Index

A

adjacency_matrix (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute)

alpha (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank attribute) (bioneuralnet.clustering.CorrelatedPageRank attribute) Autoencoder (class in bioneuralnet.downstream_task.dpmon) AutoEncoder (class in bioneuralnet.downstream_task.subject_representation)

B

B (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain attribute) (bioneuralnet.clustering.CorrelatedLouvain attribute) (bioneuralnet.clustering.hybrid_louvain.HybridLouvain attribute) (bioneuralnet.clustering.HybridLouvain attribute) bioneuralnet.clustering module bioneuralnet.clustering.correlated_louvain module bioneuralnet.clustering.correlated_pagerank module bioneuralnet.clustering.hybrid_louvain module bioneuralnet.datasets module bioneuralnet.datasets.dataset_loader module bioneuralnet.downstream_task module bioneuralnet.downstream_task.dpmon module bioneuralnet.downstream_task.subject_representation module bioneuralnet.external_tools module bioneuralnet.metrics module

bioneuralnet.metrics.correlation module bioneuralnet.metrics.evaluation module bioneuralnet.metrics.plot module bioneuralnet.network_embedding module bioneuralnet.network_embedding.gnn_embedding module bioneuralnet.network_embedding.gnn_models module bioneuralnet.utils module bioneuralnet.utils.data module bioneuralnet.utils.graph module bioneuralnet.utils.logger module bioneuralnet.utils.preprocess module bioneuralnet.utils.rdata_convert module build_omics_networks_tg() (in module bioneuralnet.downstream_task.dpmon)

C

clean_inf_nan() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) clinical_data (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) cluster_correlation() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.correlation) compare_clusters() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.plot)

CorrelatedLouvain (class in bioneuralnet.clustering) (class in bioneuralnet.clustering.correlated_louvain) CorrelatedPageRank (class in bioneuralnet.clustering) (class in bioneuralnet.clustering.correlated_pagerank) correlation_summary() (in module bioneuralnet.utils) (in module bioneuralnet.utils.data) cuda (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute)

D

DatasetLoader (class in bioneuralnet.datasets) (class in bioneuralnet.datasets.dataset_loader) DimensionAveraging (class in bioneuralnet.downstream_task.dpmon) DownstreamTaskNN (class in bioneuralnet.downstream_task.dpmon)

DPMON (class in bioneuralnet.downstream_task) (class in bioneuralnet.downstream_task.dpmon) dropout (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute)

E

embed() (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding method) (bioneuralnet.network_embedding.GNNEmbedding method) evaluate_f1m() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.evaluation) evaluate_f1w() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.evaluation) evaluate_model() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.evaluation) evaluate_rf() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.evaluation)

evaluate_single_run() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.evaluation) evaluate_xgb() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.evaluation) explore_data_stats() (in module bioneuralnet.utils) (in module bioneuralnet.utils.data) expression_summary() (in module bioneuralnet.utils) (in module bioneuralnet.utils.data)

F

fit() (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding method) (bioneuralnet.network_embedding.GNNEmbedding method) forward() (bioneuralnet.downstream_task.dpmon.Autoencoder method) (bioneuralnet.downstream_task.dpmon.DimensionAveraging method) (bioneuralnet.downstream_task.dpmon.DownstreamTaskNN method) (bioneuralnet.downstream_task.dpmon.NeuralNetwork method) (bioneuralnet.downstream_task.subject_representation.AutoEncoder method) (bioneuralnet.network_embedding.GAT method) (bioneuralnet.network_embedding.GCN method) (bioneuralnet.network_embedding.GIN method) (bioneuralnet.network_embedding.gnn_models.GAT method) (bioneuralnet.network_embedding.gnn_models.GCN method) (bioneuralnet.network_embedding.gnn_models.GIN method) (bioneuralnet.network_embedding.gnn_models.SAGE method) (bioneuralnet.network_embedding.SAGE method)

