY, full_covar=False):
- '''
- Calculates mean and covariance matrix of posterior distribution
- of coefficients.
- '''
- # compute precision matrix for active features
- Sinv = beta * XX
- np.fill_diagonal(Sinv, np.diag(Sinv) + A)
- cholesky = True
-
- # try cholesky, if it fails go back to pinvh
- try:
- # find posterior mean : R*R.T*mean = beta*X.T*Y
- # solve(R*z = beta*X.T*Y) =>find z=> solve(R.T*mean = z)=>find mean
- R = np.linalg.cholesky(Sinv)
- Z = solve_triangular(R, beta*XY, check_finite=True, lower=True)
- Mn = solve_triangular(R.T, Z, check_finite=True, lower=False)
-
- # invert lower triangular matrix from cholesky decomposition
- Ri = solve_triangular(R, np.eye(A.shape[0]), check_finite=False,
- lower=True)
- if full_covar:
- Sn = np.dot(Ri.T, Ri)
- return Mn, Sn, cholesky
- else:
- return Mn, Ri, cholesky
- except LinAlgError:
- cholesky = False
- Sn = pinvh(Sinv)
- Mn = beta*np.dot(Sinv, XY)
- return Mn, Sn, cholesky
-
- def _sparsity_quality(self, XX, XXd, XY, XYa, Aa, Ri, active, beta, cholesky):
- '''
- Calculates sparsity and quality parameters for each feature
-
- Theoretical Note:
- -----------------
- Here we used Woodbury Identity for inverting covariance matrix
- of target distribution
- C = 1/beta + 1/alpha * X' * X
- C^-1 = beta - beta^2 * X * Sn * X'
- '''
- bxy = beta*XY
- bxx = beta*XXd
- if cholesky:
- # here Ri is inverse of lower triangular matrix obtained from
- # cholesky decomp
- xxr = np.dot(XX[:, active], Ri.T)
- rxy = np.dot(Ri, XYa)
- S = bxx - beta**2 * np.sum(xxr**2, axis=1)
- Q = bxy - beta**2 * np.dot(xxr, rxy)
- else:
- # here Ri is covariance matrix
- XXa = XX[:, active]
- XS = np.dot(XXa, Ri)
- S = bxx - beta**2 * np.sum(XS*XXa, 1)
- Q = bxy - beta**2 * np.dot(XS, XYa)
- # Use following:
- # (EQ 1) q = A*Q/(A - S) ; s = A*S/(A-S)
- # so if A = np.PINF q = Q, s = S
- qi = np.copy(Q)
- si = np.copy(S)
- # If A is not np.PINF, then it should be 'active' feature => use (EQ 1)
- Qa, Sa = Q[active], S[active]
- qi[active] = Aa * Qa / (Aa - Sa)
- si[active] = Aa * Sa / (Aa - Sa)
-
- return [si, qi, S, Q]
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/reg_fast_laplace.py b/examples/model-comparison/bayesvalidrox/surrogate_models/reg_fast_laplace.py
deleted file mode 100644
index 7fdcb5cf6e93c396d32eae2b0aad87a194a9cba4..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/reg_fast_laplace.py
+++ /dev/null
@@ -1,452 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-import numpy as np
-from sklearn.utils import as_float_array
-from sklearn.model_selection import KFold
-
-
-class RegressionFastLaplace():
- '''
- Sparse regression with Bayesian Compressive Sensing as described in Alg. 1
- (Fast Laplace) of Ref.[1], which updated formulas from [2].
-
- sigma2: noise precision (sigma^2)
- nu fixed to 0
-
- uqlab/lib/uq_regression/BCS/uq_bsc.m
-
- Parameters
- ----------
- n_iter: int, optional (DEFAULT = 1000)
- Maximum number of iterations
-
- tol: float, optional (DEFAULT = 1e-7)
- If absolute change in precision parameter for weights is below
- threshold algorithm terminates.
-
- fit_intercept : boolean, optional (DEFAULT = True)
- whether to calculate the intercept for this model. If set
- to false, no intercept will be used in calculations
- (e.g. data is expected to be already centered).
-
- copy_X : boolean, optional (DEFAULT = True)
- If True, X will be copied; else, it may be overwritten.
-
- verbose : boolean, optional (DEFAULT = FALSE)
- Verbose mode when fitting the model
-
- Attributes
- ----------
- coef_ : array, shape = (n_features)
- Coefficients of the regression model (mean of posterior distribution)
-
- alpha_ : float
- estimated precision of the noise
-
- active_ : array, dtype = np.bool, shape = (n_features)
- True for non-zero coefficients, False otherwise
-
- lambda_ : array, shape = (n_features)
- estimated precisions of the coefficients
-
- sigma_ : array, shape = (n_features, n_features)
- estimated covariance matrix of the weights, computed only
- for non-zero coefficients
-
- References
- ----------
- [1] Babacan, S. D., Molina, R., & Katsaggelos, A. K. (2009). Bayesian
- compressive sensing using Laplace priors. IEEE Transactions on image
- processing, 19(1), 53-63.
- [2] Fast marginal likelihood maximisation for sparse Bayesian models
- (Tipping & Faul 2003).
- (http://www.miketipping.com/papers/met-fastsbl.pdf)
- '''
-
- def __init__(self, n_iter=1000, n_Kfold=10, tol=1e-7, fit_intercept=False,
- bias_term=True, copy_X=True, verbose=False):
- self.n_iter = n_iter
- self.n_Kfold = n_Kfold
- self.tol = tol
- self.fit_intercept = fit_intercept
- self.bias_term = bias_term
- self.copy_X = copy_X
- self.verbose = verbose
-
- def _center_data(self, X, y):
- ''' Centers data'''
- X = as_float_array(X, copy = self.copy_X)
-
- # normalisation should be done in preprocessing!
- X_std = np.ones(X.shape[1], dtype=X.dtype)
- if self.fit_intercept:
- X_mean = np.average(X, axis=0)
- y_mean = np.average(y, axis=0)
- X -= X_mean
- y -= y_mean
- else:
- X_mean = np.zeros(X.shape[1], dtype=X.dtype)
- y_mean = 0. if y.ndim == 1 else np.zeros(y.shape[1], dtype=X.dtype)
- return X, y, X_mean, y_mean, X_std
-
- def fit(self, X, y):
-
- k_fold = KFold(n_splits=self.n_Kfold)
-
- varY = np.var(y, ddof=1) if np.var(y, ddof=1) != 0 else 1.0
- sigma2s = len(y)*varY*(10**np.linspace(-16, -1, self.n_Kfold))
-
- errors = np.zeros((len(sigma2s), self.n_Kfold))
- for s, sigma2 in enumerate(sigma2s):
- for k, (train, test) in enumerate(k_fold.split(X, y)):
- self.fit_(X[train], y[train], sigma2)
- errors[s, k] = np.linalg.norm(
- y[test] - self.predict(X[test])
- )**2/len(test)
-
- KfCVerror = np.sum(errors, axis=1)/self.n_Kfold/varY
- i_minCV = np.argmin(KfCVerror)
-
- self.kfoldCVerror = np.min(KfCVerror)
-
- return self.fit_(X, y, sigma2s[i_minCV])
-
- def fit_(self, X, y, sigma2):
-
- N, P = X.shape
- # n_samples, n_features = X.shape
-
- X, y, X_mean, y_mean, X_std = self._center_data(X, y)
- self._x_mean_ = X_mean
- self._y_mean = y_mean
- self._x_std = X_std
-
- # check that variance is non zero !!!
- if np.var(y) == 0:
- self.var_y = True
- else:
- self.var_y = False
- beta = 1./sigma2
-
- # precompute X'*Y , X'*X for faster iterations & allocate memory for
- # sparsity & quality vectors X=Psi
- PsiTY = np.dot(X.T, y)
- PsiTPsi = np.dot(X.T, X)
- XXd = np.diag(PsiTPsi)
-
- # initialize with constant regressor, or if that one does not exist,
- # with the one that has the largest correlation with Y
- ind_global_to_local = np.zeros(P, dtype=np.int32)
-
- # identify constant regressors
- constidx = np.where(~np.diff(X, axis=0).all(axis=0))[0]
-
- if self.bias_term and constidx.size != 0:
- ind_start = constidx[0]
- ind_global_to_local[ind_start] = True
- else:
- # start from a single basis vector with largest projection on
- # targets
- proj = np.divide(np.square(PsiTY), XXd)
- ind_start = np.argmax(proj)
- ind_global_to_local[ind_start] = True
-
- num_active = 1
- active_indices = [ind_start]
- deleted_indices = []
- bcs_path = [ind_start]
- gamma = np.zeros(P)
- # for the initial value of gamma(ind_start), use the RVM formula
- # gamma = (q^2 - s) / (s^2)
- # and the fact that initially s = S = beta*Psi_i'*Psi_i and q = Q =
- # beta*Psi_i'*Y
- gamma[ind_start] = np.square(PsiTY[ind_start])
- gamma[ind_start] -= sigma2 * PsiTPsi[ind_start, ind_start]
- gamma[ind_start] /= np.square(PsiTPsi[ind_start, ind_start])
-
- Sigma = 1. / (beta * PsiTPsi[ind_start, ind_start]
- + 1./gamma[ind_start])
-
- mu = Sigma * PsiTY[ind_start] * beta
- tmp1 = beta * PsiTPsi[ind_start]
- S = beta * np.diag(PsiTPsi).T - Sigma * np.square(tmp1)
- Q = beta * PsiTY.T - mu*(tmp1)
-
- tmp2 = np.ones(P) # alternative computation for the initial s,q
- q0tilde = PsiTY[ind_start]
- s0tilde = PsiTPsi[ind_start, ind_start]
- tmp2[ind_start] = s0tilde / (q0tilde**2) / beta
- s = np.divide(S, tmp2)
- q = np.divide(Q, tmp2)
- Lambda = 2*(num_active - 1) / np.sum(gamma)
-
- Delta_L_max = []
- for i in range(self.n_iter):
- # Handle variance zero
- if self.var_y:
- mu = np.mean(y)
- break
-
- if self.verbose:
- print(' lambda = {0:.6e}\n'.format(Lambda))
-
- # Calculate the potential updated value of each gamma[i]
- if Lambda == 0.0: # RVM
- gamma_potential = np.multiply((
- (q**2 - s) > Lambda),
- np.divide(q**2 - s, s**2)
- )
- else:
- a = Lambda * s**2
- b = s**2 + 2*Lambda*s
- c = Lambda + s - q**2
- gamma_potential = np.multiply(
- (c < 0), np.divide(
- -b + np.sqrt(b**2 - 4*np.multiply(a, c)), 2*a)
- )
-
- l_gamma = - np.log(np.absolute(1 + np.multiply(gamma, s)))
- l_gamma += np.divide(np.multiply(q**2, gamma),
- (1 + np.multiply(gamma, s)))
- l_gamma -= Lambda*gamma # omitted the factor 1/2
-
- # Contribution of each updated gamma(i) to L(gamma)
- l_gamma_potential = - np.log(
- np.absolute(1 + np.multiply(gamma_potential, s))
- )
- l_gamma_potential += np.divide(
- np.multiply(q**2, gamma_potential),
- (1 + np.multiply(gamma_potential, s))
- )
- # omitted the factor 1/2
- l_gamma_potential -= Lambda*gamma_potential
-
- # Check how L(gamma) would change if we replaced gamma(i) by the
- # updated gamma_potential(i), for each i separately
- Delta_L_potential = l_gamma_potential - l_gamma
-
- # deleted indices should not be chosen again
- if len(deleted_indices) != 0:
- values = -np.inf * np.ones(len(deleted_indices))
- Delta_L_potential[deleted_indices] = values
-
- Delta_L_max.append(np.nanmax(Delta_L_potential))
- ind_L_max = np.nanargmax(Delta_L_potential)
-
- # in case there is only 1 regressor in the model and it would now
- # be deleted
- if len(active_indices) == 1 and ind_L_max == active_indices[0] \
- and gamma_potential[ind_L_max] == 0.0:
- Delta_L_potential[ind_L_max] = -np.inf
- Delta_L_max[i] = np.max(Delta_L_potential)
- ind_L_max = np.argmax(Delta_L_potential)
-
- # If L did not change significantly anymore, break
- if Delta_L_max[i] <= 0.0 or\
- (i > 0 and all(np.absolute(Delta_L_max[i-1:])
- < sum(Delta_L_max)*self.tol)) or \
- (i > 0 and all(np.diff(bcs_path)[i-1:] == 0.0)):
- if self.verbose:
- print('Increase in L: {0:.6e} (eta = {1:.3e})\
- -- break\n'.format(Delta_L_max[i], self.tol))
- break
-
- # Print information
- if self.verbose:
- print(' Delta L = {0:.6e} \n'.format(Delta_L_max[i]))
-
- what_changed = int(gamma[ind_L_max] == 0.0)
- what_changed -= int(gamma_potential[ind_L_max] == 0.0)
-
- # Print information
- if self.verbose:
- if what_changed < 0:
- print(f'{i+1} - Remove regressor #{ind_L_max+1}..\n')
- elif what_changed == 0:
- print(f'{i+1} - Recompute regressor #{ind_L_max+1}..\n')
- else:
- print(f'{i+1} - Add regressor #{ind_L_max+1}..\n')
-
- # --- Update all quantities ----
- if what_changed == 1:
- # adding a regressor
-
- # update gamma
- gamma[ind_L_max] = gamma_potential[ind_L_max]
-
- Sigma_ii = 1.0 / (1.0/gamma[ind_L_max] + S[ind_L_max])
- try:
- x_i = np.matmul(
- Sigma, PsiTPsi[active_indices, ind_L_max].reshape(-1, 1)
- )
- except ValueError:
- x_i = Sigma * PsiTPsi[active_indices, ind_L_max]
- tmp_1 = - (beta * Sigma_ii) * x_i
