Index

_

__init__() (DatasetRegistry method) (GCNMF method) (HyperparameterLoader method) (MethodRegistry method) (MethodRunner method) (MLPPredictor method) (QuantumSage method) (QuVINEGCNMF method) (ReproducibilityValidator method) (SeedManager method) (SplitGenerator method) (SyntheticGraphGenerator method)

A

activation (GraphGPSConfig attribute) (GraphGPSModelConfig attribute) actual_size (DatasetEntry attribute) (DatasetMetadata attribute) add() (CorpusBuilder method) (EmbeddingStore method) add_hub_nodes() (in module qbiocode.apps.quvine.data.random_graphs) add_neighbors_until_budget() (in module qbiocode.apps.quvine.data.subgraph) add_split() (DatasetRegistry method) align_direct_features() (in module qbiocode.apps.quvine.baselines.graphgps) align_features() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.baselines.graphgps) alpha (APPNPConfig attribute) apply_heat_filter() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.baselines.graphgps) (in module qbiocode.apps.quvine.embedding.quantum_filters)

apply_polynomial_filter() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.baselines.graphgps) (in module qbiocode.apps.quvine.embedding.quantum_filters) apply_rwr_filter() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.baselines.graphgps) APPNPConfig (class in qbiocode.apps.quvine.baselines.configs) as_dict() (EmbedResult method) as_list() (EmbeddingStore method) as_numpy() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.baselines.graphgps) attention_dropout (GATConfig attribute) (GATModelConfig attribute) attn_dropout (GraphGPSConfig attribute) (GraphGPSModelConfig attribute) attn_type (GraphGPSConfig attribute) (GraphGPSModelConfig attribute) available_tasks (DatasetEntry attribute)

B

BaselineFilterConfig (class in qbiocode.apps.quvine.baselines.configs) BaseWalker (class in qbiocode.apps.quvine.walks.base) betweenness_k (ComplexityConfig attribute) build() (CorpusBuilder method) (ViewBuilder method) build_appnp_config() (in module qbiocode.apps.quvine.baselines.configs) build_baseline_filter_config() (in module qbiocode.apps.quvine.baselines.configs) build_corpora() (in module qbiocode.apps.quvine.api.sgns) build_cosine_classifier() (in module qbiocode.learning.compute_qensemble) build_default_ppi_workflow() (in module qbiocode.apps.quvine.reproducibility.ppi_workflow) build_ensemble_circuit() (in module qbiocode.learning.compute_qensemble) build_gat_config() (in module qbiocode.apps.quvine.baselines.configs) build_gat_input_features() (in module qbiocode.apps.quvine.baselines.gat) build_gcnmf_config() (in module qbiocode.apps.quvine.baselines.configs)

build_graphgps_config() (in module qbiocode.apps.quvine.baselines.configs) build_graphgps_input_features() (in module qbiocode.apps.quvine.baselines.graphgps) build_graphsage_config() (in module qbiocode.apps.quvine.baselines.configs) build_netmf_config() (in module qbiocode.apps.quvine.baselines.configs) build_node2vec_config() (in module qbiocode.apps.quvine.baselines.configs) build_normalized_laplacian() (in module qbiocode.apps.quvine.baselines.gat) build_pyg_data() (in module qbiocode.apps.quvine.baselines.graphgps) build_quantum_targets() (in module qbiocode.apps.quvine.api.targets) build_quvine_filter_config() (in module qbiocode.apps.quvine.baselines.configs) build_quvine_gcnmf_config() (in module qbiocode.apps.quvine.baselines.configs) build_quvine_sgns_config() (in module qbiocode.apps.quvine.baselines.configs) build_rwr_targets_from_templates() (in module qbiocode.apps.quvine.baselines.graphgps) build_structural_features() (in module qbiocode.apps.quvine.baselines.gat) build_views() (in module qbiocode.apps.quvine.api.sgns) build_walk_targets() (in module qbiocode.apps.quvine.api.targets)

C

calculate_SLGH() (in module qbiocode.apps.sage.sage) calibrate_heat_kernel() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.baselines.graphgps) (in module qbiocode.apps.quvine.embedding.quantum_filters) calibrate_heat_kernel_fast() (in module qbiocode.apps.quvine.fusion.fuse_fixes) calibrate_polynomial_filter() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.baselines.graphgps) (in module qbiocode.apps.quvine.embedding.quantum_filters) calibrate_polynomial_filter_fast() (in module qbiocode.apps.quvine.fusion.fuse_fixes) category (MethodMetadata attribute) cca_correlation() (in module qbiocode.apps.quvine.analysis.analyze) cfg (QuvineSGNSConfig attribute) check_embedding_name() (in module qbiocode.embeddings.embed) check_torch_available() (in module qbiocode.apps.quvine.utils.torch_utils) checkpoint_restart() (in module qbiocode.utils.dataset_checkpoint) chunk_size (QuvineSGNSConfig attribute) chunkify() (in module qbiocode.apps.quvine.api.sgns) clear_results() (MethodRegistry method) clustered_heatmap (CorrelationFigures attribute) combine_results() (in module qbiocode.utils.combine_evals_results) compare_embeddings() (in module qbiocode.apps.quvine.analysis.compare) compare_graph_complexities() (in module qbiocode.evaluation.graph_evaluation) compile_corpus() (in module qbiocode.apps.quvine.corpus.operations) ComplexityConfig (class in qbiocode.evaluation.graph_evaluation) COMPONENT_OFFSETS (SeedManager attribute) compute_adjacency_spectral_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_algebraic_connectivity() (in module qbiocode.evaluation.graph_evaluation) compute_approx_path_length_metric() (in module qbiocode.evaluation.graph_evaluation) compute_betti_numbers() (in module qbiocode.evaluation.graph_evaluation) compute_centrality_concentration_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_community_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_complexity_table() (in module qbiocode.evaluation.graph_evaluation) compute_core_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_cycle_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_cyclomatic_number() (in module qbiocode.evaluation.graph_evaluation) compute_degree_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_dt() (in module qbiocode.learning.compute_dt) compute_dt_opt() (in module qbiocode.learning.compute_dt) compute_edge_features() (in module qbiocode.apps.quvine.evaluation.link_prediction) compute_effective_resistance() (in module qbiocode.evaluation.graph_evaluation) compute_enhanced_complexity_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_estrada_index() (in module qbiocode.evaluation.graph_evaluation) compute_feature_dirichlet_energy() (in module qbiocode.evaluation.graph_evaluation) compute_graph_complexity() (MethodRunner method) compute_graph_complexity_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_heat_kernel_traces() (in module qbiocode.evaluation.graph_evaluation) compute_inverse_participation_ratio() (in module qbiocode.evaluation.graph_evaluation) compute_kirchhoff_index() (in module qbiocode.evaluation.graph_evaluation) compute_kirchhoff_stats() (in module qbiocode.evaluation.graph_evaluation) compute_label_homophily() (in module qbiocode.evaluation.graph_evaluation) compute_laplacian_centrality_complexity() (in module qbiocode.evaluation.graph_evaluation)

