Index

_

__init__() (napistu_torch.data.dataset.EdgeBatchDataset method) (napistu_torch.data.dataset.SingleGraphDataset method) (napistu_torch.evaluation.manager.LocalEvaluationManager method) (napistu_torch.evaluation.manager.RemoteEvaluationManager method) (napistu_torch.lightning.datamodule.NapistuDataModule method) (napistu_torch.lightning.edge_batch_datamodule.EdgeBatchDataModule method) (napistu_torch.lightning.full_graph_datamodule.FullGraphDataModule method) (napistu_torch.load.checkpoints.Checkpoint method) (napistu_torch.load.encoders.SparseContScaler method) (napistu_torch.load.encoding_manager.EncodingManager method) (napistu_torch.ml.metrics.RelationWeightedAUC method) (napistu_torch.models.edge_encoder.EdgeEncoder method) (napistu_torch.models.heads.AttentionHead method) (napistu_torch.models.heads.ConditionalRotatEHead method) (napistu_torch.models.heads.Decoder method) (napistu_torch.models.heads.DistMultHead method) (napistu_torch.models.heads.DotProductHead method) (napistu_torch.models.heads.EdgeMLPHead method) (napistu_torch.models.heads.NodeClassificationHead method) (napistu_torch.models.heads.RelationAttentionHead method) (napistu_torch.models.heads.RelationAttentionMLPHead method) (napistu_torch.models.heads.RelationGatedMLPHead method) (napistu_torch.models.heads.RotatEHead method) (napistu_torch.models.heads.TransEHead method) (napistu_torch.models.message_passing_encoder.MessagePassingEncoder method) (napistu_torch.napistu_data.NapistuData method) (napistu_torch.napistu_data_store.NapistuDataStore method) (napistu_torch.tasks.base.BaseTask method) (napistu_torch.tasks.negative_sampler.NegativeSampler method) (napistu_torch.tasks.node_classification.NodeClassificationTask method) (napistu_torch.vertex_tensor.VertexTensor method) _abc_impl (napistu_torch.configs.DataConfig attribute) (napistu_torch.configs.ExperimentConfig attribute) (napistu_torch.configs.ModelConfig attribute) (napistu_torch.configs.RunManifest attribute) (napistu_torch.configs.TaskConfig attribute) (napistu_torch.configs.TrainingConfig attribute) (napistu_torch.configs.WandBConfig attribute) (napistu_torch.evaluation.manager.EvaluationManager attribute) (napistu_torch.evaluation.manager.LocalEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) (napistu_torch.labels.labeling_manager.LabelingManager attribute) (napistu_torch.lightning.datamodule.NapistuDataModule attribute) (napistu_torch.lightning.edge_batch_datamodule.EdgeBatchDataModule attribute) (napistu_torch.lightning.full_graph_datamodule.FullGraphDataModule attribute) (napistu_torch.load.artifacts.ArtifactDefinition attribute) (napistu_torch.load.checkpoints.CheckpointHyperparameters attribute) (napistu_torch.load.checkpoints.CheckpointStructure attribute) (napistu_torch.load.checkpoints.DataMetadata attribute) (napistu_torch.load.checkpoints.EdgeEncoderMetadata attribute) (napistu_torch.load.checkpoints.EncoderMetadata attribute) (napistu_torch.load.checkpoints.HeadMetadata attribute) (napistu_torch.load.checkpoints.ModelMetadata attribute) (napistu_torch.load.encoding_manager.EncodingConfig attribute) (napistu_torch.load.encoding_manager.SimpleEncodingConfig attribute) (napistu_torch.load.encoding_manager.TransformConfig attribute) (napistu_torch.tasks.base.BaseTask attribute) (napistu_torch.tasks.node_classification.NodeClassificationTask attribute) (napistu_torch.utils.environment_info.EnvironmentInfo attribute) _apply_heatmap_aesthetics() (in module napistu_torch.visualization.heatmaps) _apply_optional_nd_args() (in module napistu_torch.napistu_data) _apply_suptitle() (in module napistu_torch.visualization.heatmaps) _build_deduplicated_array() (in module napistu_torch.load.encoding) _build_degree_distributions() (napistu_torch.tasks.negative_sampler.NegativeSampler method) _build_edge_hash() (napistu_torch.tasks.negative_sampler.NegativeSampler method) _build_heatmap_kwargs() (in module napistu_torch.visualization.heatmaps) _build_strata_structure() (napistu_torch.tasks.negative_sampler.NegativeSampler method) _check_collisions_vectorized() (napistu_torch.tasks.negative_sampler.NegativeSampler method) _compute_dot_scores() (napistu_torch.models.heads.ConditionalRotatEHead method) _compute_per_relation_aucs() (in module napistu_torch.ml.metrics) _compute_rank_shift_for_group() (in module napistu_torch.utils.statistics) _compute_rotate_scores() (napistu_torch.models.heads.ConditionalRotatEHead method) _convert_simple_to_complex() (napistu_torch.load.encoding_manager.EncodingManager static method) _create_comprehensive_pathway_memberships() (in module napistu_torch.load.artifacts) _create_edge_prediction_data() (in module napistu_torch.load.artifacts)