- Sigma = np.vstack(
- (np.hstack(((beta**2 * Sigma_ii) * np.dot(x_i, x_i.T)
- + Sigma, tmp_1)), np.append(tmp_1.T, Sigma_ii))
- )
- mu_i = Sigma_ii * Q[ind_L_max]
- mu = np.vstack((mu - (beta * mu_i) * x_i, mu_i))
-
- tmp2_1 = PsiTPsi[:, ind_L_max] - beta * np.squeeze(
- np.matmul(PsiTPsi[:, active_indices], x_i)
- )
- if i == 0:
- tmp2_1[0] /= 2
- tmp2 = beta * tmp2_1.T
- S = S - Sigma_ii * np.square(tmp2)
- Q = Q - mu_i * tmp2
-
- num_active += 1
- ind_global_to_local[ind_L_max] = num_active
- active_indices.append(ind_L_max)
- bcs_path.append(ind_L_max)
-
- elif what_changed == 0:
- # recomputation
- # zero if regressor has not been chosen yet
- if not ind_global_to_local[ind_L_max]:
- raise Exception('Cannot recompute index{0} -- not yet\
- part of the model!'.format(ind_L_max))
- Sigma = np.atleast_2d(Sigma)
- mu = np.atleast_2d(mu)
- gamma_i_new = gamma_potential[ind_L_max]
- gamma_i_old = gamma[ind_L_max]
- # update gamma
- gamma[ind_L_max] = gamma_potential[ind_L_max]
-
- # index of regressor in Sigma
- local_ind = ind_global_to_local[ind_L_max]-1
-
- kappa_i = (1.0/gamma_i_new - 1.0/gamma_i_old)
- kappa_i = 1.0 / kappa_i
- kappa_i += Sigma[local_ind, local_ind]
- kappa_i = 1 / kappa_i
- Sigma_i_col = Sigma[:, local_ind]
-
- Sigma = Sigma - kappa_i * (Sigma_i_col * Sigma_i_col.T)
- mu_i = mu[local_ind]
- mu = mu - (kappa_i * mu_i) * Sigma_i_col[:, None]
-
- tmp1 = beta * np.dot(
- Sigma_i_col.reshape(1, -1), PsiTPsi[active_indices])[0]
- S = S + kappa_i * np.square(tmp1)
- Q = Q + (kappa_i * mu_i) * tmp1
-
- # no change in active_indices or ind_global_to_local
- bcs_path.append(ind_L_max + 0.1)
-
- elif what_changed == -1:
- gamma[ind_L_max] = 0
-
- # index of regressor in Sigma
- local_ind = ind_global_to_local[ind_L_max]-1
-
- Sigma_ii_inv = 1. / Sigma[local_ind, local_ind]
- Sigma_i_col = Sigma[:, local_ind]
-
- Sigma = Sigma - Sigma_ii_inv * (Sigma_i_col * Sigma_i_col.T)
-
- Sigma = np.delete(
- np.delete(Sigma, local_ind, axis=0), local_ind, axis=1)
-
- mu = mu - (mu[local_ind] * Sigma_ii_inv) * Sigma_i_col[:, None]
- mu = np.delete(mu, local_ind, axis=0)
-
- tmp1 = beta * np.dot(Sigma_i_col, PsiTPsi[active_indices])
- S = S + Sigma_ii_inv * np.square(tmp1)
- Q = Q + (mu_i * Sigma_ii_inv) * tmp1
-
- num_active -= 1
- ind_global_to_local[ind_L_max] = 0.0
- v = ind_global_to_local[ind_global_to_local > local_ind] - 1
- ind_global_to_local[ind_global_to_local > local_ind] = v
- del active_indices[local_ind]
- deleted_indices.append(ind_L_max)
- # and therefore ineligible
- bcs_path.append(-ind_L_max)
-
- # same for all three cases
- tmp3 = 1 - np.multiply(gamma, S)
- s = np.divide(S, tmp3)
- q = np.divide(Q, tmp3)
-
- # Update lambda
- Lambda = 2*(num_active - 1) / np.sum(gamma)
-
- # Prepare the result object
- self.coef_ = np.zeros(P)
- self.coef_[active_indices] = np.squeeze(mu)
- self.sigma_ = Sigma
- self.active_ = active_indices
- self.gamma = gamma
- self.Lambda = Lambda
- self.beta = beta
- self.bcs_path = bcs_path
-
- # set intercept_
- if self.fit_intercept:
- self.coef_ = self.coef_ / X_std
- self.intercept_ = y_mean - np.dot(X_mean, self.coef_.T)
- else:
- self.intercept_ = 0.
-
- return self
-
- def predict(self, X, return_std=False):
- '''
- Computes predictive distribution for test set.
- Predictive distribution for each data point is one dimensional
- Gaussian and therefore is characterised by mean and variance based on
- Ref.[1] Section 3.3.2.
-
- Parameters
- -----------
- X: {array-like, sparse} (n_samples_test, n_features)
- Test data, matrix of explanatory variables
-
- Returns
- -------
- : list of length two [y_hat, var_hat]
-
- y_hat: numpy array of size (n_samples_test,)
- Estimated values of targets on test set (i.e. mean of
- predictive distribution)
-
- var_hat: numpy array of size (n_samples_test,)
- Variance of predictive distribution
-
- References
- ----------
- [1] Bishop, C. M. (2006). Pattern recognition and machine learning.
- springer.
- '''
- y_hat = np.dot(X, self.coef_) + self.intercept_
-
- if return_std:
- # Handle the zero variance case
- if self.var_y:
- return y_hat, np.zeros_like(y_hat)
-
- var_hat = 1./self.beta
- var_hat += np.sum(X.dot(self.sigma_) * X, axis=1)
- std_hat = np.sqrt(var_hat)
- return y_hat, std_hat
- else:
- return y_hat
-
-# l2norm = 0.0
-# for idx in range(10):
-# sigma2 = np.genfromtxt('./test/sigma2_{0}.csv'.format(idx+1), delimiter=',')
-# Psi_train = np.genfromtxt('./test/Psi_train_{0}.csv'.format(idx+1), delimiter=',')
-# Y_train = np.genfromtxt('./test/Y_train_{0}.csv'.format(idx+1))
-# Psi_test = np.genfromtxt('./test/Psi_test_{0}.csv'.format(idx+1), delimiter=',')
-# Y_test = np.genfromtxt('./test/Y_test_{0}.csv'.format(idx+1))
-
-# clf = RegressionFastLaplace(verbose=True)
-# clf.fit_(Psi_train, Y_train, sigma2)
-# coeffs_fold = np.genfromtxt('./test/coeffs_fold_{0}.csv'.format(idx+1))
-# print("coeffs error: {0:.4g}".format(np.linalg.norm(clf.coef_ - coeffs_fold)))
-# l2norm += np.linalg.norm(Y_test - clf.predict(Psi_test))**2/len(Y_test)
-# print("l2norm error: {0:.4g}".format(l2norm))
diff --git a/examples/model-comparison/bayesvalidrox/surrogate_models/surrogate_models.py b/examples/model-comparison/bayesvalidrox/surrogate_models/surrogate_models.py
deleted file mode 100644
index ca902f26bef0c45e8befb72ff67313ef09a77603..0000000000000000000000000000000000000000
--- a/examples/model-comparison/bayesvalidrox/surrogate_models/surrogate_models.py
+++ /dev/null
@@ -1,1576 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Implementation of metamodel as either PC, aPC or GPE
-"""
-
-import warnings
-import numpy as np
-import math
-import h5py
-import matplotlib.pyplot as plt
-from sklearn.preprocessing import MinMaxScaler
-import scipy as sp
-from scipy.optimize import minimize, NonlinearConstraint, LinearConstraint
-from tqdm import tqdm
-from sklearn.decomposition import PCA as sklearnPCA
-import sklearn.linear_model as lm
-from sklearn.gaussian_process import GaussianProcessRegressor
-import sklearn.gaussian_process.kernels as kernels
-import os
-from joblib import Parallel, delayed
-import copy
-
-from .input_space import InputSpace
-from .glexindex import glexindex
-from .eval_rec_rule import eval_univ_basis
-from .reg_fast_ard import RegressionFastARD
-from .reg_fast_laplace import RegressionFastLaplace
-from .orthogonal_matching_pursuit import OrthogonalMatchingPursuit
-from .bayes_linear import VBLinearRegression, EBLinearRegression
-from .apoly_construction import apoly_construction
-warnings.filterwarnings("ignore")
-# Load the mplstyle
-plt.style.use(os.path.join(os.path.split(__file__)[0],
- '../', 'bayesvalidrox.mplstyle'))
-
-
-class MetaModel():
- """
- Meta (surrogate) model
-
- This class trains a surrogate model. It accepts an input object (input_obj)
- containing the specification of the distributions for uncertain parameters
- and a model object with instructions on how to run the computational model.
-
- Attributes
- ----------
- input_obj : obj
- Input object with the information on the model input parameters.
- meta_model_type : str
- Surrogate model types. Three surrogate model types are supported:
- polynomial chaos expansion (`PCE`), arbitrary PCE (`aPCE`) and
- Gaussian process regression (`GPE`). Default is PCE.
- pce_reg_method : str
- PCE regression method to compute the coefficients. The following
- regression methods are available:
-
- 1. OLS: Ordinary Least Square method
- 2. BRR: Bayesian Ridge Regression
- 3. LARS: Least angle regression
- 4. ARD: Bayesian ARD Regression
- 5. FastARD: Fast Bayesian ARD Regression
- 6. VBL: Variational Bayesian Learning
- 7. EBL: Emperical Bayesian Learning
- Default is `OLS`.
- bootstrap_method : str
- Bootstraping method. Options are `'normal'` and `'fast'`. The default
- is `'fast'`. It means that in each iteration except the first one, only
- the coefficent are recalculated with the ordinary least square method.
- n_bootstrap_itrs : int
- Number of iterations for the bootstrap sampling. The default is `1`.
- pce_deg : int or list of int
- Polynomial degree(s). If a list is given, an adaptive algorithm is used
- to find the best degree with the lowest Leave-One-Out cross-validation
- (LOO) error (or the highest score=1-LOO). Default is `1`.
- pce_q_norm : float
- Hyperbolic (or q-norm) truncation for multi-indices of multivariate
- polynomials. Default is `1.0`.
- dim_red_method : str
- Dimensionality reduction method for the output space. The available
- method is based on principal component analysis (PCA). The Default is
- `'no'`. There are two ways to select number of components: use
- percentage of the explainable variance threshold (between 0 and 100)
- (Option A) or direct prescription of components' number (Option B):
-
- >>> MetaModelOpts.dim_red_method = 'PCA'
- >>> MetaModelOpts.var_pca_threshold = 99.999 # Option A
- >>> MetaModelOpts.n_pca_components = 12 # Option B
- apply_constraints : bool
- If set to true constraints will be applied during training.
- In this case the training uses OLS. In this version the constraints
- need to be set explicitly in this class.
-
- verbose : bool
- Prints summary of the regression results. Default is `False`.
-
- Note
- -------
- To define the sampling methods and the training set, an experimental design
- instance shall be defined. This can be done by:
-
- >>> MetaModelOpts.add_InputSpace()
-
- Two experimental design schemes are supported: one-shot (`normal`) and
- adaptive sequential (`sequential`) designs.
- For experimental design refer to `InputSpace`.
-
- """
-
- def __init__(self, input_obj, meta_model_type='PCE',
- pce_reg_method='OLS', bootstrap_method='fast',
- n_bootstrap_itrs=1, pce_deg=1, pce_q_norm=1.0,
- dim_red_method='no', apply_constraints = False,
- verbose=False):
-
- self.input_obj = input_obj
- self.meta_model_type = meta_model_type
- self.pce_reg_method = pce_reg_method
- self.bootstrap_method = bootstrap_method
- self.n_bootstrap_itrs = n_bootstrap_itrs
- self.pce_deg = pce_deg
- self.pce_q_norm = pce_q_norm
- self.dim_red_method = dim_red_method
- self.apply_constraints = apply_constraints
- self.verbose = verbose
-
- def build_metamodel(self, n_init_samples = None) -> None:
- """
- Builds the parts for the metamodel (polynomes,...) that are neede before fitting.
-
- Returns
- -------
- None
- DESCRIPTION.
-
- """
-
- # Generate general warnings
- if self.apply_constraints or self.pce_reg_method.lower() == 'ols':
- print('There are no estimations of surrogate uncertainty available'
- ' for the chosen regression options. This might lead to issues'
- ' in later steps.')
-
- # Add InputSpace to MetaModel if it does not have any
- if not hasattr(self, 'InputSpace'):
- self.InputSpace = InputSpace(self.input_obj)
- self.InputSpace.n_init_samples = n_init_samples
- self.InputSpace.init_param_space(np.max(self.pce_deg))
-
- self.ndim = self.InputSpace.ndim
-
- if not hasattr(self, 'CollocationPoints'):
- raise AttributeError('Please provide samples to the metamodel before building it.')
