Index

A

a (BetaDistribution attribute) (DynamicLearningRateDecay attribute) (SequentialMonteCarloIterator attribute) accepted (MetropolisHastingsIterator attribute) accepted_interval (MetropolisHastingsIterator attribute) activation_per_hidden_layer (GaussianNeuralNetworkModel attribute) activation_per_hidden_layer_lst (GaussianBayesianNeuralNetworkModel attribute) active_sampler_obj (ActiveLearningClassifier attribute) ActiveLearningClassifier (class in queens.utils.classifier) Adam (class in queens.stochastic_optimizers.adam) Adamax (class in queens.stochastic_optimizers.adamax) adams_training_rate (GaussianBayesianNeuralNetworkModel attribute) (GaussianNeuralNetworkModel attribute) (HeteroskedasticGPModel attribute) AdaptiveSamplingIterator (class in queens.iterators.adaptive_sampling_iterator) add() (CollectionObject method) add_data_and_to_dict() (JobOptions method) add_nugget_to_diagonal() (in module queens.utils.numpy_utils) adjoint_file (DifferentiableSimulationModelAdjoint attribute) advi_iterations (HMCIterator attribute) (NUTSIterator attribute)

agawal09a() (in module queens.example_simulator_functions.agawal09) algorithm (OptimizationIterator attribute) alpha (DynamicLearningRateDecay attribute) animation_bool (BMFMCVisualization attribute) annotate_points() (in module queens.visualization.sa_visualization) approx_type (LogpdfGPModel attribute) as_inference_dict (PyMCIterator attribute) as_smc_rejuvenation_step (MetropolisHastingsIterator attribute) assemble_rsync_command() (in module queens.utils.rsync) assemble_x_red_stdizd() (in module queens.models.bmfmc_model) assign_hyperparameters() (GPFlowRegressionModel method) assign_variable_value() (in module queens.utils.input_to_script) at_least_2d() (in module queens.utils.numpy_utils) at_least_3d() (in module queens.utils.numpy_utils) average_computation() (ExponentialAveraging method) (IterativeAveraging method) (MovingAveraging method) (PolyakAveraging method) axs_convergence_plots (VIVisualization attribute)

B

b (BetaDistribution attribute) (DynamicLearningRateDecay attribute) (SequentialMonteCarloIterator attribute) base_dir (ExperimentalDataReader attribute) base_directory() (in module queens.utils.config_directories) base_distribution (MixtureModelVariational attribute) basis (FourierRandomField attribute) basis_dimension (FourierRandomField attribute) batch_size (GaussianNeuralNetworkModel attribute) (LogpdfGPModel attribute) BBVIIterator (class in queens.iterators.black_box_variational_bayes) BernoulliDistribution (class in queens.distributions.bernoulli) beta (RMSprop attribute) beta_1 (Adam attribute) (Adamax attribute) beta_2 (Adam attribute) (Adamax attribute) BetaDistribution (class in queens.distributions.beta) binarize() (ClassificationIterator method) block (DataProcessorPvd attribute) BMFGaussianModel (class in queens.models.likelihood_models.bayesian_mf_gaussian_likelihood) BmfiaInterface (class in queens.models.likelihood_models.bayesian_mf_gaussian_likelihood) BMFIAIterator (class in queens.iterators.bmfia_iterator) BMFIAVisualization (class in queens.visualization.bmfia_visualization)

BmfmcInterface (class in queens.models.bmfmc_model) BMFMCIterator (class in queens.iterators.bmfmc_iterator) BMFMCModel (class in queens.models.bmfmc_model) BMFMCVisualization (class in queens.visualization.bmfmc_visualization) bnn_model (GaussianBayesianNeuralNetworkModel attribute) bootstrap() (in module queens.iterators.sobol_index_gp_uncertainty.utils_estimate_indices) borehole83_hifi() (in module queens.example_simulator_functions.borehole83) borehole83_lofi() (in module queens.example_simulator_functions.borehole83) bounds (DifferentiableSimulationModelFD attribute) (LMIterator attribute) (OptimizationIterator attribute) branin78_hifi() (in module queens.example_simulator_functions.branin78) branin78_lofi() (in module queens.example_simulator_functions.branin78) branin78_medfi() (in module queens.example_simulator_functions.branin78) buffered_gradients (PyMCIterator attribute) buffered_likelihoods (PyMCIterator attribute) buffered_samples (PyMCIterator attribute) build_approximation() (BMFGaussianModel static method) (BmfiaInterface method) (BmfmcInterface method) (BMFMCModel method) (SurrogateModel method) build_html_coverage_report() (in module queens.utils.cli_utils) build_remote_environment() (RemoteConnection method)

C

c (DynamicLearningRateDecay attribute) calc_ess() (in module queens.utils.smc_utils) calc_new_ess() (SequentialMonteCarloIterator method) calc_new_gamma() (SequentialMonteCarloIterator method) calc_new_weights() (SequentialMonteCarloIterator method) calc_second_order (SobolIndexIterator attribute) calc_train_factor() (LogpdfGPModel method) calculate_basis() (DimensionMethods1D static method) (DimensionMethods2D static method) (DimensionMethods3D static method) calculate_covariance() (DimensionMethods1D static method) (DimensionMethods2D static method) (DimensionMethods3D static method) calculate_covariance_matrix() (KarhunenLoeveRandomField method) calculate_extended_gammas() (BMFMCModel method) calculate_index() (SobolIndexGPUncertaintyIterator method) calculate_indices_first_total_order() (in module queens.iterators.sobol_index_gp_uncertainty.utils_estimate_indices) calculate_indices_second_order_gp_mean() (in module queens.iterators.sobol_index_gp_uncertainty.utils_estimate_indices) calculate_indices_second_order_gp_realizations() (in module queens.iterators.sobol_index_gp_uncertainty.utils_estimate_indices) calculate_indices_third_order() (in module queens.iterators.sobol_index_gp_uncertainty.utils_estimate_indices) calculate_initial_x_train() (BMFIAIterator class method) calculate_optimal_X_train() (BMFMCIterator method) calculate_p_yhf_mean() (BMFMCModel method) calculate_p_yhf_var() (BMFMCModel method) calculate_second_order (Sampler attribute) (SobolIndexEstimator attribute) (SobolIndexGPUncertaintyIterator attribute) calculate_third_order (SobolIndexEstimatorThirdOrder attribute) (SobolIndexGPUncertaintyIterator attribute) (ThirdOrderSampler attribute) CategoricalDistribution (class in queens.distributions.categorical) categories (CategoricalDistribution attribute) cauchy_schwarz_divergence() (in module queens.iterators.adaptive_sampling_iterator) cdf() (BetaDistribution method) (ContinuousDistribution method) (DiscreteDistribution method) (ExponentialDistribution method) (FreeVariable method) (LogNormalDistribution method) (MeanFieldNormalDistribution method) (MixtureDistribution method) (MultinomialDistribution method) (NormalDistribution method) (ParticleDiscreteDistribution method) (UniformDistribution method) chains (MetropolisHastingsIterator attribute) (PyMCIterator attribute) check_1d() (ContinuousDistribution method) (DiscreteDistribution method) check_bounds() (ContinuousDistribution static method) check_convergence() (FourierRandomField method) check_coordinates_return_dimensions() (BmfiaInterface static method) check_duplicates_in_sample_space() (DiscreteDistribution static method) check_for_reference() (in module queens.utils.fcc_utils) check_if_in_desired_dat_section() (FourcDatExternalGeometry method) check_if_path_exists() (in module queens.utils.path_utils) check_if_valid_options() (in module queens.utils.valid_options_utils) check_positivity() (Distribution static method) check_precalculated() (OptimizationIterator method) check_valid_filter_options() (DataProcessorCsv class method) checkbounds() (LMIterator method) chol_k_train_train (LogpdfGPModel attribute) cholesky_k_mat (GPJittedModel attribute) choose_new_samples() (AdaptiveSamplingIterator method) classification_function (ClassificationIterator attribute) ClassificationIterator (class in queens.iterators.classification) ClassificationVisualization (class in queens.visualization.classification) classified_outputs (ClassificationIterator attribute) Classifier (class in queens.utils.classifier) classifier (ClassificationIterator attribute) classifier_obj (ActiveLearningClassifier attribute) (Classifier attribute) cli_logging() (in module queens.utils.cli_utils) client (DaskScheduler attribute) CLIError clip_by_l2_norm() (in module queens.stochastic_optimizers.stochastic_optimizer) clip_by_l2_norm_threshold (StochasticOptimizer attribute) clip_by_value() (in module queens.stochastic_optimizers.stochastic_optimizer) clip_by_value_threshold (StochasticOptimizer attribute) clip_gradient() (StochasticOptimizer method) ClusterScheduler (class in queens.schedulers.cluster_scheduler) code (QueensPythonCode attribute) coefficient (ExponentialAveraging attribute) CollectionObject (class in queens.utils.collection_utils) compute_distance() (DataProcessorEnsightInterfaceDiscrepancy method) compute_error() (SurrogateModel static method) compute_error_measures() (SurrogateModel method) compute_nash_sutcliffe_efficiency() (SurrogateModel static method) compute_pyhf_statistics() (BMFMCModel method) compute_pymc_reference() (BMFMCModel method) compute_step_with_bounds() (in module queens.utils.fd_jacobian) conditional_prediction_decorator() (in module queens.visualization.classification) ConditionalDecisionBoundaryDisplay (class in queens.visualization.classification) conduct_reparameterization() (FullRankNormalVariational method) (MeanFieldNormalVariational method) confidence_level (ElementaryEffectsIterator attribute) (SobolIndexIterator attribute)

configure_keras() (in module queens.utils.tensorflow_utils) configure_tensorflow() (in module queens.utils.tensorflow_utils) cons (OptimizationIterator attribute) construct_error_from_command() (SubprocessError class method) construct_error_from_options() (InvalidOptionError class method) construct_variational_parameters() (FullRankNormalVariational static method) (JointVariational method) (MeanFieldNormalVariational static method) (MixtureModelVariational method) (ParticleVariational method) ContinuousDistribution (class in queens.distributions.distributions) control_variate (ControlVariatesIterator attribute) control_variates_scaling_type (BBVIIterator attribute) ControlVariatesIterator (class in queens.iterators.control_variates_iterator) convert_to_dict() (in module queens.visualization.sa_visualization) (in module queens.visualization.surrogate_visualization) convert_to_pandas() (in module queens.visualization.sa_visualization) convex_hull_size (FourierRandomField attribute) coord_cols (BMFIAIterator attribute) coord_labels (BMFGaussianModel attribute) (BmfiaInterface attribute) coordinate_labels (ExperimentalDataReader attribute) coordinates (FourierRandomField attribute) coordinates_label_experimental (DataProcessorEnsight attribute) coords (RandomField attribute) coords_dict (FourcDatExternalGeometry attribute) coords_experimental_data (BMFIAIterator attribute) coords_mat (BMFGaussianModel attribute) (BmfiaInterface attribute) copy_files_to_experiment_dir() (ClusterScheduler method) (Scheduler method) copy_to_remote() (RemoteConnection method) core_run() (AdaptiveSamplingIterator method) (BBVIIterator method) (BMFIAIterator method) (BMFMCIterator method) (ClassificationIterator method) (ControlVariatesIterator method) (DataIterator method) (ElementaryEffectsIterator method) (GridIterator method) (Iterator method) (LHSIterator method) (LMIterator method) (MetropolisHastingsIterator method) (MLMCIterator method) (MonteCarloIterator method) (OptimizationIterator method) (PointsIterator method) (PolynomialChaosIterator method) (PyMCIterator method) (RPVIIterator method) (SequentialMonteCarloChopinIterator method) (SequentialMonteCarloIterator method) (SobolIndexGPUncertaintyIterator method) (SobolIndexIterator method) (SobolSequenceIterator method) (VariationalInferenceIterator method) corr_length (FourierRandomField attribute) (KarhunenLoeveRandomField attribute) cost_cv (ControlVariatesIterator attribute) cost_estimators (MLMCIterator attribute) cost_model (ControlVariatesIterator attribute) cov_matrix (KarhunenLoeveRandomField attribute) covariance (ContinuousDistribution attribute) (DiscreteDistribution attribute) (FourierRandomField attribute) (MetropolisHastingsPyMCIterator attribute) (ParticleDiscreteDistribution attribute) covariance_index (FourierRandomField attribute) create_chaospy_distribution() (in module queens.iterators.polynomial_chaos_iterator) create_chaospy_joint_distribution() (in module queens.iterators.polynomial_chaos_iterator) create_code_section() (QueensPythonCode static method) create_collection_object_from_dict() (CollectionObject class method) create_directory() (in module queens.utils.config_directories) create_folder_if_not_existent() (in module queens.utils.path_utils) create_initialization_call() (in module queens.utils.input_to_script) create_initialization_call_from_class_and_arguments() (in module queens.utils.input_to_script) create_input_templates_dict() (JobscriptDriver static method) create_latent_distribution() (PieceWiseRandomField method) create_main (QueensPythonCode attribute) create_pool() (in module queens.utils.pool_utils) create_remote_directory() (RemoteConnection method) create_script_from_input_file() (in module queens.utils.input_to_script) criterion (LHSIterator attribute) cross_validate() (SurrogateModel method) cs_div_criterion (AdaptiveSamplingIterator attribute) current_average (IterativeAveraging attribute) current_dat_section (FourcDatExternalGeometry attribute) current_gradient_value (StochasticOptimizer attribute) current_job_directory() (in module queens.utils.config_directories) current_variational_parameters (StochasticOptimizer attribute) currin88_hifi() (in module queens.example_simulator_functions.currin88) currin88_lofi() (in module queens.example_simulator_functions.currin88) cut_off (KarhunenLoeveRandomField attribute)