_create_edge_strata_by_edge_sbo_terms() (in module napistu_torch.load.artifacts) _create_edge_strata_by_node_species_type() (in module napistu_torch.load.artifacts) _create_edge_strata_by_node_type() (in module napistu_torch.load.artifacts) _create_encoding_table() (napistu_torch.load.encoding_manager.EncodingManager method), [1] _create_name_to_sid_map() (in module napistu_torch.load.artifacts) _create_relation_prediction_data() (in module napistu_torch.load.artifacts) _create_species_identifiers() (in module napistu_torch.load.artifacts) _create_species_type_prediction_data() (in module napistu_torch.load.artifacts) _create_unlabeled_data() (in module napistu_torch.load.artifacts) _extract_edge_weights() (in module napistu_torch.load.napistu_graphs) _extract_metric() (in module napistu_torch.visualization.basic_metrics) _find_cross_config_conflicts() (in module napistu_torch.load.encoding_manager) _generate_edge_attributes() (napistu_torch.tasks.negative_sampler.NegativeSampler method) _generate_relations() (napistu_torch.tasks.negative_sampler.NegativeSampler method) _get_feature_names() (in module napistu_torch.load.encoding) _get_napistu_graph_names() (in module napistu_torch.load.napistu_graphs) _get_observed_over_expected_strata() (in module napistu_torch.evaluation.edge_prediction) _get_prediction_by_strata() (in module napistu_torch.evaluation.edge_prediction) _group_identical_columns() (in module napistu_torch.load.encoding) _ignore_graph_attributes() (in module napistu_torch.load.napistu_graphs) _ignore_if_constant() (in module napistu_torch.load.napistu_graphs) _initialize_weights() (napistu_torch.models.heads.AttentionHead method) (napistu_torch.models.heads.RelationAttentionHead method) (napistu_torch.models.heads.RelationAttentionMLPHead method) _is_comparable_value() (in module napistu_torch.data.compare_napistu_data) _load_registry() (napistu_torch.napistu_data_store.NapistuDataStore method) _log_pathological_labels() (in module napistu_torch.ml.metrics) _merge_configs() (in module napistu_torch.load.encoding_manager) _name_napistu_data() (in module napistu_torch.load.napistu_graphs) _napistu_graph_to_edge_masked_napistu_data() (in module napistu_torch.load.napistu_graphs) _napistu_graph_to_inductive_napistu_data() (in module napistu_torch.load.napistu_graphs) _napistu_graph_to_unmasked_napistu_data() (in module napistu_torch.load.napistu_graphs) _napistu_graph_to_vertex_masked_napistu_data() (in module napistu_torch.load.napistu_graphs) _parse_checkpoint_filename() (in module napistu_torch.evaluation.manager) _parse_edge_weighting() (in module napistu_torch.models.message_passing_encoder) _plot_test_val_auc() (in module napistu_torch.visualization.basic_metrics) _plot_train_loss() (in module napistu_torch.visualization.basic_metrics) _predict_impl() (napistu_torch.tasks.base.BaseTask method) (napistu_torch.tasks.node_classification.NodeClassificationTask method) _prepare_continuous_labels() (in module napistu_torch.labels.create) _prepare_discrete_labels() (in module napistu_torch.labels.create) _prepare_filtering_mask() (in module napistu_torch.visualization.embeddings) _prepare_heatmap_data() (in module napistu_torch.visualization.heatmaps) _remove_deprecated_fields() (in module napistu_torch.configs) _reorder_for_clustering() (in module napistu_torch.visualization.heatmaps) _resolve_canonical_names() (in module napistu_torch.load.encoding) _resolve_checkpoint_path (napistu_torch.evaluation.manager.LocalEvaluationManager attribute) _resolve_checkpoint_path() (napistu_torch.evaluation.manager.LocalEvaluationManager method) _resolve_data_store_for_remote() (in module napistu_torch.evaluation.manager) _resolve_device() (in module napistu_torch.evaluation.edge_weights) _resolve_path() (in module napistu_torch.napistu_data_store) _rollup_pathway_similarities() (in module napistu_torch.evaluation.pathways) _sample_and_filter_batch() (napistu_torch.tasks.negative_sampler.NegativeSampler method) _sample_candidates() (napistu_torch.tasks.negative_sampler.NegativeSampler method) _sample_from_strata() (napistu_torch.tasks.negative_sampler.NegativeSampler method) _save_registry() (napistu_torch.napistu_data_store.NapistuDataStore method) _sklearn_auto_wrap_output_keys (napistu_torch.load.encoders.SparseContScaler attribute) _standardize_graph_dfs_and_encodings() (in module napistu_torch.load.napistu_graphs) _task_config_to_artifact_names_edge_prediction() (in module napistu_torch.configs) _update_model_config_with_encoder() (napistu_torch.load.checkpoints.Checkpoint method) _update_model_config_with_head() (napistu_torch.load.checkpoints.Checkpoint method) _validate_create_inputs() (in module napistu_torch.napistu_data_store) _validate_edge_encoding() (napistu_torch.napistu_data.NapistuData method) _validate_feature_aliases() (in module napistu_torch.data.compare_napistu_data) _validate_feature_names() (in module napistu_torch.data.compare_napistu_data) (in module napistu_torch.load.encoding) _validate_keys() (in module napistu_torch.data.compare_napistu_data) _validate_labels() (napistu_torch.napistu_data.NapistuData method) _validate_mask_hashes() (in module napistu_torch.data.compare_napistu_data) _validate_no_duplicate_names() (napistu_torch.napistu_data_store.NapistuDataStore method) _validate_relation_labels() (in module napistu_torch.data.compare_napistu_data) _validate_required_nd_args() (in module napistu_torch.napistu_data) _validate_structural_attributes() (in module napistu_torch.data.compare_napistu_data) _validate_vertex_encoding() (napistu_torch.napistu_data.NapistuData method) _within_category_similarity() (in module napistu_torch.evaluation.pathways)

A

accelerator (napistu_torch.configs.TrainingConfig attribute) add_optional_attr() (in module napistu_torch.utils.nd_utils) align_to_napistu_data (napistu_torch.vertex_tensor.VertexTensor attribute) align_to_napistu_data() (napistu_torch.vertex_tensor.VertexTensor method) anonymize() (napistu_torch.configs.ExperimentConfig method) artifact_type (napistu_torch.load.artifacts.ArtifactDefinition attribute)

ArtifactDefinition (class in napistu_torch.load.artifacts) assert_same_napistu_data() (napistu_torch.load.checkpoints.Checkpoint method) AttentionHead (class in napistu_torch.models.heads) augment_napistu_graph() (in module napistu_torch.load.napistu_graphs) augment_summary_types (napistu_torch.labels.labeling_manager.LabelingManager attribute), [1] auto_encode() (in module napistu_torch.load.encoding)

B

BaseTask (class in napistu_torch.tasks.base) batches_per_epoch (napistu_torch.configs.TrainingConfig attribute) best_checkpoint_path (napistu_torch.evaluation.manager.LocalEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager property)

best_checkpoint_val_auc (napistu_torch.evaluation.manager.LocalEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager property)

C

calculate_pathway_similarities() (in module napistu_torch.evaluation.pathways) calculate_rank_shift() (in module napistu_torch.utils.statistics) calculate_ranks() (in module napistu_torch.utils.pd_utils) check_no_column_conflicts() (napistu_torch.load.encoding_manager.EncodingConfig method) Checkpoint (class in napistu_torch.load.checkpoints) checkpoint (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) checkpoint_dir (napistu_torch.evaluation.manager.LocalEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager property) checkpoint_metric (napistu_torch.configs.TrainingConfig attribute) checkpoint_path (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) checkpoint_subdir (napistu_torch.configs.TrainingConfig attribute) CheckpointHyperparameters (class in napistu_torch.load.checkpoints) CheckpointStructure (class in napistu_torch.load.checkpoints) classify_encoding() (in module napistu_torch.load.encoding) cleanup_tensors() (in module napistu_torch.utils.torch_utils) columns (napistu_torch.load.encoding_manager.TransformConfig attribute) compare_top_k_union_ranks() (in module napistu_torch.utils.statistics) compose() (napistu_torch.load.encoding_manager.EncodingManager method), [1] compose_encoding_configs() (in module napistu_torch.load.encoding) compute() (napistu_torch.ml.metrics.RelationWeightedAUC method) compute_edge_feature_sensitivity() (in module napistu_torch.evaluation.edge_weights) compute_loss() (napistu_torch.tasks.base.BaseTask method) (napistu_torch.tasks.node_classification.NodeClassificationTask method) compute_mask_hashes() (in module napistu_torch.utils.nd_utils) compute_metrics() (napistu_torch.tasks.base.BaseTask method) (napistu_torch.tasks.node_classification.NodeClassificationTask method)

