codes package

Subpackages

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

Module contents