compute_laplacian_spectrum() (in module qbiocode.evaluation.graph_evaluation) compute_lr() (in module qbiocode.learning.compute_lr) compute_lr_opt() (in module qbiocode.learning.compute_lr) compute_mlp() (in module qbiocode.learning.compute_mlp) compute_mlp_opt() (in module qbiocode.learning.compute_mlp) compute_nb() (in module qbiocode.learning.compute_nb) compute_nb_opt() (in module qbiocode.learning.compute_nb) compute_nonbacktracking_spectral_radius() (in module qbiocode.evaluation.graph_evaluation) compute_odd_girth_metric() (in module qbiocode.evaluation.graph_evaluation) compute_orc_per_edge() (in module qbiocode.evaluation.graph_evaluation) compute_orc_proxy_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_orc_stats() (in module qbiocode.evaluation.graph_evaluation) compute_participation_ratio() (in module qbiocode.evaluation.graph_evaluation) compute_persistence_entropy() (in module qbiocode.evaluation.graph_evaluation) compute_pqk() (in module qbiocode.learning.compute_pqk) compute_qensemble() (in module qbiocode.learning.compute_qensemble) compute_qnn() (in module qbiocode.learning.compute_qnn) compute_qpl() (in module qbiocode.learning.compute_qpl) compute_qsvc() (in module qbiocode.learning.compute_qsvc) compute_quantum_advantage_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_quantum_complexity() (in module qbiocode.evaluation.graph_evaluation) compute_results_correlation() (in module qbiocode.visualization.visualize_correlation) compute_rf() (in module qbiocode.learning.compute_rf) compute_rf_opt() (in module qbiocode.learning.compute_rf) compute_size_density_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_sparse_spectral_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_spectral_concentration() (in module qbiocode.evaluation.graph_evaluation) compute_spectral_entropy() (in module qbiocode.evaluation.graph_evaluation) compute_spectral_gap() (in module qbiocode.evaluation.graph_evaluation) compute_structural_link_features() (in module qbiocode.apps.quvine.evaluation.link_prediction) compute_svc() (in module qbiocode.learning.compute_svc) compute_svc_opt() (in module qbiocode.learning.compute_svc) compute_topological_metrics() (in module qbiocode.evaluation.graph_evaluation) compute_von_neumann_entropy() (in module qbiocode.evaluation.graph_evaluation) compute_vqc() (in module qbiocode.learning.compute_vqc) compute_wl_compression_ratio() (in module qbiocode.evaluation.graph_evaluation) compute_xgb() (in module qbiocode.learning.compute_xgb) compute_xgb_opt() (in module qbiocode.learning.compute_xgb) config_builder (MethodMetadata attribute) config_group_for() (in module qbiocode.apps.quvine.api.aliases) constrained_view() (in module qbiocode.apps.quvine.views.views) ConvAutoencoder (class in qbiocode.embeddings.compute_autoencoder) corpus_to_embedding() (in module qbiocode.apps.quvine.embedding.word2vec) CorpusBuilder (class in qbiocode.apps.quvine.corpus.builder) CorrelationFigures (class in qbiocode.visualization.visualize_correlation) create_lr_model() (in module qbiocode.learning.compute_qpl) create_method_adapter() (in module qbiocode.apps.quvine.reproducibility.method_runner) create_mlp_model() (in module qbiocode.learning.compute_qpl) create_rf_model() (in module qbiocode.learning.compute_qpl) create_svc_model() (in module qbiocode.learning.compute_pqk) (in module qbiocode.learning.compute_qpl) create_xgb_model() (in module qbiocode.learning.compute_qpl)

D

DATA_ENV_VAR (in module qbiocode.utils.tutorial_data) dataset_name (DatasetEntry attribute) dataset_type (DatasetEntry attribute) (DatasetMetadata attribute) DatasetEntry (class in qbiocode.apps.quvine.reproducibility.dataset_registry) DatasetMetadata (class in qbiocode.apps.quvine.reproducibility.dataset_registry) DatasetRegistry (class in qbiocode.apps.quvine.reproducibility.dataset_registry) DatasetType (class in qbiocode.apps.quvine.reproducibility.dataset_registry) DEFAULT_TASKS (PPIWorkflow attribute) degree_matched_targets() (SeedTargetEvaluator method) describe_seed_plan() (SeedManager method) description (DatasetMetadata attribute) (MethodMetadata attribute) device (GATTrainConfig attribute) (GraphGPSTrainConfig attribute) (TrainConfig attribute), [1] diffusion_type (QuvineGCNMFConfig attribute)

dim (EmbedResult attribute) dimensions (APPNPConfig attribute) (GraphSAGEConfig attribute) (NetMFConfig attribute) (Node2VecConfig attribute) dir_home (in module qbiocode.apps.qprofiler.qprofiler) disease (DatasetEntry attribute) (DatasetMetadata attribute) disease_node_path (DatasetEntry attribute) distance_matched_targets() (SeedTargetEvaluator method) dot_decode() (in module qbiocode.apps.quvine.baselines.graphgps) draw_graph() (in module qbiocode.apps.quvine.utils.utilities) dropout (APPNPConfig attribute) (GATConfig attribute) (GATModelConfig attribute) (GraphGPSConfig attribute) (GraphGPSModelConfig attribute)

E

edge_batch_size (GATTrainConfig attribute) (GraphGPSTrainConfig attribute) (TrainConfig attribute), [1] edge_index_from_graph() (in module qbiocode.apps.quvine.baselines.gat) edge_scores_dot() (in module qbiocode.apps.quvine.baselines.gat) edge_triangle_support_scores() (in module qbiocode.apps.quvine.data.sparsify) EdgeIndexGATLayer (class in qbiocode.apps.quvine.baselines.gat) effective_rank() (in module qbiocode.apps.quvine.analysis.analyze) eig_tol (ComplexityConfig attribute) embed() (in module qbiocode.apps.quvine.api.core) embedding (EmbedResult attribute) (MethodResult attribute) embedding_dim (BaselineFilterConfig attribute) (GATMethodConfig attribute) (GCNMFConfig attribute) (GraphGPSMethodConfig attribute) (QuvineFilterConfig attribute) (QuvineGCNMFConfig attribute) EmbeddingStore (class in qbiocode.apps.quvine.embedding.registry) EmbedResult (class in qbiocode.apps.quvine.api.core) enabled (APPNPConfig attribute) (BaselineFilterConfig attribute) (GATMethodConfig attribute) (GCNMFConfig attribute) (GraphGPSMethodConfig attribute) (GraphSAGEConfig attribute) (NetMFConfig attribute) (Node2VecConfig attribute) (QuvineFilterConfig attribute) (QuvineGCNMFConfig attribute) (QuvineSGNSConfig attribute)

epochs (APPNPConfig attribute) (GATTrainConfig attribute) (GCNMFConfig attribute) (GraphGPSTrainConfig attribute) (GraphSAGEConfig attribute) (QuvineGCNMFConfig attribute) (TrainConfig attribute), [1] error (MethodResult attribute) evaluate() (in module qbiocode.evaluation.dataset_evaluation) (SeedTargetEvaluator method) evaluate_all_edge_feature_methods() (in module qbiocode.apps.quvine.evaluation.link_prediction) evaluate_all_label_strategies() (in module qbiocode.apps.quvine.evaluation.classification) evaluate_embeddings_ranking() (in module qbiocode.apps.quvine.evaluation.ranking) evaluate_graph() (in module qbiocode.evaluation.graph_evaluation) evaluate_link_prediction() (in module qbiocode.apps.quvine.evaluation.link_prediction) (in module qbiocode.apps.quvine.reproducibility.method_adapters) evaluate_link_prediction_cv() (in module qbiocode.apps.quvine.evaluation.link_prediction) evaluate_nc_stratified() (in module qbiocode.apps.quvine.evaluation.classification) evaluate_node_classification() (in module qbiocode.apps.quvine.evaluation.classification) evaluate_node_ranking() (in module qbiocode.apps.quvine.reproducibility.method_adapters) evaluation_metrics() (in module qbiocode.evaluation.model_evaluation) exception (MethodResult attribute) execute_circuit() (in module qbiocode.utils.qutils) execution_time (EmbedResult attribute) (MethodResult attribute) executor (MethodMetadata attribute) expand_neighborhood() (in module qbiocode.apps.quvine.data.subgraph) export_registry_csv() (DatasetRegistry method) export_registry_json() (DatasetRegistry method) extra (EmbedResult attribute)

