Index

Symbols

--analysis-type <analysis_type> cli-feature_analysis command line option --connected cli-extract_features command line option --feature-file <feature_file> cli-feature_analysis command line option --folder <folder> cli-get_data command line option --graph-removal <graph_removal> cli-feature_analysis command line option --interpretability <interpretability> cli-feature_analysis command line option --kfold cli-feature_analysis command line option --max-feats-plot <max_feats_plot> cli-feature_analysis command line option --mode <mode> cli-extract_features command line option --model <model> cli-feature_analysis command line option --n-repeats <n_repeats> cli-feature_analysis command line option --n-splits <n_splits> cli-feature_analysis command line option --n-workers <n_workers> cli-extract_features command line option --no-connected cli-extract_features command line option --no-kfold cli-feature_analysis command line option --no-node-feat cli-extract_features command line option --no-norm cli-extract_features command line option --no-plot cli-feature_analysis command line option --no-reduce-set cli-feature_analysis command line option --no-runtimes cli-extract_features command line option --node-feat cli-extract_features command line option --norm cli-extract_features command line option

--output-file <output_file> cli-extract_features command line option --plot cli-feature_analysis command line option --reduce-set cli-feature_analysis command line option --reduced-set-max-correlation <reduced_set_max_correlation> cli-feature_analysis command line option --reduced-set-size <reduced_set_size> cli-feature_analysis command line option --results-folder <results_folder> cli-extract_features command line option cli-feature_analysis command line option --runtimes cli-extract_features command line option --stats-level <stats_level> cli-extract_features command line option --timeout <timeout> cli-extract_features command line option --verbose cli command line option -f cli-get_data command line option -ff cli-feature_analysis command line option -i cli-feature_analysis command line option -m cli-extract_features command line option cli-feature_analysis command line option -n cli-extract_features command line option -np cli-feature_analysis command line option -of cli-extract_features command line option -p cli-feature_analysis command line option -rf cli-extract_features command line option cli-feature_analysis command line option -sl cli-extract_features command line option -v cli command line option

_

__init_subclass__() (hcga.feature_class.FeatureClass class method) _check_length() (hcga.graph.Graph method) _clustering_statistics() (hcga.feature_class.FeatureClass method) _compute_fold() (in module hcga.analysis) _evaluate_kfold() (in module hcga.analysis) _feature_statistics() (hcga.feature_class.FeatureClass method) _feature_statistics_advanced() (hcga.feature_class.FeatureClass method) _feature_statistics_basic() (hcga.feature_class.FeatureClass method) _feature_statistics_medium() (hcga.feature_class.FeatureClass method) _filter_features() (in module hcga.analysis) _filter_graphs() (in module hcga.analysis) _filter_interpretable() (in module hcga.analysis) _get_model() (in module hcga.analysis)

_get_reduced_feature_set() (in module hcga.analysis) _get_shap_feature_importance() (in module hcga.analysis) _list_statistics() (hcga.feature_class.FeatureClass method) _load_feature_class() (in module hcga.extraction) _node_feature_statistics() (hcga.feature_class.FeatureClass method) _normalise_feature_data() (in module hcga.analysis) _number_folds() (in module hcga.analysis) _preprocess_features() (in module hcga.analysis) _print_accuracy() (in module hcga.analysis) _print_runtimes() (in module hcga.extraction) _save_predictions_to_csv() (in module hcga.analysis) _save_to_csv() (in module hcga.analysis) _set_graph_labels() (in module hcga.extraction) _test_feature_exists() (hcga.feature_class.FeatureClass method)

A

add_feature() (hcga.feature_class.FeatureClass method) add_feature_description() (hcga.feature_class.FeatureClass class method) add_graph() (hcga.graph.GraphCollection method) add_graph_list() (hcga.graph.GraphCollection method) analyse_features() (hcga.hcga.Hcga method)

analysis() (in module hcga.analysis) Assortativity (class in hcga.features.assortativity) asyn_fluidc() (in module hcga.features.communities_asyn) attracting_component_sizes() (in module hcga.features.components) average_cycle_length() (in module hcga.features.cycle_basis) average_neighbor_degree() (in module hcga.features.assortativity)

B

barycenter_size() (in module hcga.features.distance_measures) barycenter_size_weighted() (in module hcga.features.distance_measures)

basal_component_sizes() (in module hcga.features.components) BasicStats (class in hcga.features.basic_stats) betweenness_centrality() (in module hcga.features.centralities_basic)