compute_rotate_distance() (in module napistu_torch.models.head_utils) ConditionalRotatEHead (class in napistu_torch.models.heads) config (napistu_torch.load.checkpoints.CheckpointHyperparameters attribute) (napistu_torch.models.edge_encoder.EdgeEncoder property) (napistu_torch.models.heads.Decoder property) (napistu_torch.models.message_passing_encoder.MessagePassingEncoder property) config_ (napistu_torch.load.encoding_manager.EncodingManager attribute) config_to_column_transformer() (in module napistu_torch.load.encoding) config_to_data_trimming_spec() (in module napistu_torch.configs) construct_unlabeled_napistu_data() (in module napistu_torch.load.napistu_graphs) construct_vertex_labeled_napistu_data() (in module napistu_torch.load.napistu_graphs) copy() (napistu_torch.napistu_data.NapistuData method) (napistu_torch.vertex_tensor.VertexTensor method) copy_to_store (napistu_torch.configs.DataConfig attribute) CorruptionError create() (napistu_torch.napistu_data_store.NapistuDataStore class method) create_artifact() (in module napistu_torch.load.artifacts) create_composite_edge_strata() (in module napistu_torch.load.stratification) create_install_directions() (in module napistu_torch.utils.environment_info) create_relation_labels() (in module napistu_torch.labels.create) create_single_graph_dataloader() (in module napistu_torch.data.data_utils) create_split_masks() (in module napistu_torch.ml.splitting) create_template_yaml() (in module napistu_torch.configs) create_vertex_labels() (in module napistu_torch.labels.create) created_at (napistu_torch.configs.RunManifest attribute) creation_func (napistu_torch.load.artifacts.ArtifactDefinition attribute)

D

data (napistu_torch.configs.ExperimentConfig attribute) (napistu_torch.load.checkpoints.CheckpointHyperparameters attribute) (napistu_torch.vertex_tensor.VertexTensor attribute) DataConfig (class in napistu_torch.configs) DataMetadata (class in napistu_torch.load.checkpoints) decode_labels() (in module napistu_torch.labels.apply) Decoder (class in napistu_torch.models.heads) deduplicate_features() (in module napistu_torch.load.encoding) delete_tensors() (in module napistu_torch.utils.torch_utils)

description (napistu_torch.load.artifacts.ArtifactDefinition attribute) (napistu_torch.vertex_tensor.VertexTensor attribute) detect_config_format() (in module napistu_torch.load.encoding_manager) deterministic (napistu_torch.configs.ExperimentConfig attribute) devices (napistu_torch.configs.TrainingConfig attribute) DistMultHead (class in napistu_torch.models.heads) DotProductHead (class in napistu_torch.models.heads) dropout (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.EncoderMetadata attribute)

E

early_stopping (napistu_torch.configs.TrainingConfig attribute) early_stopping_metric (napistu_torch.configs.TrainingConfig attribute) early_stopping_patience (napistu_torch.configs.TrainingConfig attribute) edge_encoder (napistu_torch.load.checkpoints.ModelMetadata attribute) edge_encoder_dim (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.EdgeEncoderMetadata attribute) edge_encoder_dropout (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.EdgeEncoderMetadata attribute) edge_encoder_init_bias (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.EdgeEncoderMetadata attribute) edge_feature_name_aliases (napistu_torch.load.checkpoints.DataMetadata attribute) edge_feature_names (napistu_torch.load.checkpoints.DataMetadata attribute) edge_in_channels (napistu_torch.load.checkpoints.EdgeEncoderMetadata attribute) (napistu_torch.load.checkpoints.EncoderMetadata attribute) edge_prediction_neg_sampling_ratio (napistu_torch.configs.TaskConfig attribute) edge_prediction_neg_sampling_strategy (napistu_torch.configs.TaskConfig attribute) edge_prediction_neg_sampling_stratify_by (napistu_torch.configs.TaskConfig attribute) EdgeBatchDataModule (class in napistu_torch.lightning.edge_batch_datamodule) EdgeBatchDataset (class in napistu_torch.data.dataset) EdgeEncoder (class in napistu_torch.models.edge_encoder) EdgeEncoderMetadata (class in napistu_torch.load.checkpoints) EdgeMLPHead (class in napistu_torch.models.heads) embedding_norm_monitoring (napistu_torch.configs.TrainingConfig attribute) embedding_norm_monitoring_log_every_n_epochs (napistu_torch.configs.TrainingConfig attribute) empty_cache() (in module napistu_torch.utils.torch_utils) enable_artifact_creation() (napistu_torch.napistu_data_store.NapistuDataStore method) encode() (napistu_torch.models.message_passing_encoder.MessagePassingEncoder method) encode_dataframe() (in module napistu_torch.load.encoding) encode_labels() (in module napistu_torch.labels.create) encode_sparse_continuous() (in module napistu_torch.load.encoders) encoder (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.EncoderMetadata attribute) (napistu_torch.load.checkpoints.ModelMetadata attribute)

EncoderMetadata (class in napistu_torch.load.checkpoints) EncodingConfig (class in napistu_torch.load.encoding_manager) EncodingManager (class in napistu_torch.load.encoding_manager) ensure() (napistu_torch.load.encoding_manager.EncodingManager class method) (napistu_torch.load.encoding_manager.EncodingManager method) ensure_artifacts() (napistu_torch.napistu_data_store.NapistuDataStore method) ensure_device() (in module napistu_torch.utils.torch_utils) ensure_path() (in module napistu_torch.utils.base_utils) ensure_strata_series() (in module napistu_torch.load.stratification) ensure_stratify_by_artifact_name() (in module napistu_torch.load.artifacts) entity (napistu_torch.configs.WandBConfig attribute) environment (napistu_torch.load.checkpoints.CheckpointHyperparameters attribute) EnvironmentInfo (class in napistu_torch.utils.environment_info) epoch (napistu_torch.load.checkpoints.CheckpointStructure attribute) epochs (napistu_torch.configs.TrainingConfig attribute) estimate_memory_footprint() (napistu_torch.napistu_data.NapistuData method) EvaluationManager (class in napistu_torch.evaluation.manager) exclude_vertex_attributes (napistu_torch.labels.labeling_manager.LabelingManager attribute), [1] expand_deduplicated_features() (in module napistu_torch.load.encoding) experiment_config (napistu_torch.configs.RunManifest attribute) (napistu_torch.evaluation.manager.EvaluationManager attribute) (napistu_torch.evaluation.manager.EvaluationManager property) experiment_dict (napistu_torch.evaluation.manager.EvaluationManager attribute), [1] (napistu_torch.evaluation.manager.LocalEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) experiment_dir (napistu_torch.evaluation.manager.LocalEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager property) experiment_name (napistu_torch.configs.RunManifest attribute) (napistu_torch.evaluation.manager.EvaluationManager attribute) (napistu_torch.evaluation.manager.EvaluationManager property) ExperimentConfig (class in napistu_torch.configs) extra_packages (napistu_torch.utils.environment_info.EnvironmentInfo attribute)