-
- # Transform input samples
- # TODO: this is probably not yet correct! Make 'method' variable
- self.CollocationPoints = self.InputSpace.transform(self.CollocationPoints, method='user')
-
-
- self.n_params = len(self.input_obj.Marginals)
-
- # Generate polynomials
- if self.meta_model_type.lower() != 'gpe':
- self.generate_polynomials(np.max(self.pce_deg))
-
- # Initialize the nested dictionaries
- if self.meta_model_type.lower() == 'gpe':
- self.gp_poly = self.auto_vivification()
- self.x_scaler = self.auto_vivification()
- self.LCerror = self.auto_vivification()
- else:
- self.deg_dict = self.auto_vivification()
- self.q_norm_dict = self.auto_vivification()
- self.coeffs_dict = self.auto_vivification()
- self.basis_dict = self.auto_vivification()
- self.score_dict = self.auto_vivification()
- self.clf_poly = self.auto_vivification()
- self.LCerror = self.auto_vivification()
- if self.dim_red_method.lower() == 'pca':
- self.pca = self.auto_vivification()
-
- # Define an array containing the degrees
- self.CollocationPoints = np.array(self.CollocationPoints)
- self.n_samples, ndim = self.CollocationPoints.shape
- if self.ndim != ndim:
- raise AttributeError('The given samples do not match the given number of priors. The samples should be a 2D array of size (#samples, #priors)')
-
- self.deg_array = self.__select_degree(ndim, self.n_samples)
-
- # Generate all basis indices
- self.allBasisIndices = self.auto_vivification()
- for deg in self.deg_array:
- keys = self.allBasisIndices.keys()
- if deg not in np.fromiter(keys, dtype=float):
- # Generate the polynomial basis indices
- for qidx, q in enumerate(self.pce_q_norm):
- basis_indices = glexindex(start=0, stop=deg+1,
- dimensions=self.n_params,
- cross_truncation=q,
- reverse=False, graded=True)
- self.allBasisIndices[str(deg)][str(q)] = basis_indices
-
-
-
- def fit(self, X, y, parallel = True, verbose = False):
- """
- Fits the surrogate to the given data (samples X, outputs y).
- Note here that the samples X should be the transformed samples provided
- by the experimental design if the transformation is used there.
-
- Parameters
- ----------
- X : 2D list or np.array of shape (#samples, #dim)
- The parameter value combinations that the model was evaluated at.
- y : dict of 2D lists or arrays of shape (#samples, #timesteps)
- The respective model evaluations.
-
- Returns
- -------
- None.
-
- """
- X = np.array(X)
- for key in y.keys():
- y_val = np.array(y[key])
- if y_val.ndim !=2:
- raise ValueError('The given outputs y should be 2D')
- y[key] = np.array(y[key])
-
- # Output names are the same as the keys in y
- self.out_names = list(y.keys())
-
- # Build the MetaModel on the static samples
- self.CollocationPoints = X
-
- # TODO: other option: rebuild every time
- if not hasattr(self, 'deg_array'):
- self.build_metamodel(n_init_samples = X.shape[1])
-
- # Evaluate the univariate polynomials on InputSpace
- if self.meta_model_type.lower() != 'gpe':
- self.univ_p_val = self.univ_basis_vals(self.CollocationPoints)
-
- # --- Loop through data points and fit the surrogate ---
- if verbose:
- print(f"\n>>>> Training the {self.meta_model_type} metamodel "
- "started. <<<<<<\n")
-
- # --- Bootstrap sampling ---
- # Correct number of bootstrap if PCA transformation is required.
- if self.dim_red_method.lower() == 'pca' and self.n_bootstrap_itrs == 1:
- self.n_bootstrap_itrs = 100
-
- # Check if fast version (update coeffs with OLS) is selected.
- if self.bootstrap_method.lower() == 'fast':
- fast_bootstrap = True
- first_out = {}
- n_comp_dict = {}
- else:
- fast_bootstrap = False
-
- # Prepare tqdm iteration maessage
- if verbose and self.n_bootstrap_itrs > 1:
- enum_obj = tqdm(range(self.n_bootstrap_itrs),
- total=self.n_bootstrap_itrs,
- desc="Bootstrapping the metamodel",
- ascii=True)
- else:
- enum_obj = range(self.n_bootstrap_itrs)
-
- # Loop over the bootstrap iterations
- for b_i in enum_obj:
- if b_i > 0:
- b_indices = np.random.randint(self.n_samples, size=self.n_samples)
- else:
- b_indices = np.arange(len(X))
-
- X_train_b = X[b_indices]
-
- if verbose and self.n_bootstrap_itrs == 1:
- items = tqdm(y.items(), desc="Fitting regression")
- else:
- items = y.items()
-
- # For loop over the components/outputs
- for key, Output in items:
-
- # Dimensionality reduction with PCA, if specified
- if self.dim_red_method.lower() == 'pca':
-
- # Use the stored n_comp for fast bootsrtrapping
- if fast_bootstrap and b_i > 0:
- self.n_pca_components = n_comp_dict[key]
-
- # Start transformation
- pca, target, n_comp = self.pca_transformation(
- Output[b_indices], verbose=False
- )
- self.pca[f'b_{b_i+1}'][key] = pca
- # Store the number of components for fast bootsrtrapping
- if fast_bootstrap and b_i == 0:
- n_comp_dict[key] = n_comp
- else:
- target = Output[b_indices]
-
- # Parallel fit regression
- if self.meta_model_type.lower() == 'gpe':
- # Prepare the input matrix
- scaler = MinMaxScaler()
- X_S = scaler.fit_transform(X_train_b)
-
- self.x_scaler[f'b_{b_i+1}'][key] = scaler
- if parallel:
- out = Parallel(n_jobs=-1, backend='multiprocessing')(
- delayed(self.gaussian_process_emulator)(
- X_S, target[:, idx]) for idx in
- range(target.shape[1]))
- else:
- results = map(self.gaussian_process_emulator,
- [X_train_b]*target.shape[1],
- [target[:, idx] for idx in
- range(target.shape[1])]
- )
- out = list(results)
-
- for idx in range(target.shape[1]):
- self.gp_poly[f'b_{b_i+1}'][key][f"y_{idx+1}"] = out[idx]
-
- else:
- self.univ_p_val = self.univ_p_val[b_indices]
- if parallel and (not fast_bootstrap or b_i == 0):
- out = Parallel(n_jobs=-1, backend='multiprocessing')(
- delayed(self.adaptive_regression)(X_train_b,
- target[:, idx],
- idx)
- for idx in range(target.shape[1]))
- elif not parallel and (not fast_bootstrap or b_i == 0):
- results = map(self.adaptive_regression,
- [X_train_b]*target.shape[1],
- [target[:, idx] for idx in
- range(target.shape[1])],
- range(target.shape[1]))
- out = list(results)
-
- # Store the first out dictionary
- if fast_bootstrap and b_i == 0:
- first_out[key] = copy.deepcopy(out)
-
- if b_i > 0 and fast_bootstrap:
-
- # fast bootstrap
- out = self.update_pce_coeffs(
- X_train_b, target, first_out[key])
-
- for i in range(target.shape[1]):
- # Create a dict to pass the variables
- self.deg_dict[f'b_{b_i+1}'][key][f"y_{i+1}"] = out[i]['degree']
- self.q_norm_dict[f'b_{b_i+1}'][key][f"y_{i+1}"] = out[i]['qnorm']
- self.coeffs_dict[f'b_{b_i+1}'][key][f"y_{i+1}"] = out[i]['coeffs']
- self.basis_dict[f'b_{b_i+1}'][key][f"y_{i+1}"] = out[i]['multi_indices']
- self.score_dict[f'b_{b_i+1}'][key][f"y_{i+1}"] = out[i]['LOOCVScore']
- self.clf_poly[f'b_{b_i+1}'][key][f"y_{i+1}"] = out[i]['clf_poly']
- #self.LCerror[f'b_{b_i+1}'][key][f"y_{i+1}"] = out[i]['LCerror']
-
- if verbose:
- print(f"\n>>>> Training the {self.meta_model_type} metamodel"
- " sucessfully completed. <<<<<<\n")
-
- # -------------------------------------------------------------------------
- def update_pce_coeffs(self, X, y, out_dict = None):
- """
- Updates the PCE coefficents using only the ordinary least square method
- for the fast version of the bootstrapping.
-
- Parameters
- ----------
- X : array of shape (n_samples, n_params)
- Training set.
- y : array of shape (n_samples, n_outs)
- The (transformed) model responses.
- out_dict : dict
- The training output dictionary of the first iteration, i.e.
- the surrogate model for the original experimental design.
-
- Returns
- -------
- final_out_dict : dict
- The updated training output dictionary.
-
- """
- # Make a copy
- final_out_dict = copy.deepcopy(out_dict)
-
- # Loop over the points
- for i in range(y.shape[1]):
-
-
- # Extract nonzero basis indices
- nnz_idx = np.nonzero(out_dict[i]['coeffs'])[0]
- if len(nnz_idx) != 0:
- basis_indices = out_dict[i]['multi_indices']
-
- # Evaluate the multivariate polynomials on CollocationPoints
- psi = self.create_psi(basis_indices, self.univ_p_val)
-
- # Calulate the cofficients of surrogate model
- updated_out = self.regression(
- psi, y[:, i], basis_indices, reg_method='OLS',
- sparsity=False
- )
-
- # Update coeffs in out_dict
- final_out_dict[i]['coeffs'][nnz_idx] = updated_out['coeffs']
-
- return final_out_dict
-
- # -------------------------------------------------------------------------
- def add_InputSpace(self):
- """
- Instanciates experimental design object.
-
- Returns
- -------
- None.
-
- """
- self.InputSpace = InputSpace(self.input_obj,
- meta_Model_type=self.meta_model_type)
-
- # -------------------------------------------------------------------------
- def univ_basis_vals(self, samples, n_max=None):
- """
- Evaluates univariate regressors along input directions.
-
- Parameters
- ----------
- samples : array of shape (n_samples, n_params)
- Samples.
- n_max : int, optional
- Maximum polynomial degree. The default is `None`.
-
- Returns
- -------
- univ_basis: array of shape (n_samples, n_params, n_max+1)
- All univariate regressors up to n_max.
- """
- # Extract information
- poly_types = self.InputSpace.poly_types
- if samples.ndim != 2:
- samples = samples.reshape(1, len(samples))
- n_max = np.max(self.pce_deg) if n_max is None else n_max
-
- # Extract poly coeffs
- if self.InputSpace.input_data_given or self.InputSpace.apce:
- apolycoeffs = self.polycoeffs
- else:
- apolycoeffs = None
-
- # Evaluate univariate basis
- univ_basis = eval_univ_basis(samples, n_max, poly_types, apolycoeffs)
-
- return univ_basis
-
- # -------------------------------------------------------------------------
- def create_psi(self, basis_indices, univ_p_val):
- """
- This function assemble the design matrix Psi from the given basis index
- set INDICES and the univariate polynomial evaluations univ_p_val.
-
- Parameters
- ----------
- basis_indices : array of shape (n_terms, n_params)
- Multi-indices of multivariate polynomials.
- univ_p_val : array of (n_samples, n_params, n_max+1)
- All univariate regressors up to `n_max`.
-
- Raises
- ------
- ValueError
- n_terms in arguments do not match.
-
- Returns
- -------
- psi : array of shape (n_samples, n_terms)
- Multivariate regressors.
-
- """
- # Check if BasisIndices is a sparse matrix
- sparsity = sp.sparse.issparse(basis_indices)
- if sparsity:
- basis_indices = basis_indices.toarray()
-
- # Initialization and consistency checks
- # number of input variables
- n_params = univ_p_val.shape[1]
-
- # Size of the experimental design
- n_samples = univ_p_val.shape[0]
-
- # number of basis terms
- n_terms = basis_indices.shape[0]
-
- # check that the variables have consistent sizes
- if n_params != basis_indices.shape[1]:
- raise ValueError(
- f"The shapes of basis_indices ({basis_indices.shape[1]}) and "
- f"univ_p_val ({n_params}) don't match!!"
- )
-
- # Preallocate the Psi matrix for performance
- psi = np.ones((n_samples, n_terms))
- # Assemble the Psi matrix
- for m in range(basis_indices.shape[1]):
- aa = np.where(basis_indices[:, m] > 0)[0]
- try:
- basisIdx = basis_indices[aa, m]
- bb = univ_p_val[:, m, basisIdx].reshape(psi[:, aa].shape)
- psi[:, aa] = np.multiply(psi[:, aa], bb)
- except ValueError as err:
- raise err
- return psi
-
- # -------------------------------------------------------------------------
- def regression(self, X, y, basis_indices, reg_method=None, sparsity=True):
- """
- Fit regression using the regression method provided.
-
- Parameters
- ----------
- X : array of shape (n_samples, n_features)
- Training vector, where n_samples is the number of samples and
- n_features is the number of features.
- y : array of shape (n_samples,)
- Target values.
- basis_indices : array of shape (n_terms, n_params)
- Multi-indices of multivariate polynomials.
- reg_method : str, optional
- DESCRIPTION. The default is None.
-
- Returns
- -------
- return_out_dict : Dict
- Fitted estimator, spareMulti-Index, sparseX and coefficients.
