Index

_

__call__() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) __getitem__() (GNNGraphDataset method) (GNNGraphDatasetInMemory method) __init__() (Decoder method) (EarlyStopper method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GNNGraphDataset method) (GNNGraphDatasetInMemory method) (GraphData method) (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchMinMaxScaler method) (TorchRNNWrapper method) (TorchStandardScaler method), [1] _available_activ_fn (GNNEPDBaseModel attribute), [1], [2] _best_model_state (EarlyStopper attribute) _best_optimizer_state (EarlyStopper attribute) _best_training_epoch (EarlyStopper attribute) _check_best_state_file() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] _check_edges_indexes_matrix() (GraphData method) (GraphData static method) _check_maximum() (TorchMinMaxScaler method), [1] _check_mean() (TorchStandardScaler method), [1] _check_minimum() (TorchMinMaxScaler method), [1] _check_state_file() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] _check_std() (TorchStandardScaler method), [1], [2], [3] _check_tensor() (TorchMinMaxScaler method), [1] (TorchStandardScaler method), [1] _data_scalers (GNNEPDBaseModel attribute), [1], [2] _dataset_basename (GNNGraphDataset attribute) _dataset_directory (GNNGraphDataset attribute) _dataset_sample_files (GNNGraphDataset attribute) _dataset_samples (GNNGraphDataset attribute) (GNNGraphDatasetInMemory attribute) _dec_edge_hidden_activ_type (GNNEPDBaseModel attribute), [1], [2] _dec_edge_output_activ_type (GNNEPDBaseModel attribute), [1], [2] _dec_global_hidden_activ_type (GNNEPDBaseModel attribute), [1], [2] _dec_global_output_activ_type (GNNEPDBaseModel attribute), [1], [2] _dec_n_hidden_layers (GNNEPDBaseModel attribute), [1], [2] _dec_node_hidden_activ_type (GNNEPDBaseModel attribute), [1], [2] _dec_node_output_activ_type (GNNEPDBaseModel attribute), [1], [2] _decoder (EncodeProcessDecode attribute), [1] _device (GNNEPDBaseModel attribute), [1], [2] (TorchMinMaxScaler attribute) (TorchStandardScaler attribute), [1] _device_type (GNNEPDBaseModel attribute), [1], [2] _edge_features_matrix (GraphData attribute) _edge_fn (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] _edge_targets_matrix (GraphData attribute) _edges_indexes (GraphData attribute) _enc_edge_hidden_activ_type (GNNEPDBaseModel attribute), [1], [2] _enc_edge_output_activ_type (GNNEPDBaseModel attribute), [1], [2] _enc_global_hidden_activ_type (GNNEPDBaseModel attribute), [1], [2] _enc_global_output_activ_type (GNNEPDBaseModel attribute), [1], [2] _enc_n_hidden_layers (GNNEPDBaseModel attribute), [1], [2] _enc_node_hidden_activ_type (GNNEPDBaseModel attribute), [1], [2] _enc_node_output_activ_type (GNNEPDBaseModel attribute), [1], [2] _encoder (EncodeProcessDecode attribute), [1] _get_backward_hooks() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) _get_edges_from_local_radius() (GraphData method) (GraphData static method) _global_features_matrix (GraphData attribute) _global_fn (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] _global_targets_matrix (GraphData attribute) _gnn_epd_model (GNNEPDBaseModel attribute), [1], [2] _hidden_layer_size (GNNEPDBaseModel attribute), [1], [2] _improvement_tolerance (EarlyStopper attribute) _init_data_scalers() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] _is_norm_layer (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] _is_skip_unset_update (GraphIndependentNetwork attribute), [1] _is_store_dataset (GNNGraphDataset attribute) _load_from_state_dict() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) _maximum (TorchMinMaxScaler attribute) _mean (TorchStandardScaler attribute), [1] _metadata (GraphData attribute) _min_validation_loss (EarlyStopper attribute) _minimum (TorchMinMaxScaler attribute) _n_dim (GraphData attribute) _n_edge (GraphData attribute) _n_edge_in (GNNEPDBaseModel attribute), [1], [2] (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] (Processor attribute)