D

DaskScheduler (class in queens.schedulers.dask_scheduler) dat_sections (FourcDatExternalGeometry attribute) data (MovingAveraging attribute) data_attribute (DataProcessorPvd attribute) data_processor (ExperimentalDataReader attribute) (JobscriptDriver attribute) DataIterator (class in queens.iterators.data_iterator) DataProcessor (class in queens.data_processor.data_processor) DataProcessorCsv (class in queens.data_processor.data_processor_csv) DataProcessorEnsight (class in queens.data_processor.data_processor_ensight) DataProcessorEnsightInterfaceDiscrepancy (class in queens.data_processor.data_processor_ensight_interface) DataProcessorNumpy (class in queens.data_processor.data_processor_numpy) DataProcessorPvd (class in queens.data_processor.data_processor_pvd) DataProcessorTxt (class in queens.data_processor.data_processor_txt) debug (GlobalSettings attribute) decay_factor (StepwiseLearningRateDecay attribute) decay_interval (StepwiseLearningRateDecay attribute) default_classification_function() (in module queens.iterators.classification) deformed_grid() (DataProcessorEnsightInterfaceDiscrepancy method) desired_dat_sections (FourcDatExternalGeometry attribute) dict (Parameters attribute) dict_replace_infs() (in module queens.utils.input_to_script) DifferentiableSimulationModelAdjoint (class in queens.models.differentiable_simulation_model_adjoint) DifferentiableSimulationModelFD (class in queens.models.differentiable_simulation_model_fd) dim (ParticlesChopinDistribution property) dim_coords (RandomField attribute) dimension (ContinuousDistribution attribute) (DiscreteDistribution attribute) (FourierRandomField attribute) (KarhunenLoeveRandomField attribute) (ParticleDiscreteDistribution attribute) (ParticleVariational attribute) (RandomField attribute) (VariationalDistribution attribute) dimension_lengthscales (GPFlowRegressionModel attribute) (GPflowSVGPModel attribute) dimension_output (GPflowSVGPModel attribute) DimensionMethods1D (class in queens.parameters.fields.fourier_field) DimensionMethods2D (class in queens.parameters.fields.fourier_field) DimensionMethods3D (class in queens.parameters.fields.fourier_field) discard_tuned_samples (PyMCIterator attribute) DiscreteDistribution (class in queens.distributions.distributions)

displacement_fields (DataProcessorEnsightInterfaceDiscrepancy attribute) distances() (in module queens.models.logpdf_gp_model) Distribution (class in queens.distributions.distributions) distribution (PieceWiseRandomField attribute) (PolynomialChaosIterator attribute) (RandomField attribute) distributions (JointVariational attribute) distributions_dimension (JointVariational attribute) distributions_n_parameters (JointVariational attribute) diverse_subset_design() (BMFMCIterator method) do_mh_step() (MetropolisHastingsIterator method) do_processing() (in module queens.utils.process_outputs) do_single_iteration() (StochasticOptimizer method) done (StochasticOptimizer attribute) draw() (BetaDistribution method) (CategoricalDistribution method) (ContinuousDistribution method) (DiscreteDistribution method) (Distribution method) (ExponentialDistribution method) (FourierRandomField method) (FreeVariable method) (FullRankNormalVariational method) (JointVariational method) (KarhunenLoeveRandomField method) (LogNormalDistribution method) (MeanFieldNormalDistribution method) (MeanFieldNormalVariational method) (MixtureDistribution method) (MixtureModelVariational method) (MultinomialDistribution method) (NormalDistribution method) (ParticleDiscreteDistribution method) (ParticleVariational method) (PieceWiseRandomField method) (RandomField method) (UniformDistribution method) (VariationalDistribution method) draw_samples() (Parameters method) draw_trace() (SequentialMonteCarloIterator method) Driver (class in queens.drivers.driver) driver (SimulationModel attribute) DynamicLearningRateDecay (class in queens.stochastic_optimizers.learning_rate_decay)

E

early_max_treedepth (NUTSIterator attribute) eigenbasis (KarhunenLoeveRandomField attribute) eigendecomp_cov_matrix() (KarhunenLoeveRandomField method) eigenfunc (DataIterator attribute) eigenfunc_random_fields (BMFMCModel attribute) eigenvals (BMFMCModel attribute) eigenvalues (KarhunenLoeveRandomField attribute) eigenvectors (KarhunenLoeveRandomField attribute) elbo (VariationalInferenceIterator attribute) element_centers (FourcDatExternalGeometry attribute) element_topology (FourcDatExternalGeometry attribute) ElementaryEffectsIterator (class in queens.iterators.elementary_effects_iterator) eps (Adam attribute) (Adamax attribute) (RMSprop attribute) error_measures (SurrogateModel attribute) ess (BBVIIterator attribute) (SequentialMonteCarloIterator attribute) ess_cur (SequentialMonteCarloIterator attribute) estimate() (SobolIndexEstimator method) (SobolIndexEstimatorThirdOrder method) estimate_bandwidth_for_kde() (in module queens.utils.pdf_estimation) (in module queens.utils.process_outputs) estimate_cdf() (in module queens.utils.process_outputs) estimate_cov() (in module queens.utils.process_outputs) estimate_icdf() (in module queens.utils.process_outputs) estimate_mean() (in module queens.utils.process_outputs) estimate_pdf() (in module queens.utils.pdf_estimation) (in module queens.utils.process_outputs) estimate_result_interval() (in module queens.utils.process_outputs) estimate_var() (in module queens.utils.process_outputs) estimates_first_order (SobolIndexEstimator attribute) estimates_second_order (SobolIndexEstimator attribute) estimates_third_order (SobolIndexEstimatorThirdOrder attribute) estimates_total_order (SobolIndexEstimator attribute) eval_fit (SurrogateModel attribute) eval_log_likelihood() (AdaptiveSamplingIterator method) (BBVIIterator method) (MetropolisHastingsIterator method) (MetropolisHastingsPyMCIterator method) (PyMCIterator method) (SequentialMonteCarloChopinIterator method) (SequentialMonteCarloIterator method) eval_log_likelihood_grad() (MetropolisHastingsPyMCIterator method) (PyMCIterator method) eval_log_prior() (MetropolisHastingsIterator method) (PyMCIterator method) (SequentialMonteCarloIterator method) eval_log_prior_grad() (MetropolisHastingsPyMCIterator method) (PyMCIterator method) eval_model() (BMFIAIterator method) (OptimizationIterator method) eval_surrogate_accuracy() (SurrogateModel method) eval_surrogate_accuracy_cv() (SurrogateModel method) evaluate() (BMFGaussianModel method) (BmfiaInterface method) (BmfmcInterface method) (BMFMCModel method) (DaskScheduler method) (DifferentiableSimulationModelFD method) (GaussianLikelihood method) (LikelihoodModel method) (LogpdfGPModel method) (Model method) (PoolScheduler method) (Scheduler method) (SimulationModel method) (StatisticsSecondOrderEstimates method) (StatisticsSobolIndexEstimates method) (StatisticsThirdOrderSobolIndexEstimates method) (SurrogateModel method)

evaluate_and_gradient() (BmfiaInterface method) (Model method) (RPVIIterator method) evaluate_and_gradient_bool (Model attribute) evaluate_and_gradient_method (BmfiaInterface attribute) evaluate_and_gradient_per_coordinate() (BmfiaInterface static method) evaluate_and_gradient_per_time_step() (BmfiaInterface static method) evaluate_fd_positions() (OptimizationIterator method) evaluate_finite_differences() (DifferentiableSimulationModelFD method) evaluate_from_output() (BMFGaussianModel method) evaluate_HF_model_for_X_train() (BMFIAIterator method) evaluate_LF_model_for_X_train() (BMFIAIterator method) evaluate_mean_and_std() (LogpdfGPModel static method) evaluate_method (BmfiaInterface attribute) evaluate_mf_likelihood() (BMFGaussianModel method) evaluate_per_coordinate() (BmfiaInterface static method) evaluate_per_time_step() (BmfiaInterface static method) evaluate_statistics() (SobolIndexGPUncertaintyIterator method) example_simulator_function_by_name() (in module queens.example_simulator_functions) expand_random_field_realization() (Parameters method) expand_training_data() (BMFIAIterator method) expanded_representation() (FourierRandomField method) (KarhunenLoeveRandomField method) (PieceWiseRandomField method) (RandomField method) expectation_cv (ControlVariatesIterator attribute) expected_filter_by_range (DataProcessorCsv attribute) expected_filter_by_row_index (DataProcessorCsv attribute) expected_filter_by_target_values (DataProcessorCsv attribute) expected_filter_entire_file (DataProcessorCsv attribute) experiment_dir (JobOptions attribute) (Scheduler attribute) experiment_directory() (in module queens.utils.config_directories) experiment_name (GlobalSettings attribute) (JobOptions attribute) (Scheduler attribute) experimental_data (DataProcessorEnsight attribute) experimental_ref_data_lst (DataProcessorEnsightInterfaceDiscrepancy attribute) ExperimentalDataReader (class in queens.utils.experimental_data_reader) experiments_base_directory() (in module queens.utils.config_directories) explained_variance (KarhunenLoeveRandomField attribute) ExponentialAveraging (class in queens.utils.iterative_averaging_utils) ExponentialDistribution (class in queens.distributions.exponential) export() (SimulationMetadata method) export_dict() (Distribution method) (FullRankNormalVariational method) (JointVariational method) (MeanFieldNormalVariational method) (MixtureDistribution method) (MixtureModelVariational method) (ParticleVariational method) (VariationalDistribution method) extern_imports (QueensPythonCode attribute) external_geometry (DataProcessorEnsight attribute) ExternalGeometry (class in queens.external_geometry.external_geometry) extract_block_diag() (in module queens.utils.gpf_utils) extract_parameters_of_parameter_distributions() (in module queens.iterators.sobol_index_iterator)