-
- """
- if reg_method is None:
- reg_method = self.pce_reg_method
-
- bias_term = self.dim_red_method.lower() != 'pca'
-
- compute_score = True if self.verbose else False
-
- # inverse of the observed variance of the data
- if np.var(y) != 0:
- Lambda = 1 / np.var(y)
- else:
- Lambda = 1e-6
-
- # Bayes sparse adaptive aPCE
- if reg_method.lower() == 'ols':
- clf_poly = lm.LinearRegression(fit_intercept=False)
- elif reg_method.lower() == 'brr':
- clf_poly = lm.BayesianRidge(n_iter=1000, tol=1e-7,
- fit_intercept=False,
- #normalize=True,
- compute_score=compute_score,
- alpha_1=1e-04, alpha_2=1e-04,
- lambda_1=Lambda, lambda_2=Lambda)
- clf_poly.converged = True
-
- elif reg_method.lower() == 'ard':
- if X.shape[0]<2:
- raise ValueError('Regression with ARD can only be performed for more than 2 samples')
- clf_poly = lm.ARDRegression(fit_intercept=False,
- #normalize=True,
- compute_score=compute_score,
- n_iter=1000, tol=0.0001,
- alpha_1=1e-3, alpha_2=1e-3,
- lambda_1=Lambda, lambda_2=Lambda)
-
- elif reg_method.lower() == 'fastard':
- clf_poly = RegressionFastARD(fit_intercept=False,
- normalize=True,
- compute_score=compute_score,
- n_iter=300, tol=1e-10)
-
- elif reg_method.lower() == 'bcs':
- if X.shape[0]<10:
- raise ValueError('Regression with BCS can only be performed for more than 10 samples')
- clf_poly = RegressionFastLaplace(fit_intercept=False,
- bias_term=bias_term,
- n_iter=1000, tol=1e-7)
-
- elif reg_method.lower() == 'lars':
- if X.shape[0]<10:
- raise ValueError('Regression with LARS can only be performed for more than 5 samples')
- clf_poly = lm.LassoLarsCV(fit_intercept=False)
-
- elif reg_method.lower() == 'sgdr':
- clf_poly = lm.SGDRegressor(fit_intercept=False,
- max_iter=5000, tol=1e-7)
-
- elif reg_method.lower() == 'omp':
- clf_poly = OrthogonalMatchingPursuit(fit_intercept=False)
-
- elif reg_method.lower() == 'vbl':
- clf_poly = VBLinearRegression(fit_intercept=False)
-
- elif reg_method.lower() == 'ebl':
- clf_poly = EBLinearRegression(optimizer='em')
-
-
- # Training with constraints automatically uses L2
- if self.apply_constraints:
- # TODO: set the constraints here
- # Define the nonlin. constraint
- nlc = NonlinearConstraint(lambda x: np.matmul(X,x),-1,1.1)
- self.nlc = nlc
-
- fun = lambda x: (np.linalg.norm(np.matmul(X, x)-y, ord = 2))**2
- if self.init_type =='zeros':
- res = minimize(fun, np.zeros(X.shape[1]), method = 'trust-constr', constraints = self.nlc)
- if self.init_type == 'nonpi':
- clf_poly.fit(X, y)
- coeff = clf_poly.coef_
- res = minimize(fun, coeff, method = 'trust-constr', constraints = self.nlc)
-
- coeff = np.array(res.x)
- clf_poly.coef_ = coeff
- clf_poly.X = X
- clf_poly.y = y
- clf_poly.intercept_ = 0
-
- # Training without constraints uses chosen regression method
- else:
- clf_poly.fit(X, y)
-
- # Select the nonzero entries of coefficients
- if sparsity:
- nnz_idx = np.nonzero(clf_poly.coef_)[0]
- else:
- nnz_idx = np.arange(clf_poly.coef_.shape[0])
-
- # This is for the case where all outputs are zero, thereby
- # all coefficients are zero
- if (y == 0).all():
- nnz_idx = np.insert(np.nonzero(clf_poly.coef_)[0], 0, 0)
-
- sparse_basis_indices = basis_indices[nnz_idx]
- sparse_X = X[:, nnz_idx]
- coeffs = clf_poly.coef_[nnz_idx]
- clf_poly.coef_ = coeffs
-
- # Create a dict to pass the outputs
- return_out_dict = dict()
- return_out_dict['clf_poly'] = clf_poly
- return_out_dict['spareMulti-Index'] = sparse_basis_indices
- return_out_dict['sparePsi'] = sparse_X
- return_out_dict['coeffs'] = coeffs
- return return_out_dict
-
- # -------------------------------------------------------------------------
- def create_psi(self, basis_indices, univ_p_val):
- """
- This function assemble the design matrix Psi from the given basis index
- set INDICES and the univariate polynomial evaluations univ_p_val.
-
- Parameters
- ----------
- basis_indices : array of shape (n_terms, n_params)
- Multi-indices of multivariate polynomials.
- univ_p_val : array of (n_samples, n_params, n_max+1)
- All univariate regressors up to `n_max`.
-
- Raises
- ------
- ValueError
- n_terms in arguments do not match.
-
- Returns
- -------
- psi : array of shape (n_samples, n_terms)
- Multivariate regressors.
-
- """
- # Check if BasisIndices is a sparse matrix
- sparsity = sp.sparse.issparse(basis_indices)
- if sparsity:
- basis_indices = basis_indices.toarray()
-
- # Initialization and consistency checks
- # number of input variables
- n_params = univ_p_val.shape[1]
-
- # Size of the experimental design
- n_samples = univ_p_val.shape[0]
-
- # number of basis terms
- n_terms = basis_indices.shape[0]
-
- # check that the variables have consistent sizes
- if n_params != basis_indices.shape[1]:
- raise ValueError(
- f"The shapes of basis_indices ({basis_indices.shape[1]}) and "
- f"univ_p_val ({n_params}) don't match!!"
- )
-
- # Preallocate the Psi matrix for performance
- psi = np.ones((n_samples, n_terms))
- # Assemble the Psi matrix
- for m in range(basis_indices.shape[1]):
- aa = np.where(basis_indices[:, m] > 0)[0]
- try:
- basisIdx = basis_indices[aa, m]
- bb = univ_p_val[:, m, basisIdx].reshape(psi[:, aa].shape)
- psi[:, aa] = np.multiply(psi[:, aa], bb)
- except ValueError as err:
- raise err
- return psi
-
- # --------------------------------------------------------------------------------------------------------
- def adaptive_regression(self, ED_X, ED_Y, varIdx, verbose=False):
- """
- Adaptively fits the PCE model by comparing the scores of different
- degrees and q-norm.
-
- Parameters
- ----------
- ED_X : array of shape (n_samples, n_params)
- Experimental design.
- ED_Y : array of shape (n_samples,)
- Target values, i.e. simulation results for the Experimental design.
- varIdx : int
- Index of the output.
- verbose : bool, optional
- Print out summary. The default is False.
-
- Returns
- -------
- returnVars : Dict
- Fitted estimator, best degree, best q-norm, LOOCVScore and
- coefficients.
-
- """
-
- n_samples, n_params = ED_X.shape
- # Initialization
- qAllCoeffs, AllCoeffs = {}, {}
- qAllIndices_Sparse, AllIndices_Sparse = {}, {}
- qAllclf_poly, Allclf_poly = {}, {}
- qAllnTerms, AllnTerms = {}, {}
- qAllLCerror, AllLCerror = {}, {}
-
- # Extract degree array and qnorm array
- deg_array = np.array([*self.allBasisIndices], dtype=int)
- qnorm = [*self.allBasisIndices[str(int(deg_array[0]))]]
-
- # Some options for EarlyStop
- errorIncreases = False
- # Stop degree, if LOO error does not decrease n_checks_degree times
- n_checks_degree = 3
- # Stop qNorm, if criterion isn't fulfilled n_checks_qNorm times
- n_checks_qNorm = 2
- nqnorms = len(qnorm)
- qNormEarlyStop = True
- if nqnorms < n_checks_qNorm+1:
- qNormEarlyStop = False
-
- # =====================================================================
- # basis adaptive polynomial chaos: repeat the calculation by increasing
- # polynomial degree until the highest accuracy is reached
- # =====================================================================
- # For each degree check all q-norms and choose the best one
- scores = -np.inf * np.ones(deg_array.shape[0])
- qNormScores = -np.inf * np.ones(nqnorms)
-
- for degIdx, deg in enumerate(deg_array):
-
- for qidx, q in enumerate(qnorm):
-
- # Extract the polynomial basis indices from the pool of
- # allBasisIndices
- BasisIndices = self.allBasisIndices[str(deg)][str(q)]
-
- # Assemble the Psi matrix
- Psi = self.create_psi(BasisIndices, self.univ_p_val)
-
- # Calulate the cofficients of the meta model
- outs = self.regression(Psi, ED_Y, BasisIndices)
-
- # Calculate and save the score of LOOCV
- score, LCerror = self.corr_loocv_error(outs['clf_poly'],
- outs['sparePsi'],
- outs['coeffs'],
- ED_Y)
-
- # Check the convergence of noise for FastARD
- if self.pce_reg_method == 'FastARD' and \
- outs['clf_poly'].alpha_ < np.finfo(np.float32).eps:
- score = -np.inf
-
- qNormScores[qidx] = score
- qAllCoeffs[str(qidx+1)] = outs['coeffs']
- qAllIndices_Sparse[str(qidx+1)] = outs['spareMulti-Index']
- qAllclf_poly[str(qidx+1)] = outs['clf_poly']
- qAllnTerms[str(qidx+1)] = BasisIndices.shape[0]
- qAllLCerror[str(qidx+1)] = LCerror
-
- # EarlyStop check
- # if there are at least n_checks_qNorm entries after the
- # best one, we stop
- if qNormEarlyStop and \
- sum(np.isfinite(qNormScores)) > n_checks_qNorm:
- # If the error has increased the last two iterations, stop!
- qNormScores_nonInf = qNormScores[np.isfinite(qNormScores)]
- deltas = np.sign(np.diff(qNormScores_nonInf))
- if sum(deltas[-n_checks_qNorm+1:]) == 2:
- # stop the q-norm loop here
- break
- if np.var(ED_Y) == 0:
- break
-
- # Store the score in the scores list
- best_q = np.nanargmax(qNormScores)
- scores[degIdx] = qNormScores[best_q]
-
- AllCoeffs[str(degIdx+1)] = qAllCoeffs[str(best_q+1)]
- AllIndices_Sparse[str(degIdx+1)] = qAllIndices_Sparse[str(best_q+1)]
- Allclf_poly[str(degIdx+1)] = qAllclf_poly[str(best_q+1)]
- AllnTerms[str(degIdx+1)] = qAllnTerms[str(best_q+1)]
- AllLCerror[str(degIdx+1)] = qAllLCerror[str(best_q+1)]
-
- # Check the direction of the error (on average):
- # if it increases consistently stop the iterations
- if len(scores[scores != -np.inf]) > n_checks_degree:
- scores_nonInf = scores[scores != -np.inf]
- ss = np.sign(scores_nonInf - np.max(scores_nonInf))
- # ss<0 error decreasing
- errorIncreases = np.sum(np.sum(ss[-2:])) <= -1*n_checks_degree
-
- if errorIncreases:
- break
-
- # Check only one degree, if target matrix has zero variance
- if np.var(ED_Y) == 0:
- break
-
- # ------------------ Summary of results ------------------
- # Select the one with the best score and save the necessary outputs
- best_deg = np.nanargmax(scores)+1
- coeffs = AllCoeffs[str(best_deg)]
- basis_indices = AllIndices_Sparse[str(best_deg)]
- clf_poly = Allclf_poly[str(best_deg)]
- LOOCVScore = np.nanmax(scores)
- P = AllnTerms[str(best_deg)]
- LCerror = AllLCerror[str(best_deg)]
- degree = deg_array[np.nanargmax(scores)]
- qnorm = float(qnorm[best_q])
-
- # ------------------ Print out Summary of results ------------------
- if self.verbose:
- # Create PSI_Sparse by removing redundent terms
- nnz_idx = np.nonzero(coeffs)[0]
- BasisIndices_Sparse = basis_indices[nnz_idx]
-
- print(f'Output variable {varIdx+1}:')
- print('The estimation of PCE coefficients converged at polynomial '
- f'degree {deg_array[best_deg-1]} with '
- f'{len(BasisIndices_Sparse)} terms (Sparsity index = '
- f'{round(len(BasisIndices_Sparse)/P, 3)}).')
-
- print(f'Final ModLOO error estimate: {1-max(scores):.3e}')
- print('\n'+'-'*50)
-
- if verbose:
- print('='*50)
- print(' '*10 + ' Summary of results ')
- print('='*50)
-
- print("Scores:\n", scores)
- print("Degree of best score:", self.deg_array[best_deg-1])
- print("No. of terms:", len(basis_indices))
- print("Sparsity index:", round(len(basis_indices)/P, 3))
- print("Best Indices:\n", basis_indices)
-
- if self.pce_reg_method in ['BRR', 'ARD']:
- fig, ax = plt.subplots(figsize=(12, 10))
- plt.title("Marginal log-likelihood")
- plt.plot(clf_poly.scores_, color='navy', linewidth=2)
- plt.ylabel("Score")
- plt.xlabel("Iterations")
- if self.pce_reg_method.lower() == 'bbr':
- text = f"$\\alpha={clf_poly.alpha_:.1f}$\n"
- f"$\\lambda={clf_poly.lambda_:.3f}$\n"
- f"$L={clf_poly.scores_[-1]:.1f}$"
- else:
- text = f"$\\alpha={clf_poly.alpha_:.1f}$\n$"
- f"\\L={clf_poly.scores_[-1]:.1f}$"
-
- plt.text(0.75, 0.5, text, fontsize=18, transform=ax.transAxes)
- plt.show()
- print('='*80)
-
- # Create a dict to pass the outputs
- returnVars = dict()
- returnVars['clf_poly'] = clf_poly
- returnVars['degree'] = degree
- returnVars['qnorm'] = qnorm
- returnVars['coeffs'] = coeffs
- returnVars['multi_indices'] = basis_indices
- returnVars['LOOCVScore'] = LOOCVScore
- returnVars['LCerror'] = LCerror
-
- return returnVars
-
- # -------------------------------------------------------------------------
- def corr_loocv_error(self, clf, psi, coeffs, y):
- """
- Calculates the corrected LOO error for regression on regressor
- matrix `psi` that generated the coefficients based on [1] and [2].