_n_edge_out (EncodeProcessDecode attribute), [1] (GNNEPDBaseModel attribute), [1], [2] (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] (Processor attribute) _n_features (TorchMinMaxScaler attribute) (TorchStandardScaler attribute), [1] _n_global_in (GNNEPDBaseModel attribute), [1], [2] (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] (Processor attribute) _n_global_out (EncodeProcessDecode attribute), [1] (GNNEPDBaseModel attribute), [1], [2] (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] (Processor attribute) _n_message_steps (EncodeProcessDecode attribute), [1] (GNNEPDBaseModel attribute), [1], [2] _n_node (GraphData attribute) _n_node_in (GNNEPDBaseModel attribute), [1], [2] (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] (Processor attribute) _n_node_out (EncodeProcessDecode attribute), [1] (GNNEPDBaseModel attribute), [1], [2] (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] (Processor attribute) _n_not_improve (EarlyStopper attribute) _n_time_edge (EncodeProcessDecode attribute), [1] (GNNEPDBaseModel attribute), [1], [2] (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] (Processor attribute) _n_time_global (EncodeProcessDecode attribute), [1] (GNNEPDBaseModel attribute), [1], [2] (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] (Processor attribute) _n_time_node (EncodeProcessDecode attribute), [1] (GNNEPDBaseModel attribute), [1], [2] (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] (Processor attribute) _named_members() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) _node_features_matrix (GraphData attribute) _node_fn (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] _node_targets_matrix (GraphData attribute) _nodes_coords (GraphData attribute) _pro_edge_hidden_activ_type (GNNEPDBaseModel attribute), [1], [2] _pro_edge_output_activ_type (GNNEPDBaseModel attribute), [1], [2] _pro_edge_to_node_aggr (GNNEPDBaseModel attribute), [1], [2] _pro_global_hidden_activ_type (GNNEPDBaseModel attribute), [1], [2] _pro_global_output_activ_type (GNNEPDBaseModel attribute), [1], [2] _pro_n_hidden_layers (GNNEPDBaseModel attribute), [1], [2] _pro_node_hidden_activ_type (GNNEPDBaseModel attribute), [1], [2] _pro_node_output_activ_type (GNNEPDBaseModel attribute), [1], [2] _pro_node_to_global_aggr (GNNEPDBaseModel attribute), [1], [2] _processor (EncodeProcessDecode attribute), [1] (Processor attribute) _register_load_state_dict_pre_hook() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) _register_state_dict_hook() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) _remove_best_state_files() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] _remove_posterior_state_files() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] _save_to_state_dict() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) _std (TorchStandardScaler attribute), [1] _trigger_tolerance (EarlyStopper attribute) _update_dataset_directory() (GNNGraphDataset method), [1] _validate_model() (EarlyStopper method) _validation_frequency (EarlyStopper attribute) _validation_loss_history (EarlyStopper attribute) _validation_size (EarlyStopper attribute) _validation_steps_history (EarlyStopper attribute) _version (Decoder attribute) (EncodeProcessDecode attribute), [1] (Encoder attribute) (GNNEPDBaseModel attribute), [1], [2] (GraphIndependentNetwork attribute), [1] (GraphInteractionNetwork attribute), [1] (Processor attribute) (TorchRNNWrapper attribute)

A

add_metadata() (GraphData method), [1] add_module() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

aggregate() (GraphInteractionNetwork method), [1] (Processor method) apply() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

B

bfloat16() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) buffers() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

build_fnn() (in module graphorge.gnn_base_model.model.gnn_architectures) (in module graphorge.gnn_base_model.model.gnn_epd_model) build_rnn() (in module graphorge.gnn_base_model.model.gnn_architectures) (in module graphorge.gnn_base_model.model.gnn_epd_model)

C

check_normalized_return() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] children() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) clear() (OrderedDict method) compile() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

compute_sample_prediction_loss() (in module graphorge.gnn_base_model.predict.prediction) copy() (OrderedDict method) cpu() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) cuda() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

D

data_scaler_transform() (GNNEPDBaseModel method), [1], [2] Decoder (class in graphorge.gnn_base_model.model.gnn_epd_model) display_hydra_job_header() (in module graphorge.gnn_base_model.optimization.hydra_optimization_template) double() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

dummy_function() (in module graphorge.gnn_base_model.optimization.hydra_optimization_template)