F

feature_encoding() (in module qbiocode.utils.helper_fn) features (BaselineFilterConfig attribute) (QuvineFilterConfig attribute) fiedler_eigenvalue_sparse() (in module qbiocode.evaluation.graph_evaluation) fill_degree_matched_until_budget() (in module qbiocode.apps.quvine.data.subgraph) fill_random_until_budget() (in module qbiocode.apps.quvine.data.subgraph) filter_type (BaselineFilterConfig attribute) (QuvineFilterConfig attribute) find_duplicate_files() (in module qbiocode.utils.find_duplicates) find_string_in_files() (in module qbiocode.utils.find_string) fixed_heat_time_grid() (in module qbiocode.apps.quvine.baselines.graphgps) flatten_classification_results() (in module qbiocode.apps.quvine.evaluation.classification) forward() (ConvAutoencoder method) (EdgeIndexGATLayer method) (GATEncoder method) (GATNodeClassifier method) (GCNLayer method) (GCNMF method) (MLPPredictor method) (PyGGraphGPS method) (QuVINEGCNMF method)

from_dict() (DatasetEntry class method) fuse_best_across_types() (in module qbiocode.apps.quvine.fusion.fuse) fuse_by_method_type() (in module qbiocode.apps.quvine.fusion.fuse) fuse_embeddings() (in module qbiocode.apps.quvine.fusion.fuse) fuse_embeddings_attention() (in module qbiocode.apps.quvine.fusion.fuse) fuse_embeddings_attention_fixed() (in module qbiocode.apps.quvine.fusion.fuse_fixes) fuse_embeddings_consensus_gated() (in module qbiocode.apps.quvine.fusion.fuse_fixes) fuse_embeddings_graphreg() (in module qbiocode.apps.quvine.fusion.fuse) fuse_embeddings_hybrid() (in module qbiocode.apps.quvine.fusion.fuse) fuse_embeddings_svd() (in module qbiocode.apps.quvine.fusion.fuse) fuse_embeddings_svd_shared_private() (in module qbiocode.apps.quvine.fusion.fuse) fuse_embeddings_uniform_mean() (in module qbiocode.apps.quvine.fusion.fuse_fixes)

G

GATConfig (class in qbiocode.apps.quvine.baselines.gat) GATEncoder (class in qbiocode.apps.quvine.baselines.gat) GATMethodConfig (class in qbiocode.apps.quvine.baselines.configs) GATModelConfig (class in qbiocode.apps.quvine.baselines.configs) GATNodeClassifier (class in qbiocode.apps.quvine.baselines.gat) GATTrainConfig (class in qbiocode.apps.quvine.baselines.configs) GCNLayer (class in qbiocode.apps.quvine.baselines.gcn_mf) GCNMF (class in qbiocode.apps.quvine.baselines.gcn_mf) GCNMFConfig (class in qbiocode.apps.quvine.baselines.configs) generate_all() (PPIGraphGenerator method) (SyntheticGraphGenerator method) generate_all_splits() (SplitGenerator method) generate_appnp_embedding() (in module qbiocode.apps.quvine.baselines.appnp) generate_barabasi_albert() (in module qbiocode.apps.quvine.data.random_graphs) generate_baseline_filter_embedding() (in module qbiocode.apps.quvine.embedding.quantum_filters) generate_baseline_filter_embedding_wrapper() (in module qbiocode.apps.quvine.baselines.gcn_mf) generate_baseline_gcnmf_embedding() (in module qbiocode.apps.quvine.baselines.gcn_mf) generate_baseline_heat_embedding() (in module qbiocode.apps.quvine.embedding.quantum_filters) generate_baseline_poly_embedding() (in module qbiocode.apps.quvine.embedding.quantum_filters) generate_bipartite_random() (in module qbiocode.apps.quvine.data.random_graphs) generate_blobs_datasets() (in module qbiocode.data_generation.make_blobs) generate_centrality_labels() (in module qbiocode.apps.quvine.evaluation.classification) generate_circles_datasets() (in module qbiocode.data_generation.make_circles) generate_classification_datasets() (in module qbiocode.data_generation.make_class) generate_community_labels() (in module qbiocode.apps.quvine.evaluation.classification) generate_comprehensive_dataset() (in module qbiocode.apps.quvine.data.random_graphs) generate_configuration_model_graph() (in module qbiocode.apps.quvine.data.random_graphs) generate_core_periphery() (in module qbiocode.apps.quvine.data.random_graphs) generate_core_periphery_labels() (in module qbiocode.apps.quvine.evaluation.classification) generate_ctqw_hiperwalk_scores() (in module qbiocode.apps.quvine.walks.ctqw) generate_CTQW_walks() (in module qbiocode.apps.quvine.walks.ctqw) generate_data() (in module qbiocode.data_generation.generator) generate_default_blobs_datasets() (in module qbiocode.data_generation.make_blobs) generate_degree_corrected_sbm() (in module qbiocode.apps.quvine.data.random_graphs) generate_degree_labels() (in module qbiocode.apps.quvine.evaluation.classification) generate_DTQW_walks() (in module qbiocode.apps.quvine.walks.dtqw) generate_erdos_renyi() (in module qbiocode.apps.quvine.data.random_graphs) generate_gat_embedding() (in module qbiocode.apps.quvine.baselines.gat) generate_gat_embedding_by_method_name() (in module qbiocode.apps.quvine.baselines.gat) generate_graph_with_seeds_and_targets() (in module qbiocode.apps.quvine.data.random_graphs) generate_graphgps_embedding() (in module qbiocode.apps.quvine.baselines.graphgps) generate_graphgps_embedding_by_method_name() (in module qbiocode.apps.quvine.baselines.graphgps) generate_grid_torus_lattice() (in module qbiocode.apps.quvine.data.random_graphs) generate_heterophilic_sbm() (in module qbiocode.apps.quvine.data.random_graphs) generate_hierarchical_network() (in module qbiocode.apps.quvine.data.random_graphs) generate_homophily_labels() (in module qbiocode.apps.quvine.evaluation.classification) generate_link_prediction_split() (SplitGenerator method) generate_modular_network() (in module qbiocode.apps.quvine.data.random_graphs) generate_moons_datasets() (in module qbiocode.data_generation.make_moons) generate_multiple_gat_embeddings() (in module qbiocode.apps.quvine.baselines.gat) generate_multiple_graphgps_embeddings() (in module qbiocode.apps.quvine.baselines.graphgps) generate_node_classification_split() (SplitGenerator method) generate_node_ranking_split() (SplitGenerator method) generate_points_in_nd_sphere() (in module qbiocode.data_generation.make_spheres) generate_powerlaw_cluster() (in module qbiocode.apps.quvine.data.random_graphs) generate_qcaliber_gcnmf_heat_embedding() (in module qbiocode.apps.quvine.baselines.gcn_mf) generate_qcaliber_gcnmf_poly_embedding() (in module qbiocode.apps.quvine.baselines.gcn_mf) generate_qml_experiment_configs() (in module qbiocode.utils.generate_qml_configs) generate_quantum_targets_from_walks() (in module qbiocode.apps.quvine.reproducibility.method_adapters) generate_quvine_gcnmf_embedding() (in module qbiocode.apps.quvine.baselines.gcn_mf) generate_quvine_heat_embedding() (in module qbiocode.apps.quvine.embedding.quantum_filters) generate_quvine_poly_embedding() (in module qbiocode.apps.quvine.embedding.quantum_filters) generate_random_geometric() (in module qbiocode.apps.quvine.data.random_graphs) generate_random_regular_expander_like() (in module qbiocode.apps.quvine.data.random_graphs) generate_RWR_pagerank_walks() (in module qbiocode.apps.quvine.walks.rwr) generate_s_curve_datasets() (in module qbiocode.data_generation.make_s_curve) generate_single() (PPIGraphGenerator method) (SyntheticGraphGenerator method) generate_spheres_datasets() (in module qbiocode.data_generation.make_spheres) generate_spirals_datasets() (in module qbiocode.data_generation.make_spirals) generate_stochastic_block_model() (in module qbiocode.apps.quvine.data.random_graphs)