F

fast_dev_run (napistu_torch.configs.ExperimentConfig attribute) feature_names (napistu_torch.vertex_tensor.VertexTensor attribute) filter_and_reorder_df() (in module napistu_torch.utils.pd_utils) find_best_checkpoint() (in module napistu_torch.evaluation.manager) fit() (napistu_torch.load.encoders.SparseContScaler method) fit_encoders() (in module napistu_torch.load.encoding) format_edge_feature_sensitivity() (in module napistu_torch.evaluation.edge_weights) format_metric_label() (in module napistu_torch.utils.labeling_utils) format_metrics_as_markdown() (in module napistu_torch.utils.table_utils) format_summary() (in module napistu_torch.utils.nd_utils) forward() (napistu_torch.models.edge_encoder.EdgeEncoder method) (napistu_torch.models.heads.AttentionHead method) (napistu_torch.models.heads.ConditionalRotatEHead method) (napistu_torch.models.heads.Decoder method) (napistu_torch.models.heads.DistMultHead method) (napistu_torch.models.heads.DotProductHead method) (napistu_torch.models.heads.EdgeMLPHead method) (napistu_torch.models.heads.NodeClassificationHead method) (napistu_torch.models.heads.RelationAttentionHead method) (napistu_torch.models.heads.RelationAttentionMLPHead method) (napistu_torch.models.heads.RelationGatedMLPHead method) (napistu_torch.models.heads.RotatEHead method) (napistu_torch.models.heads.TransEHead method) (napistu_torch.models.message_passing_encoder.MessagePassingEncoder method) (napistu_torch.tasks.base.BaseTask method)

from_config() (napistu_torch.models.heads.Decoder class method) (napistu_torch.models.message_passing_encoder.MessagePassingEncoder class method) (napistu_torch.napistu_data_store.NapistuDataStore class method) from_current_env() (napistu_torch.utils.environment_info.EnvironmentInfo class method) from_dict (napistu_torch.labels.labeling_manager.LabelingManager attribute) from_dict() (napistu_torch.labels.labeling_manager.LabelingManager class method) from_huggingface (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) from_huggingface() (napistu_torch.configs.RunManifest class method) (napistu_torch.evaluation.manager.RemoteEvaluationManager class method) (napistu_torch.napistu_data_store.NapistuDataStore class method) from_json() (napistu_torch.configs.ExperimentConfig class method) from_task_and_data() (napistu_torch.load.checkpoints.CheckpointHyperparameters class method) from_yaml() (napistu_torch.configs.ExperimentConfig class method) (napistu_torch.configs.RunManifest class method) FullGraphDataModule (class in napistu_torch.lightning.full_graph_datamodule)

G

gat_concat (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.EncoderMetadata attribute) gat_heads (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.EncoderMetadata attribute) gcs_model_to_store() (in module napistu_torch.load.gcs) get_architecture_string() (napistu_torch.configs.ModelConfig method) get_artifact_info() (in module napistu_torch.load.artifacts) get_checkpoint_dir() (napistu_torch.configs.TrainingConfig method) get_comprehensive_source_membership() (in module napistu_torch.evaluation.pathways) get_config() (napistu_torch.load.encoding_manager.EncodingManager method), [1] get_data_summary() (napistu_torch.load.checkpoints.Checkpoint method) get_edge_encoder_config() (napistu_torch.load.checkpoints.Checkpoint method) get_edge_feature_names() (napistu_torch.napistu_data.NapistuData method) get_edge_indices() (napistu_torch.napistu_data.NapistuData method) get_edge_names() (napistu_torch.napistu_data.NapistuData method) get_edge_weights() (napistu_torch.napistu_data.NapistuData method) get_embeddings() (napistu_torch.tasks.base.BaseTask method) get_encoder_config() (napistu_torch.load.checkpoints.Checkpoint method) get_encoding_table() (napistu_torch.load.encoding_manager.EncodingManager method), [1] get_enhanced_tags() (napistu_torch.configs.WandBConfig method) get_environment_info() (napistu_torch.load.checkpoints.Checkpoint method) get_experiment_dict (napistu_torch.evaluation.manager.EvaluationManager attribute) get_experiment_dict() (napistu_torch.evaluation.manager.EvaluationManager method) get_experiment_name() (napistu_torch.configs.ExperimentConfig method) get_feature_by_name() (napistu_torch.napistu_data.NapistuData method) get_feature_names_out() (napistu_torch.load.encoders.SparseContScaler method) get_features_by_regex() (napistu_torch.napistu_data.NapistuData method) get_head_config() (napistu_torch.load.checkpoints.Checkpoint method) get_install_directions() (napistu_torch.utils.environment_info.EnvironmentInfo method) get_label_names (napistu_torch.labels.labeling_manager.LabelingManager attribute)

get_label_names() (napistu_torch.labels.labeling_manager.LabelingManager method) get_learned_edge_weights() (napistu_torch.tasks.base.BaseTask method) get_missing_artifacts() (napistu_torch.napistu_data_store.NapistuDataStore method) get_node2vec_model() (in module napistu_torch.models.node2vec) get_node2vec_training_loop() (in module napistu_torch.models.node2vec) get_node2vec_training_regime() (in module napistu_torch.models.node2vec) get_num_relations() (napistu_torch.napistu_data.NapistuData method) get_run_summary (napistu_torch.evaluation.manager.EvaluationManager attribute) get_run_summary() (napistu_torch.configs.RunManifest method) (napistu_torch.evaluation.manager.EvaluationManager method) (napistu_torch.evaluation.manager.RemoteEvaluationManager method) get_save_dir() (napistu_torch.configs.WandBConfig method) get_store (napistu_torch.evaluation.manager.EvaluationManager attribute) get_store() (napistu_torch.evaluation.manager.EvaluationManager method) get_summary() (napistu_torch.models.edge_encoder.EdgeEncoder method) (napistu_torch.models.heads.Decoder method) (napistu_torch.models.message_passing_encoder.MessagePassingEncoder method) (napistu_torch.napistu_data.NapistuData method) (napistu_torch.tasks.base.BaseTask method) (napistu_torch.utils.environment_info.EnvironmentInfo method) get_summary_string (napistu_torch.evaluation.manager.EvaluationManager attribute) get_summary_string() (napistu_torch.evaluation.manager.EvaluationManager method) get_symmetrical_relation_indices() (napistu_torch.napistu_data.NapistuData method) get_vertex_feature_names() (napistu_torch.napistu_data.NapistuData method) get_vertex_indices() (napistu_torch.napistu_data.NapistuData method) get_vertex_names() (napistu_torch.napistu_data.NapistuData method) global_step (napistu_torch.load.checkpoints.CheckpointStructure attribute) gradient_clip_val (napistu_torch.configs.TrainingConfig attribute) graph_conv_aggregator (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.EncoderMetadata attribute) group (napistu_torch.configs.WandBConfig attribute)