E

EarlyStopper (class in graphorge.gnn_base_model.train.training) edge_update() (GraphInteractionNetwork method), [1] (Processor method) edge_updater() (GraphInteractionNetwork method), [1] (Processor method) EncodeProcessDecode (class in graphorge.gnn_base_model.model.gnn_epd_model) (class in graphorge.gnn_base_model.model.gnn_model) Encoder (class in graphorge.gnn_base_model.model.gnn_epd_model) eval() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

evaluate_criterion() (EarlyStopper method), [1] extra_repr() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) extract_data_torch_data_object() (GraphData static method)

F

find_unique_file_with_regex() (in module graphorge.ioput.iostandard) fit() (TorchMinMaxScaler method), [1] (TorchStandardScaler method), [1], [2], [3] fit_data_scalers() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] float() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

forward() (Decoder method) (EncodeProcessDecode method), [1], [2], [3] (Encoder method) (GNNEPDBaseModel method), [1], [2], [3], [4], [5] (GraphIndependentNetwork method), [1], [2], [3] (GraphInteractionNetwork method), [1], [2], [3] (Processor method), [1] (TorchRNNWrapper method), [1] fromkeys() (OrderedDict class method)

G

get() (OrderedDict method) get_buffer() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) get_dataset_basename() (GNNGraphDataset method), [1] get_dataset_directory() (GNNGraphDataset method), [1] get_dataset_sample_files() (GNNGraphDataset method), [1] get_dataset_sample_files_from_dir() (in module graphorge.gnn_base_model.data.graph_dataset) get_device() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] get_edge_features_matrix() (GraphData method), [1] get_edge_targets_matrix() (GraphData method), [1] get_edges_indexes_mesh() (GraphData static method) get_extra_state() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) get_fitted_data_scaler() (GNNEPDBaseModel method), [1], [2], [3], [4], [5], [6], [7], [8] get_global_features_matrix() (GraphData method), [1] get_global_targets_matrix() (GraphData method), [1] get_graph_edges_indexes() (GraphData method), [1] get_input_features_from_graph() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] get_learning_rate_scheduler() (in module graphorge.gnn_base_model.train.training) get_metadata() (GraphData method), [1] get_metadata_from_graph() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] get_model_summary() (in module graphorge.gnn_base_model.model.model_summary) get_n_edge() (GraphData method), [1] get_n_model_parameters() (in module graphorge.gnn_base_model.model.model_summary) get_n_node() (GraphData method), [1] get_node_features_matrix() (GraphData method), [1] get_node_targets_matrix() (GraphData method), [1] get_nodes_coords() (GraphData method), [1] get_output_features_from_graph() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] get_parameter() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) get_pyg_data_loader() (in module graphorge.gnn_base_model.data.graph_dataset) get_pytorch_activation() (GNNEPDBaseModel class method), [1], [2] get_pytorch_loss() (in module graphorge.gnn_base_model.predict.prediction) (in module graphorge.gnn_base_model.train.torch_loss) (in module graphorge.gnn_base_model.train.training) get_pytorch_optimizer() (in module graphorge.gnn_base_model.train.training) get_submodule() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) get_subset_indices_mapping() (in module graphorge.gnn_base_model.data.graph_dataset) get_torch_data_object() (GraphData method), [1] get_undirected_unique_edges() (GraphData method) (GraphData static method)