generate_swiss_roll_datasets() (in module qbiocode.data_generation.make_swiss_roll) generate_watts_strogatz() (in module qbiocode.apps.quvine.data.random_graphs) generation_params (DatasetMetadata attribute) get() (DatasetRegistry method) (EmbeddingStore method) get_adapter() (in module qbiocode.apps.quvine.baselines.adapters) get_all_datasets() (DatasetRegistry method) get_ansatz() (in module qbiocode.utils.qutils) get_backend_session() (in module qbiocode.utils.qutils) get_coefficient_var() (in module qbiocode.evaluation.dataset_evaluation) get_coined_hiperwalk_scores() (in module qbiocode.apps.quvine.walks.dtqw) get_complexity() (in module qbiocode.evaluation.dataset_evaluation) get_component_seed() (SeedManager method) get_condition_number() (in module qbiocode.evaluation.dataset_evaluation) get_creds() (in module qbiocode.utils.ibm_account) get_device() (in module qbiocode.apps.quvine.utils.torch_utils) get_dimensions() (in module qbiocode.evaluation.dataset_evaluation) get_direct_walk_features() (in module qbiocode.apps.quvine.baselines.gat) get_ego_net_nodes_quvine() (in module qbiocode.apps.quvine.embedding.quantum_filters) get_embedding_dim() (in module qbiocode.apps.quvine.baselines.configs) get_embeddings() (GATNodeClassifier method) (GCNMF method) (in module qbiocode.embeddings.embed) (QuVINEGCNMF method) get_entries_for_dataset() (DatasetRegistry method) get_entropy() (in module qbiocode.evaluation.dataset_evaluation) get_estimator() (in module qbiocode.utils.qutils) get_fdr() (in module qbiocode.evaluation.dataset_evaluation) get_feature_map() (in module qbiocode.utils.qutils) get_fractal_dim() (in module qbiocode.evaluation.dataset_evaluation) get_global_loader() (in module qbiocode.apps.quvine.baselines.hyperparameter_loader) get_graph_statistics() (in module qbiocode.apps.quvine.data.random_graphs) get_intrinsic_dim() (in module qbiocode.evaluation.dataset_evaluation) get_laplacian() (in module qbiocode.apps.quvine.baselines.graphgps) (in module qbiocode.apps.quvine.embedding.quantum_filters) get_log_density() (in module qbiocode.evaluation.dataset_evaluation) get_low_var_features() (in module qbiocode.evaluation.dataset_evaluation) get_metadata() (MethodRegistry method) get_method_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) get_method_params() (HyperparameterLoader method) get_moments() (in module qbiocode.evaluation.dataset_evaluation) get_mutual_information() (in module qbiocode.evaluation.dataset_evaluation) get_nnz() (in module qbiocode.evaluation.dataset_evaluation) get_nodelist() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.evaluation.graph_evaluation) get_observable() (in module qbiocode.utils.qutils) get_optimizer() (in module qbiocode.utils.qutils) get_repetitions() (DatasetRegistry method) get_result() (MethodRegistry method) get_results() (MethodRegistry method) get_RWR_pagerank_scores() (in module qbiocode.apps.quvine.walks.rwr) get_sampler() (in module qbiocode.utils.qutils) get_seed() (SeedManager method) get_sparse_adjacency() (in module qbiocode.evaluation.graph_evaluation) get_sparse_laplacian() (in module qbiocode.evaluation.graph_evaluation) get_split_seed() (SeedManager method) get_stats() (in module qbiocode.apps.quvine.utils.utilities) get_summary() (DatasetRegistry method) get_task_seed() (SeedManager method) get_torch_info() (in module qbiocode.apps.quvine.utils.torch_utils) get_total_correlation() (in module qbiocode.evaluation.dataset_evaluation) get_validation_report() (ReproducibilityValidator method) get_variance() (in module qbiocode.evaluation.dataset_evaluation) get_volume() (in module qbiocode.evaluation.dataset_evaluation) gini_coefficient() (in module qbiocode.evaluation.graph_evaluation) graph_path (DatasetEntry attribute) graph_to_edge_index() (in module qbiocode.apps.quvine.baselines.graphgps) GraphGPSConfig (class in qbiocode.apps.quvine.baselines.graphgps) GraphGPSMethodConfig (class in qbiocode.apps.quvine.baselines.configs) GraphGPSModelConfig (class in qbiocode.apps.quvine.baselines.configs) GraphGPSTrainConfig (class in qbiocode.apps.quvine.baselines.configs) GraphSAGEConfig (class in qbiocode.apps.quvine.baselines.configs)

H

has_node_features (DatasetMetadata attribute) has_node_labels (DatasetMetadata attribute) heads (GATConfig attribute) (GATModelConfig attribute) (GraphGPSConfig attribute) (GraphGPSModelConfig attribute) heat_kernel_n_probes (ComplexityConfig attribute) heat_kernel_t_values (ComplexityConfig attribute) heat_t (GATMethodConfig attribute) (GraphGPSMethodConfig attribute) heat_taylor_coeffs() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.baselines.graphgps)

hidden_dim (APPNPConfig attribute) (GATConfig attribute) (GATModelConfig attribute) (GCNMFConfig attribute) (GraphGPSConfig attribute) (GraphGPSModelConfig attribute) (GraphSAGEConfig attribute) (QuvineGCNMFConfig attribute) hierarchical_fusion() (in module qbiocode.apps.quvine.fusion.fuse) HyperparameterLoader (class in qbiocode.apps.quvine.baselines.hyperparameter_loader)

I

importance_sample_centers() (in module qbiocode.apps.quvine.embedding.quantum_filters) induce_subgraph_by_nodes() (in module qbiocode.apps.quvine.data.subgraph) instantiate_runtime_service() (in module qbiocode.utils.ibm_account)

is_directed (DatasetMetadata attribute) is_enabled() (MethodRegistry method) is_transductive() (in module qbiocode.embeddings.embed) items() (EmbeddingStore method)

K

K (APPNPConfig attribute) (BaselineFilterConfig attribute) (QuvineFilterConfig attribute) (QuvineGCNMFConfig attribute)

keep_largest_connected_component() (in module qbiocode.apps.quvine.data.prepare) kind (EmbedResult attribute) knn_overlap() (in module qbiocode.apps.quvine.analysis.analyze) knn_sets() (in module qbiocode.apps.quvine.analysis.analyze)