F

f_mean_train (BMFMCModel attribute) fd_jacobian() (in module queens.utils.fd_jacobian) features_config (BMFIAIterator attribute) (BMFMCModel attribute) feynman_kac_model (SequentialMonteCarloChopinIterator attribute) field_dimension (FourierRandomField attribute) field_name (DataProcessorPvd attribute) fig_convergence_plots (VIVisualization attribute) figures (SAVisualization attribute) (SurrogateVisualization attribute) file_name (ExperimentalDataReader attribute) file_name_identifier (DataProcessor attribute) file_options_dict (DataProcessor attribute) file_path (SimulationMetadata attribute) files_to_be_deleted_regex_lst (DataProcessor attribute) files_to_copy (Driver attribute) FileTypeError filter() (LogFilter method) filter_and_manipulate_raw_data() (DataProcessor method) (DataProcessorCsv method) (DataProcessorEnsight method) (DataProcessorEnsightInterfaceDiscrepancy method) (DataProcessorNumpy method) (DataProcessorPvd method) (DataProcessorTxt method) filter_range (DataProcessorCsv attribute) filter_target_values (DataProcessorCsv attribute) filter_tol (DataProcessorCsv attribute) filter_type (DataProcessorCsv attribute) fim_dampening_bool (VariationalInferenceIterator attribute) fim_dampening_coefficient (VariationalInferenceIterator attribute) fim_dampening_lower_bound (VariationalInferenceIterator attribute) fim_decay_start_iter (VariationalInferenceIterator attribute) finish_and_clean() (ExternalGeometry method) (FourcDatExternalGeometry method) finite_difference_method (DifferentiableSimulationModelFD attribute) first_effect_variance() (in module queens.example_simulator_functions.ishigami90) (in module queens.example_simulator_functions.sobol_g_function) first_order_estimator (SobolIndexEstimator attribute) first_order_indices() (in module queens.example_simulator_functions.ishigami90) (in module queens.example_simulator_functions.sobol_g_function) fisher_information_matrix() (FullRankNormalVariational method) (JointVariational method) (MeanFieldNormalVariational method) (MixtureModelVariational method) (ParticleVariational method) (VariationalDistribution method)

fit() (IdentityScaler method) (Scaler method) (StandardScaler method) format() (NewLineFormatter method) forward_model (LikelihoodModel attribute) FourcDatExternalGeometry (class in queens.external_geometry.fourc_dat_geometry) FourcDriver (class in queens.drivers.fourc_driver) FourierRandomField (class in queens.parameters.fields.fourier_field) FreeVariable (class in queens.distributions.free) from_config_create() (BMFIAVisualization class method) (BMFMCVisualization class method) (ClassificationVisualization class method) (GridIteratorVisualization class method) (Predictor class method) (Sampler class method) (SAVisualization class method) (SobolIndexEstimator class method) (SobolIndexEstimatorThirdOrder class method) (StatisticsSobolIndexEstimates class method) (StatisticsThirdOrderSobolIndexEstimates class method) (SurrogateVisualization class method) (ThirdOrderSampler class method) (VIVisualization class method) from_config_create_distribution() (MixtureDistribution class method) from_config_create_fields_code() (in module queens.utils.input_to_script) from_config_create_iterator() (in module queens.utils.fcc_utils) from_config_create_object() (in module queens.utils.fcc_utils) from_config_create_parameters() (in module queens.parameters.parameters) (in module queens.utils.input_to_script) from_config_create_pymc_distribution() (in module queens.utils.pymc) from_config_create_pymc_distribution_dict() (in module queens.utils.pymc) from_config_create_script() (in module queens.utils.input_to_script) from_estimator() (ConditionalDecisionBoundaryDisplay class method) FullRankNormalVariational (class in queens.variational_distributions.full_rank_normal) function (FunctionDriver attribute) function_requires_job_id (FunctionDriver attribute) function_wrapper() (FunctionDriver static method) FunctionDriver (class in queens.drivers.function_driver)

G

gamma (MetropolisHastingsIterator attribute) gamma_cur (SequentialMonteCarloIterator attribute) gammas (SequentialMonteCarloIterator attribute) gammas_ext_mc (BMFMCModel attribute) gammas_ext_train (BMFMCModel attribute) gardner14a() (in module queens.example_simulator_functions.gardner14a) gather_metadata_and_write_to_csv() (in module queens.utils.cli_utils) gaussian_1d_logpdf() (in module queens.example_simulator_functions.gaussian_logpdf) gaussian_2d_logpdf() (in module queens.example_simulator_functions.gaussian_logpdf) gaussian_4d_logpdf() (in module queens.example_simulator_functions.gaussian_logpdf) gaussian_mixture_4d_logpdf() (in module queens.example_simulator_functions.gaussian_mixture_logpdf) GaussianBayesianNeuralNetworkModel (class in queens.models.surrogate_models.bayesian_neural_network) GaussianLikelihood (class in queens.models.likelihood_models.gaussian_likelihood) GaussianNeuralNetworkModel (class in queens.models.surrogate_models.gaussian_neural_network) generate_code() (QueensPythonCode method) generate_output_cfbgp() (LogpdfGPModel static method) generate_output_cgpmap_2() (LogpdfGPModel static method) generate_output_gpmap_1() (LogpdfGPModel static method) generate_script() (QueensPythonCode method) geometric_set_data (DataProcessorEnsight attribute) geometric_target (DataProcessorEnsight attribute) get_all_samples() (SobolIndexIterator method) get_check_array_dimension_and_reshape() (MeanFieldNormalDistribution static method) get_cli_options() (in module queens.utils.cli_utils) get_coordinates_of_desired_geometric_sets() (FourcDatExternalGeometry method) get_current_dat_section() (FourcDatExternalGeometry method) get_data_from_file() (DataProcessor method) get_design_method() (BMFIAIterator class method) (BMFMCIterator method) get_desired_dat_sections() (FourcDatExternalGeometry method) get_dim() (DimensionMethods1D static method) (DimensionMethods2D static method) (DimensionMethods3D static method) get_dimension_hyperparameters() (GPFlowRegressionModel method) get_elements_belonging_to_desired_material() (FourcDatExternalGeometry method) get_experimental_data() (ExperimentalDataReader method) get_free_local_port() (RemoteConnection method) get_free_remote_port() (RemoteConnection method) get_gradient_function() (VariationalInferenceIterator method) get_hf_training_data() (BMFMCModel method) get_importance_sampling_weights() (BBVIIterator method) get_job_ids() (Scheduler method) get_log_posterior_unnormalized() (BBVIIterator method) get_log_prior() (BBVIIterator method) get_materials() (FourcDatExternalGeometry method) get_metadata_from_experiment_dir() (in module queens.utils.metadata) get_module_attribute() (in module queens.utils.import_utils) get_module_class() (in module queens.utils.import_utils) (in module queens.utils.input_to_script) get_nodes_of_interest() (FourcDatExternalGeometry method) get_only_desired_coordinates() (FourcDatExternalGeometry method) get_only_desired_topology() (FourcDatExternalGeometry method) get_option() (in module queens.utils.valid_options_utils) get_particles_and_weights() (AdaptiveSamplingIterator method) get_plotter() (GridIteratorVisualization method) get_port() (in module queens.utils.remote_operations) get_positions() (in module queens.utils.fd_jacobian) get_positions_raw_2pointperturb() (LMIterator method) get_random_fields_and_truncated_basis() (BMFMCModel method) get_raw_data_from_file() (DataProcessor method) (DataProcessorCsv method) (DataProcessorEnsight method) (DataProcessorEnsightInterfaceDiscrepancy method) (DataProcessorNumpy method) (DataProcessorPvd method) (DataProcessorTxt method) get_read_in_jobscript_template() (JobscriptDriver static method) get_state() (GPJittedModel method) get_str_table() (in module queens.utils.print_utils) get_topology() (FourcDatExternalGeometry method) git_hash (GlobalSettings attribute)

global_settings (Iterator attribute) (QueensPythonCode attribute) global_settings_context (QueensPythonCode attribute) GlobalSettings (class in queens.global_settings) gnuplot_gp_convergence() (in module queens.visualization.gnuplot_vis) gp_model (Predictor attribute) GPFlowRegressionModel (class in queens.models.surrogate_models.gp_approximation_gpflow) GPflowSVGPModel (class in queens.models.surrogate_models.gp_approximation_gpflow_svgp) GPJittedModel (class in queens.models.surrogate_models.gp_approximation_jitted) grad() (BMFGaussianModel method) (BMFMCModel method) (DifferentiableSimulationModelAdjoint method) (DifferentiableSimulationModelFD method) (GaussianBayesianNeuralNetworkModel method) (GaussianLikelihood method) (GaussianNeuralNetworkModel method) (GPFlowRegressionModel method) (GPflowSVGPModel method) (GPJittedModel method) (HeteroskedasticGPModel method) (LikelihoodModel method) (LogpdfGPModel method) (Model method) (PymcDistributionWrapper method) (SimulationModel method) (SurrogateModel method) grad_joint_logpdf() (Parameters method) grad_log_evidence_matern_3_2() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) grad_log_evidence_squared_exponential() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) grad_log_evidence_value (GPJittedModel attribute) grad_log_pdf_d_ylf() (BMFGaussianModel method) grad_logpdf() (BetaDistribution method) (ContinuousDistribution method) (ExponentialDistribution method) (FourierRandomField method) (FreeVariable method) (KarhunenLoeveRandomField method) (LogNormalDistribution method) (MeanFieldNormalDistribution method) (MixtureDistribution method) (NormalDistribution method) (PieceWiseRandomField method) (RandomField method) (UniformDistribution method) grad_logpdf_var() (MeanFieldNormalDistribution method) grad_params_log_variational_mat (BBVIIterator attribute) grad_params_logpdf() (FullRankNormalVariational method) (JointVariational method) (MeanFieldNormalVariational method) (MixtureModelVariational method) (ParticleVariational method) (VariationalDistribution method) grad_params_reparameterization() (FullRankNormalVariational method) (MeanFieldNormalVariational method) grad_posterior_mean_matern_3_2() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) grad_posterior_mean_squared_exponential() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) grad_posterior_var_matern_3_2() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) grad_posterior_var_squared_exponential() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) grad_sample_logpdf() (FullRankNormalVariational method) (MeanFieldNormalVariational method) gradient (StochasticOptimizer attribute) gradient_data_processor (JobscriptDriver attribute) gradient_driver (DifferentiableSimulationModelAdjoint attribute) gradient_func (PymcGradientWrapper attribute) gradient_identity_multi_fidelity_mean_fun() (GPJittedModel static method) gradient_mean_function (GaussianNeuralNetworkModel attribute) (GPJittedModel attribute) gradient_sinus_test_fun() (in module queens.example_simulator_functions.sinus) gradient_zero_mean_fun() (GPJittedModel static method) grid_dict (GridIterator attribute) GridIterator (class in queens.iterators.grid_iterator) GridIteratorVisualization (class in queens.visualization.grid_iterator_visualization)

H

handle_gradient_nan() (VariationalInferenceIterator method) havebounds (LMIterator attribute) header_row (DataProcessorCsv attribute) HeteroskedasticGPModel (class in queens.models.surrogate_models.gp_heteroskedastic_gpflow) hf_data_iterator (BMFMCModel attribute) hf_model (BMFIAIterator attribute) high_fidelity_model (BMFMCModel attribute)

hmc_burn_in (LogpdfGPModel attribute) hmc_steps (LogpdfGPModel attribute) HMCIterator (class in queens.iterators.hmc_iterator) hyper_params (GPJittedModel attribute) hyperparameter_log_likelihood() (LogpdfGPModel static method) hyperparameter_log_prior() (LogpdfGPModel static method) hyperparameter_log_prob() (LogpdfGPModel static method) hyperparameters (LogpdfGPModel attribute)

I

identity_multi_fidelity_mean_fun() (GPJittedModel static method) IdentityScaler (class in queens.utils.random_process_scaler) imports (QueensPythonCode attribute) index_column (DataProcessorCsv attribute) index_estimator (SobolIndexGPUncertaintyIterator attribute) init_distribution_wrapper() (MetropolisHastingsPyMCIterator method) (PyMCIterator method) init_mcmc_method() (HMCIterator method) (MetropolisHastingsPyMCIterator method) (NUTSIterator method) (PyMCIterator method) init_reg (LMIterator attribute) init_scaler() (in module queens.utils.gpf_utils) init_strategy (HMCIterator attribute) (NUTSIterator attribute) initial_design (BMFMCIterator attribute) initial_guess (LMIterator attribute) (OptimizationIterator attribute) initial_train_iterator (AdaptiveSamplingIterator attribute) initialize() (LogpdfGPModel method) initialize_bmfia_iterator() (BMFGaussianModel static method) initialize_feynman_kac() (SequentialMonteCarloChopinIterator method) initialize_variational_parameters() (FullRankNormalVariational method) (JointVariational method) (MeanFieldNormalVariational method) (MixtureModelVariational method) (ParticleVariational method) (VariationalDistribution method) initvals (PyMCIterator attribute) inject() (in module queens.utils.injector) inject_in_template() (in module queens.utils.injector) inject_template_cli() (in module queens.utils.cli_utils) input_dim_red() (BMFMCModel method) input_files (JobOptions attribute) input_templates (JobscriptDriver attribute) input_to_script_cli() (in module queens.utils.cli_utils) inputs (SimulationMetadata attribute)

insert_new_obj() (in module queens.utils.fcc_utils) (in module queens.utils.input_to_script) instantiate_per_coordinate() (BmfiaInterface static method) instantiate_per_time_step() (BmfiaInterface static method) instantiate_probabilistic_mappings (BmfiaInterface attribute) interface (BMFMCModel attribute) InvalidOptionError inverse_cdf_transform() (Parameters method) inverse_transform_grad_mean() (IdentityScaler method) (StandardScaler method) inverse_transform_grad_var() (IdentityScaler method) (StandardScaler method) inverse_transform_mean() (IdentityScaler method) (Scaler method) (StandardScaler method) inverse_transform_std() (IdentityScaler method) (Scaler method) (StandardScaler method) is_active (ActiveLearningClassifier attribute) (Classifier attribute) is_cov (HMCIterator attribute) (NUTSIterator attribute) is_empty() (in module queens.utils.path_utils) is_trained (SurrogateModel attribute) ishigami90() (in module queens.example_simulator_functions.ishigami90) items() (CollectionObject method) iter_opt (LMIterator attribute) iterate_over_time_steps() (BmfiaInterface static method) iteration (LogLinearLearningRateDecay attribute) (StepwiseLearningRateDecay attribute) (StochasticOptimizer attribute) iteration_counter (PolyakAveraging attribute) iteration_data (VariationalInferenceIterator attribute) IterativeAveraging (class in queens.utils.iterative_averaging_utils) Iterator (class in queens.iterators.iterator) itypes (PymcDistributionWrapper attribute) (PymcGradientWrapper attribute)