get_validation_loss_history() (EarlyStopper method), [1] GNNEPDBaseModel (class in graphorge.gnn_base_model.model.gnn_model) (class in graphorge.gnn_base_model.predict.prediction) (class in graphorge.gnn_base_model.train.training) GNNGraphDataset (class in graphorge.gnn_base_model.data.graph_dataset) GNNGraphDatasetInMemory (class in graphorge.gnn_base_model.data.graph_dataset) graph_standard_partial_fit() (in module graphorge.gnn_base_model.model.gnn_model) GraphData (class in graphorge.gnn_base_model.data.graph_data) GraphIndependentNetwork (class in graphorge.gnn_base_model.model.gnn_architectures) (class in graphorge.gnn_base_model.model.gnn_epd_model) GraphInteractionNetwork (class in graphorge.gnn_base_model.model.gnn_architectures) (class in graphorge.gnn_base_model.model.gnn_epd_model) graphorge module graphorge.gnn_base_model module graphorge.gnn_base_model.data module graphorge.gnn_base_model.data.graph_data module graphorge.gnn_base_model.data.graph_dataset module graphorge.gnn_base_model.model module graphorge.gnn_base_model.model.gnn_architectures module graphorge.gnn_base_model.model.gnn_epd_model module graphorge.gnn_base_model.model.gnn_model module graphorge.gnn_base_model.model.model_summary module graphorge.gnn_base_model.optimization module graphorge.gnn_base_model.optimization.hydra_optimization_plots module graphorge.gnn_base_model.optimization.hydra_optimization_template module graphorge.gnn_base_model.predict module graphorge.gnn_base_model.predict.prediction module graphorge.gnn_base_model.predict.prediction_plots module graphorge.gnn_base_model.train module graphorge.gnn_base_model.train.cross_validation module graphorge.gnn_base_model.train.torch_loss module graphorge.gnn_base_model.train.training module graphorge.gnn_base_model.train.training_plots module graphorge.ioput module graphorge.ioput.iostandard module graphorge.ioput.plots module graphorge.utilities module graphorge.utilities.data_scalers module grouped_bar_chart() (in module graphorge.gnn_base_model.train.training_plots) (in module graphorge.ioput.plots)

H

half() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

I

init_model_from_file() (GNNEPDBaseModel method), [1], [2] (GNNEPDBaseModel static method), [1], [2] inverse_transform() (TorchMinMaxScaler method), [1] (TorchStandardScaler method), [1], [2], [3] ipu() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

is_evaluate_criterion() (EarlyStopper method), [1] is_model_in_normalized (GNNEPDBaseModel attribute), [1], [2] is_model_out_normalized (GNNEPDBaseModel attribute), [1], [2] items() (OrderedDict method)

J

jittable() (GraphInteractionNetwork method), [1] (Processor method)

K

keys() (OrderedDict method)

kfold_cross_validation() (in module graphorge.gnn_base_model.train.cross_validation)

L

load_best_performance_state() (EarlyStopper method), [1] load_dataset() (GNNGraphDataset method) (GNNGraphDataset static method) load_loss_history() (in module graphorge.gnn_base_model.train.training) load_lr_history() (in module graphorge.gnn_base_model.train.training) load_model_data_scalers_from_file() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] load_model_state() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] load_sample_predictions() (in module graphorge.gnn_base_model.predict.prediction)

load_state_dict() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) load_training_state() (in module graphorge.gnn_base_model.train.training)

M

make_directory() (in module graphorge.gnn_base_model.predict.prediction) (in module graphorge.gnn_base_model.train.cross_validation) (in module graphorge.ioput.iostandard) make_predictions_subdir() (in module graphorge.gnn_base_model.predict.prediction) message() (GraphInteractionNetwork method), [1], [2], [3] (Processor method) message_and_aggregate() (GraphInteractionNetwork method), [1] (Processor method) model_directory (GNNEPDBaseModel attribute), [1], [2] model_name (GNNEPDBaseModel attribute), [1], [2] module graphorge graphorge.gnn_base_model graphorge.gnn_base_model.data graphorge.gnn_base_model.data.graph_data graphorge.gnn_base_model.data.graph_dataset graphorge.gnn_base_model.model graphorge.gnn_base_model.model.gnn_architectures graphorge.gnn_base_model.model.gnn_epd_model graphorge.gnn_base_model.model.gnn_model graphorge.gnn_base_model.model.model_summary graphorge.gnn_base_model.optimization graphorge.gnn_base_model.optimization.hydra_optimization_plots graphorge.gnn_base_model.optimization.hydra_optimization_template graphorge.gnn_base_model.predict graphorge.gnn_base_model.predict.prediction graphorge.gnn_base_model.predict.prediction_plots graphorge.gnn_base_model.train graphorge.gnn_base_model.train.cross_validation graphorge.gnn_base_model.train.torch_loss graphorge.gnn_base_model.train.training graphorge.gnn_base_model.train.training_plots graphorge.ioput graphorge.ioput.iostandard graphorge.ioput.plots graphorge.utilities graphorge.utilities.data_scalers

modules() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) move_time_dimension_axis() (GraphData static method) move_to_end() (OrderedDict method)