L

l2_normalize() (in module qbiocode.apps.quvine.evaluation.ranking) label_to_array() (in module qbiocode.utils.data_encoding) lap_pe_dim (GraphGPSConfig attribute) (GraphGPSModelConfig attribute) largest_connected_component_size (DatasetMetadata attribute) list_methods() (in module qbiocode.apps.quvine.api.aliases) (MethodRegistry method) load() (DatasetRegistry method) load_and_override_config() (in module qbiocode.apps.quvine.baselines.hyperparameter_loader) load_comprehensive_dataset() (in module qbiocode.apps.quvine.data.random_graphs) load_config() (in module qbiocode.apps.quvine.api.config) load_graph() (in module qbiocode.apps.quvine.data.data_loader) (MethodRunner method) (SyntheticGraphGenerator method) load_gwas_data() (in module qbiocode.apps.quvine.data.data_loader) load_hyperparameters() (HyperparameterLoader method)

load_pegasus_results() (in module qbiocode.apps.quvine.data.data_loader) load_seed_registry() (SeedManager method) load_seeds_and_targets() (in module qbiocode.apps.quvine.data.data_loader) load_split() (MethodRunner method) (SplitGenerator method) load_train_graph() (MethodRunner method) LOCAL_DATA_DIRS (in module qbiocode.utils.tutorial_data) local_gnn (GraphGPSConfig attribute) (GraphGPSModelConfig attribute) log_torch_info() (in module qbiocode.apps.quvine.utils.torch_utils) lr (APPNPConfig attribute) (GATTrainConfig attribute) (GCNMFConfig attribute) (GraphGPSTrainConfig attribute) (GraphSAGEConfig attribute) (QuvineGCNMFConfig attribute) (TrainConfig attribute), [1]

M

main() (in module qbiocode.apps.qprofiler.cli) (in module qbiocode.apps.qprofiler.qprofiler) (in module qbiocode.apps.qprofiler.qprofiler_batchmode) (in module qbiocode.apps.quvine.cli) (in module qbiocode.apps.quvine.main) (in module qbiocode.apps.sage.sage) make_base_features() (in module qbiocode.apps.quvine.baselines.graphgps) make_edge_batch() (in module qbiocode.apps.quvine.baselines.gat) make_spirals() (in module qbiocode.data_generation.make_spirals) materialize_undirected_simple_graph() (in module qbiocode.apps.quvine.data.sparsify) (in module qbiocode.apps.quvine.data.subgraph) max_degree (PrepareGraphConfig attribute) max_nodes (PrepareGraphConfig attribute) max_seed_cosine_scores() (in module qbiocode.apps.quvine.evaluation.ranking) metadata (MethodResult attribute) metadata_path (DatasetEntry attribute) method (EmbedResult attribute) MethodMetadata (class in qbiocode.apps.quvine.baselines.registry) MethodRegistry (class in qbiocode.apps.quvine.baselines.registry) MethodResult (class in qbiocode.apps.quvine.baselines.registry) MethodRunner (class in qbiocode.apps.quvine.reproducibility.method_runner) mf_dim (GCNMFConfig attribute) (QuvineGCNMFConfig attribute) min_count (Node2VecConfig attribute) MLPPredictor (class in qbiocode.apps.quvine.baselines.appnp) model (GATMethodConfig attribute) (GraphGPSMethodConfig attribute) model_run() (in module qbiocode.evaluation.model_run) modeleval() (in module qbiocode.evaluation.model_evaluation) module qbiocode qbiocode.apps qbiocode.apps.qprofiler qbiocode.apps.qprofiler.cli qbiocode.apps.qprofiler.configs qbiocode.apps.qprofiler.qprofiler qbiocode.apps.qprofiler.qprofiler_batchmode qbiocode.apps.quvine qbiocode.apps.quvine.analysis qbiocode.apps.quvine.analysis.analyze qbiocode.apps.quvine.analysis.compare qbiocode.apps.quvine.api qbiocode.apps.quvine.api.aliases qbiocode.apps.quvine.api.config qbiocode.apps.quvine.api.core qbiocode.apps.quvine.api.sgns qbiocode.apps.quvine.api.targets qbiocode.apps.quvine.baselines qbiocode.apps.quvine.baselines.adapters qbiocode.apps.quvine.baselines.appnp qbiocode.apps.quvine.baselines.configs qbiocode.apps.quvine.baselines.gat qbiocode.apps.quvine.baselines.gcn_mf qbiocode.apps.quvine.baselines.graphgps qbiocode.apps.quvine.baselines.graphsage qbiocode.apps.quvine.baselines.hyperparameter_loader qbiocode.apps.quvine.baselines.netmf qbiocode.apps.quvine.baselines.node2vec qbiocode.apps.quvine.baselines.registration qbiocode.apps.quvine.baselines.registry qbiocode.apps.quvine.cli qbiocode.apps.quvine.configs qbiocode.apps.quvine.corpus qbiocode.apps.quvine.corpus.builder qbiocode.apps.quvine.corpus.operations qbiocode.apps.quvine.data qbiocode.apps.quvine.data.data_loader qbiocode.apps.quvine.data.prepare qbiocode.apps.quvine.data.random_graphs qbiocode.apps.quvine.data.random_graphs_extended qbiocode.apps.quvine.data.sparsify qbiocode.apps.quvine.data.subgraph qbiocode.apps.quvine.embedding qbiocode.apps.quvine.embedding.quantum_filters qbiocode.apps.quvine.embedding.registry qbiocode.apps.quvine.embedding.word2vec qbiocode.apps.quvine.evaluation qbiocode.apps.quvine.evaluation.classification qbiocode.apps.quvine.evaluation.link_prediction qbiocode.apps.quvine.evaluation.ranking qbiocode.apps.quvine.fusion qbiocode.apps.quvine.fusion.fuse qbiocode.apps.quvine.fusion.fuse_fixes qbiocode.apps.quvine.main qbiocode.apps.quvine.pipeline qbiocode.apps.quvine.reproducibility qbiocode.apps.quvine.reproducibility.dataset_registry qbiocode.apps.quvine.reproducibility.graph_generator qbiocode.apps.quvine.reproducibility.method_adapters qbiocode.apps.quvine.reproducibility.method_runner qbiocode.apps.quvine.reproducibility.ppi_workflow qbiocode.apps.quvine.reproducibility.seed_manager qbiocode.apps.quvine.reproducibility.split_generator qbiocode.apps.quvine.reproducibility.validator qbiocode.apps.quvine.utils qbiocode.apps.quvine.utils.io qbiocode.apps.quvine.utils.logging qbiocode.apps.quvine.utils.seed qbiocode.apps.quvine.utils.torch_utils qbiocode.apps.quvine.utils.utilities qbiocode.apps.quvine.views qbiocode.apps.quvine.views.generator qbiocode.apps.quvine.views.views qbiocode.apps.quvine.walks qbiocode.apps.quvine.walks.base qbiocode.apps.quvine.walks.ctqw qbiocode.apps.quvine.walks.dtqw qbiocode.apps.quvine.walks.rwr qbiocode.apps.sage qbiocode.apps.sage.sage qbiocode.data_generation qbiocode.data_generation.generator qbiocode.data_generation.make_blobs qbiocode.data_generation.make_circles qbiocode.data_generation.make_class qbiocode.data_generation.make_moons qbiocode.data_generation.make_s_curve qbiocode.data_generation.make_spheres qbiocode.data_generation.make_spirals qbiocode.data_generation.make_swiss_roll qbiocode.embeddings qbiocode.embeddings.compute_autoencoder qbiocode.embeddings.embed qbiocode.evaluation qbiocode.evaluation.dataset_evaluation qbiocode.evaluation.graph_evaluation qbiocode.evaluation.model_evaluation qbiocode.evaluation.model_run qbiocode.learning qbiocode.learning.compute_dt qbiocode.learning.compute_lr qbiocode.learning.compute_mlp qbiocode.learning.compute_nb qbiocode.learning.compute_pqk qbiocode.learning.compute_qensemble qbiocode.learning.compute_qnn qbiocode.learning.compute_qpl qbiocode.learning.compute_qsvc qbiocode.learning.compute_rf qbiocode.learning.compute_svc qbiocode.learning.compute_vqc qbiocode.learning.compute_xgb qbiocode.utils qbiocode.utils.combine_evals_results qbiocode.utils.data_encoding qbiocode.utils.dataset_checkpoint qbiocode.utils.find_duplicates qbiocode.utils.find_string qbiocode.utils.generate_qml_configs qbiocode.utils.helper_fn qbiocode.utils.ibm_account qbiocode.utils.qc_winner_finder qbiocode.utils.qutils qbiocode.utils.tutorial_data qbiocode.version qbiocode.visualization qbiocode.visualization.visualize_correlation

