Index _ | A | B | C | D | E | F | G | I | L | M | N | O | P | R | S | T | W _ _prepare_t() (codes.surrogates.Polynomial method) A AbstractSurrogateModel (class in codes.surrogates) (class in codes.surrogates.surrogates) activation (codes.surrogates.Decoder attribute) (codes.surrogates.Encoder attribute) (codes.surrogates.ODE attribute) B BranchNet (class in codes.surrogates) C check_and_load_data() (in module codes.utils) (in module codes.utils.data_utils) check_benchmark() (in module codes.benchmark) (in module codes.benchmark.bench_utils) check_surrogate() (in module codes.benchmark) (in module codes.benchmark.bench_utils) check_training_status() (in module codes.utils) (in module codes.utils.utils) ChemDataset (class in codes.surrogates) clean_metrics() (in module codes.benchmark) (in module codes.benchmark.bench_utils) codes module codes.benchmark module, [1] codes.benchmark.bench_fcts module, [1] codes.benchmark.bench_plots module, [1] codes.benchmark.bench_utils module, [1] codes.surrogates module, [1] codes.surrogates.surrogate_classes module codes.surrogates.surrogates module, [1] codes.train module, [1] codes.train.train_fcts module, [1] codes.utils module, [1] codes.utils.data_utils module, [1] codes.utils.utils module, [1] coef (codes.surrogates.Polynomial attribute) compare_batchsize() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) compare_dynamic_accuracy() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) compare_extrapolation() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) compare_inference_time() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) compare_interpolation() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) compare_MAE() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) compare_main_losses() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) compare_models() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) compare_relative_errors() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) compare_sparse() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) compare_UQ() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) config (codes.surrogates.AbstractSurrogateModel attribute) (codes.surrogates.LatentNeuralODE attribute) (codes.surrogates.LatentPoly attribute) (codes.surrogates.ModelWrapper attribute) (codes.surrogates.surrogates.AbstractSurrogateModel attribute) convert_dict_to_scientific_notation() (in module codes.benchmark) (in module codes.benchmark.bench_utils) convert_to_standard_types() (in module codes.benchmark) (in module codes.benchmark.bench_utils) count_trainable_parameters() (in module codes.benchmark) (in module codes.benchmark.bench_utils) create_dataloader() (codes.surrogates.FullyConnected method) (codes.surrogates.MultiONet method) create_dataset() (in module codes.utils) (in module codes.utils.data_utils) create_hdf5_dataset() (in module codes.utils) (in module codes.utils.data_utils) create_model_dir() (in module codes.utils) (in module codes.utils.utils) create_task_list_for_surrogate() (in module codes.train) (in module codes.train.train_fcts) D DatasetError Decoder (class in codes.surrogates) decoder (codes.surrogates.ModelWrapper attribute) degree (codes.surrogates.Polynomial attribute) denormalize() (codes.surrogates.AbstractSurrogateModel method) (codes.surrogates.surrogates.AbstractSurrogateModel method) deriv() (codes.surrogates.ModelWrapper class method) (codes.surrogates.ModelWrapper method) deriv2() (codes.surrogates.ModelWrapper class method) (codes.surrogates.ModelWrapper method) deriv2_loss() (codes.surrogates.ModelWrapper class method) (codes.surrogates.ModelWrapper method) deriv_loss() (codes.surrogates.ModelWrapper class method) (codes.surrogates.ModelWrapper method) device (codes.surrogates.AbstractSurrogateModel attribute) (codes.surrogates.LatentPoly attribute) (codes.surrogates.surrogates.AbstractSurrogateModel attribute) dimension (codes.surrogates.Polynomial attribute) discard_numpy_entries() (in module codes.benchmark) (in module codes.benchmark.bench_utils) download_data() (in module codes.utils) (in module codes.utils.data_utils) E Encoder (class in codes.surrogates) encoder (codes.surrogates.ModelWrapper attribute) epoch() (codes.surrogates.FullyConnected method) (codes.surrogates.MultiONet method) evaluate_accuracy() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) evaluate_batchsize() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) evaluate_compute() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) evaluate_dynamic_accuracy() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) evaluate_extrapolation() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) evaluate_interpolation() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) evaluate_sparse() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) evaluate_UQ() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) F