N

named_buffers() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) named_children() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) named_modules() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

named_parameters() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) new_file_path_with_int() (in module graphorge.gnn_base_model.data.graph_data) (in module graphorge.ioput.iostandard)

O

OrderedDict (class in graphorge.gnn_base_model.model.model_summary)

P

parameters() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) plot_boxplots() (in module graphorge.ioput.plots) plot_dle_error_histogram() (in module graphorge.gnn_base_model.predict.prediction_plots) plot_graph() (GraphData method), [1] plot_histogram() (in module graphorge.gnn_base_model.predict.prediction_plots) (in module graphorge.ioput.plots) plot_histogram_2d() (in module graphorge.ioput.plots) plot_kfold_cross_validation() (in module graphorge.gnn_base_model.train.training_plots) plot_loss_convergence_test() (in module graphorge.gnn_base_model.train.training_plots) plot_optimization_history() (in module graphorge.gnn_base_model.optimization.hydra_optimization_plots) plot_prediction_loss_history() (in module graphorge.gnn_base_model.predict.prediction_plots) plot_training_loss_and_lr_history() (in module graphorge.gnn_base_model.train.training_plots)

plot_training_loss_history() (in module graphorge.gnn_base_model.train.training_plots) plot_truth_vs_prediction() (in module graphorge.gnn_base_model.predict.prediction_plots) plot_xny_data() (in module graphorge.gnn_base_model.train.training_plots) (in module graphorge.ioput.plots) plot_xy2_data() (in module graphorge.gnn_base_model.train.training_plots) (in module graphorge.ioput.plots) plot_xy_data() (in module graphorge.gnn_base_model.optimization.hydra_optimization_plots) (in module graphorge.gnn_base_model.predict.prediction_plots) (in module graphorge.gnn_base_model.train.training_plots) (in module graphorge.ioput.plots) plot_xyz_data() (in module graphorge.ioput.plots) pop() (OrderedDict method) popitem() (OrderedDict method) predict() (in module graphorge.gnn_base_model.predict.prediction) (in module graphorge.gnn_base_model.train.cross_validation) (in module graphorge.gnn_base_model.train.training) predict_output_features() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] Processor (class in graphorge.gnn_base_model.model.gnn_epd_model) propagate() (GraphInteractionNetwork method), [1] (Processor method)

R

read_loss_history_from_file() (in module graphorge.gnn_base_model.train.training) read_lr_history_from_file() (in module graphorge.gnn_base_model.train.training) register_aggregate_forward_hook() (GraphInteractionNetwork method), [1] (Processor method) register_aggregate_forward_pre_hook() (GraphInteractionNetwork method), [1] (Processor method) register_backward_hook() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) register_buffer() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) register_edge_update_forward_hook() (GraphInteractionNetwork method), [1] (Processor method) register_edge_update_forward_pre_hook() (GraphInteractionNetwork method), [1] (Processor method) register_forward_hook() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) register_forward_pre_hook() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) register_full_backward_hook() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) register_full_backward_pre_hook() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

register_load_state_dict_post_hook() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) register_message_and_aggregate_forward_hook() (GraphInteractionNetwork method), [1] (Processor method) register_message_and_aggregate_forward_pre_hook() (GraphInteractionNetwork method), [1] (Processor method) register_message_forward_hook() (GraphInteractionNetwork method), [1] (Processor method) register_message_forward_pre_hook() (GraphInteractionNetwork method), [1] (Processor method) register_module() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) register_parameter() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) register_propagate_forward_hook() (GraphInteractionNetwork method), [1] (Processor method) register_propagate_forward_pre_hook() (GraphInteractionNetwork method), [1] (Processor method) register_state_dict_pre_hook() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) remove_posterior_optim_state_files() (in module graphorge.gnn_base_model.train.training) requires_grad_() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) reset_parameters() (GraphInteractionNetwork method), [1] (Processor method)