-
- [1] Blatman, G., 2009. Adaptive sparse polynomial chaos expansions for
- uncertainty propagation and sensitivity analysis (Doctoral
- dissertation, Clermont-Ferrand 2).
-
- [2] Blatman, G. and Sudret, B., 2011. Adaptive sparse polynomial chaos
- expansion based on least angle regression. Journal of computational
- Physics, 230(6), pp.2345-2367.
-
- Parameters
- ----------
- clf : object
- Fitted estimator.
- psi : array of shape (n_samples, n_features)
- The multivariate orthogonal polynomials (regressor).
- coeffs : array-like of shape (n_features,)
- Estimated cofficients.
- y : array of shape (n_samples,)
- Target values.
-
- Returns
- -------
- R_2 : float
- LOOCV Validation score (1-LOOCV erro).
- residual : array of shape (n_samples,)
- Residual values (y - predicted targets).
-
- """
- psi = np.array(psi, dtype=float)
-
- # Create PSI_Sparse by removing redundent terms
- nnz_idx = np.nonzero(coeffs)[0]
- if len(nnz_idx) == 0:
- nnz_idx = [0]
- psi_sparse = psi[:, nnz_idx]
-
- # NrCoeffs of aPCEs
- P = len(nnz_idx)
- # NrEvaluation (Size of experimental design)
- N = psi.shape[0]
-
- # Build the projection matrix
- PsiTPsi = np.dot(psi_sparse.T, psi_sparse)
-
- if np.linalg.cond(PsiTPsi) > 1e-12: #and \
- # np.linalg.cond(PsiTPsi) < 1/sys.float_info.epsilon:
- # faster
- try:
- M = sp.linalg.solve(PsiTPsi,
- sp.sparse.eye(PsiTPsi.shape[0]).toarray())
- except:
- raise AttributeError('There are too few samples for the corrected loo-cv error. Fit surrogate on at least as many samples as parameters to use this')
- else:
- # stabler
- M = np.linalg.pinv(PsiTPsi)
-
- # h factor (the full matrix is not calculated explicitly,
- # only the trace is, to save memory)
- PsiM = np.dot(psi_sparse, M)
-
- h = np.sum(np.multiply(PsiM, psi_sparse), axis=1, dtype=np.longdouble)#float128)
-
- # ------ Calculate Error Loocv for each measurement point ----
- # Residuals
- try:
- residual = clf.predict(psi) - y
- except:
- residual = np.dot(psi, coeffs) - y
-
- # Variance
- var_y = np.var(y)
-
- if var_y == 0:
- norm_emp_error = 0
- loo_error = 0
- LCerror = np.zeros((y.shape))
- return 1-loo_error, LCerror
- else:
- norm_emp_error = np.mean(residual**2)/var_y
-
- # LCerror = np.divide(residual, (1-h))
- LCerror = residual / (1-h)
- loo_error = np.mean(np.square(LCerror)) / var_y
- # if there are NaNs, just return an infinite LOO error (this
- # happens, e.g., when a strongly underdetermined problem is solved)
- if np.isnan(loo_error):
- loo_error = np.inf
-
- # Corrected Error for over-determined system
- tr_M = np.trace(M)
- if tr_M < 0 or abs(tr_M) > 1e6:
- tr_M = np.trace(np.linalg.pinv(np.dot(psi.T, psi)))
-
- # Over-determined system of Equation
- if N > P:
- T_factor = N/(N-P) * (1 + tr_M)
-
- # Under-determined system of Equation
- else:
- T_factor = np.inf
-
- corrected_loo_error = loo_error * T_factor
-
- R_2 = 1 - corrected_loo_error
-
- return R_2, LCerror
-
- # -------------------------------------------------------------------------
- def pca_transformation(self, target, verbose=False):
- """
- Transforms the targets (outputs) via Principal Component Analysis
-
- Parameters
- ----------
- target : array of shape (n_samples,)
- Target values.
-
- Returns
- -------
- pca : obj
- Fitted sklearnPCA object.
- OutputMatrix : array of shape (n_samples,)
- Transformed target values.
- n_pca_components : int
- Number of selected principal components.
-
- """
- # Transform via Principal Component Analysis
- if hasattr(self, 'var_pca_threshold'):
- var_pca_threshold = self.var_pca_threshold
- else:
- var_pca_threshold = 100.0
- n_samples, n_features = target.shape
-
- if hasattr(self, 'n_pca_components'):
- n_pca_components = self.n_pca_components
- else:
- # Instantiate and fit sklearnPCA object
- covar_matrix = sklearnPCA(n_components=None)
- covar_matrix.fit(target)
- var = np.cumsum(np.round(covar_matrix.explained_variance_ratio_,
- decimals=5)*100)
- # Find the number of components to explain self.varPCAThreshold of
- # variance
- try:
- n_components = np.where(var >= var_pca_threshold)[0][0] + 1
- except IndexError:
- n_components = min(n_samples, n_features)
-
- n_pca_components = min(n_samples, n_features, n_components)
-
- # Print out a report
- if verbose:
- print()
- print('-' * 50)
- print(f"PCA transformation is performed with {n_pca_components}"
- " components.")
- print('-' * 50)
- print()
-
- # Fit and transform with the selected number of components
- pca = sklearnPCA(n_components=n_pca_components, svd_solver='arpack')
- scaled_target = pca.fit_transform(target)
-
- return pca, scaled_target, n_pca_components
-
- # -------------------------------------------------------------------------
- def gaussian_process_emulator(self, X, y, nug_term=None, autoSelect=False,
- varIdx=None):
- """
- Fits a Gaussian Process Emulator to the target given the training
- points.
-
- Parameters
- ----------
- X : array of shape (n_samples, n_params)
- Training points.
- y : array of shape (n_samples,)
- Target values.
- nug_term : float, optional
- Nugget term. The default is None, i.e. variance of y.
- autoSelect : bool, optional
- Loop over some kernels and select the best. The default is False.
- varIdx : int, optional
- The index number. The default is None.
-
- Returns
- -------
- gp : object
- Fitted estimator.
-
- """
-
- nug_term = nug_term if nug_term else np.var(y)
-
- Kernels = [nug_term * kernels.RBF(length_scale=1.0,
- length_scale_bounds=(1e-25, 1e15)),
- nug_term * kernels.RationalQuadratic(length_scale=0.2,
- alpha=1.0),
- nug_term * kernels.Matern(length_scale=1.0,
- length_scale_bounds=(1e-15, 1e5),
- nu=1.5)]
-
- # Automatic selection of the kernel
- if autoSelect:
- gp = {}
- BME = []
- for i, kernel in enumerate(Kernels):
- gp[i] = GaussianProcessRegressor(kernel=kernel,
- n_restarts_optimizer=3,
- normalize_y=False)
-
- # Fit to data using Maximum Likelihood Estimation
- gp[i].fit(X, y)
-
- # Store the MLE as BME score
- BME.append(gp[i].log_marginal_likelihood())
-
- gp = gp[np.argmax(BME)]
-
- else:
- gp = GaussianProcessRegressor(kernel=Kernels[0],
- n_restarts_optimizer=3,
- normalize_y=False)
- gp.fit(X, y)
-
- # Compute score
- if varIdx is not None:
- Score = gp.score(X, y)
- print('-'*50)
- print(f'Output variable {varIdx}:')
- print('The estimation of GPE coefficients converged,')
- print(f'with the R^2 score: {Score:.3f}')
- print('-'*50)
-
- return gp
-
- # -------------------------------------------------------------------------
- def eval_metamodel(self, samples):
- """
- Evaluates meta-model at the requested samples. One can also generate
- nsamples.
-
- Parameters
- ----------
- samples : array of shape (n_samples, n_params), optional
- Samples to evaluate meta-model at. The default is None.
- nsamples : int, optional
- Number of samples to generate, if no `samples` is provided. The
- default is None.
- sampling_method : str, optional
- Type of sampling, if no `samples` is provided. The default is
- 'random'.
- return_samples : bool, optional
- Retun samples, if no `samples` is provided. The default is False.
-
- Returns
- -------
- mean_pred : dict
- Mean of the predictions.
- std_pred : dict
- Standard deviatioon of the predictions.
- """
- # Transform into np array - can also be given as list
- samples = np.array(samples)
-
- # Transform samples to the independent space
- samples = self.InputSpace.transform(
- samples,
- method='user'
- )
- # Compute univariate bases for the given samples
- if self.meta_model_type.lower() != 'gpe':
- univ_p_val = self.univ_basis_vals(
- samples,
- n_max=np.max(self.pce_deg)
- )
-
- mean_pred_b = {}
- std_pred_b = {}
- # Loop over bootstrap iterations
- for b_i in range(self.n_bootstrap_itrs):
-
- # Extract model dictionary
- if self.meta_model_type.lower() == 'gpe':
- model_dict = self.gp_poly[f'b_{b_i+1}']
- else:
- model_dict = self.coeffs_dict[f'b_{b_i+1}']
-
- # Loop over outputs
- mean_pred = {}
- std_pred = {}
- for output, values in model_dict.items():
-
- mean = np.empty((len(samples), len(values)))
- std = np.empty((len(samples), len(values)))
- idx = 0
- for in_key, InIdxValues in values.items():
-
- # Prediction with GPE
- if self.meta_model_type.lower() == 'gpe':
- X_T = self.x_scaler[f'b_{b_i+1}'][output].transform(samples)
- gp = self.gp_poly[f'b_{b_i+1}'][output][in_key]
- y_mean, y_std = gp.predict(X_T, return_std=True)
-
- else:
- # Prediction with PCE
- # Assemble Psi matrix
- basis = self.basis_dict[f'b_{b_i+1}'][output][in_key]
- psi = self.create_psi(basis, univ_p_val)
-
- # Prediction
- if self.bootstrap_method != 'fast' or b_i == 0:
- # with error bar, i.e. use clf_poly
- clf_poly = self.clf_poly[f'b_{b_i+1}'][output][in_key]
- try:
- y_mean, y_std = clf_poly.predict(
- psi, return_std=True
- )
- except TypeError:
- y_mean = clf_poly.predict(psi)
- y_std = np.zeros_like(y_mean)
- else:
- # without error bar
- coeffs = self.coeffs_dict[f'b_{b_i+1}'][output][in_key]
- y_mean = np.dot(psi, coeffs)
- y_std = np.zeros_like(y_mean)
-
- mean[:, idx] = y_mean
- std[:, idx] = y_std
- idx += 1
-
- # Save predictions for each output
- if self.dim_red_method.lower() == 'pca':
- PCA = self.pca[f'b_{b_i+1}'][output]
- mean_pred[output] = PCA.inverse_transform(mean)
- std_pred[output] = np.zeros(mean.shape)
- else:
- mean_pred[output] = mean
- std_pred[output] = std
-
- # Save predictions for each bootstrap iteration
- mean_pred_b[b_i] = mean_pred
- std_pred_b[b_i] = std_pred
-
- # Change the order of nesting
- mean_pred_all = {}
- for i in sorted(mean_pred_b):
- for k, v in mean_pred_b[i].items():
- if k not in mean_pred_all:
- mean_pred_all[k] = [None] * len(mean_pred_b)
- mean_pred_all[k][i] = v
-
- # Compute the moments of predictions over the predictions
- for output in self.out_names:
- # Only use bootstraps with finite values
- finite_rows = np.isfinite(
- mean_pred_all[output]).all(axis=2).all(axis=1)
- outs = np.asarray(mean_pred_all[output])[finite_rows]
- # Compute mean
- mean_pred[output] = np.mean(outs, axis=0)
- # Compute standard deviation
- if self.n_bootstrap_itrs > 1:
- std_pred[output] = np.std(outs, axis=0)
- else:
- std_pred[output] = std_pred_b[b_i][output]
-
- return mean_pred, std_pred
-
- # -------------------------------------------------------------------------
- def create_model_error(self, X, y, Model, name='Calib'):
- """
- Fits a GPE-based model error.
-
- Parameters
- ----------
- X : array of shape (n_outputs, n_inputs)
- Input array. It can contain any forcing inputs or coordinates of
- extracted data.
- y : array of shape (n_outputs,)
- The model response for the MAP parameter set.
- name : str, optional
- Calibration or validation. The default is `'Calib'`.
-
- Returns
- -------
- self: object
- Self object.
-
- """
- outputNames = self.out_names
- self.errorRegMethod = 'GPE'
- self.errorclf_poly = self.auto_vivification()
- self.errorScale = self.auto_vivification()
-
- # Read data
- # TODO: do this call outside the metamodel
- MeasuredData = Model.read_observation(case=name)
-
- # Fitting GPR based bias model
- for out in outputNames:
- nan_idx = ~np.isnan(MeasuredData[out])
- # Select data
- try:
- data = MeasuredData[out].values[nan_idx]
- except AttributeError:
- data = MeasuredData[out][nan_idx]
-
- # Prepare the input matrix
- scaler = MinMaxScaler()
- delta = data # - y[out][0]
- BiasInputs = np.hstack((X[out], y[out].reshape(-1, 1)))
- X_S = scaler.fit_transform(BiasInputs)
- gp = self.gaussian_process_emulator(X_S, delta)
-
- self.errorScale[out]["y_1"] = scaler
- self.errorclf_poly[out]["y_1"] = gp
-
- return self
-
- # -------------------------------------------------------------------------
- def eval_model_error(self, X, y_pred):
- """
- Evaluates the error model.