J

jac_abs_step (LMIterator attribute) jac_method (OptimizationIterator attribute) jac_rel_step (LMIterator attribute) (OptimizationIterator attribute) jacobian() (OptimizationIterator method) jacobian_and_residual() (LMIterator method) jit_func_generate_output (LogpdfGPModel attribute) jitter (LogpdfGPModel attribute) job_dir (JobOptions attribute)

job_dirs_in_experiment_dir() (in module queens.utils.config_directories) job_id (JobOptions attribute) (SimulationMetadata attribute) JobOptions (class in queens.drivers.jobscript_driver) jobscript_file_name (JobscriptDriver attribute) jobscript_options (JobscriptDriver attribute) jobscript_template (JobscriptDriver attribute) JobscriptDriver (class in queens.drivers.jobscript_driver) joint_logpdf() (Parameters method) JointVariational (class in queens.variational_distributions.joint)

K

k (DynamicLearningRateDecay attribute) k_mat (GPJittedModel attribute) k_mat_inv (GPJittedModel attribute) k_min (DynamicLearningRateDecay attribute)

KarhunenLoeveRandomField (class in queens.parameters.fields.kl_field) kernel_initializer (GaussianNeuralNetworkModel attribute) kernel_type (GPJittedModel attribute) keys() (CollectionObject method)

L

l1_norm() (in module queens.utils.iterative_averaging_utils) l2_norm() (in module queens.utils.iterative_averaging_utils) latent_1d_distribution (PieceWiseRandomField attribute) latent_grad() (Parameters method) latent_gradient() (FourierRandomField method) (KarhunenLoeveRandomField method) (PieceWiseRandomField method) (RandomField method) latent_index (FourierRandomField attribute) LazyLoader (class in queens.utils.import_utils) learning_rate (StochasticOptimizer attribute) learning_rate_decay (StochasticOptimizer attribute) LearningRateDecay (class in queens.stochastic_optimizers.learning_rate_decay) level (LogFilter attribute) lf_data_iterators (BMFMCModel attribute) lf_model (BMFIAIterator attribute) LHSIterator (class in queens.iterators.lhs_iterator) likelihood_counter (BMFGaussianModel attribute) likelihood_evals_for_refinement (BMFGaussianModel attribute) likelihood_model (AdaptiveSamplingIterator attribute) (StaticStateSpaceModel attribute) LikelihoodModel (class in queens.models.likelihood_models.likelihood_model) line_topology (FourcDatExternalGeometry attribute) linear_scale_a_to_b() (in module queens.models.bmfmc_model) list_associated_material_numbers (FourcDatExternalGeometry attribute) list_geometric_sets (FourcDatExternalGeometry attribute) list_replace_infs() (in module queens.utils.input_to_script) LMIterator (class in queens.iterators.lm_iterator) load() (Classifier method) load_input_file() (in module queens.utils.io_utils) load_pickle() (in module queens.utils.pickle_utils) load_result() (in module queens.utils.io_utils) load_results (QueensPythonCode attribute) load_sampling_data() (BMFMCModel method) local_optimization (ElementaryEffectsIterator attribute) LocalScheduler (class in queens.schedulers.local_scheduler) log_evidence() (GPJittedModel method) log_init_args() (in module queens.utils.logger_settings) log_like (PyMCIterator attribute) log_likelihood (MetropolisHastingsIterator attribute) (SequentialMonteCarloIterator attribute) log_posterior (MetropolisHastingsIterator attribute) (SequentialMonteCarloIterator attribute) log_posterior_unnormalized (BBVIIterator attribute) log_posterior_unnormalized_list (BBVIIterator attribute) log_prior (MetropolisHastingsIterator attribute) (PyMCIterator attribute) (SequentialMonteCarloIterator attribute)

log_variational_mat (BBVIIterator attribute) LogFilter (class in queens.utils.logger_settings) loglik() (StaticStateSpaceModel method) LogLinearLearningRateDecay (class in queens.stochastic_optimizers.learning_rate_decay) LogNormalDistribution (class in queens.distributions.lognormal) logpdf (PymcDistributionWrapper attribute) logpdf() (BetaDistribution method) (CategoricalDistribution method) (ContinuousDistribution method) (DiscreteDistribution method) (Distribution method) (ExponentialDistribution method) (FourierRandomField method) (FreeVariable method) (FullRankNormalVariational method) (JointVariational method) (KarhunenLoeveRandomField method) (LogNormalDistribution method) (MeanFieldNormalDistribution method) (MeanFieldNormalVariational method) (MixtureDistribution method) (MixtureModelVariational method) (MultinomialDistribution method) (NormalDistribution method) (ParticleDiscreteDistribution method) (ParticlesChopinDistribution method) (ParticleVariational method) (PieceWiseRandomField method) (RandomField method) (UniformDistribution method) (VariationalDistribution method) logpdf_const (ExponentialDistribution attribute) (NormalDistribution attribute) (UniformDistribution attribute) logpdf_grad (PymcDistributionWrapper attribute) logpdf_gradients (PymcDistributionWrapper attribute) LogpdfGPModel (class in queens.models.logpdf_gp_model) logpyt() (StaticStateSpaceModel method) loo_cv_bool (BBVIIterator attribute) loss_plot_path (GaussianNeuralNetworkModel attribute) low_chol (NormalDistribution attribute) lower_bound (BetaDistribution attribute) (UniformDistribution attribute) lowesterror (LMIterator attribute)

M

m (Adam attribute) (Adamax attribute) m_f_mc (BMFMCModel attribute) ma09() (in module queens.example_simulator_functions.ma09) main() (in module queens.example_simulator_functions.executable_park91a_hifi_on_grid_with_gradients) (in module queens.main) main_run() (ExternalGeometry method) matern_3_2() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) max_feval (BBVIIterator attribute) (LMIterator attribute) (OptimizationIterator attribute) (SequentialMonteCarloChopinIterator attribute) (VariationalInferenceIterator attribute) max_iteration (StochasticOptimizer attribute) max_steps (HMCIterator attribute) max_treedepth (NUTSIterator attribute) mcmc_kernel (SequentialMonteCarloIterator attribute) mean (ContinuousDistribution attribute) (DiscreteDistribution attribute) (FourierRandomField attribute) (KarhunenLoeveRandomField attribute) (ParticleDiscreteDistribution attribute) (Scaler attribute) mean_field_variational_distribution() (GaussianBayesianNeuralNetworkModel static method) mean_function (GaussianNeuralNetworkModel attribute) (GPJittedModel attribute) MeanFieldNormalDistribution (class in queens.distributions.mean_field_normal) MeanFieldNormalVariational (class in queens.variational_distributions.mean_field_normal) memory (BBVIIterator attribute) MetropolisHastingsIterator (class in queens.iterators.metropolis_hastings_iterator) MetropolisHastingsPyMCIterator (class in queens.iterators.metropolis_hastings_pymc_iterator) mf_interface (BMFGaussianModel attribute) mf_subiterator (BMFGaussianModel attribute) mh_select() (in module queens.utils.mcmc_utils) mini_batch_size (GPflowSVGPModel attribute) minimize() (in module queens.utils.jax_minimize_wrapper) MixtureDistribution (class in queens.distributions.mixture) MixtureModelVariational (class in queens.variational_distributions.mixture_model) MLMCIterator (class in queens.iterators.mlmc_iterator) model (BMFMCIterator attribute) Model (class in queens.models.model) model (ControlVariatesIterator attribute) (GPFlowRegressionModel attribute) (GPflowSVGPModel attribute) (HeteroskedasticGPModel attribute) (Iterator attribute) model_eval_iteration_period (BBVIIterator attribute) model_fwd_evals (PyMCIterator attribute) model_grad_evals (PyMCIterator attribute) model_outputs (AdaptiveSamplingIterator attribute) model_realizations_lst (GaussianBayesianNeuralNetworkModel attribute) models (MLMCIterator attribute) module queens queens.data_processor queens.data_processor.data_processor queens.data_processor.data_processor_csv queens.data_processor.data_processor_ensight queens.data_processor.data_processor_ensight_interface queens.data_processor.data_processor_numpy queens.data_processor.data_processor_pvd queens.data_processor.data_processor_txt queens.distributions queens.distributions.bernoulli queens.distributions.beta queens.distributions.categorical queens.distributions.distributions queens.distributions.exponential queens.distributions.free queens.distributions.lognormal queens.distributions.mean_field_normal queens.distributions.mixture queens.distributions.multinomial queens.distributions.normal queens.distributions.particles queens.distributions.uniform queens.distributions.uniform_discrete queens.drivers queens.drivers.driver queens.drivers.fourc_driver queens.drivers.function_driver queens.drivers.jobscript_driver queens.drivers.mpi_driver queens.example_simulator_functions queens.example_simulator_functions.agawal09 queens.example_simulator_functions.borehole83 queens.example_simulator_functions.branin78 queens.example_simulator_functions.currin88 queens.example_simulator_functions.executable_park91a_hifi_on_grid_with_gradients queens.example_simulator_functions.gardner14a queens.example_simulator_functions.gaussian_logpdf queens.example_simulator_functions.gaussian_mixture_logpdf queens.example_simulator_functions.ishigami90 queens.example_simulator_functions.ma09 queens.example_simulator_functions.oakley_ohagan04 queens.example_simulator_functions.parabola_residual queens.example_simulator_functions.paraboloid queens.example_simulator_functions.park91a queens.example_simulator_functions.park91b queens.example_simulator_functions.perdikaris17 queens.example_simulator_functions.rezende15 queens.example_simulator_functions.rosenbrock60 queens.example_simulator_functions.sinus queens.example_simulator_functions.sobol_g_function queens.external_geometry queens.external_geometry.external_geometry queens.external_geometry.fourc_dat_geometry queens.global_settings queens.iterators queens.iterators.adaptive_sampling_iterator queens.iterators.black_box_variational_bayes queens.iterators.bmfia_iterator queens.iterators.bmfmc_iterator queens.iterators.classification queens.iterators.control_variates_iterator queens.iterators.data_iterator queens.iterators.elementary_effects_iterator queens.iterators.grid_iterator queens.iterators.hmc_iterator queens.iterators.iterator queens.iterators.lhs_iterator queens.iterators.lm_iterator queens.iterators.metropolis_hastings_iterator queens.iterators.metropolis_hastings_pymc_iterator queens.iterators.mlmc_iterator queens.iterators.monte_carlo_iterator queens.iterators.nuts_iterator queens.iterators.optimization_iterator queens.iterators.points_iterator queens.iterators.polynomial_chaos_iterator queens.iterators.pymc_iterator queens.iterators.reparameteriztion_based_variational_inference queens.iterators.sequential_monte_carlo_chopin queens.iterators.sequential_monte_carlo_iterator queens.iterators.sobol_index_gp_uncertainty queens.iterators.sobol_index_gp_uncertainty.estimator queens.iterators.sobol_index_gp_uncertainty.predictor queens.iterators.sobol_index_gp_uncertainty.sampler queens.iterators.sobol_index_gp_uncertainty.statistics queens.iterators.sobol_index_gp_uncertainty.utils_estimate_indices queens.iterators.sobol_index_gp_uncertainty_iterator queens.iterators.sobol_index_iterator queens.iterators.sobol_sequence_iterator queens.iterators.variational_inference queens.main queens.models queens.models.bmfmc_model queens.models.differentiable_simulation_model_adjoint queens.models.differentiable_simulation_model_fd queens.models.likelihood_models queens.models.likelihood_models.bayesian_mf_gaussian_likelihood queens.models.likelihood_models.gaussian_likelihood queens.models.likelihood_models.likelihood_model queens.models.logpdf_gp_model queens.models.model queens.models.simulation_model queens.models.surrogate_models queens.models.surrogate_models.bayesian_neural_network queens.models.surrogate_models.gaussian_neural_network queens.models.surrogate_models.gp_approximation_gpflow queens.models.surrogate_models.gp_approximation_gpflow_svgp queens.models.surrogate_models.gp_approximation_jitted queens.models.surrogate_models.gp_heteroskedastic_gpflow queens.models.surrogate_models.surrogate_model queens.models.surrogate_models.utils queens.models.surrogate_models.utils.kernel_utils_jitted queens.parameters queens.parameters.fields queens.parameters.fields.fourier_field queens.parameters.fields.kl_field queens.parameters.fields.piece_wise_field queens.parameters.fields.random_fields queens.parameters.parameters queens.schedulers queens.schedulers.cluster_scheduler queens.schedulers.dask_scheduler queens.schedulers.local_scheduler queens.schedulers.pool_scheduler queens.schedulers.scheduler queens.stochastic_optimizers queens.stochastic_optimizers.adam queens.stochastic_optimizers.adamax queens.stochastic_optimizers.learning_rate_decay queens.stochastic_optimizers.rms_prop queens.stochastic_optimizers.sgd queens.stochastic_optimizers.stochastic_optimizer queens.utils queens.utils.ascii_art queens.utils.classifier queens.utils.cli_utils queens.utils.collection_utils queens.utils.config_directories queens.utils.exceptions queens.utils.experimental_data_reader queens.utils.fcc_utils queens.utils.fd_jacobian queens.utils.gpf_utils queens.utils.import_utils queens.utils.injector queens.utils.input_to_script queens.utils.io_utils queens.utils.iterative_averaging_utils queens.utils.jax_minimize_wrapper queens.utils.logger_settings queens.utils.mcmc_utils queens.utils.metadata queens.utils.numpy_utils queens.utils.path_utils queens.utils.pdf_estimation queens.utils.pickle_utils queens.utils.plot_outputs queens.utils.pool_utils queens.utils.print_utils queens.utils.process_outputs queens.utils.pymc queens.utils.random_process_scaler queens.utils.remote_build queens.utils.remote_operations queens.utils.rsync queens.utils.run_subprocess queens.utils.smc_utils queens.utils.sobol_sequence queens.utils.start_dask_cluster queens.utils.tensorflow_utils queens.utils.valid_options_utils queens.variational_distributions queens.variational_distributions.full_rank_normal queens.variational_distributions.joint queens.variational_distributions.mean_field_normal queens.variational_distributions.mixture_model queens.variational_distributions.particle queens.variational_distributions.variational_distribution queens.visualization queens.visualization.bmfia_visualization queens.visualization.bmfmc_visualization queens.visualization.classification queens.visualization.gaussian_neural_network_vis queens.visualization.gnuplot_vis queens.visualization.grid_iterator_visualization queens.visualization.sa_visualization queens.visualization.surrogate_visualization queens.visualization.variational_inference_visualization