N

n_jobs (QuvineSGNSConfig attribute) n_layers (APPNPConfig attribute) (GCNMFConfig attribute) (GraphSAGEConfig attribute) (QuvineGCNMFConfig attribute) name (DatasetMetadata attribute) (MethodMetadata attribute) (MethodResult attribute) names() (EmbeddingStore method) neg_samples (GraphSAGEConfig attribute) negative (NetMFConfig attribute) negative_slope (GATConfig attribute) (GATModelConfig attribute) NetMFConfig (class in qbiocode.apps.quvine.baselines.configs) Node2VecConfig (class in qbiocode.apps.quvine.baselines.configs)

node_order (EmbedResult attribute) nonbacktracking_max_directed_edges (ComplexityConfig attribute) normalize (BaselineFilterConfig attribute) (QuvineFilterConfig attribute) normalize() (in module qbiocode.apps.quvine.analysis.analyze) normalize_adjacency() (in module qbiocode.apps.quvine.baselines.appnp) (in module qbiocode.apps.quvine.baselines.gcn_mf) normalize_data() (in module qbiocode.utils.data_encoding) normalize_laplacian (QuvineGCNMFConfig attribute) num_edges (DatasetMetadata attribute) num_layers (GATConfig attribute) (GATModelConfig attribute) (GraphGPSConfig attribute) (GraphGPSModelConfig attribute) num_nodes (DatasetMetadata attribute) num_walks (Node2VecConfig attribute)

O

odd_girth_max_sources (ComplexityConfig attribute) odd_girth_min_cycle_break (ComplexityConfig attribute) ordered_heatmap (CorrelationFigures attribute) output_dim (GATConfig attribute) (GATModelConfig attribute) (GraphGPSConfig attribute) (GraphGPSModelConfig attribute)

override_config() (HyperparameterLoader method) override_nested_config() (HyperparameterLoader method)

P

p (Node2VecConfig attribute) pagerank_alpha (ComplexityConfig attribute) pagerank_max_iter (ComplexityConfig attribute) pagerank_tol (ComplexityConfig attribute) parse_args() (in module qbiocode.apps.qprofiler.qprofiler_batchmode) path_num_sources (ComplexityConfig attribute) patience (GATTrainConfig attribute) (GraphGPSTrainConfig attribute) (TrainConfig attribute), [1] per_node_consensus_gate() (in module qbiocode.apps.quvine.fusion.fuse_fixes) personalized_pagerank_propagation() (in module qbiocode.apps.quvine.baselines.appnp) Pipeline (class in qbiocode.apps.quvine.pipeline) plot_metric() (in module qbiocode.apps.quvine.utils.utilities) plot_metric_vs_k() (in module qbiocode.apps.quvine.utils.utilities) plot_precision_recall() (in module qbiocode.apps.quvine.utils.utilities) plot_results() (QuantumSage method) plot_results_correlation() (in module qbiocode.visualization.visualize_correlation) plot_singular_values() (in module qbiocode.apps.quvine.analysis.analyze) poly_K (GATMethodConfig attribute) (GraphGPSMethodConfig attribute) poly_ridge (GATMethodConfig attribute) (GraphGPSMethodConfig attribute)

PPI (DatasetType attribute) ppi_source (DatasetEntry attribute) (DatasetMetadata attribute) PPIGraphGenerator (class in qbiocode.apps.quvine.reproducibility.graph_generator) PPIWorkflow (class in qbiocode.apps.quvine.reproducibility.ppi_workflow) pqk() (in module qbiocode.embeddings.embed) precision_at_k() (SeedTargetEvaluator method) precompute_quantum_diffusion() (in module qbiocode.apps.quvine.baselines.gcn_mf) predict() (QuantumSage method) prepare_graph() (in module qbiocode.apps.quvine.data.prepare) prepare_training_set() (in module qbiocode.utils.data_encoding) PrepareGraphConfig (class in qbiocode.apps.quvine.data.prepare) preprocess_all() (PPIWorkflow method) preprocess_single() (PPIWorkflow method) print_results() (in module qbiocode.utils.helper_fn) process_root() (in module qbiocode.apps.quvine.api.sgns) process_root_chunk() (in module qbiocode.apps.quvine.api.sgns) procrustes_residual() (in module qbiocode.apps.quvine.analysis.analyze) PUBLICATION_STYLE (in module qbiocode.visualization.visualize_correlation) publication_style() (in module qbiocode.visualization.visualize_correlation) PyGGraphGPS (class in qbiocode.apps.quvine.baselines.graphgps)

Q

q (Node2VecConfig attribute) qbiocode module qbiocode.apps module qbiocode.apps.qprofiler module qbiocode.apps.qprofiler.cli module qbiocode.apps.qprofiler.configs module qbiocode.apps.qprofiler.qprofiler module qbiocode.apps.qprofiler.qprofiler_batchmode module qbiocode.apps.quvine module qbiocode.apps.quvine.analysis module qbiocode.apps.quvine.analysis.analyze module qbiocode.apps.quvine.analysis.compare module qbiocode.apps.quvine.api module qbiocode.apps.quvine.api.aliases module qbiocode.apps.quvine.api.config module qbiocode.apps.quvine.api.core module qbiocode.apps.quvine.api.sgns module qbiocode.apps.quvine.api.targets module qbiocode.apps.quvine.baselines module qbiocode.apps.quvine.baselines.adapters module qbiocode.apps.quvine.baselines.appnp module qbiocode.apps.quvine.baselines.configs module qbiocode.apps.quvine.baselines.gat module qbiocode.apps.quvine.baselines.gcn_mf module qbiocode.apps.quvine.baselines.graphgps module qbiocode.apps.quvine.baselines.graphsage module qbiocode.apps.quvine.baselines.hyperparameter_loader module qbiocode.apps.quvine.baselines.netmf module qbiocode.apps.quvine.baselines.node2vec module qbiocode.apps.quvine.baselines.registration module qbiocode.apps.quvine.baselines.registry module qbiocode.apps.quvine.cli module qbiocode.apps.quvine.configs module qbiocode.apps.quvine.corpus module qbiocode.apps.quvine.corpus.builder module qbiocode.apps.quvine.corpus.operations module qbiocode.apps.quvine.data module qbiocode.apps.quvine.data.data_loader module qbiocode.apps.quvine.data.prepare module qbiocode.apps.quvine.data.random_graphs module qbiocode.apps.quvine.data.random_graphs_extended module qbiocode.apps.quvine.data.sparsify module qbiocode.apps.quvine.data.subgraph module qbiocode.apps.quvine.embedding module qbiocode.apps.quvine.embedding.quantum_filters module qbiocode.apps.quvine.embedding.registry module qbiocode.apps.quvine.embedding.word2vec module qbiocode.apps.quvine.evaluation module qbiocode.apps.quvine.evaluation.classification module qbiocode.apps.quvine.evaluation.link_prediction module qbiocode.apps.quvine.evaluation.ranking module qbiocode.apps.quvine.fusion module qbiocode.apps.quvine.fusion.fuse module qbiocode.apps.quvine.fusion.fuse_fixes module qbiocode.apps.quvine.main module qbiocode.apps.quvine.pipeline module qbiocode.apps.quvine.reproducibility module qbiocode.apps.quvine.reproducibility.dataset_registry module qbiocode.apps.quvine.reproducibility.graph_generator module qbiocode.apps.quvine.reproducibility.method_adapters module qbiocode.apps.quvine.reproducibility.method_runner module qbiocode.apps.quvine.reproducibility.ppi_workflow module qbiocode.apps.quvine.reproducibility.seed_manager module qbiocode.apps.quvine.reproducibility.split_generator module qbiocode.apps.quvine.reproducibility.validator module qbiocode.apps.quvine.utils module qbiocode.apps.quvine.utils.io module