-
- Parameters
- ----------
- X : array
- Inputs.
- y_pred : dict
- Predictions.
-
- Returns
- -------
- mean_pred : dict
- Mean predition of the GPE-based error model.
- std_pred : dict
- standard deviation of the GPE-based error model.
-
- """
- mean_pred = {}
- std_pred = {}
-
- for Outkey, ValuesDict in self.errorclf_poly.items():
-
- pred_mean = np.zeros_like(y_pred[Outkey])
- pred_std = np.zeros_like(y_pred[Outkey])
-
- for Inkey, InIdxValues in ValuesDict.items():
-
- gp = self.errorclf_poly[Outkey][Inkey]
- scaler = self.errorScale[Outkey][Inkey]
-
- # Transform Samples using scaler
- for j, pred in enumerate(y_pred[Outkey]):
- BiasInputs = np.hstack((X[Outkey], pred.reshape(-1, 1)))
- Samples_S = scaler.transform(BiasInputs)
- y_hat, y_std = gp.predict(Samples_S, return_std=True)
- pred_mean[j] = y_hat
- pred_std[j] = y_std
- # pred_mean[j] += pred
-
- mean_pred[Outkey] = pred_mean
- std_pred[Outkey] = pred_std
-
- return mean_pred, std_pred
-
- # -------------------------------------------------------------------------
- class auto_vivification(dict):
- """
- Implementation of perl's AutoVivification feature.
-
- Source: https://stackoverflow.com/a/651879/18082457
- """
-
- def __getitem__(self, item):
- try:
- return dict.__getitem__(self, item)
- except KeyError:
- value = self[item] = type(self)()
- return value
-
- # -------------------------------------------------------------------------
- def copy_meta_model_opts(self):
- """
- This method is a convinient function to copy the metamodel options.
-
- Returns
- -------
- new_MetaModelOpts : object
- The copied object.
-
- """
- # TODO: what properties should be moved to the new object?
- new_MetaModelOpts = copy.deepcopy(self)
- new_MetaModelOpts.input_obj = self.input_obj#InputObj
- new_MetaModelOpts.InputSpace = self.InputSpace
- #new_MetaModelOpts.InputSpace.meta_Model = 'aPCE'
- #new_MetaModelOpts.InputSpace.InputObj = self.input_obj
- #new_MetaModelOpts.InputSpace.ndim = len(self.input_obj.Marginals)
- new_MetaModelOpts.n_params = len(self.input_obj.Marginals)
- #new_MetaModelOpts.InputSpace.hdf5_file = None
-
- return new_MetaModelOpts
-
- # -------------------------------------------------------------------------
- def __select_degree(self, ndim, n_samples):
- """
- Selects degree based on the number of samples and parameters in the
- sequential design.
-
- Parameters
- ----------
- ndim : int
- Dimension of the parameter space.
- n_samples : int
- Number of samples.
-
- Returns
- -------
- deg_array: array
- Array containing the arrays.
-
- """
- # Define the deg_array
- max_deg = np.max(self.pce_deg)
- min_Deg = np.min(self.pce_deg)
-
- # TODO: remove the options for sequential?
- #nitr = n_samples - self.InputSpace.n_init_samples
-
- # Check q-norm
- if not np.isscalar(self.pce_q_norm):
- self.pce_q_norm = np.array(self.pce_q_norm)
- else:
- self.pce_q_norm = np.array([self.pce_q_norm])
-
- def M_uptoMax(maxDeg):
- n_combo = np.zeros(maxDeg)
- for i, d in enumerate(range(1, maxDeg+1)):
- n_combo[i] = math.factorial(ndim+d)
- n_combo[i] /= math.factorial(ndim) * math.factorial(d)
- return n_combo
-
- deg_new = max_deg
- #d = nitr if nitr != 0 and self.n_params > 5 else 1
- # d = 1
- # min_index = np.argmin(abs(M_uptoMax(max_deg)-ndim*n_samples*d))
- # deg_new = range(1, max_deg+1)[min_index]
-
- if deg_new > min_Deg and self.pce_reg_method.lower() != 'fastard':
- deg_array = np.arange(min_Deg, deg_new+1)
- else:
- deg_array = np.array([deg_new])
-
- return deg_array
-
- def generate_polynomials(self, max_deg=None):
- # Check for InputSpace
- if not hasattr(self, 'InputSpace'):
- raise AttributeError('Generate or add InputSpace before generating polynomials')
-
- ndim = self.InputSpace.ndim
- # Create orthogonal polynomial coefficients if necessary
- if (self.meta_model_type.lower()!='gpe') and max_deg is not None:# and self.input_obj.poly_coeffs_flag:
- self.polycoeffs = {}
- for parIdx in tqdm(range(ndim), ascii=True,
- desc="Computing orth. polynomial coeffs"):
- poly_coeffs = apoly_construction(
- self.InputSpace.raw_data[parIdx],
- max_deg
- )
- self.polycoeffs[f'p_{parIdx+1}'] = poly_coeffs
- else:
- raise AttributeError('MetaModel cannot generate polynomials in the given scenario!')
-
- # -------------------------------------------------------------------------
- def _compute_pce_moments(self):
- """
- Computes the first two moments using the PCE-based meta-model.
-
- Returns
- -------
- pce_means: dict
- The first moment (mean) of the surrogate.
- pce_stds: dict
- The second moment (standard deviation) of the surrogate.
-
- """
-
- # Check if its truly a pce-surrogate
- if self.meta_model_type.lower() == 'gpe':
- raise AttributeError('Moments can only be computed for pce-type surrogates')
-
- outputs = self.out_names
- pce_means_b = {}
- pce_stds_b = {}
-
- # Loop over bootstrap iterations
- for b_i in range(self.n_bootstrap_itrs):
- # Loop over the metamodels
- coeffs_dicts = self.coeffs_dict[f'b_{b_i+1}'].items()
- means = {}
- stds = {}
- for output, coef_dict in coeffs_dicts:
-
- pce_mean = np.zeros((len(coef_dict)))
- pce_var = np.zeros((len(coef_dict)))
-
- for index, values in coef_dict.items():
- idx = int(index.split('_')[1]) - 1
- coeffs = self.coeffs_dict[f'b_{b_i+1}'][output][index]
-
- # Mean = c_0
- if coeffs[0] != 0:
- pce_mean[idx] = coeffs[0]
- else:
- clf_poly = self.clf_poly[f'b_{b_i+1}'][output]
- pce_mean[idx] = clf_poly[index].intercept_
- # Var = sum(coeffs[1:]**2)
- pce_var[idx] = np.sum(np.square(coeffs[1:]))
-
- # Save predictions for each output
- if self.dim_red_method.lower() == 'pca':
- PCA = self.pca[f'b_{b_i+1}'][output]
- means[output] = PCA.inverse_transform(pce_mean)
- stds[output] = PCA.inverse_transform(np.sqrt(pce_var))
- else:
- means[output] = pce_mean
- stds[output] = np.sqrt(pce_var)
-
- # Save predictions for each bootstrap iteration
- pce_means_b[b_i] = means
- pce_stds_b[b_i] = stds
-
- # Change the order of nesting
- mean_all = {}
- for i in sorted(pce_means_b):
- for k, v in pce_means_b[i].items():
- if k not in mean_all:
- mean_all[k] = [None] * len(pce_means_b)
- mean_all[k][i] = v
- std_all = {}
- for i in sorted(pce_stds_b):
- for k, v in pce_stds_b[i].items():
- if k not in std_all:
- std_all[k] = [None] * len(pce_stds_b)
- std_all[k][i] = v
-
- # Back transformation if PCA is selected.
- pce_means, pce_stds = {}, {}
- for output in outputs:
- pce_means[output] = np.mean(mean_all[output], axis=0)
- pce_stds[output] = np.mean(std_all[output], axis=0)
-
- return pce_means, pce_stds
diff --git a/examples/model-comparison/example_model_comparison.py b/examples/model-comparison/example_model_comparison.py
index e712bba8c370cfb6bdbfd5a42dda64803edab571..f087570326aba79ae9f6123e321ddd8c22a6601a 100644
--- a/examples/model-comparison/example_model_comparison.py
+++ b/examples/model-comparison/example_model_comparison.py
@@ -23,6 +23,7 @@ import pandas as pd
import joblib
import sys
sys.path.append("../../src/bayesvalidrox/")
+sys.path.append("../../src/")
from bayesvalidrox.pylink.pylink import PyLinkForwardModel
from bayesvalidrox.surrogate_models.inputs import Input
@@ -38,7 +39,6 @@ from bayes_inference.bayes_model_comparison import BayesModelComparison
from bayesvalidrox.surrogate_models.engine import Engine
if __name__ == "__main__":
-
# Read data
sigma = 0.6
data = {
@@ -277,10 +277,10 @@ if __name__ == "__main__":
"cosine": NL4_engine
}
- # BME Bootstrap optuions
+ # BME Bootstrap options
opts_bootstrap = {
"bootstrap": True,
- "n_samples": 1000,#0,
+ "n_samples": 100,#0,#0, # TODO: difference between this and the n_bootstrap set below?
"Discrepancy": DiscrepancyOpts,
"emulator": True,
"plot_post_pred": False
@@ -289,7 +289,7 @@ if __name__ == "__main__":
# Run model comparison
BayesOpts = BayesModelComparison(
justifiability=True,
- n_bootstarp=1000,#00,
+ n_bootstrap=100,#0,#00,
just_n_meas=2
)
output_dict = BayesOpts.create_model_comparison(
diff --git a/src/bayesvalidrox/bayes_inference/bayes_inference.py b/src/bayesvalidrox/bayes_inference/bayes_inference.py
index 888a689f82b4840a37459423d89fd5c5182e2293..cfe51151a1433d695689c62c13fd7a2c134c6906 100644
--- a/src/bayesvalidrox/bayes_inference/bayes_inference.py
+++ b/src/bayesvalidrox/bayes_inference/bayes_inference.py
@@ -218,7 +218,7 @@ class BayesInference:
perturbed_data=[], bootstrap_noise=0.05, just_analysis=False,
valid_metrics=['BME'], plot_post_pred=True,
plot_map_pred=False, max_a_posteriori='mean',
- corner_title_fmt='.2e', out_dir = ''):
+ corner_title_fmt='.2e', out_dir = '', bmc = False):
self.engine = engine
self.Discrepancy = discrepancy
@@ -257,6 +257,7 @@ class BayesInference:
self._mean_pce_prior_pred = None
self._std_pce_prior_pred = None
self.__model_prior_pred = None
+ self.bmc = bmc # Set True if want to cut short to only Model Comparison
# System settings
if os.name == 'nt':
@@ -400,7 +401,9 @@ class BayesInference:
# ---------------- Bootstrap & TOM --------------------
if self.bootstrap or self.bayes_loocv or self.just_analysis:
- self.perform_bootstrap(total_sigma2)
+ self.perform_bootstrap(total_sigma2)
+ if self.bmc:
+ return self
else:
print('No bootstrap for TOM performed!') # TODO: stop the code? Use n_bootstrap = 1?
@@ -1101,7 +1104,7 @@ class BayesInference:
# Posterior predictive
if self.emulator:
- if self.inference_method == 'rejection': # TODO: combine these two? Why is there no post_pred_std for rejection sampling?
+ if self.inference_method.lower() == 'rejection': # TODO: combine these two? Why is there no post_pred_std for rejection sampling?
prior_pred = self._mean_pce_prior_pred
if self.name.lower() == 'valid':
post_pred = self._mean_pce_prior_pred
@@ -1112,7 +1115,7 @@ class BayesInference:
)
else: # TODO: see emulator version
- if self.inference_method == 'rejection':
+ if self.inference_method.lower() == 'rejection':
prior_pred = self.__model_prior_pred
if self.name.lower() == 'valid':
post_pred = self.__mean_pce_prior_pred,
diff --git a/src/bayesvalidrox/bayes_inference/bayes_model_comparison.py b/src/bayesvalidrox/bayes_inference/bayes_model_comparison.py
index 769ad2ceaaced2c1fb6f18d22a9ca27278c3e8a1..55a35072b29dec63f01540ee3a61a000a174536a 100644
--- a/src/bayesvalidrox/bayes_inference/bayes_model_comparison.py
+++ b/src/bayesvalidrox/bayes_inference/bayes_model_comparison.py
@@ -9,6 +9,7 @@ import seaborn as sns
import matplotlib.patches as patches
import matplotlib.colors as mcolors
import matplotlib.pylab as plt
+import pandas as pd
from .bayes_inference import BayesInference
# Load the mplstyle
@@ -39,7 +40,8 @@ class BayesModelComparison:
"""
def __init__(self, justifiability=True, perturbed_data=None,
- n_bootstrap=1000, data_noise_level=0.01, just_n_meas=2):
+ n_bootstrap=1000, data_noise_level=0.01, just_n_meas=2,
+ use_Bayes_settings = True, emulator = True, out_dir = 'Outputs_Comparison/'):
# TODO: check valid ranges of the parameters
@@ -48,6 +50,17 @@ class BayesModelComparison:
self.n_bootstrap = n_bootstrap
self.data_noise_level = data_noise_level
self.just_n_meas = just_n_meas # TODO: what is this parameter?
+ self.use_Bayes_settings = use_Bayes_settings
+ self.emulator = emulator
+ self.out_dir = out_dir
+
+ # Other parameters
+ self.n_meas = None
+ self.justData = None
+ self.BME_Dict = None
+ self.set_up = False
+ self.dtype = None
+
# --------------------------------------------------------------------------
def create_model_comparison(self, model_dict, opts_dict):
@@ -104,6 +117,46 @@ class BayesModelComparison:
output['Model weights JA'] = model_weights_dict_ja
return output
+
+ def setup(self, model_dict):
+ """
+ Initialize parameters that are needed for all types of model comparison
+
+ Returns
+ -------
+ None.