MonteCarloIterator (class in queens.iterators.monte_carlo_iterator) MovingAveraging (class in queens.utils.iterative_averaging_utils) MpiDriver (class in queens.drivers.mpi_driver) MultinomialDistribution (class in queens.distributions.multinomial)

N

n_components (MixtureModelVariational attribute) n_parameters (FullRankNormalVariational attribute) (JointVariational attribute) (MeanFieldNormalVariational attribute) (MixtureModelVariational attribute) n_params (ActiveLearningClassifier attribute) (Classifier attribute) n_samples_per_iter (VariationalInferenceIterator attribute) n_sims (SequentialMonteCarloChopinIterator attribute) (StaticStateSpaceModel attribute) (VariationalInferenceIterator attribute) names (Parameters attribute) nan_in_gradient_counter (VariationalInferenceIterator attribute) natural_gradient_bool (VariationalInferenceIterator attribute) negative_log_likelihood() (GaussianBayesianNeuralNetworkModel static method) (GaussianNeuralNetworkModel static method) new_material_numbers (FourcDatExternalGeometry attribute) new_nodes_lst (FourcDatExternalGeometry attribute) new_value (IterativeAveraging attribute) NewLineFormatter (class in queens.utils.logger_settings) next_job_id (Scheduler attribute) nn_model (GaussianNeuralNetworkModel attribute) no_features_comparison_bool (BMFMCModel attribute) no_features_ref (BMFMCVisualization attribute) node_coordinates (FourcDatExternalGeometry attribute) node_topology (FourcDatExternalGeometry attribute) nodes_of_interest (FourcDatExternalGeometry attribute) nodes_per_hidden_layer (GaussianNeuralNetworkModel attribute) nodes_per_hidden_layer_lst (GaussianBayesianNeuralNetworkModel attribute) nodes_written (FourcDatExternalGeometry attribute) noise_type (GaussianLikelihood attribute) noise_var (BMFGaussianModel attribute) noise_var_iterative_averaging (GaussianLikelihood attribute) noise_variance_lower_bound (GPJittedModel attribute) normal_distribution (BMFGaussianModel attribute) (GaussianLikelihood attribute) (LogNormalDistribution attribute), [1] NormalDistribution (class in queens.distributions.normal) nugget_noise_variance (GaussianLikelihood attribute) nugget_std (GaussianNeuralNetworkModel attribute) nugget_variance (KarhunenLoeveRandomField attribute) num_bootstrap_samples (ElementaryEffectsIterator attribute) (MLMCIterator attribute) (SobolIndexIterator attribute) num_burn_in (MetropolisHastingsIterator attribute) (PyMCIterator attribute) num_chains (MetropolisHastingsIterator attribute) (PyMCIterator attribute) num_collocation_points (PolynomialChaosIterator attribute) num_dim (LogpdfGPModel attribute) num_epochs (GaussianBayesianNeuralNetworkModel attribute) (GaussianNeuralNetworkModel attribute) (HeteroskedasticGPModel attribute) num_features (BMFIAIterator attribute) (BMFMCModel attribute) num_grid_points_per_axis (GridIterator attribute) num_hyper (LogpdfGPModel attribute) num_inducing_points (GPflowSVGPModel attribute) (HeteroskedasticGPModel attribute)

num_iter_for_avg (MovingAveraging attribute) num_iterations (LHSIterator attribute) num_jobs (Scheduler attribute) num_levels (ElementaryEffectsIterator attribute) num_model_calls (ClassificationIterator attribute) num_new_samples (AdaptiveSamplingIterator attribute) num_optimal_trajectories (ElementaryEffectsIterator attribute) num_optimizations (LogpdfGPModel attribute) num_parameters (GridIterator attribute) (Parameters attribute) (VariationalInferenceIterator attribute) num_params (SobolIndexIterator attribute) num_particles (SequentialMonteCarloChopinIterator attribute) (SequentialMonteCarloIterator attribute) num_posterior_samples (GaussianBayesianNeuralNetworkModel attribute) (HeteroskedasticGPModel attribute) num_processors_multi_processing (BmfiaInterface attribute) num_procs (DaskScheduler attribute) (JobOptions attribute) (SobolIndexGPUncertaintyIterator attribute) num_refinement_samples (BMFGaussianModel attribute) num_refinements (GaussianNeuralNetworkModel attribute) num_rejuvenation_steps (SequentialMonteCarloChopinIterator attribute) num_sample_points (ClassificationIterator attribute) num_samples (ControlVariatesIterator attribute) (LHSIterator attribute) (MetropolisHastingsIterator attribute) (MLMCIterator attribute) (MonteCarloIterator attribute) (PyMCIterator attribute) (SobolIndexIterator attribute) num_samples_cv (ControlVariatesIterator attribute) num_samples_statistics (GaussianBayesianNeuralNetworkModel attribute) num_samples_stats (HeteroskedasticGPModel attribute) num_steps (AdaptiveSamplingIterator attribute) num_trajectories (ElementaryEffectsIterator attribute) num_variables (SequentialMonteCarloChopinIterator attribute) (SequentialMonteCarloIterator attribute) number_bootstrap_samples (SobolIndexEstimator attribute) (StatisticsSobolIndexEstimates attribute) number_expansion_terms (FourierRandomField attribute) number_gp_realizations (Predictor attribute) (SobolIndexEstimator attribute) (StatisticsSobolIndexEstimates attribute) number_input_dimensions (GPFlowRegressionModel attribute) (GPflowSVGPModel attribute) number_monte_carlo_samples (Sampler attribute) (SobolIndexEstimator attribute) number_of_samples (SobolSequenceIterator attribute) number_parameters (Sampler attribute) (SobolIndexEstimator attribute) (StatisticsSobolIndexEstimates attribute) number_posterior_samples (GPFlowRegressionModel attribute) (GPflowSVGPModel attribute) number_restarts (GPFlowRegressionModel attribute) number_training_iterations (GPFlowRegressionModel attribute) (GPflowSVGPModel attribute) numpy_to_particles_array() (StaticStateSpaceModel method) NUTSIterator (class in queens.iterators.nuts_iterator)

O

oakley_ohagan04() (in module queens.example_simulator_functions.oakley_ohagan04) objective() (OptimizationIterator method) objective_and_jacobian (OptimizationIterator attribute) open() (RemoteConnection method) open_port_forwarding() (RemoteConnection method) OptimizationIterator (class in queens.iterators.optimization_iterator) optimize_hyper_params() (BmfiaInterface static method) optimize_hyperparameters() (LogpdfGPModel method) optimizer (HeteroskedasticGPModel attribute) optimizer_seed (GaussianBayesianNeuralNetworkModel attribute) (GaussianNeuralNetworkModel attribute) organize_sections() (ExternalGeometry method) (FourcDatExternalGeometry method) original_materials_in_dat (FourcDatExternalGeometry attribute) otypes (PymcDistributionWrapper attribute) (PymcGradientWrapper attribute)

output (BMFMCIterator attribute) (ControlVariatesIterator attribute) (DataIterator attribute) (ElementaryEffectsIterator attribute) (GridIterator attribute) (LHSIterator attribute) (MLMCIterator attribute) (MonteCarloIterator attribute) (PointsIterator attribute) (SobolIndexIterator attribute) (SobolSequenceIterator attribute) output_dir (GlobalSettings attribute) (JobOptions attribute) output_file (JobOptions attribute) output_label (BMFGaussianModel attribute) (ExperimentalDataReader attribute) outputs (SimulationMetadata attribute)