fit() (codes.surrogates.AbstractSurrogateModel method) (codes.surrogates.FullyConnected method) (codes.surrogates.LatentNeuralODE method), [1] (codes.surrogates.LatentPoly method), [1] (codes.surrogates.MultiONet method) (codes.surrogates.surrogates.AbstractSurrogateModel method) flatten_dict() (in module codes.benchmark) (in module codes.benchmark.bench_utils) format_seconds() (in module codes.benchmark) (in module codes.benchmark.bench_utils) format_time() (in module codes.benchmark) (in module codes.benchmark.bench_utils) forward() (codes.surrogates.AbstractSurrogateModel method) (codes.surrogates.BranchNet method) (codes.surrogates.Decoder method), [1] (codes.surrogates.Encoder method), [1] (codes.surrogates.FullyConnected method) (codes.surrogates.FullyConnectedNet method) (codes.surrogates.LatentNeuralODE method), [1] (codes.surrogates.LatentPoly method), [1] (codes.surrogates.ModelWrapper method), [1] (codes.surrogates.MultiONet method) (codes.surrogates.ODE method), [1] (codes.surrogates.Polynomial method), [1] (codes.surrogates.surrogates.AbstractSurrogateModel method) (codes.surrogates.TrunkNet method) FullyConnected (class in codes.surrogates) FullyConnectedNet (class in codes.surrogates) G get_custom_palette() (in module codes.benchmark) (in module codes.benchmark.bench_plots) get_data_subset() (in module codes.utils) (in module codes.utils.data_utils) get_model_config() (in module codes.benchmark) (in module codes.benchmark.bench_utils) get_progress_bar() (in module codes.utils) (in module codes.utils.utils) get_required_models_list() (in module codes.benchmark) (in module codes.benchmark.bench_utils) get_surrogate() (in module codes.benchmark) (in module codes.benchmark.bench_utils) I identity_loss() (codes.surrogates.ModelWrapper method), [1] in_features (codes.surrogates.Encoder attribute) inference_time_bar_plot() (in module codes.benchmark) (in module codes.benchmark.bench_plots) int_ext_sparse() (in module codes.benchmark) (in module codes.benchmark.bench_plots) L L1 (codes.surrogates.AbstractSurrogateModel attribute) (codes.surrogates.surrogates.AbstractSurrogateModel attribute) l2_loss() (codes.surrogates.ModelWrapper class method) (codes.surrogates.ModelWrapper method) latent_features (codes.surrogates.Decoder attribute) (codes.surrogates.Encoder attribute) LatentNeuralODE (class in codes.surrogates) LatentPoly (class in codes.surrogates) load() (codes.surrogates.AbstractSurrogateModel method) (codes.surrogates.surrogates.AbstractSurrogateModel method) load_and_save_config() (in module codes.utils) (in module codes.utils.utils) load_model() (in module codes.benchmark) (in module codes.benchmark.bench_utils) load_task_list() (in module codes.utils) (in module codes.utils.utils) loss_weights (codes.surrogates.ModelWrapper attribute) M MAE (codes.surrogates.AbstractSurrogateModel attribute) (codes.surrogates.surrogates.AbstractSurrogateModel attribute) make_comparison_csv() (in module codes.benchmark) (in module codes.benchmark.bench_utils) make_description() (in module codes.utils) (in module codes.utils.utils) measure_memory_footprint() (in module codes.benchmark) (in module codes.benchmark.bench_utils) mlp (codes.surrogates.Decoder attribute) (codes.surrogates.Encoder attribute) (codes.surrogates.ODE attribute) model (codes.surrogates.LatentNeuralODE attribute) (codes.surrogates.LatentPoly attribute) ModelWrapper (class in codes.surrogates) module codes codes.benchmark, [1] codes.benchmark.bench_fcts, [1] codes.benchmark.bench_plots, [1] codes.benchmark.bench_utils, [1] codes.surrogates, [1] codes.surrogates.surrogate_classes codes.surrogates.surrogates, [1] codes.train, [1] codes.train.train_fcts, [1] codes.utils, [1] codes.utils.data_utils, [1] codes.utils.utils, [1] MultiONet (class in codes.surrogates) N n_chemicals (codes.surrogates.AbstractSurrogateModel attribute) (codes.surrogates.surrogates.AbstractSurrogateModel attribute) n_hidden (codes.surrogates.Encoder attribute) n_timesteps (codes.surrogates.AbstractSurrogateModel attribute) (codes.surrogates.surrogates.AbstractSurrogateModel attribute) nice_print() (in module codes.utils) (in module codes.utils.utils) normalisation (codes.surrogates.AbstractSurrogateModel attribute) (codes.surrogates.surrogates.AbstractSurrogateModel attribute) normalize_data() (in module codes.utils) (in module codes.utils.data_utils) O ODE (class in codes.surrogates) ode (codes.surrogates.ModelWrapper attribute) out_features (codes.surrogates.Decoder attribute) P parallel_training() (in