H

has_edges() (napistu_torch.napistu_data.NapistuData method) head (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.HeadMetadata attribute) (napistu_torch.load.checkpoints.ModelMetadata attribute) HeadMetadata (class in napistu_torch.load.checkpoints) hf_repo_id (napistu_torch.configs.DataConfig attribute)

hf_revision (napistu_torch.configs.DataConfig attribute) hidden_channels (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.EncoderMetadata attribute) (napistu_torch.load.checkpoints.HeadMetadata attribute) hierarchical_cluster() (in module napistu_torch.visualization.heatmaps) hyper_parameters (napistu_torch.load.checkpoints.CheckpointStructure attribute)

I

identity_collate() (in module napistu_torch.data.data_utils) import_bionty() (in module napistu_torch.utils.optional) import_gradio_client() (in module napistu_torch.utils.optional) import_lightning() (in module napistu_torch.utils.optional) import_modelgenerator() (in module napistu_torch.utils.optional) import_scdataloader() (in module napistu_torch.utils.optional)

import_scgpt() (in module napistu_torch.utils.optional) import_scprint() (in module napistu_torch.utils.optional) import_seaborn() (in module napistu_torch.utils.optional) import_torchtext() (in module napistu_torch.utils.optional) in_channels (napistu_torch.load.checkpoints.EncoderMetadata attribute) init_head_as_identity (napistu_torch.configs.ModelConfig attribute)

L

label_attribute (napistu_torch.labels.labeling_manager.LabelingManager attribute), [1] label_names (napistu_torch.labels.labeling_manager.LabelingManager attribute), [1] LabelingManager (class in napistu_torch.labels.labeling_manager) layout_tsne() (in module napistu_torch.visualization.embeddings) layout_umap() (in module napistu_torch.visualization.embeddings) limit_train_batches (napistu_torch.configs.ExperimentConfig attribute) limit_val_batches (napistu_torch.configs.ExperimentConfig attribute) list_artifacts() (napistu_torch.napistu_data_store.NapistuDataStore method) list_available_artifacts() (in module napistu_torch.load.artifacts) list_napistu_datas() (napistu_torch.napistu_data_store.NapistuDataStore method) list_pandas_dfs() (napistu_torch.napistu_data_store.NapistuDataStore method) list_vertex_tensors() (napistu_torch.napistu_data_store.NapistuDataStore method) load (napistu_torch.vertex_tensor.VertexTensor attribute) load() (napistu_torch.load.checkpoints.Checkpoint class method) (napistu_torch.napistu_data.NapistuData class method) (napistu_torch.vertex_tensor.VertexTensor class method) load_artifact() (napistu_torch.napistu_data_store.NapistuDataStore method) load_model_from_checkpoint (napistu_torch.evaluation.manager.EvaluationManager attribute) (napistu_torch.evaluation.manager.LocalEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) load_model_from_checkpoint() (napistu_torch.evaluation.manager.EvaluationManager method) (napistu_torch.evaluation.manager.LocalEvaluationManager method) (napistu_torch.evaluation.manager.RemoteEvaluationManager method)

load_napistu_data (napistu_torch.evaluation.manager.EvaluationManager attribute) load_napistu_data() (napistu_torch.evaluation.manager.EvaluationManager method) (napistu_torch.napistu_data_store.NapistuDataStore method) load_napistu_graph() (napistu_torch.napistu_data_store.NapistuDataStore method) load_pandas_df() (napistu_torch.napistu_data_store.NapistuDataStore method) load_sbml_dfs() (napistu_torch.napistu_data_store.NapistuDataStore method) load_vertex_tensor() (napistu_torch.napistu_data_store.NapistuDataStore method) LocalEvaluationManager (class in napistu_torch.evaluation.manager) log_memory_usage() (in module napistu_torch.utils.torch_utils) log_model (napistu_torch.configs.WandBConfig attribute) log_summary() (napistu_torch.load.encoding_manager.EncodingManager method), [1] loss_type (napistu_torch.models.heads.AttentionHead attribute) (napistu_torch.models.heads.ConditionalRotatEHead attribute) (napistu_torch.models.heads.Decoder property) (napistu_torch.models.heads.DistMultHead attribute) (napistu_torch.models.heads.DotProductHead attribute) (napistu_torch.models.heads.EdgeMLPHead attribute) (napistu_torch.models.heads.RelationAttentionHead attribute) (napistu_torch.models.heads.RelationAttentionMLPHead attribute) (napistu_torch.models.heads.RelationGatedMLPHead attribute) (napistu_torch.models.heads.RotatEHead attribute) (napistu_torch.models.heads.TransEHead attribute) loss_weight_alpha (napistu_torch.configs.TaskConfig attribute) lr (napistu_torch.configs.TrainingConfig attribute)