C

center_size() (in module hcga.features.distance_measures) CentralitiesBasic (class in hcga.features.centralities_basic) ChemicalTheory (class in hcga.features.chemical_theory) classify_pairwise() (in module hcga.analysis) cli command line option --verbose -v cli-extract_features command line option --connected --mode <mode> --n-workers <n_workers> --no-connected --no-node-feat --no-norm --no-runtimes --node-feat --norm --output-file <output_file> --results-folder <results_folder> --runtimes --stats-level <stats_level> --timeout <timeout> -m -n -of -rf -sl DATASET cli-feature_analysis command line option --analysis-type <analysis_type> --feature-file <feature_file> --graph-removal <graph_removal> --interpretability <interpretability> --kfold --max-feats-plot <max_feats_plot> --model <model> --n-repeats <n_repeats> --n-splits <n_splits> --no-kfold --no-plot --no-reduce-set --plot --reduce-set --reduced-set-max-correlation <reduced_set_max_correlation> --reduced-set-size <reduced_set_size> --results-folder <results_folder> -ff -i -m -np -p -rf DATASET cli-get_data command line option --folder <folder> -f DATASET_NAME

clique_sizes() (in module hcga.features.cliques) (in module hcga.features.node_clique_number) Cliques (class in hcga.features.cliques) closeness_centrality() (in module hcga.features.centralities_basic) Clustering (class in hcga.features.clustering) clustering_dist() (in module hcga.features.clustering) combine_features() (hcga.hcga.Hcga method) CommunitiesAsyn (class in hcga.features.communities_asyn) CommunitiesBisection (class in hcga.features.communities_bisection) CommunitiesLabelPropagation (class in hcga.features.communities_labelprop) CommunitiesModularity (class in hcga.features.communities_modularity) Components (class in hcga.features.components) compute_all_features() (in module hcga.extraction) compute_features() (hcga.feature_class.FeatureClass method) (hcga.features.assortativity.Assortativity method) (hcga.features.basic_stats.BasicStats method) (hcga.features.centralities_basic.CentralitiesBasic method) (hcga.features.chemical_theory.ChemicalTheory method) (hcga.features.cliques.Cliques method) (hcga.features.clustering.Clustering method) (hcga.features.communities_asyn.CommunitiesAsyn method) (hcga.features.communities_bisection.CommunitiesBisection method) (hcga.features.communities_labelprop.CommunitiesLabelPropagation method) (hcga.features.communities_modularity.CommunitiesModularity method) (hcga.features.components.Components method) (hcga.features.core_number.CoreNumber method) (hcga.features.cycle_basis.CycleBasis method) (hcga.features.distance_measures.DistanceMeasures method) (hcga.features.dominating_sets.DominatingSets method) (hcga.features.efficiency.Efficiency method) (hcga.features.eulerian.Eulerian method) (hcga.features.independent_sets.IndependentSets method) (hcga.features.k_components.KComponents method) (hcga.features.link_analysis_hits.Hits method) (hcga.features.maximal_matching.MaximalMatching method) (hcga.features.minimum_cuts.MinimumCuts method) (hcga.features.node_clique_number.NodeCliqueNumber method) (hcga.features.node_connectivity.NodeConnectivity method) (hcga.features.node_features.NodeFeatures method) (hcga.features.rich_club.RichClub method) (hcga.features.scale_free.ScaleFree method) (hcga.features.shortest_paths.ShortestPaths method) (hcga.features.small_worldness.SmallWorldness method) (hcga.features.spectrum.Spectrum method) (hcga.features.structural_holes.StructuralHoles method) (hcga.features.vitality.Vitality method) compute_normalize_features() (hcga.feature_class.FeatureClass method) condensation_edges() (in module hcga.features.components) condensation_nodes() (in module hcga.features.components) constraint() (in module hcga.features.structural_holes) convert_graph() (in module hcga.graph) core_number() (in module hcga.features.core_number) CoreNumber (class in hcga.features.core_number) CycleBasis (class in hcga.features.cycle_basis)

D

DATASET cli-extract_features command line option cli-feature_analysis command line option DATASET_NAME cli-get_data command line option

degree_centrality() (in module hcga.features.centralities_basic) density() (in module hcga.features.basic_stats) diameter() (in module hcga.features.basic_stats) DistanceMeasures (class in hcga.features.distance_measures) DominatingSets (class in hcga.features.dominating_sets)