module codes.train) (in module codes.train.train_fcts) plot_average_errors_over_time() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_average_uncertainty_over_time() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_comparative_dynamic_correlation_heatmaps() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_comparative_error_correlation_heatmaps() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_dynamic_correlation() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_dynamic_correlation_heatmap() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_error_correlation_heatmap() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_error_distribution_comparative() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_error_distribution_per_chemical() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_example_predictions_with_uncertainty() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_generalization_error_comparison() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_generalization_errors() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_loss_comparison() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_losses() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_MAE_comparison() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_MAE_comparison_train_duration() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_relative_errors() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_relative_errors_over_time() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_surr_losses() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_uncertainty_over_time_comparison() (in module codes.benchmark) (in module codes.benchmark.bench_plots) plot_uncertainty_vs_errors() (in module codes.benchmark) (in module codes.benchmark.bench_plots) Polynomial (class in codes.surrogates) predict() (codes.surrogates.AbstractSurrogateModel method) (codes.surrogates.surrogates.AbstractSurrogateModel method) prepare_data() (codes.surrogates.AbstractSurrogateModel method) (codes.surrogates.FullyConnected method) (codes.surrogates.LatentNeuralODE method) (codes.surrogates.LatentPoly method), [1] (codes.surrogates.MultiONet method) (codes.surrogates.surrogates.AbstractSurrogateModel method) R read_yaml_config() (in module codes.benchmark) (in module codes.benchmark.bench_utils) (in module codes.utils) (in module codes.utils.utils) reg_factor (codes.surrogates.ODE attribute) rel_errors_and_uq() (in module codes.benchmark) (in module codes.benchmark.bench_plots) renormalize_loss_weights() (codes.surrogates.ModelWrapper method), [1] run_benchmark() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) S save() (codes.surrogates.AbstractSurrogateModel method) (codes.surrogates.surrogates.AbstractSurrogateModel method) save_plot() (in module codes.benchmark) (in module codes.benchmark.bench_plots) save_plot_counter() (in module codes.benchmark) (in module codes.benchmark.bench_plots) save_task_list() (in module codes.utils) (in module codes.utils.utils) sequential_training() (in module codes.train) (in module codes.train.train_fcts) set_random_seeds() (in module codes.utils) (in module codes.utils.utils) setup_criterion() (codes.surrogates.MultiONet method) setup_optimizer_and_scheduler() (codes.surrogates.FullyConnected method) (codes.surrogates.MultiONet method) setup_progress_bar() (codes.surrogates.AbstractSurrogateModel method) (codes.surrogates.surrogates.AbstractSurrogateModel method) surrogate_classes (in module codes.surrogates) T t_matrix (codes.surrogates.Polynomial attribute) tabular_comparison() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) tanh_reg (codes.surrogates.ODE attribute) test_loss (codes.surrogates.AbstractSurrogateModel attribute) (codes.surrogates.surrogates.AbstractSurrogateModel attribute) time_execution() (in module codes.utils) (in module codes.utils.utils) time_inference() (in module codes.benchmark) (in module codes.benchmark.bench_fcts) total_loss() (codes.surrogates.ModelWrapper method), [1] train_and_save_model() (in module codes.train) (in module codes.train.train_fcts) train_duration (codes.surrogates.AbstractSurrogateModel attribute) (codes.surrogates.surrogates.AbstractSurrogateModel attribute) train_loss (codes.surrogates.AbstractSurrogateModel attribute) (codes.surrogates.surrogates.AbstractSurrogateModel attribute) TrunkNet (class in codes.surrogates) W width_list (codes.surrogates.Decoder attribute) (codes.surrogates.Encoder attribute) worker() (in module codes.train) (in module codes.train.train_fcts) worker_init_fn() (in module codes.utils) (in module codes.utils.utils) write_metrics_to_yaml() (in module codes.benchmark) (in module codes.benchmark.bench_utils)