qbiocode.apps.quvine.utils.logging module qbiocode.apps.quvine.utils.seed module qbiocode.apps.quvine.utils.torch_utils module qbiocode.apps.quvine.utils.utilities module qbiocode.apps.quvine.views module qbiocode.apps.quvine.views.generator module qbiocode.apps.quvine.views.views module qbiocode.apps.quvine.walks module qbiocode.apps.quvine.walks.base module qbiocode.apps.quvine.walks.ctqw module qbiocode.apps.quvine.walks.dtqw module qbiocode.apps.quvine.walks.rwr module qbiocode.apps.sage module qbiocode.apps.sage.sage module qbiocode.data_generation module qbiocode.data_generation.generator module qbiocode.data_generation.make_blobs module qbiocode.data_generation.make_circles module qbiocode.data_generation.make_class module qbiocode.data_generation.make_moons module qbiocode.data_generation.make_s_curve module qbiocode.data_generation.make_spheres module qbiocode.data_generation.make_spirals module qbiocode.data_generation.make_swiss_roll module qbiocode.embeddings module qbiocode.embeddings.compute_autoencoder module qbiocode.embeddings.embed module qbiocode.evaluation module qbiocode.evaluation.dataset_evaluation module qbiocode.evaluation.graph_evaluation module qbiocode.evaluation.model_evaluation module qbiocode.evaluation.model_run module qbiocode.learning module qbiocode.learning.compute_dt module qbiocode.learning.compute_lr module qbiocode.learning.compute_mlp module qbiocode.learning.compute_nb module qbiocode.learning.compute_pqk module qbiocode.learning.compute_qensemble module qbiocode.learning.compute_qnn module qbiocode.learning.compute_qpl module qbiocode.learning.compute_qsvc module qbiocode.learning.compute_rf module qbiocode.learning.compute_svc module qbiocode.learning.compute_vqc module qbiocode.learning.compute_xgb module qbiocode.utils module qbiocode.utils.combine_evals_results module qbiocode.utils.data_encoding module qbiocode.utils.dataset_checkpoint module qbiocode.utils.find_duplicates module qbiocode.utils.find_string module qbiocode.utils.generate_qml_configs module qbiocode.utils.helper_fn module qbiocode.utils.ibm_account module qbiocode.utils.qc_winner_finder module qbiocode.utils.qutils module qbiocode.utils.tutorial_data module qbiocode.version module qbiocode.visualization module qbiocode.visualization.visualize_correlation module qml_winner() (in module qbiocode.utils.qc_winner_finder) QuantumSage (class in qbiocode.apps.sage.sage) QUVINE_HEADLINE_METHODS (in module qbiocode.embeddings.embed) QUVINE_METHODS (in module qbiocode.embeddings.embed) QuvineFilterConfig (class in qbiocode.apps.quvine.baselines.configs) QuVINEGCNMF (class in qbiocode.apps.quvine.baselines.gcn_mf) QuvineGCNMFConfig (class in qbiocode.apps.quvine.baselines.configs) QuvineMethodError QuvineSGNSConfig (class in qbiocode.apps.quvine.baselines.configs)

R

radius (PrepareGraphConfig attribute) random_state (BaselineFilterConfig attribute) (ComplexityConfig attribute) (GATTrainConfig attribute) (GCNMFConfig attribute) (GraphGPSTrainConfig attribute) (QuvineFilterConfig attribute) (QuvineGCNMFConfig attribute) (TrainConfig attribute), [1] rank (NetMFConfig attribute) rank_graphs_by_complexity() (in module qbiocode.evaluation.graph_evaluation) REAL_WORLD (DatasetType attribute) recall_at_k() (SeedTargetEvaluator method) register() (DatasetRegistry method) (MethodRegistry method) register_all_methods() (in module qbiocode.apps.quvine.baselines.registration) register_multiple() (MethodRegistry method) registry_group (DatasetEntry attribute) repetition_id (DatasetEntry attribute) REPO_DATA_DIRS (in module qbiocode.utils.tutorial_data) ReproducibilityValidator (class in qbiocode.apps.quvine.reproducibility.validator) requested_method (EmbedResult attribute) requested_size (DatasetEntry attribute) (DatasetMetadata attribute) require_torch() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.utils.torch_utils) requires_graph (MethodMetadata attribute) requires_q_targets (MethodMetadata attribute) reset_parameters() (EdgeIndexGATLayer method) (GCNLayer method) residual (GATConfig attribute) (GATModelConfig attribute) resolve_method() (in module qbiocode.apps.quvine.api.aliases) retain_ratio (PrepareGraphConfig attribute) retrieve_probabilities() (in module qbiocode.utils.qutils) ridge (QuvineFilterConfig attribute) (QuvineGCNMFConfig attribute) row_normalize() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.baselines.graphgps) rsa_corr() (in module qbiocode.apps.quvine.analysis.analyze) run() (BaseWalker method) (Pipeline method) run_all() (MethodRegistry method) run_appnp() (in module qbiocode.apps.quvine.baselines.appnp) run_appnp_adapter() (in module qbiocode.apps.quvine.baselines.adapters) (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_baseline_filter_adapter() (in module qbiocode.apps.quvine.baselines.adapters) (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_baseline_filter_heat_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_baseline_filter_poly_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_baseline_gcnmf_adapter() (in module qbiocode.apps.quvine.baselines.adapters) (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_category() (MethodRegistry method) run_ctqw_fusion_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_dtqw_fusion_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_filter_ctqw_heat_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_filter_ctqw_poly_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters)

run_filter_rwr_heat_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_filter_rwr_poly_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_adapter() (in module qbiocode.apps.quvine.baselines.adapters) (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_baseline_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_ctqw_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_ctqw_heat_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_ctqw_poly_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_dtqw_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_dtqw_heat_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_dtqw_poly_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_heat_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_poly_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_rwr_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_rwr_heat_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_gat_rwr_poly_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_adapter() (in module qbiocode.apps.quvine.baselines.adapters) (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_baseline_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_ctqw_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_ctqw_heat_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_ctqw_poly_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_dtqw_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_dtqw_heat_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_dtqw_poly_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_heat_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_poly_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_rwr_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_rwr_heat_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphgps_rwr_poly_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_graphsage() (in module qbiocode.apps.quvine.baselines.graphsage) run_graphsage_adapter() (in module qbiocode.apps.quvine.baselines.adapters) (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_job() (in module qbiocode.apps.qprofiler.qprofiler_batchmode) run_method() (MethodRegistry method) (MethodRunner method) run_netmf() (in module qbiocode.apps.quvine.baselines.netmf) run_netmf_adapter() (in module qbiocode.apps.quvine.baselines.adapters) (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_node2vec() (in module qbiocode.apps.quvine.baselines.node2vec) run_node2vec_adapter() (in module qbiocode.apps.quvine.baselines.adapters) (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_quvine_ctqw_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_quvine_dtqw_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_quvine_gcnmf_adapter() (in module qbiocode.apps.quvine.baselines.adapters) run_quvine_heat_adapter() (in module qbiocode.apps.quvine.baselines.adapters) run_quvine_poly_adapter() (in module qbiocode.apps.quvine.baselines.adapters) run_quvine_rwr_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_quvine_sgns() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_quvine_sgns_adapter() (in module qbiocode.apps.quvine.baselines.adapters) run_rwr_fusion_adapter() (in module qbiocode.apps.quvine.reproducibility.method_adapters) run_sgns() (in module qbiocode.apps.quvine.api.sgns) run_walks_for_root() (in module qbiocode.apps.quvine.api.sgns) rwr_alpha (GATMethodConfig attribute) (GraphGPSMethodConfig attribute) rwr_steps (GATMethodConfig attribute) (GraphGPSMethodConfig attribute)