M

manifest (napistu_torch.evaluation.manager.EvaluationManager attribute), [1] (napistu_torch.evaluation.manager.LocalEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) map_identifiers_to_vertex_names() (in module napistu_torch.utils.napistu_utils) margin (napistu_torch.models.heads.Decoder property) memory_manager() (in module napistu_torch.utils.torch_utils) merge_rare_strata() (in module napistu_torch.load.stratification) MessagePassingEncoder (class in napistu_torch.models.message_passing_encoder) metrics (napistu_torch.configs.TaskConfig attribute) mlp_dropout (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.HeadMetadata attribute) mlp_hidden_dim (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.HeadMetadata attribute) mlp_num_layers (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.HeadMetadata attribute) mode (napistu_torch.configs.WandBConfig attribute) model (napistu_torch.configs.ExperimentConfig attribute) (napistu_torch.load.checkpoints.CheckpointHyperparameters attribute) model_config (napistu_torch.configs.DataConfig attribute) (napistu_torch.configs.ExperimentConfig attribute) (napistu_torch.configs.ModelConfig attribute) (napistu_torch.configs.RunManifest attribute) (napistu_torch.configs.TaskConfig attribute) (napistu_torch.configs.TrainingConfig attribute) (napistu_torch.configs.WandBConfig attribute) (napistu_torch.labels.labeling_manager.LabelingManager attribute) (napistu_torch.load.artifacts.ArtifactDefinition attribute) (napistu_torch.load.checkpoints.CheckpointHyperparameters attribute) (napistu_torch.load.checkpoints.CheckpointStructure attribute) (napistu_torch.load.checkpoints.DataMetadata attribute) (napistu_torch.load.checkpoints.EdgeEncoderMetadata attribute) (napistu_torch.load.checkpoints.EncoderMetadata attribute) (napistu_torch.load.checkpoints.HeadMetadata attribute) (napistu_torch.load.checkpoints.ModelMetadata attribute) (napistu_torch.load.encoding_manager.EncodingConfig attribute) (napistu_torch.load.encoding_manager.SimpleEncodingConfig attribute) (napistu_torch.load.encoding_manager.TransformConfig attribute) (napistu_torch.utils.environment_info.EnvironmentInfo attribute) ModelConfig (class in napistu_torch.configs) ModelMetadata (class in napistu_torch.load.checkpoints) module napistu_torch napistu_torch.configs napistu_torch.constants napistu_torch.data napistu_torch.data.compare_napistu_data napistu_torch.data.constants napistu_torch.data.data_utils napistu_torch.data.dataset napistu_torch.evaluation napistu_torch.evaluation.constants napistu_torch.evaluation.edge_prediction napistu_torch.evaluation.edge_weights napistu_torch.evaluation.manager napistu_torch.evaluation.pathways napistu_torch.labels napistu_torch.labels.apply napistu_torch.labels.constants napistu_torch.labels.create napistu_torch.labels.labeling_manager napistu_torch.lightning napistu_torch.lightning.constants napistu_torch.lightning.datamodule napistu_torch.lightning.edge_batch_datamodule napistu_torch.lightning.full_graph_datamodule napistu_torch.load napistu_torch.load.artifacts napistu_torch.load.checkpoints napistu_torch.load.constants napistu_torch.load.encoders napistu_torch.load.encoding napistu_torch.load.encoding_manager napistu_torch.load.gcs napistu_torch.load.napistu_graphs napistu_torch.load.stratification napistu_torch.ml napistu_torch.ml.constants napistu_torch.ml.metrics napistu_torch.ml.splitting napistu_torch.models napistu_torch.models.constants napistu_torch.models.edge_encoder napistu_torch.models.head_utils napistu_torch.models.heads napistu_torch.models.message_passing_encoder napistu_torch.models.node2vec napistu_torch.napistu_data napistu_torch.napistu_data_store napistu_torch.tasks napistu_torch.tasks.base napistu_torch.tasks.constants napistu_torch.tasks.negative_sampler napistu_torch.tasks.node_classification napistu_torch.utils napistu_torch.utils.base_utils napistu_torch.utils.constants napistu_torch.utils.environment_info napistu_torch.utils.labeling_utils napistu_torch.utils.napistu_utils napistu_torch.utils.nd_utils napistu_torch.utils.optional napistu_torch.utils.pd_utils napistu_torch.utils.statistics napistu_torch.utils.string_utils napistu_torch.utils.table_utils napistu_torch.utils.torch_utils napistu_torch.vertex_tensor napistu_torch.visualization napistu_torch.visualization.advanced_metrics napistu_torch.visualization.basic_metrics napistu_torch.visualization.constants napistu_torch.visualization.embeddings napistu_torch.visualization.heatmaps

N

name (napistu_torch.configs.ExperimentConfig attribute) (napistu_torch.load.artifacts.ArtifactDefinition attribute) (napistu_torch.load.checkpoints.DataMetadata attribute) (napistu_torch.vertex_tensor.VertexTensor attribute) napistu_data_name (napistu_torch.configs.DataConfig attribute) napistu_data_store (napistu_torch.evaluation.manager.EvaluationManager attribute), [1] (napistu_torch.evaluation.manager.LocalEvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) napistu_graph_path (napistu_torch.configs.DataConfig attribute) napistu_graph_to_napistu_data() (in module napistu_torch.load.napistu_graphs) napistu_torch module napistu_torch.configs module napistu_torch.constants module napistu_torch.data module napistu_torch.data.compare_napistu_data module napistu_torch.data.constants module napistu_torch.data.data_utils module napistu_torch.data.dataset module napistu_torch.evaluation module napistu_torch.evaluation.constants module napistu_torch.evaluation.edge_prediction module napistu_torch.evaluation.edge_weights module napistu_torch.evaluation.manager module napistu_torch.evaluation.pathways module napistu_torch.labels module napistu_torch.labels.apply module napistu_torch.labels.constants module napistu_torch.labels.create module napistu_torch.labels.labeling_manager module napistu_torch.lightning module napistu_torch.lightning.constants module napistu_torch.lightning.datamodule module napistu_torch.lightning.edge_batch_datamodule module napistu_torch.lightning.full_graph_datamodule module napistu_torch.load module napistu_torch.load.artifacts module napistu_torch.load.checkpoints module napistu_torch.load.constants module napistu_torch.load.encoders module napistu_torch.load.encoding module napistu_torch.load.encoding_manager module napistu_torch.load.gcs module napistu_torch.load.napistu_graphs module napistu_torch.load.stratification module napistu_torch.ml module napistu_torch.ml.constants module napistu_torch.ml.metrics module napistu_torch.ml.splitting module napistu_torch.models module napistu_torch.models.constants module

napistu_torch.models.edge_encoder module napistu_torch.models.head_utils module napistu_torch.models.heads module napistu_torch.models.message_passing_encoder module napistu_torch.models.node2vec module napistu_torch.napistu_data module napistu_torch.napistu_data_store module napistu_torch.tasks module napistu_torch.tasks.base module napistu_torch.tasks.constants module napistu_torch.tasks.negative_sampler module napistu_torch.tasks.node_classification module napistu_torch.utils module napistu_torch.utils.base_utils module napistu_torch.utils.constants module napistu_torch.utils.environment_info module napistu_torch.utils.labeling_utils module napistu_torch.utils.napistu_utils module napistu_torch.utils.nd_utils module napistu_torch.utils.optional module napistu_torch.utils.pd_utils module napistu_torch.utils.statistics module napistu_torch.utils.string_utils module napistu_torch.utils.table_utils module napistu_torch.utils.torch_utils module napistu_torch.vertex_tensor module napistu_torch.visualization module napistu_torch.visualization.advanced_metrics module napistu_torch.visualization.basic_metrics module napistu_torch.visualization.constants module napistu_torch.visualization.embeddings module napistu_torch.visualization.heatmaps module napistu_torch_version (napistu_torch.utils.environment_info.EnvironmentInfo attribute) napistu_version (napistu_torch.utils.environment_info.EnvironmentInfo attribute) NapistuData (class in napistu_torch.napistu_data) NapistuDataModule (class in napistu_torch.lightning.datamodule) NapistuDataStore (class in napistu_torch.napistu_data_store) nc_dropout (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.HeadMetadata attribute) NegativeSampler (class in napistu_torch.tasks.negative_sampler) NodeClassificationHead (class in napistu_torch.models.heads) NodeClassificationTask (class in napistu_torch.tasks.node_classification) normalize_and_validate_indices() (in module napistu_torch.utils.base_utils) normalized_distances_to_probs() (in module napistu_torch.models.head_utils) num_classes (napistu_torch.load.checkpoints.HeadMetadata attribute) num_edge_features (napistu_torch.lightning.datamodule.NapistuDataModule property) (napistu_torch.load.checkpoints.DataMetadata attribute) num_edges (napistu_torch.load.checkpoints.DataMetadata attribute) num_layers (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.EncoderMetadata attribute) num_node_features (napistu_torch.lightning.datamodule.NapistuDataModule property) (napistu_torch.load.checkpoints.DataMetadata attribute) num_nodes (napistu_torch.load.checkpoints.DataMetadata attribute) num_relations (napistu_torch.load.checkpoints.HeadMetadata attribute) num_test_edges (napistu_torch.load.checkpoints.DataMetadata attribute) num_train_edges (napistu_torch.load.checkpoints.DataMetadata attribute) num_unique_relations (napistu_torch.load.checkpoints.DataMetadata attribute) num_val_edges (napistu_torch.load.checkpoints.DataMetadata attribute)