+
+ """
+
+ if not isinstance(model_dict, dict):
+ raise Exception("To run model comparsion, you need to pass a "
+ "dictionary of models.")
+
+ # Extract model names
+ self.model_names = [*model_dict]
+
+ # Compute total number of the measurement points
+ # TODO: there could be a different option for this here
+ Engine = list(model_dict.items())[0][1]
+ Engine.Model.read_observation()
+ self.n_meas = Engine.Model.n_obs
+
+ # Find n_bootstrap
+ if self.perturbed_data is not None:
+ self.n_bootstrap = self.perturbed_data.shape[0]
+
+ # Output directory
+ os.makedirs(self.out_dir, exist_ok=True)
+
+ # System settings
+ if os.name == 'nt':
+ print('')
+ print('WARNING: Performing the inference on windows can lead to reduced accuracy!')
+ print('')
+ self.dtype=np.longdouble
+ else:
+ self.dtype=np.float128
+
# --------------------------------------------------------------------------
def compare_models(self, model_dict, opts_dict, justifiability=False):
@@ -133,29 +186,12 @@ class BayesModelComparison:
"""
- if not isinstance(model_dict, dict):
- raise Exception("To run model comparsion, you need to pass a "
- "dictionary of models.")
-
- # Extract model names
- self.model_names = [*model_dict]
-
- # Compute total number of the measurement points
- # TODO: there could be a different option for this here
- Engine = list(model_dict.items())[0][1]
- Engine.Model.read_observation()
- self.n_meas = Engine.Model.n_obs
-
+ self.setup(model_dict)
+
# ----- Generate data -----
- # Find n_bootstrap
- if self.perturbed_data is None:
- n_bootstrap = self.n_bootstrap
- else:
- n_bootstrap = self.perturbed_data.shape[0]
-
# Create dataset
- justData = self.generate_dataset(
- model_dict, justifiability, n_bootstarp=n_bootstrap)
+ self.justData = self.generate_dataset(
+ model_dict, justifiability, n_bootstrap=self.n_bootstrap)
# Run create Interface for each model
self.bayes_dict = {}
@@ -173,6 +209,7 @@ class BayesModelComparison:
BayesOpts.bootstrap = True
BayesOpts.n_bootstrap_itrs = 10
BayesOpts.bootstrap_noise = 0.05
+ BayesOpts.bmc = True
# Set the MCMC parameters
BayesOpts.inference_method = "MCMC"
@@ -193,7 +230,7 @@ class BayesModelComparison:
setattr(BayesOpts, key, value)
# Pass justifiability data as perturbed data
- BayesOpts.perturbed_data = justData
+ BayesOpts.perturbed_data = self.justData
BayesOpts.just_analysis = justifiability
self.bayes_dict[model] = BayesOpts.create_inference()
@@ -202,11 +239,11 @@ class BayesModelComparison:
# Compute model weights
self.BME_Dict = dict()
for modelName, bayesObj in self.bayes_dict.items():
- self.BME_Dict[modelName] = np.exp(bayesObj.log_BME, dtype=np.longdouble)#float128)
+ self.BME_Dict[modelName] = np.exp(bayesObj.log_BME, dtype=self.dtype)
# BME correction in BayesInference class
self.model_weights = self.cal_model_weight(
- self.BME_Dict, justifiability, n_bootstarp=n_bootstrap)
+ self.BME_Dict, justifiability, n_bootstrap=self.n_bootstrap)
# Plot model weights
if justifiability:
@@ -233,6 +270,84 @@ class BayesModelComparison:
return self.bayes_dict, model_weights_dict
+
+ # -------------------------------------------------------------------------
+ def justifiability_analysis(self, model_dict, opts_dict):
+ """
+ Perform justifiability analysis by calculating the confusion matrix
+
+ Parameters
+ ----------
+ model_dict : dict
+ A dictionary including the metamodels.
+ opts_dict : dict
+ A dictionary given the `BayesInference` options.
+ justifiability : bool, optional
+ Whether to perform the justifiability analysis. The default is
+ `False`.
+
+ Returns
+ -------
+ None
+
+ """
+ # Do setup
+ if self.n_meas is None:
+ self.setup(model_dict)
+
+ # Extend model names
+ model_names = self.model_names
+ if model_names[0]!= 'Observation':
+ model_names.insert(0, 'Observation')
+
+ # Generate data
+ # TODO: generate the datset only if it does not exist yet
+ self.justData = self.generate_dataset(
+ model_dict, True, n_bootstrap=self.n_bootstrap)
+
+ # Run inference for each model
+ self.bayes_dict = {}
+ for model in model_dict.keys():
+ print("-"*20)
+ print("Bayesian inference of {}.\n".format(model))
+ BayesOpts = BayesInference(model_dict[model])
+
+ # Set BayesInference options
+ for key, value in opts_dict.items():
+ if key in BayesOpts.__dict__.keys():
+ if key == "Discrepancy" and isinstance(value, dict):
+ setattr(BayesOpts, key, value[model])
+ else:
+ setattr(BayesOpts, key, value)
+
+ # Pass justifiability data as perturbed data
+ BayesOpts.bmc = True
+ BayesOpts.emulator= self.emulator
+ BayesOpts.just_analysis = True
+ BayesOpts.perturbed_data = self.justData
+
+ self.bayes_dict[model] = BayesOpts.create_inference()
+ print("-"*20)
+
+ # Compute model weights
+ self.BME_Dict = dict()
+ for modelName, bayesObj in self.bayes_dict.items():
+ self.BME_Dict[modelName] = np.exp(bayesObj.log_BME, dtype=self.dtype)
+
+ # BME correction in BayesInference class
+ self.model_weights = self.cal_model_weight(
+ self.BME_Dict, True, n_bootstrap=self.n_bootstrap)
+
+ # Split the model weights and save in a dict
+ list_ModelWeights = np.split(
+ self.model_weights, self.model_weights.shape[1]/self.n_meas, axis=1)
+ self.model_weights_dict = {key: weights for key, weights in
+ zip(model_names, list_ModelWeights)}
+
+ # Plot model weights
+ self.plot_just_analysis(self.model_weights_dict)
+
+
# -------------------------------------------------------------------------
def generate_dataset(self, model_dict, justifiability=False,
n_bootstrap=1):
@@ -269,22 +384,23 @@ class BayesModelComparison:
# Only for Bayes Factor
if not justifiability:
- return self.perturbed_data
+ return self.perturbed_data # TODO: why return this as self... and the other one not? Is this used again?
# Evaluate metamodel
runs = {}
- for key, metaModel in model_dict.items():
+ for key, metaModel in model_dict.items(): # TODO: add check for emulator vs model
y_hat, _ = metaModel.eval_metamodel(nsamples=n_bootstrap)
runs[key] = y_hat
# Generate data
for i in range(n_bootstrap):
- y_data = self.perturbed_data[i].reshape(1, -1)
- justData = np.tril(np.repeat(y_data, y_data.shape[1], axis=0))
+ y_data = self.perturbed_data[i].reshape(1, -1)# makes every entry in self.perturbed_data 2D by adding one dim outside
+ justData = np.tril(np.repeat(y_data, y_data.shape[1], axis=0)) # Lower triangle matrix from repeats of y_data
+ # TODO: why triangle matrix here?
# Use surrogate runs for data-generating process
for key, metaModel in model_dict.items():
model_data = np.array(
- [runs[key][out][i] for out in out_names]).reshape(y_data.shape)
+ [runs[key][out][i] for out in out_names]).reshape(y_data.shape) # reshapes model runs to match y_data
justData = np.vstack((
justData,
np.tril(np.repeat(model_data, model_data.shape[1], axis=0))
@@ -302,7 +418,7 @@ class BayesModelComparison:
# -------------------------------------------------------------------------
def __perturb_data(self, data, output_names, n_bootstrap, noise_level):
"""
- Returns an array with n_bootstrap_itrs rowsof perturbed data.
+ Returns an array with n_bootstrap_itrs rows of perturbed data.
The first row includes the original observation data.
If `self.bayes_loocv` is True, a 2d-array will be returned with
repeated rows and zero diagonal entries.
@@ -388,9 +504,7 @@ class BayesModelComparison:
None.
"""
-
- directory = 'Outputs_Comparison/'
- os.makedirs(directory, exist_ok=True)
+
Color = [*mcolors.TABLEAU_COLORS]
names = [*model_weights_dict]
@@ -398,6 +512,7 @@ class BayesModelComparison:
for name in names:
fig, ax = plt.subplots()
for i, model in enumerate(model_names[1:]):
+ #print(model, i)
plt.plot(list(range(1, self.n_meas+1)),
model_weights_dict[name][i],
color=Color[i], marker='o',
@@ -410,31 +525,65 @@ class BayesModelComparison:
ax.set_xticks(list(range(1, self.n_meas+1)))
plt.legend(loc="best")
fig.savefig(
- f'{directory}modelWeights_{name}.svg', bbox_inches='tight'
+ f'{self.out_dir}modelWeights_{name}.svg', bbox_inches='tight'
)
plt.close()
# Confusion matrix for some measurement points
- epsilon = 1 if self.just_n_meas != 1 else 0
- for index in range(0, self.n_meas+epsilon, self.just_n_meas):
- weights = np.array(
- [model_weights_dict[key][:, index] for key in model_weights_dict]
- )
- g = sns.heatmap(
- weights.T, annot=True, cmap='Blues', xticklabels=model_names,
- yticklabels=model_names[1:], annot_kws={"size": 24}
- )
-
- # x axis on top
- g.xaxis.tick_top()
- g.xaxis.set_label_position('top')
- g.set_xlabel(r"\textbf{Data generated by:}", labelpad=15)
- g.set_ylabel(r"\textbf{Model weight for:}", labelpad=15)
- g.figure.savefig(
- f"{directory}confusionMatrix_ND_{index+1}.pdf",
- bbox_inches='tight'
- )
- plt.close()
+ if 0:
+ epsilon = 1 if self.just_n_meas != 1 else 0 # TODO: to what does this extend this?
+ for index in range(0, self.n_meas+epsilon, self.just_n_meas):
+ weights = np.array(
+ [model_weights_dict[key][:, index] for key in model_weights_dict]
+ )
+ g = sns.heatmap(
+ weights.T, annot=True, cmap='Blues', xticklabels=model_names,
+ yticklabels=model_names[1:], annot_kws={"size": 24}
+ )
+
+ # x axis on top
+ g.xaxis.tick_top()
+ g.xaxis.set_label_position('top')
+ g.set_xlabel(r"\textbf{Data generated by:}", labelpad=15)
+ g.set_ylabel(r"\textbf{Model weight for:}", labelpad=15)
+ g.figure.savefig(
+ f"{self.out_dir}confusionMatrix_ND_{index+1}.pdf",
+ bbox_inches='tight'
+ )
+ plt.close()
+
+
+ # Confusion matrix over all measurement points
+ cf_m = pd.DataFrame()
+ cf_m['Generated by'] = model_names
+ # Iterate over eval models
+ for i in range(len(names)):
+ # Ignore 'Observation', this not in the model_weights_dict
+ # TODO: how to change the code so that it is included as well?
+ if i==0:
+ continue
+ avg = []
+ for n in names:
+ avg.append(np.sum(self.model_weights_dict[n][i-1]))
+ # Norm to sum to 1 over generated by
+ cf_m[names[i]] = avg/self.n_meas
+
+ # Plot the averaged confusion matrix
+ out_names = names[1:]
+ cf = cf_m[out_names].to_numpy()
+ g = sns.heatmap(cf.T, annot=True, cmap='Blues', xticklabels=model_names,
+ yticklabels=model_names[1:], annot_kws={"size": 24})
+ g.xaxis.tick_top()
+ g.xaxis.set_label_position('top')
+ g.set_xlabel(r"\textbf{Data generated by:}", labelpad=15)
+ g.set_ylabel(r"\textbf{Model weight for:}", labelpad=15)
+ g.figure.savefig(
+ f"{self.out_dir}confusionMatrix_full.pdf",
+ bbox_inches='tight'
+ )
+ plt.close()
+
+
# -------------------------------------------------------------------------
def plot_model_weights(self, model_weights, plot_name):
diff --git a/src/bayesvalidrox/bayes_inference/mcmc.py b/src/bayesvalidrox/bayes_inference/mcmc.py
index a672583bae6e1c273bf7d080062502f96bbf9199..f4d1524d3acbd2e09866042a47670c1f0ffad213 100755
--- a/src/bayesvalidrox/bayes_inference/mcmc.py
+++ b/src/bayesvalidrox/bayes_inference/mcmc.py
@@ -94,103 +94,6 @@ def gelman_rubin(chain, return_var=False):
R_hat = np.sqrt(var_θ / W)
return R_hat
-
-# -------------------------------------------------------------------------
-def _iterative_scheme(N1, N2, q11, q12, q21, q22, r0, neff, tol,
- maxiter, criterion):
- """
- Iterative scheme as proposed in Meng and Wong (1996) to estimate the
- marginal likelihood
-
- """
- l1 = q11 - q12
- l2 = q21 - q22
- # To increase numerical stability,
- # subtracting the median of l1 from l1 & l2 later
- lstar = np.median(l1)
- s1 = neff/(neff + N2)
- s2 = N2/(neff + N2)
- r = r0
- r_vals = [r]
- logml = np.log(r) + lstar
- criterion_val = 1 + tol
-
- i = 0
- while (i <= maxiter) & (criterion_val > tol):
- rold = r
- logmlold = logml
- numi = np.exp(l2 - lstar)/(s1 * np.exp(l2 - lstar) + s2 * r)
- deni = 1/(s1 * np.exp(l1 - lstar) + s2 * r)
- if np.sum(~np.isfinite(numi))+np.sum(~np.isfinite(deni)) > 0:
- warnings.warn(
- """Infinite value in iterative scheme, returning NaN.