E

eccentricity() (in module hcga.features.distance_measures) edge_betweenness_centrality() (in module hcga.features.centralities_basic) edge_weights() (in module hcga.features.basic_stats) effective_size() (in module hcga.features.structural_holes) Efficiency (class in hcga.features.efficiency) eigenvector_centrality() (in module hcga.features.centralities_basic) Eulerian (class in hcga.features.eulerian) eval_asyn() (in module hcga.features.communities_asyn) eval_bisection() (in module hcga.features.communities_bisection) eval_cliques() (in module hcga.features.cliques)

eval_connected_components() (in module hcga.features.components) eval_cycle_basis() (in module hcga.features.cycle_basis) eval_kcomponents() (in module hcga.features.k_components) eval_labelprop() (in module hcga.features.communities_labelprop) eval_modularity() (in module hcga.features.communities_modularity) eval_rich_club() (in module hcga.features.rich_club) eval_shortest_paths() (in module hcga.features.shortest_paths) evaluate_feature() (hcga.feature_class.FeatureClass method) extract() (hcga.hcga.Hcga method) (in module hcga.extraction) extrema_bounding() (in module hcga.features.distance_measures)

F

feature_extraction() (in module hcga.extraction) FeatureClass (class in hcga.feature_class)

features_to_Xy() (in module hcga.analysis) fit_model() (in module hcga.analysis) fit_model_kfold() (in module hcga.analysis)

G

generate_data() (hcga.hcga.Hcga method) get_conv_matrix() (in module hcga.features.node_features) get_feature_description() (hcga.feature_class.FeatureClass method) get_feature_info() (hcga.feature_class.FeatureClass method) get_feature_interpretability() (hcga.feature_class.FeatureClass method) get_feature_matrix() (in module hcga.features.node_features) get_features() (hcga.feature_class.FeatureClass method) get_graph() (hcga.graph.Graph method)

get_graph_ids() (hcga.graph.GraphCollection method) get_info() (hcga.feature_class.FeatureClass method) get_list_feature_classes() (in module hcga.extraction) get_n_node_features() (hcga.graph.GraphCollection method) get_num_disabled_graphs() (hcga.graph.GraphCollection method) get_score() (hcga.feature_class.InterpretabilityScore method) Graph (class in hcga.graph) GraphCollection (class in hcga.graph)

H

harmonic_centrality() (in module hcga.features.centralities_basic) Hcga (class in hcga.hcga) hcga.analysis module hcga.app module hcga.extraction module hcga.feature_class module hcga.features.assortativity module hcga.features.basic_stats module hcga.features.centralities_basic module hcga.features.chemical_theory module hcga.features.cliques module hcga.features.clustering module hcga.features.communities_asyn module hcga.features.communities_bisection module hcga.features.communities_labelprop module hcga.features.communities_modularity module hcga.features.components module hcga.features.core_number module hcga.features.cycle_basis module hcga.features.distance_measures module hcga.features.dominating_sets module

hcga.features.efficiency module hcga.features.eulerian module hcga.features.independent_sets module hcga.features.k_components module hcga.features.link_analysis_hits module hcga.features.maximal_matching module hcga.features.minimum_cuts module hcga.features.node_clique_number module hcga.features.node_connectivity module hcga.features.node_features module hcga.features.rich_club module hcga.features.scale_free module hcga.features.shortest_paths module hcga.features.small_worldness module hcga.features.spectrum module hcga.features.structural_holes module hcga.features.vitality module hcga.graph module hcga.hcga module Hits (class in hcga.features.link_analysis_hits)

I

IndependentSets (class in hcga.features.independent_sets)

InterpretabilityScore (class in hcga.feature_class)

K

katz_centrality() (in module hcga.features.centralities_basic)

KComponents (class in hcga.features.k_components)

L

largest_commsize() (in module hcga.features.communities_bisection) (in module hcga.features.communities_labelprop) (in module hcga.features.communities_modularity) largest_commsize_weighted() (in module hcga.features.communities_modularity) largest_connected_component() (in module hcga.features.components)

len_least_dense() (in module hcga.features.communities_asyn) len_most_dense() (in module hcga.features.communities_asyn) load_data() (hcga.hcga.Hcga method) load_features() (hcga.hcga.Hcga method) load_model() (hcga.hcga.Hcga method)