O

optimizer (napistu_torch.configs.TrainingConfig attribute)

other_artifacts (napistu_torch.configs.DataConfig attribute) output_dir (napistu_torch.configs.ExperimentConfig attribute)

P

platform_release (napistu_torch.utils.environment_info.EnvironmentInfo attribute) platform_system (napistu_torch.utils.environment_info.EnvironmentInfo attribute) plot_auc_only() (in module napistu_torch.visualization.basic_metrics) plot_combined_grouped_barplot() (in module napistu_torch.visualization.advanced_metrics) plot_coordinates_with_masks() (in module napistu_torch.visualization.embeddings) plot_edge_feature_sensitivity() (in module napistu_torch.evaluation.edge_weights) plot_edge_predictions_by_strata() (in module napistu_torch.evaluation.edge_prediction) plot_grouped_barplot() (in module napistu_torch.visualization.advanced_metrics) plot_heatmap() (in module napistu_torch.visualization.heatmaps) plot_model_comparison() (in module napistu_torch.visualization.basic_metrics) precision (napistu_torch.configs.TrainingConfig attribute) predict() (napistu_torch.tasks.base.BaseTask method) predict_dataloader() (napistu_torch.lightning.datamodule.NapistuDataModule method) (napistu_torch.lightning.edge_batch_datamodule.EdgeBatchDataModule method) (napistu_torch.lightning.full_graph_datamodule.FullGraphDataModule method) prepare_batch() (napistu_torch.tasks.base.BaseTask method) (napistu_torch.tasks.node_classification.NodeClassificationTask method)

pretrained_model_freeze_encoder_weights (napistu_torch.configs.ModelConfig attribute) pretrained_model_freeze_head_weights (napistu_torch.configs.ModelConfig attribute) pretrained_model_load_head (napistu_torch.configs.ModelConfig attribute) pretrained_model_path (napistu_torch.configs.ModelConfig attribute) pretrained_model_revision (napistu_torch.configs.ModelConfig attribute) pretrained_model_source (napistu_torch.configs.ModelConfig attribute) project (napistu_torch.configs.WandBConfig attribute) Properties (napistu_torch.evaluation.manager.EvaluationManager attribute) (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) publish_store_to_huggingface() (napistu_torch.napistu_data_store.NapistuDataStore method) publish_to_huggingface (napistu_torch.evaluation.manager.LocalEvaluationManager attribute) publish_to_huggingface() (napistu_torch.evaluation.manager.LocalEvaluationManager method) (napistu_torch.evaluation.manager.RemoteEvaluationManager method) python_implementation (napistu_torch.utils.environment_info.EnvironmentInfo attribute) python_version (napistu_torch.utils.environment_info.EnvironmentInfo attribute) pytorch_lightning_version (napistu_torch.load.checkpoints.CheckpointStructure attribute) (napistu_torch.utils.environment_info.EnvironmentInfo attribute)

R

relation_attention_heads (napistu_torch.configs.ModelConfig attribute) relation_emb_dim (napistu_torch.configs.ModelConfig attribute) relation_type_labels (napistu_torch.load.checkpoints.DataMetadata attribute) RelationAttentionHead (class in napistu_torch.models.heads) RelationAttentionMLPHead (class in napistu_torch.models.heads) RelationGatedMLPHead (class in napistu_torch.models.heads) RelationWeightedAUC (class in napistu_torch.ml.metrics) RemoteEvaluationManager (class in napistu_torch.evaluation.manager) remove_deprecated_fields() (napistu_torch.configs.DataConfig class method) (napistu_torch.configs.ModelConfig class method) reorder_multindex_by_categorical_and_numeric() (in module napistu_torch.utils.pd_utils) repo_id (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) repo_url (napistu_torch.evaluation.manager.RemoteEvaluationManager property) require_bionty() (in module napistu_torch.utils.optional)

require_gradio_client() (in module napistu_torch.utils.optional) require_lightning() (in module napistu_torch.utils.optional) require_modelgenerator() (in module napistu_torch.utils.optional) require_scdataloader() (in module napistu_torch.utils.optional) require_scgpt() (in module napistu_torch.utils.optional) require_scprint() (in module napistu_torch.utils.optional) require_seaborn() (in module napistu_torch.utils.optional) require_torchtext() (in module napistu_torch.utils.optional) reverse_edges() (napistu_torch.napistu_data.NapistuData method) revision (napistu_torch.evaluation.manager.RemoteEvaluationManager attribute) rotate_margin (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.HeadMetadata attribute) RotatEHead (class in napistu_torch.models.heads) RunManifest (class in napistu_torch.configs)

S

sage_aggregator (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.EncoderMetadata attribute) sample() (napistu_torch.tasks.negative_sampler.NegativeSampler method) sanitize_filename() (in module napistu_torch.utils.string_utils) save (napistu_torch.vertex_tensor.VertexTensor attribute) save() (napistu_torch.napistu_data.NapistuData method) (napistu_torch.vertex_tensor.VertexTensor method) save_checkpoints (napistu_torch.configs.TrainingConfig attribute) save_napistu_data() (napistu_torch.napistu_data_store.NapistuDataStore method) save_pandas_df() (napistu_torch.napistu_data_store.NapistuDataStore method) save_vertex_tensor() (napistu_torch.napistu_data_store.NapistuDataStore method) sbml_dfs_path (napistu_torch.configs.DataConfig attribute) scheduler (napistu_torch.configs.TrainingConfig attribute) score_distribution_monitoring (napistu_torch.configs.TrainingConfig attribute) score_distribution_monitoring_log_every_n_epochs (napistu_torch.configs.TrainingConfig attribute) scores_to_probs() (napistu_torch.models.heads.ConditionalRotatEHead method) (napistu_torch.models.heads.RotatEHead method) (napistu_torch.models.heads.TransEHead method)

seed (napistu_torch.configs.ExperimentConfig attribute) select_device() (in module napistu_torch.utils.torch_utils) setup() (napistu_torch.lightning.datamodule.NapistuDataModule method) shortest_common_prefix() (in module napistu_torch.utils.base_utils) show_memory_footprint() (napistu_torch.napistu_data.NapistuData method) show_summary() (napistu_torch.napistu_data.NapistuData method) SimpleEncodingConfig (class in napistu_torch.load.encoding_manager) SingleGraphDataset (class in napistu_torch.data.dataset) SparseContScaler (class in napistu_torch.load.encoders) splitting_strategy (napistu_torch.load.checkpoints.DataMetadata attribute) state_dict (napistu_torch.load.checkpoints.CheckpointStructure attribute) store_dir (napistu_torch.configs.DataConfig attribute) summarize_edge_predictions_by_strata() (in module napistu_torch.evaluation.edge_prediction) summary() (napistu_torch.napistu_data_store.NapistuDataStore method) supports_relations (napistu_torch.models.heads.Decoder property)