P

p_yhf_mc (BMFMCModel attribute) p_yhf_mean (BMFMCModel attribute) p_yhf_var (BMFMCModel attribute) p_ylf_mc (BMFMCModel attribute) parabola_residual() (in module queens.example_simulator_functions.parabola_residual) paraboloid() (in module queens.example_simulator_functions.paraboloid) param_current (LMIterator attribute) param_opt (LMIterator attribute) parameter_list (BBVIIterator attribute) parameter_names (Sampler attribute) (SobolIndexEstimator attribute) (SobolIndexIterator attribute) (StatisticsSobolIndexEstimates attribute) (SurrogateVisualization attribute) parameters (BMFMCModel attribute) Parameters (class in queens.parameters.parameters) parameters (Driver attribute) (Iterator attribute) (QueensPythonCode attribute) (Sampler attribute) parameters_keys (Parameters attribute) park91a_hifi() (in module queens.example_simulator_functions.park91a) park91a_hifi_coords() (in module queens.example_simulator_functions.executable_park91a_hifi_on_grid_with_gradients) park91a_hifi_on_grid() (in module queens.example_simulator_functions.park91a) park91a_hifi_on_grid_with_gradients() (in module queens.example_simulator_functions.park91a) park91a_lofi() (in module queens.example_simulator_functions.park91a) park91a_lofi_on_grid() (in module queens.example_simulator_functions.park91a) park91a_lofi_on_grid_with_gradients() (in module queens.example_simulator_functions.park91a) park91b_hifi() (in module queens.example_simulator_functions.park91b) park91b_lofi() (in module queens.example_simulator_functions.park91b) parse_arguments() (in module queens.utils.start_dask_cluster) partial_derivatives_hyper_params (GPJittedModel attribute) partial_grad_evaluate() (BMFGaussianModel method) partial_hyperparameter_log_prob (LogpdfGPModel attribute) ParticleDiscreteDistribution (class in queens.distributions.particles) particles (SequentialMonteCarloIterator attribute) particles_array_to_numpy() (StaticStateSpaceModel method) particles_obj (ParticleVariational attribute) ParticlesChopinDistribution (class in queens.iterators.sequential_monte_carlo_chopin) ParticleVariational (class in queens.variational_distributions.particle) path (VIVisualization attribute) path_length (HMCIterator attribute) path_to_dat_file (FourcDatExternalGeometry attribute) path_to_data (DataIterator attribute) path_to_preprocessed_dat_file (FourcDatExternalGeometry attribute) paths (BMFIAVisualization attribute) (BMFMCVisualization attribute) pdf() (BetaDistribution method) (CategoricalDistribution method) (ContinuousDistribution method) (DiscreteDistribution method) (Distribution method) (ExponentialDistribution method) (FreeVariable method) (FullRankNormalVariational method) (JointVariational method) (LogNormalDistribution method) (MeanFieldNormalDistribution method) (MeanFieldNormalVariational method) (MixtureDistribution method) (MixtureModelVariational method) (MultinomialDistribution method) (NormalDistribution method) (ParticleDiscreteDistribution method) (ParticlesChopinDistribution method) (ParticleVariational method) (UniformDistribution method) (VariationalDistribution method) pdf_const (ExponentialDistribution attribute) (UniformDistribution attribute) perdikaris17_hifi() (in module queens.example_simulator_functions.perdikaris17) perdikaris17_lofi() (in module queens.example_simulator_functions.perdikaris17) perform() (PymcDistributionWrapper method) (PymcGradientWrapper method) perform_kde() (in module queens.utils.process_outputs) PieceWiseRandomField (class in queens.parameters.fields.piece_wise_field) plot() (BMFIAVisualization method) (in module queens.visualization.gnuplot_vis) (SAVisualization method) (SurrogateVisualization method) plot_1d() (SurrogateVisualization method) plot_2d() (SurrogateVisualization method) plot_basename (ClassificationVisualization attribute) plot_bool (ClassificationVisualization attribute) plot_boolean (VIVisualization attribute) plot_booleans (BMFIAVisualization attribute) (BMFMCVisualization attribute) (GridIteratorVisualization attribute) plot_cdf() (in module queens.utils.plot_outputs) plot_convergence() (VIVisualization method) plot_decision_boundary() (ClassificationVisualization method) plot_feature_ranking() (BMFMCVisualization method) plot_gp_from_gpflow() (SurrogateVisualization method) plot_icdf() (in module queens.utils.plot_outputs) plot_loss() (in module queens.visualization.gaussian_neural_network_vis) plot_manifold() (BMFMCVisualization method) plot_model_dependency() (in module queens.visualization.bmfia_visualization) plot_one_d() (GridIteratorVisualization method) plot_pdf() (in module queens.utils.plot_outputs) plot_pdfs() (BMFMCVisualization method) plot_posterior_from_samples() (BMFIAVisualization method) plot_qoi_grid() (GridIteratorVisualization method) plot_refresh_rate (GPJittedModel attribute) plot_results() (SobolIndexIterator method) plot_si_bar() (SAVisualization method) plot_si_scatter() (SAVisualization method) plot_trace_every (SequentialMonteCarloIterator attribute) plot_two_d() (GridIteratorVisualization method) points (PointsIterator attribute) points_array (PointsIterator attribute) PointsIterator (class in queens.iterators.points_iterator) PolyakAveraging (class in queens.utils.iterative_averaging_utils) polynomial_chaos_approach (PolynomialChaosIterator attribute) polynomial_order (PolynomialChaosIterator attribute) PolynomialChaosIterator (class in queens.iterators.polynomial_chaos_iterator) pool (PoolScheduler attribute) PoolScheduler (class in queens.schedulers.pool_scheduler) post_run() (AdaptiveSamplingIterator method) (BMFMCIterator method) (ClassificationIterator method) (ControlVariatesIterator method) (DataIterator method) (ElementaryEffectsIterator method) (GridIterator method) (Iterator method) (LHSIterator method) (LMIterator method) (MetropolisHastingsIterator method) (MetropolisHastingsPyMCIterator method) (MLMCIterator method) (MonteCarloIterator method) (OptimizationIterator method) (PointsIterator method) (PolynomialChaosIterator method) (PyMCIterator method) (SequentialMonteCarloChopinIterator method) (SequentialMonteCarloIterator method) (SobolIndexGPUncertaintyIterator method) (SobolIndexIterator method) (SobolSequenceIterator method) (VariationalInferenceIterator method)

posterior_cov_mat_y (HeteroskedasticGPModel attribute) posterior_mean_matern_3_2() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) posterior_mean_squared_exponential() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) posterior_var_matern_3_2() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) posterior_var_squared_exponential() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) ppf() (BetaDistribution method) (ContinuousDistribution method) (DiscreteDistribution method) (ExponentialDistribution method) (FreeVariable method) (LogNormalDistribution method) (MeanFieldNormalDistribution method) (MixtureDistribution method) (MultinomialDistribution method) (NormalDistribution method) (ParticleDiscreteDistribution method) (ParticlesChopinDistribution method) (UniformDistribution method) pre_run() (AdaptiveSamplingIterator method) (ControlVariatesIterator method) (ElementaryEffectsIterator method) (GridIterator method) (Iterator method) (LHSIterator method) (LMIterator method) (MetropolisHastingsIterator method) (MLMCIterator method) (MonteCarloIterator method) (OptimizationIterator method) (PointsIterator method) (PolynomialChaosIterator method) (PyMCIterator method) (SequentialMonteCarloChopinIterator method) (SequentialMonteCarloIterator method) (SobolIndexGPUncertaintyIterator method) (SobolIndexIterator method) (SobolSequenceIterator method) (VariationalInferenceIterator method) precalculated_positions (OptimizationIterator attribute) precision (NormalDistribution attribute) precoefficient (StochasticOptimizer attribute) predict() (Classifier method) (GaussianBayesianNeuralNetworkModel method) (GaussianNeuralNetworkModel method) (GPFlowRegressionModel method) (GPflowSVGPModel method) (GPJittedModel method) (HeteroskedasticGPModel method) (Predictor method) (SurrogateModel method) predict_and_gradient() (GaussianNeuralNetworkModel method) predict_f() (GaussianBayesianNeuralNetworkModel method) predict_f_samples() (GaussianBayesianNeuralNetworkModel method) (HeteroskedasticGPModel method) predict_y() (GaussianBayesianNeuralNetworkModel method) (GaussianNeuralNetworkModel method) (HeteroskedasticGPModel method) predict_y_samples() (GaussianBayesianNeuralNetworkModel method) predictive_var (BMFMCVisualization attribute) predictive_var_bool (BMFMCModel attribute) Predictor (class in queens.iterators.sobol_index_gp_uncertainty.predictor) predictor (SobolIndexGPUncertaintyIterator attribute) prepare_input_files() (JobscriptDriver method) prepare_z_lf_for_time_steps() (BmfiaInterface static method) print_banner() (in module queens.utils.ascii_art) print_banner_and_description() (in module queens.utils.ascii_art) print_bmfia_acceleration() (in module queens.utils.ascii_art) print_centered_multiline() (in module queens.utils.ascii_art) print_centered_multiline_block() (in module queens.utils.ascii_art) print_classification() (in module queens.utils.ascii_art) print_crown() (in module queens.utils.ascii_art) print_git_information() (GlobalSettings method) print_greeting_message() (in module queens.utils.cli_utils) print_pickle_data_cli() (in module queens.utils.cli_utils) print_pickled_data() (in module queens.utils.pickle_utils) print_points_iterator() (in module queens.utils.ascii_art) print_results() (ElementaryEffectsIterator method) (SobolIndexIterator method) printstep() (LMIterator method) prior (SequentialMonteCarloChopinIterator attribute) prior_gp_mean (LogpdfGPModel attribute) prior_rate (LogpdfGPModel attribute) prior_trainable() (GaussianBayesianNeuralNetworkModel static method) probabilistic_mapping (BmfmcInterface attribute) probabilistic_mapping_obj_lst (BmfiaInterface attribute) probabilities (CategoricalDistribution attribute) (DiscreteDistribution attribute) (ParticleDiscreteDistribution attribute) problem_dimension (DataProcessorEnsightInterfaceDiscrepancy attribute) process_outputs() (in module queens.utils.process_outputs) process_results() (ElementaryEffectsIterator method) (SobolIndexIterator method) progressbar (PyMCIterator attribute) project_samples_on_truncated_basis() (in module queens.models.bmfmc_model) proposal_distribution (MetropolisHastingsIterator attribute) pymc_model (PyMCIterator attribute) pymc_sampler_stats (PyMCIterator attribute) PymcDistributionWrapper (class in queens.utils.pymc) PymcGradientWrapper (class in queens.utils.pymc) PyMCIterator (class in queens.iterators.pymc_iterator)

Q

quantile (LogpdfGPModel attribute) queens module queens.data_processor module queens.data_processor.data_processor module queens.data_processor.data_processor_csv module queens.data_processor.data_processor_ensight module queens.data_processor.data_processor_ensight_interface module queens.data_processor.data_processor_numpy module queens.data_processor.data_processor_pvd module queens.data_processor.data_processor_txt module queens.distributions module queens.distributions.bernoulli module queens.distributions.beta module queens.distributions.categorical module queens.distributions.distributions module queens.distributions.exponential module queens.distributions.free module queens.distributions.lognormal module queens.distributions.mean_field_normal module queens.distributions.mixture module queens.distributions.multinomial module queens.distributions.normal module queens.distributions.particles module queens.distributions.uniform module queens.distributions.uniform_discrete module queens.drivers module queens.drivers.driver module queens.drivers.fourc_driver module queens.drivers.function_driver module queens.drivers.jobscript_driver module queens.drivers.mpi_driver module queens.example_simulator_functions module queens.example_simulator_functions.agawal09 module queens.example_simulator_functions.borehole83 module queens.example_simulator_functions.branin78 module queens.example_simulator_functions.currin88 module queens.example_simulator_functions.executable_park91a_hifi_on_grid_with_gradients module queens.example_simulator_functions.gardner14a module queens.example_simulator_functions.gaussian_logpdf module queens.example_simulator_functions.gaussian_mixture_logpdf module queens.example_simulator_functions.ishigami90 module queens.example_simulator_functions.ma09 module queens.example_simulator_functions.oakley_ohagan04 module queens.example_simulator_functions.parabola_residual module queens.example_simulator_functions.paraboloid module queens.example_simulator_functions.park91a module queens.example_simulator_functions.park91b module queens.example_simulator_functions.perdikaris17 module queens.example_simulator_functions.rezende15 module queens.example_simulator_functions.rosenbrock60 module queens.example_simulator_functions.sinus module queens.example_simulator_functions.sobol_g_function module queens.external_geometry module queens.external_geometry.external_geometry module queens.external_geometry.fourc_dat_geometry module queens.global_settings module queens.iterators module queens.iterators.adaptive_sampling_iterator module queens.iterators.black_box_variational_bayes module queens.iterators.bmfia_iterator module queens.iterators.bmfmc_iterator module queens.iterators.classification module queens.iterators.control_variates_iterator module queens.iterators.data_iterator module queens.iterators.elementary_effects_iterator module queens.iterators.grid_iterator module queens.iterators.hmc_iterator module queens.iterators.iterator module queens.iterators.lhs_iterator module queens.iterators.lm_iterator module queens.iterators.metropolis_hastings_iterator module queens.iterators.metropolis_hastings_pymc_iterator module queens.iterators.mlmc_iterator module queens.iterators.monte_carlo_iterator module queens.iterators.nuts_iterator module queens.iterators.optimization_iterator module queens.iterators.points_iterator module queens.iterators.polynomial_chaos_iterator module queens.iterators.pymc_iterator module queens.iterators.reparameteriztion_based_variational_inference module queens.iterators.sequential_monte_carlo_chopin module queens.iterators.sequential_monte_carlo_iterator module queens.iterators.sobol_index_gp_uncertainty module queens.iterators.sobol_index_gp_uncertainty.estimator module queens.iterators.sobol_index_gp_uncertainty.predictor module queens.iterators.sobol_index_gp_uncertainty.sampler module queens.iterators.sobol_index_gp_uncertainty.statistics module queens.iterators.sobol_index_gp_uncertainty.utils_estimate_indices module queens.iterators.sobol_index_gp_uncertainty_iterator module queens.iterators.sobol_index_iterator module queens.iterators.sobol_sequence_iterator module queens.iterators.variational_inference module queens.main module queens.models module queens.models.bmfmc_model module queens.models.differentiable_simulation_model_adjoint module