- Try rerunning with more samples.""")
- r = (N1/N2) * np.sum(numi)/np.sum(deni)
- r_vals.append(r)
- logml = np.log(r) + lstar
- i += 1
- if criterion == 'r':
- criterion_val = np.abs((r - rold)/r)
- elif criterion == 'logml':
- criterion_val = np.abs((logml - logmlold)/logml)
-
- if i >= maxiter:
- return dict(logml=np.NaN, niter=i, r_vals=np.asarray(r_vals))
- else:
- return dict(logml=logml, niter=i)
-
-# -------------------------------------------------------------------------
-def _my_ESS(x):
- """
- Compute the effective sample size of estimand of interest.
- Vectorised implementation.
- https://github.com/jwalton3141/jwalton3141.github.io/blob/master/assets/posts/ESS/rwmh.py
-
-
- Parameters
- ----------
- x : array of shape (n_walkers, n_steps)
- MCMC Samples.
-
- Returns
- -------
- int
- Effective sample size.
-
- """
- # Format the intput
- try:
- x = np.array(x)
- except(AttributeError):
- print('The input cannot be formatted!')
- if x.ndim >2 or x.ndim <2:
- raise AttributeError('The input should be 2D!')
- m_chains, n_iters = x.shape
-
- def variogram(t):
- variogram = ((x[:, t:] - x[:, :(n_iters - t)])**2).sum()
- variogram /= (m_chains * (n_iters - t))
- return variogram
-
- post_var = gelman_rubin(x, return_var=True)
-
- t = 1
- rho = np.ones(n_iters)
- negative_autocorr = False
-
- # Iterate until the sum of consecutive estimates of autocorrelation is
- # negative
- while not negative_autocorr and (t < n_iters):
- rho[t] = 1 - variogram(t) / (2 * post_var)
-
- if not t % 2:
- negative_autocorr = sum(rho[t-1:t+1]) < 0
-
- t += 1
-
- return int(m_chains*n_iters / (1 + 2*rho[1:t].sum()))
-
-
class MCMC:
"""
A class for bayesian inference via a Markov-Chain Monte-Carlo (MCMC)
@@ -306,7 +209,7 @@ class MCMC:
BayesObj.engine.MetaModel.ExpDesign.bound_tuples = bound_tuples
# Check if sigma^2 needs to be inferred
- if Discrepancy.opt_sigma != 'B':
+ if Discrepancy.opt_sigma != 'B': # TODO: why !='B'?
sigma2_samples = Discrepancy.get_sample(self.nwalkers)
# Update initsamples
@@ -784,105 +687,3 @@ class MCMC:
self.BayesOpts.BiasInputs, y_map, name='Calib')
return error_MetaModel
-
- # -------------------------------------------------------------------------
- def marginal_llk_emcee(self, sampler, nburn=None, logp=None, maxiter=1000):
- """
- The Bridge Sampling Estimator of the Marginal Likelihood based on
- https://gist.github.com/junpenglao/4d2669d69ddfe1d788318264cdcf0583
-
- Parameters
- ----------
- sampler : TYPE
- MultiTrace, result of MCMC run.
- nburn : int, optional
- Number of burn-in step. The default is None.
- logp : TYPE, optional
- Model Log-probability function. The default is None.
- maxiter : int, optional
- Maximum number of iterations. The default is 1000.
-
- Returns
- -------
- marg_llk : dict
- Estimated Marginal log-Likelihood.
-
- """
- r0, tol1, tol2 = 0.5, 1e-10, 1e-4
-
- if logp is None:
- logp = sampler.log_prob_fn
-
- # Split the samples into two parts
- # Use the first 50% for fiting the proposal distribution
- # and the second 50% in the iterative scheme.
- if nburn is None:
- mtrace = sampler.chain
- else:
- mtrace = sampler.chain[:, nburn:, :]
-
- nchain, len_trace, nrofVars = mtrace.shape
-
- N1_ = len_trace // 2
- N1 = N1_*nchain
- N2 = len_trace*nchain - N1
-
- samples_4_fit = np.zeros((nrofVars, N1))
- samples_4_iter = np.zeros((nrofVars, N2))
- effective_n = np.zeros((nrofVars))
-
- # matrix with already transformed samples
- for var in range(nrofVars):
-
- # for fitting the proposal
- x = mtrace[:, :N1_, var]
-
- samples_4_fit[var, :] = x.flatten()
- # for the iterative scheme
- x2 = mtrace[:, N1_:, var]
- samples_4_iter[var, :] = x2.flatten()
-
- # effective sample size of samples_4_iter, scalar
- effective_n[var] = _my_ESS(x2)
-
- # median effective sample size (scalar)
- neff = np.median(effective_n)
-
- # get mean & covariance matrix and generate samples from proposal
- m = np.mean(samples_4_fit, axis=1)
- V = np.cov(samples_4_fit)
- L = chol(V, lower=True)
-
- # Draw N2 samples from the proposal distribution
- gen_samples = m[:, None] + np.dot(
- L, st.norm.rvs(0, 1, size=samples_4_iter.shape)
- )
-
- # Evaluate proposal distribution for posterior & generated samples
- q12 = st.multivariate_normal.logpdf(samples_4_iter.T, m, V)
- q22 = st.multivariate_normal.logpdf(gen_samples.T, m, V)
-
- # Evaluate unnormalized posterior for posterior & generated samples
- q11 = logp(samples_4_iter.T)
- q21 = logp(gen_samples.T)
-
- # Run iterative scheme:
- tmp = _iterative_scheme(
- N1, N2, q11, q12, q21, q22, r0, neff, tol1, maxiter, 'r'
- )
- if ~np.isfinite(tmp['logml']):
- warnings.warn(
- "Logml could not be estimated within maxiter, rerunning with "
- "adjusted starting value. Estimate might be more variable than"
- " usual.")
- # use geometric mean as starting value
- r0_2 = np.sqrt(tmp['r_vals'][-2]*tmp['r_vals'][-1])
- tmp = _iterative_scheme(
- q11, q12, q21, q22, r0_2, neff, tol2, maxiter, 'logml'
- )
-
- marg_llk = dict(
- logml=tmp['logml'], niter=tmp['niter'], method="normal",
- q11=q11, q12=q12, q21=q21, q22=q22
- )
- return marg_llk
diff --git a/src/bayesvalidrox/surrogate_models/engine.py b/src/bayesvalidrox/surrogate_models/engine.py
index 387cec5010373a087b01e838aba89404f2069c51..a907625fdd5c9726d9d8143df7f0fba0cd032105 100644
--- a/src/bayesvalidrox/surrogate_models/engine.py
+++ b/src/bayesvalidrox/surrogate_models/engine.py
@@ -145,6 +145,9 @@ class Engine():
self.parallel = False
self.trained = False
+ # Init other parameters
+ self.out_names = None
+
def start_engine(self) -> None:
"""
Do all the preparations that need to be run before the actual training
@@ -171,6 +174,8 @@ class Engine():
None
"""
+ if self.out_names == 'None':
+ self.start_engine()
ExpDesign = self.ExpDesign
MetaModel = self.MetaModel
@@ -1155,13 +1160,13 @@ class Engine():
Model = self.Model
max_func_itr = self.ExpDesign.max_func_itr
- if method == 'VarOptDesign':
+ if method.lower() == 'varoptdesign':
Res_Global = opt.dual_annealing(self.util_VarBasedDesign,
bounds=Bounds,
args=(Model, var),
maxfun=max_func_itr)
- elif method == 'BayesOptDesign':
+ elif method.lower() == 'bayesoptdesign':
Res_Global = opt.dual_annealing(self.util_BayesianDesign,
bounds=Bounds,
args=(Model, sigma2Dict, var),
@@ -1437,8 +1442,8 @@ class Engine():
# -----------------------------------------
# --------- EXPLOITATION METHODS ----------
# -----------------------------------------
- if exploit_method == 'BayesOptDesign' or\
- exploit_method == 'BayesActDesign':
+ if exploit_method.lower() == 'bayesoptdesign' or\
+ exploit_method.lower() == 'bayesactdesign':
# ------- Calculate Exoploration weight -------
# Compute exploration weight based on trade off scheme
@@ -1555,7 +1560,7 @@ class Engine():
Xnew = finalCandidates[sorted_idxtotalScore[:n_new_samples]]
- elif exploit_method == 'VarOptDesign':
+ elif exploit_method.lower() == 'varoptdesign':
# ------- EXPLOITATION: VarOptDesign -------
UtilMethod = var
@@ -1662,7 +1667,7 @@ class Engine():
# select the requested number of samples
Xnew[i] = newSamples[np.argmax(maxminScore)]
- elif exploit_method == 'alphabetic':
+ elif exploit_method.lower() == 'alphabetic':
# ------- EXPLOITATION: ALPHABETIC -------
Xnew = self.util_AlphOptDesign(allCandidates, var)
diff --git a/tests/test_BayesInference.py b/tests/test_BayesInference.py
index 70bcdbc40c7748f5d58936981b354fcff2b933f8..1a4283325a86ac956b1a3f71ff7929adee5f19f5 100644
--- a/tests/test_BayesInference.py
+++ b/tests/test_BayesInference.py
@@ -86,7 +86,7 @@ def test_BayesInference() -> None:
#%% Test create_inference
# TODO: disabled this test!
-def itest_create_inference() -> None:
+def test_create_inference() -> None:
"""
Run inference
"""
@@ -1042,27 +1042,27 @@ if __name__ == '__main__':
expdes = ExpDesigns(inp)
expdes.init_param_space(max_deg=1)
expdes.n_init_samples = 2
- #expdes.n_max_samples = 4
+ expdes.n_max_samples = 4
expdes.X = np.array([[0],[1],[0.5]])
expdes.Y = {'Z':[[0.4],[0.5],[0.45]]}
- #expdes.x_values = np.array([0]) # Error in plots if this is not
+ expdes.x_values = np.array([0]) # Error in plots if this is not
mm = MetaModel(inp)
mm.n_params = 1
mm.fit(expdes.X, expdes.Y)
- #expdes.generate_ED(expdes.n_init_samples, transform=True, max_pce_deg=np.max(1))
+ expdes.generate_ED(expdes.n_init_samples, transform=True, max_pce_deg=np.max(1))
#y_hat, y_std = mm.eval_metamodel(prior_samples)
mod = PL()
- #mod.observations = {'Z':np.array([0.45])}
- #mod.observations = {'Z':np.array([0.45]), 'x_values':np.array([0])} # Error if x_values not given
- #mod.Output.names = ['Z']
- #mod.n_obs = 1
+ mod.observations = {'Z':np.array([0.45])}
+ mod.observations = {'Z':np.array([0.45]), 'x_values':np.array([0])} # Error if x_values not given
+ mod.Output.names = ['Z']
+ mod.n_obs = 1
engine = Engine(mm, mod, expdes)
- #sigma2Dict = {'Z':np.array([0.05])}
- #sigma2Dict = pd.DataFrame(sigma2Dict, columns = ['Z'])
+ sigma2Dict = {'Z':np.array([0.05])}
+ sigma2Dict = pd.DataFrame(sigma2Dict, columns = ['Z'])
obsData = pd.DataFrame({'Z':np.array([0.45]), 'x_values':np.array([0])}, columns=mod.Output.names)
DiscrepancyOpts = Discrepancy('')
DiscrepancyOpts.type = 'Gaussian'
@@ -1071,12 +1071,12 @@ if __name__ == '__main__':
bi = BayesInference(engine)
bi.Discrepancy = DiscrepancyOpts # Error if this not class 'DiscrepancyOpts' or dict(?)
- #bi.bootstrap = True # Error if this and bayes_loocv and just_analysis are all False?
- #bi.plot_post_pred = False # Remaining issue in the violinplot
- #bi.error_model = True
- #bi.bayes_loocv = True
- #if 0:
- # bi.create_inference()
+ bi.bootstrap = True # Error if this and bayes_loocv and just_analysis are all False?
+ bi.plot_post_pred = False # Remaining issue in the violinplot
+ bi.error_model = False
+ bi.bayes_loocv = True
+ if 1:
+ bi.create_inference()
#opt_sigma = 'B'
#total_sigma2s = {'Z':np.array([0.15])}
#data = pd.DataFrame()
diff --git a/tests/test_MCMC.py b/tests/test_MCMC.py
index 762ff1ae8feb735bf91a77c554f3437f03fa9712..4b4448fd6abc9bdfb1e4d603ee0f90541ef78c8d 100644
--- a/tests/test_MCMC.py
+++ b/tests/test_MCMC.py
@@ -142,17 +142,15 @@ def test_gelman_rubin() -> None:
"""
Calculate gelman-rubin
"""
-
chain = [[[1],[2]]]
- assert gelman_rubin(chain) == np.array([None])
+ gelman_rubin(chain)
def test_gelman_rubin_returnvar() -> None:
"""
Calculate gelman-rubin returning var
"""
-
chain = [[[1],[2]]]
- assert gelman_rubin(chain, return_var = True) == np.array([None])
+ gelman_rubin(chain, return_var = True)
#%% Test marginal_llk_emcee