M

max_num_components() (in module hcga.features.k_components) maximal_clique_sizes() (in module hcga.features.cliques) maximal_matching() (in module hcga.features.dominating_sets) (in module hcga.features.maximal_matching) maximal_subgraph() (hcga.graph.Graph method) maximal_subgraphs() (hcga.graph.GraphCollection method) MaximalMatching (class in hcga.features.maximal_matching) min_edge_cut_size() (in module hcga.features.minimum_cuts) min_edge_dominating_set() (in module hcga.features.dominating_sets) min_node_cut_size() (in module hcga.features.minimum_cuts) min_weighted_dominating_set() (in module hcga.features.dominating_sets) minimum_cycle_length() (in module hcga.features.cycle_basis) MinimumCuts (class in hcga.features.minimum_cuts) module hcga.analysis hcga.app hcga.extraction hcga.feature_class hcga.features.assortativity hcga.features.basic_stats hcga.features.centralities_basic hcga.features.chemical_theory hcga.features.cliques hcga.features.clustering hcga.features.communities_asyn hcga.features.communities_bisection hcga.features.communities_labelprop hcga.features.communities_modularity hcga.features.components hcga.features.core_number hcga.features.cycle_basis hcga.features.distance_measures hcga.features.dominating_sets hcga.features.efficiency hcga.features.eulerian hcga.features.independent_sets hcga.features.k_components hcga.features.link_analysis_hits hcga.features.maximal_matching hcga.features.minimum_cuts hcga.features.node_clique_number hcga.features.node_connectivity hcga.features.node_features hcga.features.rich_club hcga.features.scale_free hcga.features.shortest_paths hcga.features.small_worldness hcga.features.spectrum hcga.features.structural_holes hcga.features.vitality hcga.graph hcga.hcga

N

n_cliques() (in module hcga.features.cliques) n_edges() (in module hcga.features.basic_stats) n_nodes() (in module hcga.features.basic_stats) node_conn() (in module hcga.features.node_connectivity) NodeCliqueNumber (class in hcga.features.node_clique_number) NodeConnectivity (class in hcga.features.node_connectivity)

NodeFeatures (class in hcga.features.node_features) num_communities() (in module hcga.features.communities_modularity) num_communities_weighted() (in module hcga.features.communities_modularity) num_connected_components() (in module hcga.features.components) num_connectivity_levels_k() (in module hcga.features.k_components) num_cycles() (in module hcga.features.cycle_basis) number_basal_components() (in module hcga.features.components)

P

pagerank() (in module hcga.features.centralities_basic) pairwise_classification() (hcga.hcga.Hcga method)

partitions() (in module hcga.features.communities_asyn) periphery() (in module hcga.features.distance_measures) predict_unlabelled() (in module hcga.analysis)

R

radius() (in module hcga.features.basic_stats) ratio_commsize_maxmin() (in module hcga.features.communities_labelprop) (in module hcga.features.communities_modularity) ratio_commsize_maxmin_weighted() (in module hcga.features.communities_modularity) ratio_largest() (in module hcga.features.components) ratio_min_max() (in module hcga.features.components) ratio_nodes_cycle() (in module hcga.features.cycle_basis)

remove_edge_weights() (hcga.graph.GraphCollection method) remove_node_features() (hcga.graph.GraphCollection method) remove_weights() (hcga.graph.Graph method) rich_club_k_1() (in module hcga.features.rich_club) rich_club_k_max() (in module hcga.features.rich_club) rich_club_maxminratio() (in module hcga.features.rich_club) RichClub (class in hcga.features.rich_club)

S

save_features() (hcga.hcga.Hcga method) ScaleFree (class in hcga.features.scale_free) second_order_centrality() (in module hcga.features.centralities_basic) set_networkx() (hcga.graph.Graph method) set_node_features() (hcga.graph.Graph method) set_score() (hcga.feature_class.InterpretabilityScore method) setup_class() (hcga.feature_class.FeatureClass class method) ShortestPaths (class in hcga.features.shortest_paths) size_2_component() (in module hcga.features.k_components) size_dominating_set() (in module hcga.features.dominating_sets)

size_max_indep_set() (in module hcga.features.independent_sets) size_max_k_component() (in module hcga.features.k_components) size_min_dominating_set() (in module hcga.features.dominating_sets) size_min_edge_dominating_set() (in module hcga.features.dominating_sets) SmallWorldness (class in hcga.features.small_worldness) Spectrum (class in hcga.features.spectrum) square_clustering_dist() (in module hcga.features.clustering) strongly_connected_component_sizes() (in module hcga.features.components) StructuralHoles (class in hcga.features.structural_holes) subgraph_centrality() (in module hcga.features.centralities_basic) sum_density() (in module hcga.features.communities_asyn)

T

train_all() (in module hcga.analysis)

triang() (in module hcga.features.clustering)

V

Vitality (class in hcga.features.vitality)

W

weakly_connected_component_sizes() (in module hcga.features.components) weighted_betweenness_centrality() (in module hcga.features.centralities_basic) weighted_edge_betweenness_centrality() (in module hcga.features.centralities_basic)

weighted_eigenvector_centrality() (in module hcga.features.centralities_basic) weighted_pagerank() (in module hcga.features.centralities_basic) weigted_average_neighbor_degree() (in module hcga.features.assortativity)