queens.models.differentiable_simulation_model_fd module queens.models.likelihood_models module queens.models.likelihood_models.bayesian_mf_gaussian_likelihood module queens.models.likelihood_models.gaussian_likelihood module queens.models.likelihood_models.likelihood_model module queens.models.logpdf_gp_model module queens.models.model module queens.models.simulation_model module queens.models.surrogate_models module queens.models.surrogate_models.bayesian_neural_network module queens.models.surrogate_models.gaussian_neural_network module queens.models.surrogate_models.gp_approximation_gpflow module queens.models.surrogate_models.gp_approximation_gpflow_svgp module queens.models.surrogate_models.gp_approximation_jitted module queens.models.surrogate_models.gp_heteroskedastic_gpflow module queens.models.surrogate_models.surrogate_model module queens.models.surrogate_models.utils module queens.models.surrogate_models.utils.kernel_utils_jitted module queens.parameters module queens.parameters.fields module queens.parameters.fields.fourier_field module queens.parameters.fields.kl_field module queens.parameters.fields.piece_wise_field module queens.parameters.fields.random_fields module queens.parameters.parameters module queens.schedulers module queens.schedulers.cluster_scheduler module queens.schedulers.dask_scheduler module queens.schedulers.local_scheduler module queens.schedulers.pool_scheduler module queens.schedulers.scheduler module queens.stochastic_optimizers module queens.stochastic_optimizers.adam module queens.stochastic_optimizers.adamax module queens.stochastic_optimizers.learning_rate_decay module queens.stochastic_optimizers.rms_prop module queens.stochastic_optimizers.sgd module queens.stochastic_optimizers.stochastic_optimizer module queens.utils module queens.utils.ascii_art module queens.utils.classifier module queens.utils.cli_utils module queens.utils.collection_utils module queens.utils.config_directories module queens.utils.exceptions module queens.utils.experimental_data_reader module queens.utils.fcc_utils module queens.utils.fd_jacobian module queens.utils.gpf_utils module queens.utils.import_utils module queens.utils.injector module queens.utils.input_to_script module queens.utils.io_utils module queens.utils.iterative_averaging_utils module queens.utils.jax_minimize_wrapper module queens.utils.logger_settings module queens.utils.mcmc_utils module queens.utils.metadata module queens.utils.numpy_utils module queens.utils.path_utils module queens.utils.pdf_estimation module queens.utils.pickle_utils module queens.utils.plot_outputs module queens.utils.pool_utils module queens.utils.print_utils module queens.utils.process_outputs module queens.utils.pymc module queens.utils.random_process_scaler module queens.utils.remote_build module queens.utils.remote_operations module queens.utils.rsync module queens.utils.run_subprocess module queens.utils.smc_utils module queens.utils.sobol_sequence module queens.utils.start_dask_cluster module queens.utils.tensorflow_utils module queens.utils.valid_options_utils module queens.variational_distributions module queens.variational_distributions.full_rank_normal module queens.variational_distributions.joint module queens.variational_distributions.mean_field_normal module queens.variational_distributions.mixture_model module queens.variational_distributions.particle module queens.variational_distributions.variational_distribution module queens.visualization module queens.visualization.bmfia_visualization module queens.visualization.bmfmc_visualization module queens.visualization.classification module queens.visualization.gaussian_neural_network_vis module queens.visualization.gnuplot_vis module queens.visualization.grid_iterator_visualization module queens.visualization.sa_visualization module queens.visualization.surrogate_visualization module queens.visualization.variational_inference_visualization module QueensException QueensPythonCode (class in queens.utils.input_to_script)

R

R_op() (PymcDistributionWrapper method) (PymcGradientWrapper method) raise_error_on_jobscript_failure (JobscriptDriver attribute) random_design() (BMFIAIterator static method) (BMFMCIterator method) random_dirich_flag (FourcDatExternalGeometry attribute) random_field_flag (Parameters attribute) random_fields (FourcDatExternalGeometry attribute) random_neumann_flag (FourcDatExternalGeometry attribute) random_sampling_frequency (ClassificationIterator attribute) random_seed (BBVIIterator attribute) (HeteroskedasticGPModel attribute) (VariationalInferenceIterator attribute) random_transport_dirich_flag (FourcDatExternalGeometry attribute) RandomField (class in queens.parameters.fields.random_fields) randomize (SobolSequenceIterator attribute) rate (ExponentialDistribution attribute) rbf() (in module queens.models.logpdf_gp_model) rbf_by_dists() (in module queens.models.logpdf_gp_model) read_external_data() (ExternalGeometry method) (FourcDatExternalGeometry method) read_file() (in module queens.utils.io_utils) read_geometry_coordinates() (DataProcessorEnsight static method) read_geometry_from_dat_file() (FourcDatExternalGeometry method) read_input_file() (in module queens.example_simulator_functions.executable_park91a_hifi_on_grid_with_gradients) read_monitorfile() (DataProcessorEnsightInterfaceDiscrepancy static method) read_pickle_file() (DataIterator method) reconstruct_distribution_parameters() (FullRankNormalVariational method) (JointVariational method) (MeanFieldNormalVariational method) (MixtureModelVariational method) (ParticleVariational method) (VariationalDistribution method) refinement_epochs_decay (GaussianNeuralNetworkModel attribute) reg_param (LMIterator attribute) rel_l1_change (IterativeAveraging attribute) (StochasticOptimizer attribute) rel_l1_change_threshold (StochasticOptimizer attribute) rel_l2_change (IterativeAveraging attribute) (StochasticOptimizer attribute) rel_l2_change_threshold (StochasticOptimizer attribute) relative_change() (in module queens.utils.iterative_averaging_utils) relative_path_from_queens() (in module queens.utils.path_utils) relative_path_from_source() (in module queens.utils.path_utils) remote_python (RemoteConnection attribute) remote_queens_repository (RemoteConnection attribute) RemoteConnection (class in queens.utils.remote_operations) remove_html_coverage_report() (in module queens.utils.cli_utils) render_template() (in module queens.utils.injector) resample (BBVIIterator attribute) resample() (SequentialMonteCarloIterator method) resampling_method (SequentialMonteCarloChopinIterator attribute) resampling_threshold (SequentialMonteCarloChopinIterator attribute) reset_logging() (in module queens.utils.logger_settings) response (Model attribute) responsibilities() (MixtureDistribution method)

restart_file (AdaptiveSamplingIterator attribute) restart_max_value (GPFlowRegressionModel attribute) restart_min_value (GPFlowRegressionModel attribute) restart_worker() (ClusterScheduler method) (DaskScheduler method) (LocalScheduler method) restart_workers (DaskScheduler attribute) result_description (BMFMCIterator attribute) (ClassificationIterator attribute) (DataIterator attribute) (ElementaryEffectsIterator attribute) (GridIterator attribute) (LHSIterator attribute) (LMIterator attribute) (MetropolisHastingsIterator attribute) (MonteCarloIterator attribute) (OptimizationIterator attribute) (PointsIterator attribute) (PolynomialChaosIterator attribute) (PyMCIterator attribute) (SequentialMonteCarloChopinIterator attribute) (SequentialMonteCarloIterator attribute) (SobolIndexGPUncertaintyIterator attribute) (SobolIndexIterator attribute) (SobolSequenceIterator attribute) (VariationalInferenceIterator attribute) result_dict (PolynomialChaosIterator attribute) result_file() (GlobalSettings method) results (PyMCIterator attribute) (SobolIndexGPUncertaintyIterator attribute) results_dict (PyMCIterator attribute) returned_filter_format (DataProcessorCsv attribute) rezende15_potential1() (in module queens.example_simulator_functions.rezende15) rho_min (DynamicLearningRateDecay attribute) RMSprop (class in queens.stochastic_optimizers.rms_prop) rosenbrock60() (in module queens.example_simulator_functions.rosenbrock60) rosenbrock60_residual() (in module queens.example_simulator_functions.rosenbrock60) rosenbrock60_residual_1d() (in module queens.example_simulator_functions.rosenbrock60) rosenbrock60_residual_3d() (in module queens.example_simulator_functions.rosenbrock60) RPVIIterator (class in queens.iterators.reparameteriztion_based_variational_inference) rsync() (in module queens.utils.rsync) run() (Driver method) (FunctionDriver method) (in module queens.main) (Iterator method) (JobscriptDriver method) run_BMFMC() (BMFMCModel method) run_BMFMC_without_features() (BMFMCModel method) run_function() (RemoteConnection method) run_iterator (QueensPythonCode attribute) run_iterator() (in module queens.main) run_optimization() (StochasticOptimizer method) run_subprocess() (in module queens.utils.run_subprocess) run_type_adjoint() (in module queens.example_simulator_functions.executable_park91a_hifi_on_grid_with_gradients) run_type_provided_gradient() (in module queens.example_simulator_functions.executable_park91a_hifi_on_grid_with_gradients) run_type_standard() (in module queens.example_simulator_functions.executable_park91a_hifi_on_grid_with_gradients) rvs() (ParticlesChopinDistribution method)

S

safe_cholesky() (in module queens.utils.numpy_utils) salib_problem (ElementaryEffectsIterator attribute) (SobolIndexIterator attribute) sample() (Sampler method) (ThirdOrderSampler method) sample_as_dict() (Parameters method) sample_hyperparameters() (LogpdfGPModel method) sample_set (BBVIIterator attribute) sample_sobol_sequence() (in module queens.utils.sobol_sequence) sample_space (DiscreteDistribution attribute) (ParticleDiscreteDistribution attribute) Sampler (class in queens.iterators.sobol_index_gp_uncertainty.sampler) sampler (SobolIndexGPUncertaintyIterator attribute) samples (ClassificationIterator attribute) (ControlVariatesIterator attribute) (DataIterator attribute) (ElementaryEffectsIterator attribute) (GridIterator attribute) (LHSIterator attribute) (MLMCIterator attribute) (MonteCarloIterator attribute) (PolynomialChaosIterator attribute) (SobolIndexIterator attribute) (SobolSequenceIterator attribute) samples_list (BBVIIterator attribute) sampling_approach (Sampler attribute) sampling_bool (BBVIIterator attribute) sampling_rule (PolynomialChaosIterator attribute) save_bool (ClassificationVisualization attribute) (VIVisualization attribute) save_bools (BMFIAVisualization attribute) (BMFMCVisualization attribute) (GridIteratorVisualization attribute) save_plots() (VIVisualization method) saving_path (ClassificationVisualization attribute) saving_paths (SAVisualization attribute) (SurrogateVisualization attribute) saving_paths_list (GridIteratorVisualization attribute) SAVisualization (class in queens.visualization.sa_visualization) scale (ExponentialDistribution attribute) scale_covariance (MetropolisHastingsIterator attribute) scale_type (GridIterator attribute) scale_types_list (GridIteratorVisualization attribute) Scaler (class in queens.utils.random_process_scaler) scaler_x (GaussianNeuralNetworkModel attribute) (GPFlowRegressionModel attribute) (GPflowSVGPModel attribute) (GPJittedModel attribute) (LogpdfGPModel attribute) scaler_y (GaussianNeuralNetworkModel attribute) (GPFlowRegressionModel attribute) (GPflowSVGPModel attribute) (GPJittedModel attribute) (LogpdfGPModel attribute) scaling (HMCIterator attribute) (MetropolisHastingsPyMCIterator attribute) (NUTSIterator attribute) Scheduler (class in queens.schedulers.scheduler) scheduler (SimulationModel attribute) scheme_specific_gradient() (Adam method) (Adamax method) (RMSprop method) (SGD method) (StochasticOptimizer method) scipy_beta (BetaDistribution attribute) score_function_bool (RPVIIterator attribute) section_match_dict (FourcDatExternalGeometry attribute) seed (AdaptiveSamplingIterator attribute) (ControlVariatesIterator attribute) (ElementaryEffectsIterator attribute) (GPflowSVGPModel attribute) (LHSIterator attribute) (MetropolisHastingsIterator attribute) (MLMCIterator attribute) (MonteCarloIterator attribute) (PolynomialChaosIterator attribute) (PyMCIterator attribute) (SequentialMonteCarloChopinIterator attribute) (SequentialMonteCarloIterator attribute) (SobolIndexIterator attribute) (SobolSequenceIterator attribute)