T

tags (napistu_torch.configs.WandBConfig attribute) task (napistu_torch.configs.ExperimentConfig attribute) (napistu_torch.configs.TaskConfig attribute) task_config_to_artifact_names() (in module napistu_torch.configs) TaskConfig (class in napistu_torch.configs) test_dataloader() (napistu_torch.lightning.datamodule.NapistuDataModule method) (napistu_torch.lightning.edge_batch_datamodule.EdgeBatchDataModule method) (napistu_torch.lightning.full_graph_datamodule.FullGraphDataModule method) test_mask_hash (napistu_torch.load.checkpoints.DataMetadata attribute) test_step() (napistu_torch.tasks.base.BaseTask method) to_dict (napistu_torch.labels.labeling_manager.LabelingManager attribute) to_dict() (napistu_torch.configs.ExperimentConfig method) (napistu_torch.labels.labeling_manager.LabelingManager method) to_json() (napistu_torch.configs.ExperimentConfig method) to_yaml() (napistu_torch.configs.ExperimentConfig method) (napistu_torch.configs.RunManifest method) torch_geometric_version (napistu_torch.utils.environment_info.EnvironmentInfo attribute)

torch_version (napistu_torch.utils.environment_info.EnvironmentInfo attribute) train_dataloader() (napistu_torch.lightning.datamodule.NapistuDataModule method) (napistu_torch.lightning.edge_batch_datamodule.EdgeBatchDataModule method) (napistu_torch.lightning.full_graph_datamodule.FullGraphDataModule method) train_mask_hash (napistu_torch.load.checkpoints.DataMetadata attribute) train_test_val_split() (in module napistu_torch.ml.splitting) training (napistu_torch.configs.ExperimentConfig attribute) training_step() (napistu_torch.tasks.base.BaseTask method) TrainingConfig (class in napistu_torch.configs) transe_margin (napistu_torch.configs.ModelConfig attribute) (napistu_torch.load.checkpoints.HeadMetadata attribute) TransEHead (class in napistu_torch.models.heads) transform() (napistu_torch.load.encoders.SparseContScaler method) transform_dataframe() (in module napistu_torch.load.encoding) TransformConfig (class in napistu_torch.load.encoding_manager) transformer (napistu_torch.load.encoding_manager.TransformConfig attribute) trim() (napistu_torch.napistu_data.NapistuData method)

U

unencode_features() (napistu_torch.napistu_data.NapistuData method) update_model_config() (napistu_torch.load.checkpoints.Checkpoint method)

use_edge_encoder (napistu_torch.configs.ModelConfig attribute) use_pretrained_model (napistu_torch.configs.ModelConfig attribute)

V

val_dataloader() (napistu_torch.lightning.datamodule.NapistuDataModule method) (napistu_torch.lightning.edge_batch_datamodule.EdgeBatchDataModule method) (napistu_torch.lightning.full_graph_datamodule.FullGraphDataModule method) val_mask_hash (napistu_torch.load.checkpoints.DataMetadata attribute) validate() (napistu_torch.load.encoding_manager.EncodingManager method), [1] (napistu_torch.napistu_data_store.NapistuDataStore method) validate_all_values_are_column_collections() (napistu_torch.load.encoding_manager.SimpleEncodingConfig method) validate_artifact_name() (napistu_torch.napistu_data_store.NapistuDataStore method) validate_artifact_registry() (in module napistu_torch.load.artifacts) validate_artifact_type() (napistu_torch.load.artifacts.ArtifactDefinition class method) validate_columns() (napistu_torch.load.encoding_manager.TransformConfig class method) validate_edge_strata_alignment() (in module napistu_torch.load.stratification) validate_encoder() (napistu_torch.configs.ModelConfig class method) validate_exclude_attributes() (napistu_torch.labels.labeling_manager.LabelingManager class method) validate_graph_alignment() (napistu_torch.napistu_data.NapistuData method) validate_head() (napistu_torch.configs.ModelConfig class method) validate_label_attribute() (napistu_torch.labels.labeling_manager.LabelingManager class method)

validate_mode() (napistu_torch.configs.WandBConfig class method) validate_name() (napistu_torch.load.artifacts.ArtifactDefinition class method) validate_optimizer() (napistu_torch.configs.TrainingConfig class method) validate_paths() (napistu_torch.configs.DataConfig method) validate_power_of_2() (napistu_torch.configs.ModelConfig class method) validate_pretrained_model() (napistu_torch.configs.ModelConfig method) validate_same_data() (in module napistu_torch.data.compare_napistu_data) validate_scheduler() (napistu_torch.configs.TrainingConfig class method) validate_state_dict_not_empty() (napistu_torch.load.checkpoints.CheckpointStructure class method) validate_summary_types() (napistu_torch.labels.labeling_manager.LabelingManager class method) validate_symmetric_relation_indices() (in module napistu_torch.models.head_utils) validate_task() (napistu_torch.configs.TaskConfig class method) validate_transformer() (napistu_torch.load.encoding_manager.TransformConfig class method) validation_step() (napistu_torch.tasks.base.BaseTask method) vertex_feature_name_aliases (napistu_torch.load.checkpoints.DataMetadata attribute) vertex_feature_names (napistu_torch.load.checkpoints.DataMetadata attribute) vertex_names (napistu_torch.vertex_tensor.VertexTensor attribute) VertexTensor (class in napistu_torch.vertex_tensor)

W

wandb (napistu_torch.configs.ExperimentConfig attribute) wandb_entity (napistu_torch.configs.RunManifest attribute) (napistu_torch.evaluation.manager.EvaluationManager attribute) (napistu_torch.evaluation.manager.EvaluationManager property) wandb_project (napistu_torch.configs.RunManifest attribute) (napistu_torch.evaluation.manager.EvaluationManager attribute) (napistu_torch.evaluation.manager.EvaluationManager property) wandb_run_id (napistu_torch.configs.RunManifest attribute) (napistu_torch.evaluation.manager.EvaluationManager attribute) (napistu_torch.evaluation.manager.EvaluationManager property)

wandb_run_url (napistu_torch.configs.RunManifest attribute) (napistu_torch.evaluation.manager.EvaluationManager attribute) (napistu_torch.evaluation.manager.EvaluationManager property) wandb_subdir (napistu_torch.configs.WandBConfig attribute) WandBConfig (class in napistu_torch.configs) weight_decay (napistu_torch.configs.TrainingConfig attribute) weight_loss_by_relation_frequency (napistu_torch.configs.TaskConfig attribute) weight_monitoring (napistu_torch.configs.TrainingConfig attribute)