S

save_dataset() (GNNGraphDataset method), [1] save_figure() (in module graphorge.gnn_base_model.optimization.hydra_optimization_plots) (in module graphorge.gnn_base_model.predict.prediction_plots) (in module graphorge.gnn_base_model.train.training_plots) (in module graphorge.ioput.plots) save_loss_history() (in module graphorge.gnn_base_model.train.training) save_model_init_file() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] save_model_init_state() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] save_model_state() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] save_sample_predictions() (in module graphorge.gnn_base_model.predict.prediction) save_training_state() (in module graphorge.gnn_base_model.train.training) scatter_xy_data() (in module graphorge.gnn_base_model.predict.prediction_plots) (in module graphorge.ioput.plots) seed_worker() (in module graphorge.gnn_base_model.predict.prediction) (in module graphorge.gnn_base_model.train.training) set_data_scalers() (GNNEPDBaseModel method), [1], [2] set_dataset_basename() (GNNGraphDataset method), [1] set_device() (GNNEPDBaseModel method), [1], [2], [3], [4], [5] (TorchMinMaxScaler method), [1] (TorchStandardScaler method), [1], [2], [3] set_edge_features_matrix() (GraphData method), [1] set_edge_targets_matrix() (GraphData method), [1] set_extra_state() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

set_global_features_matrix() (GraphData method), [1] set_global_targets_matrix() (GraphData method), [1] set_graph_edges_indexes() (GraphData method), [1] set_maximum() (TorchMinMaxScaler method), [1] set_mean() (TorchStandardScaler method), [1], [2], [3] set_mean_and_std() (TorchStandardScaler method), [1] set_metadata() (GraphData method), [1] set_minimum() (TorchMinMaxScaler method), [1] set_minimum_and_maximum() (TorchMinMaxScaler method), [1] set_node_features_matrix() (GraphData method), [1] set_node_targets_matrix() (GraphData method), [1] set_std() (TorchStandardScaler method), [1], [2], [3] setdefault() (OrderedDict method) share_memory() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) split_dataset() (in module graphorge.gnn_base_model.data.graph_dataset) state_dict() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

T

tex_str() (in module graphorge.ioput.plots) to() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) to_empty() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) TorchMinMaxScaler (class in graphorge.utilities.data_scalers) TorchRNNWrapper (class in graphorge.gnn_base_model.model.gnn_architectures) TorchStandardScaler (class in graphorge.gnn_base_model.model.gnn_model) (class in graphorge.utilities.data_scalers)

train() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method) train_model() (in module graphorge.gnn_base_model.train.cross_validation) (in module graphorge.gnn_base_model.train.training) transform() (TorchMinMaxScaler method), [1] (TorchStandardScaler method), [1], [2], [3] type() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

U

update() (GraphInteractionNetwork method), [1], [2], [3] (OrderedDict method) (Processor method)

update_dataset_file_internal_directory() (GNNGraphDataset method) (GNNGraphDataset static method) update_global() (GraphInteractionNetwork method), [1]

V

values() (OrderedDict method)

W

write_cross_validation_summary_file() (in module graphorge.gnn_base_model.train.cross_validation) write_graph_dataset_summary_file() (in module graphorge.gnn_base_model.data.graph_dataset) write_prediction_summary_file() (in module graphorge.gnn_base_model.predict.prediction) write_summary_file() (in module graphorge.gnn_base_model.data.graph_dataset) (in module graphorge.gnn_base_model.optimization.hydra_optimization_template) (in module graphorge.gnn_base_model.predict.prediction) (in module graphorge.gnn_base_model.train.cross_validation) (in module graphorge.gnn_base_model.train.training) (in module graphorge.ioput.iostandard)

write_training_summary_file() (in module graphorge.gnn_base_model.train.training)

X

xpu() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)

Z

zero_grad() (Decoder method) (EncodeProcessDecode method), [1] (Encoder method) (GNNEPDBaseModel method), [1], [2] (GraphIndependentNetwork method), [1] (GraphInteractionNetwork method), [1] (Processor method) (TorchRNNWrapper method)