S

safe_eigsh() (in module qbiocode.evaluation.graph_evaluation) safe_float() (in module qbiocode.evaluation.graph_evaluation) safe_torch_import() (in module qbiocode.apps.quvine.utils.torch_utils) sample_degree_sequence() (in module qbiocode.apps.quvine.data.random_graphs) sample_negative_edges() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.evaluation.link_prediction) sample_walks_from_distribution() (in module qbiocode.apps.quvine.utils.utilities) sanitize_graph() (in module qbiocode.evaluation.graph_evaluation) save() (DatasetRegistry method) save_config() (in module qbiocode.apps.quvine.utils.io) save_seed_registry() (SeedManager method) scale_train_test() (in module qbiocode.utils.helper_fn) scaler_fn() (in module qbiocode.utils.helper_fn) scatter (CorrelationFigures attribute) scatter_ax (CorrelationFigures attribute) scipy_sparse_to_torch_coo() (in module qbiocode.apps.quvine.baselines.gat) scoring (PrepareGraphConfig attribute) seed (APPNPConfig attribute) (DatasetEntry attribute) (GraphSAGEConfig attribute) (NetMFConfig attribute) (Node2VecConfig attribute) seed_centroid_scores() (in module qbiocode.apps.quvine.evaluation.ranking) SeedManager (class in qbiocode.apps.quvine.reproducibility.seed_manager) SeedTargetEvaluator (class in qbiocode.apps.quvine.evaluation.ranking) select_calibration_seeds() (in module qbiocode.apps.quvine.api.targets) set_global_loader() (in module qbiocode.apps.quvine.baselines.hyperparameter_loader) set_global_seed() (in module qbiocode.apps.quvine.utils.seed) set_seed() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.baselines.graphgps) (QuantumSage method)

setup_logging() (in module qbiocode.apps.quvine.utils.logging) SKLEARN_METHODS (in module qbiocode.embeddings.embed) sparsify_edges (PrepareGraphConfig attribute) sparsify_edges_biological() (in module qbiocode.apps.quvine.data.sparsify) spectral_info() (in module qbiocode.apps.quvine.analysis.analyze) spectral_k (ComplexityConfig attribute) split_edges() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.evaluation.link_prediction) split_paths (DatasetEntry attribute) SplitGenerator (class in qbiocode.apps.quvine.reproducibility.split_generator) standardize_columns() (in module qbiocode.apps.quvine.baselines.gat) (in module qbiocode.apps.quvine.baselines.graphgps) standardize_features (GraphGPSConfig attribute) (GraphGPSModelConfig attribute) subsample_nodes (PrepareGraphConfig attribute) subsample_nodes() (in module qbiocode.apps.quvine.data.subgraph) subsample_nodes_with_protected() (in module qbiocode.apps.quvine.data.subgraph) success (MethodResult attribute) summarize_classification_results() (in module qbiocode.apps.quvine.evaluation.classification) summarize_link_prediction_results() (in module qbiocode.apps.quvine.evaluation.link_prediction) SUPPORTED_ENTANGLEMENTS (in module qbiocode.utils.qutils) SUPPORTED_FEATURE_MAPS (in module qbiocode.utils.qutils) SUPPORTED_OPTIMIZERS (in module qbiocode.utils.qutils) sweep_configuration_model_graphs() (in module qbiocode.apps.quvine.data.random_graphs) sweep_degree_corrected_sbm() (in module qbiocode.apps.quvine.data.random_graphs) sweep_grid_torus_lattice() (in module qbiocode.apps.quvine.data.random_graphs) sweep_heterophilic_sbm() (in module qbiocode.apps.quvine.data.random_graphs) sweep_random_regular_expander_like() (in module qbiocode.apps.quvine.data.random_graphs) SYNTHETIC (DatasetType attribute) SYNTHETIC_FAMILIES (SyntheticGraphGenerator attribute) SyntheticGraphGenerator (class in qbiocode.apps.quvine.reproducibility.graph_generator)

T

t (BaselineFilterConfig attribute) (QuvineFilterConfig attribute) task (GraphGPSTrainConfig attribute) (TrainConfig attribute) TASK_TO_COMPONENT (SeedManager attribute) TASK_TO_SPLIT_COMPONENT (SeedManager attribute) to_dict() (DatasetEntry method) torch_optional() (in module qbiocode.apps.quvine.utils.torch_utils) TorchNotAvailableError track_progress() (in module qbiocode.utils.combine_evals_results) train (GATMethodConfig attribute) (GraphGPSMethodConfig attribute)

train_classifier() (in module qbiocode.apps.quvine.reproducibility.method_adapters) train_embeddings() (in module qbiocode.apps.quvine.api.sgns) train_gat_link_reconstruction() (in module qbiocode.apps.quvine.baselines.gat) train_gat_node_classifier() (in module qbiocode.apps.quvine.baselines.gat) train_gcn_mf() (in module qbiocode.apps.quvine.baselines.gcn_mf) train_graphgps_link_reconstruction() (in module qbiocode.apps.quvine.baselines.graphgps) train_graphgps_node_classifier() (in module qbiocode.apps.quvine.baselines.graphgps) train_sub_sages() (QuantumSage method) TrainConfig (class in qbiocode.apps.quvine.baselines.gat) (class in qbiocode.apps.quvine.baselines.graphgps) transpile_circuit() (in module qbiocode.utils.qutils) tutorial_data_dirs() (in module qbiocode.utils.tutorial_data) tutorial_data_path() (in module qbiocode.utils.tutorial_data)

U

UNAVAILABLE (in module qbiocode.apps.quvine.baselines) unit_coefficient_data_map() (in module qbiocode.utils.qutils) use_features (BaselineFilterConfig attribute) (QuvineFilterConfig attribute)

use_largest_cc_for_path (ComplexityConfig attribute) use_layer_norm (GraphGPSConfig attribute) (GraphGPSModelConfig attribute) used_quantum_targets (EmbedResult attribute)

V

val_edge_fraction (GATTrainConfig attribute) (GraphGPSTrainConfig attribute) (TrainConfig attribute), [1] validate_all_datasets() (ReproducibilityValidator method) validate_consistency() (DatasetRegistry method) validate_dataset() (ReproducibilityValidator method) validate_experiment_consistency() (ReproducibilityValidator method) validate_seed_consistency() (SeedManager method) validate_split_consistency() (ReproducibilityValidator method)

validate_torch_tensor() (in module qbiocode.apps.quvine.utils.torch_utils) variant (GATMethodConfig attribute) (GraphGPSMethodConfig attribute) variant_for() (in module qbiocode.apps.quvine.api.aliases) verbose (GATTrainConfig attribute) (GraphGPSTrainConfig attribute) (PrepareGraphConfig attribute) (TrainConfig attribute), [1] ViewBuilder (class in qbiocode.apps.quvine.views.generator)

W

walk_kind (QuvineSGNSConfig attribute) walk_length (Node2VecConfig attribute) weight_decay (APPNPConfig attribute) (GATTrainConfig attribute) (GCNMFConfig attribute) (GraphGPSTrainConfig attribute) (QuvineGCNMFConfig attribute) (TrainConfig attribute), [1]

window (Node2VecConfig attribute) window_size (NetMFConfig attribute) wl_iterations (ComplexityConfig attribute) workers (Node2VecConfig attribute)