seed_bootstrap_samples (SobolIndexEstimator attribute) seed_monte_carlo (Sampler attribute) seed_posterior_samples (Predictor attribute) sensitivity_indices (SobolIndexIterator attribute) SequentialMonteCarloChopinIterator (class in queens.iterators.sequential_monte_carlo_chopin) SequentialMonteCarloIterator (class in queens.iterators.sequential_monte_carlo_iterator) set_feature_strategy() (BMFIAIterator method) (BMFMCModel method) set_gradient_function() (StochasticOptimizer method) set_optimized_state_of_probabilistic_mappings() (BmfiaInterface method) set_state() (GPJittedModel method) set_transform_function() (in module queens.utils.gpf_utils) setup() (GaussianBayesianNeuralNetworkModel method) (GaussianNeuralNetworkModel method) (GPFlowRegressionModel method) (GPflowSVGPModel method) (GPJittedModel method) (HeteroskedasticGPModel method) (SurrogateModel method) setup_basic_logging() (in module queens.utils.logger_settings) setup_cli_logging() (in module queens.utils.logger_settings) setup_cluster_logging() (in module queens.utils.logger_settings) setup_file_handler() (in module queens.utils.logger_settings) setup_logger() (in module queens.utils.logger_settings) setup_stream_handler() (in module queens.utils.logger_settings) SGD (class in queens.stochastic_optimizers.sgd) should_be_displayed (SAVisualization attribute) (SurrogateVisualization attribute) should_be_saved (SAVisualization attribute) (SurrogateVisualization attribute) shutdown_client() (DaskScheduler method) si (ElementaryEffectsIterator attribute) SimulationMetadata (class in queens.utils.metadata) SimulationModel (class in queens.models.simulation_model) sinus_test_fun() (in module queens.example_simulator_functions.sinus) skip_rows (DataProcessorCsv attribute) skip_values (SobolIndexIterator attribute) slope (LogLinearLearningRateDecay attribute) smc_obj (SequentialMonteCarloChopinIterator attribute) sobol_g_function() (in module queens.example_simulator_functions.sobol_g_function) SobolIndexEstimator (class in queens.iterators.sobol_index_gp_uncertainty.estimator) SobolIndexEstimatorThirdOrder (class in queens.iterators.sobol_index_gp_uncertainty.estimator) SobolIndexGPUncertaintyIterator (class in queens.iterators.sobol_index_gp_uncertainty_iterator) SobolIndexIterator (class in queens.iterators.sobol_index_iterator) SobolSequenceIterator (class in queens.iterators.sobol_sequence_iterator) solution (LMIterator attribute) (OptimizationIterator attribute) solving_iterator (AdaptiveSamplingIterator attribute) sparse (PolynomialChaosIterator attribute) split_array_by_chunk_sizes() (in module queens.variational_distributions.joint) squared_exponential() (in module queens.models.surrogate_models.utils.kernel_utils_jitted) standard_deviation (MeanFieldNormalDistribution attribute) (Scaler attribute) StandardScaler (class in queens.utils.random_process_scaler) start_cluster() (RemoteConnection method) start_subprocess() (in module queens.utils.run_subprocess) StaticStateSpaceModel (class in queens.utils.smc_utils) statistics (SobolIndexGPUncertaintyIterator attribute) StatisticsSecondOrderEstimates (class in queens.iterators.sobol_index_gp_uncertainty.statistics) StatisticsSobolIndexEstimates (class in queens.iterators.sobol_index_gp_uncertainty.statistics) StatisticsThirdOrderSobolIndexEstimates (class in queens.iterators.sobol_index_gp_uncertainty.statistics) std (FourierRandomField attribute) (KarhunenLoeveRandomField attribute) step (PyMCIterator attribute) step_size (DifferentiableSimulationModelFD attribute) (HMCIterator attribute) (NUTSIterator attribute) StepwiseLearningRateDecay (class in queens.stochastic_optimizers.learning_rate_decay) stochastic_optimizer (GPJittedModel attribute) (VariationalInferenceIterator attribute) StochasticOptimizer (class in queens.stochastic_optimizers.stochastic_optimizer) str_to_bool() (in module queens.utils.cli_utils) stretch_vector() (DataProcessorEnsightInterfaceDiscrepancy method) stringify() (in module queens.utils.input_to_script) SubprocessError sum_over_iter (PolyakAveraging attribute) summary (PyMCIterator attribute) surface_topology (FourcDatExternalGeometry attribute) SurrogateModel (class in queens.models.surrogate_models.surrogate_model) SurrogateVisualization (class in queens.visualization.surrogate_visualization) sync_remote_repository() (RemoteConnection method)

T

target_accept (HMCIterator attribute) (NUTSIterator attribute) target_time_lst (DataProcessorEnsight attribute) temper (MetropolisHastingsIterator attribute) (SequentialMonteCarloIterator attribute) temper_factory() (in module queens.utils.smc_utils) temper_logpdf_bayes() (in module queens.utils.smc_utils) temper_logpdf_generic() (in module queens.utils.smc_utils) testing_iterator (SurrogateModel attribute) third_order_parameters (SobolIndexEstimatorThirdOrder attribute) (StatisticsThirdOrderSobolIndexEstimates attribute) (ThirdOrderSampler attribute) ThirdOrderSampler (class in queens.iterators.sobol_index_gp_uncertainty.sampler) time_code() (SimulationMetadata method) time_label (ExperimentalDataReader attribute) time_label_experimental (DataProcessorEnsight attribute) time_steps (DataProcessorPvd attribute) time_tol (DataProcessorEnsight attribute) (DataProcessorEnsightInterfaceDiscrepancy attribute) time_vec (BMFGaussianModel attribute) (BmfiaInterface attribute) (BMFIAIterator attribute) timedelta_to_str() (in module queens.schedulers.cluster_scheduler) times (SimulationMetadata attribute) timestamp (SimulationMetadata attribute) to_dict() (CollectionObject method) (JobOptions method) (SimulationMetadata method) to_dict_with_standard_types() (in module queens.utils.io_utils) to_distribution_list() (Parameters method) to_list() (Parameters method)

tolerance (LMIterator attribute) tot_num_samples (MetropolisHastingsIterator attribute) total_grad_params_logpdf() (FullRankNormalVariational method) (MeanFieldNormalVariational method) total_order_indices() (in module queens.example_simulator_functions.ishigami90) (in module queens.example_simulator_functions.sobol_g_function) train() (ActiveLearningClassifier method) (Classifier method) (GaussianBayesianNeuralNetworkModel method) (GaussianNeuralNetworkModel method) (GPFlowRegressionModel method) (GPflowSVGPModel method) (GPJittedModel method) (HeteroskedasticGPModel method) (SurrogateModel method) train_inducing_points_location (GPflowSVGPModel attribute) train_likelihood_variance (GPFlowRegressionModel attribute) (GPflowSVGPModel attribute) train_probabilistic_mappings_in_parallel() (BmfiaInterface static method) training_data (GPflowSVGPModel attribute) training_indices (BMFMCModel attribute) training_iterator (SurrogateModel attribute) transform() (IdentityScaler method) (Scaler method) (StandardScaler method) transform_hyperparameters() (GPFlowRegressionModel method) trunc_threshold (FourierRandomField attribute) tune (MetropolisHastingsIterator attribute) tune_interval (MetropolisHastingsIterator attribute) (MetropolisHastingsPyMCIterator attribute) tune_scale_covariance() (in module queens.utils.mcmc_utils)

U

u (Adamax attribute) uncertain_parameters (BMFMCModel attribute) UniformDiscreteDistribution (class in queens.distributions.uniform_discrete) UniformDistribution (class in queens.distributions.uniform) unit_bounding() (in module queens.example_simulator_functions.park91a) update_average() (IterativeAveraging method) update_covariance() (GaussianLikelihood method) (NormalDistribution method) update_ess() (SequentialMonteCarloIterator method) update_gamma() (SequentialMonteCarloIterator method) update_mappings_method (BmfiaInterface attribute) update_mappings_per_coordinate() (BmfiaInterface static method) update_mappings_per_time_step() (BmfiaInterface static method) update_mean() (MeanFieldNormalDistribution method)

update_probabilistic_mapping_with_features() (BMFIAIterator method) (BMFMCModel method) update_reg (LMIterator attribute) update_training_data() (GaussianNeuralNetworkModel method) update_variance() (MeanFieldNormalDistribution method) update_weights() (SequentialMonteCarloIterator method) upper_bound (BetaDistribution attribute) (LogpdfGPModel attribute) (UniformDistribution attribute) use_cols_lst (DataProcessorCsv attribute) use_optimal_num_samples (ControlVariatesIterator attribute) (MLMCIterator attribute) use_queens_prior (PyMCIterator attribute) use_rows_lst (DataProcessorCsv attribute)

V

v (Adam attribute) (RMSprop attribute) v_train (LogpdfGPModel attribute) valid_kernels_dict (GPJittedModel attribute) valid_probabilistic_mappings_configurations (BmfiaInterface attribute) values() (CollectionObject method) var_names_list (GridIteratorVisualization attribute) var_y_mc (BMFMCModel attribute) variability (FourierRandomField attribute) VariableName (class in queens.utils.input_to_script) variance() (in module queens.example_simulator_functions.ishigami90) (in module queens.example_simulator_functions.sobol_g_function) variance_cv_mean_estimator (ControlVariatesIterator attribute) variational_distribution (VariationalInferenceIterator attribute) variational_params (VariationalInferenceIterator attribute) variational_params_initialization_approach (VariationalInferenceIterator attribute) variational_transformation (VariationalInferenceIterator attribute) VariationalDistribution (class in queens.variational_distributions.variational_distribution)

VariationalInferenceIterator (class in queens.iterators.variational_inference) verbose (Scheduler attribute) verbose_every_n_iter (VariationalInferenceIterator attribute) verbose_output (LMIterator attribute) (OptimizationIterator attribute) verbosity_on (GaussianBayesianNeuralNetworkModel attribute) (GaussianNeuralNetworkModel attribute) visualization (BMFMCIterator attribute) (BMFMCModel attribute) (ElementaryEffectsIterator attribute) (GridIterator attribute) (SurrogateModel attribute) visualization_bool (DataProcessorEnsightInterfaceDiscrepancy attribute) visualization_obj (ClassificationIterator attribute) VIVisualization (class in queens.visualization.variational_inference_visualization) volume_topology (FourcDatExternalGeometry attribute) vtk_array_type (DataProcessorEnsight attribute) vtk_field_components (DataProcessorEnsight attribute) vtk_field_label (DataProcessorEnsight attribute)

W

waste_free (SequentialMonteCarloChopinIterator attribute) weights (SequentialMonteCarloIterator attribute) width (UniformDistribution attribute) write_metadata_to_csv() (in module queens.utils.metadata)

write_random_fields_to_dat() (FourcDatExternalGeometry method) write_results() (AdaptiveSamplingIterator method) (in module queens.example_simulator_functions.executable_park91a_hifi_on_grid_with_gradients) (in module queens.utils.process_outputs) write_to_csv() (in module queens.utils.io_utils)

X

x3_x4_grid_eval() (in module queens.example_simulator_functions.park91a) x_cols (BMFIAIterator attribute) X_cols (BMFMCModel attribute) X_mc (BMFMCModel attribute) x_train (AdaptiveSamplingIterator attribute)

X_train (BMFIAIterator attribute) (BMFMCIterator attribute) (BMFMCModel attribute) x_train (LogpdfGPModel attribute) (SurrogateModel attribute) x_train_new (AdaptiveSamplingIterator attribute)

Y

Y_HF_mc (BMFMCModel attribute) Y_HF_train (BMFIAIterator attribute) (BMFMCModel attribute) Y_LF_train (BMFIAIterator attribute) Y_LFs_mc (BMFMCModel attribute) Y_LFs_train (BMFMCIterator attribute) (BMFMCModel attribute)

y_obs (LikelihoodModel attribute) y_obs_vec (BMFIAIterator attribute) y_pdf_support (BMFMCModel attribute) y_train (AdaptiveSamplingIterator attribute) (LogpdfGPModel attribute) (SurrogateModel attribute)

Z

Z_mc (BMFMCModel attribute) Z_train (BMFIAIterator attribute) (BMFMCModel attribute)

zero_mean_fun() (GPJittedModel static method)