G

G (bioneuralnet.clustering.hybrid_louvain.HybridLouvain attribute) (bioneuralnet.clustering.HybridLouvain attribute) GAT (class in bioneuralnet.network_embedding) (class in bioneuralnet.network_embedding.gnn_models) GCN (class in bioneuralnet.network_embedding) (class in bioneuralnet.network_embedding.gnn_models) gen_correlation_graph() (in module bioneuralnet.utils) (in module bioneuralnet.utils.graph) gen_gaussian_knn_graph() (in module bioneuralnet.utils) (in module bioneuralnet.utils.graph) gen_lasso_graph() (in module bioneuralnet.utils) (in module bioneuralnet.utils.graph) gen_mst_graph() (in module bioneuralnet.utils) (in module bioneuralnet.utils.graph) gen_similarity_graph() (in module bioneuralnet.utils) (in module bioneuralnet.utils.graph) gen_snn_graph() (in module bioneuralnet.utils) (in module bioneuralnet.utils.graph) gen_threshold_graph() (in module bioneuralnet.utils) (in module bioneuralnet.utils.graph) generate_hidden_dims() (in module bioneuralnet.downstream_task.subject_representation) generate_weighted_personalization() (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank method) (bioneuralnet.clustering.CorrelatedPageRank method) get_activation() (in module bioneuralnet.downstream_task.subject_representation) (in module bioneuralnet.network_embedding.gnn_models)

get_embeddings() (bioneuralnet.network_embedding.GAT method) (bioneuralnet.network_embedding.GCN method) (bioneuralnet.network_embedding.GIN method) (bioneuralnet.network_embedding.gnn_models.GAT method) (bioneuralnet.network_embedding.gnn_models.GCN method) (bioneuralnet.network_embedding.gnn_models.GIN method) (bioneuralnet.network_embedding.gnn_models.SAGE method) (bioneuralnet.network_embedding.SAGE method) get_logger() (in module bioneuralnet.utils) (in module bioneuralnet.utils.logger) get_quality() (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain method) (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank method) (bioneuralnet.clustering.CorrelatedLouvain method) (bioneuralnet.clustering.CorrelatedPageRank method) GIN (class in bioneuralnet.network_embedding) (class in bioneuralnet.network_embedding.gnn_models) gnn_hidden_dim (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) GNNEmbedding (class in bioneuralnet.network_embedding) (class in bioneuralnet.network_embedding.gnn_embedding) gpu (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute)

H

hidden_dim (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute)

HybridLouvain (class in bioneuralnet.clustering) (class in bioneuralnet.clustering.hybrid_louvain)

K

k (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank attribute) (bioneuralnet.clustering.CorrelatedPageRank attribute) k3 (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain attribute) (bioneuralnet.clustering.CorrelatedLouvain attribute) (bioneuralnet.clustering.hybrid_louvain.HybridLouvain attribute) (bioneuralnet.clustering.HybridLouvain attribute)

k4 (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain attribute) (bioneuralnet.clustering.CorrelatedLouvain attribute) (bioneuralnet.clustering.hybrid_louvain.HybridLouvain attribute) (bioneuralnet.clustering.HybridLouvain attribute)

L

layer_num (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) louvain_to_adjacency() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.correlation)

lr (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute)

M

max_iter (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank attribute) (bioneuralnet.clustering.CorrelatedPageRank attribute) (bioneuralnet.clustering.hybrid_louvain.HybridLouvain attribute) (bioneuralnet.clustering.HybridLouvain attribute) model (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) model_type (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) module bioneuralnet.clustering bioneuralnet.clustering.correlated_louvain bioneuralnet.clustering.correlated_pagerank bioneuralnet.clustering.hybrid_louvain bioneuralnet.datasets bioneuralnet.datasets.dataset_loader bioneuralnet.downstream_task bioneuralnet.downstream_task.dpmon bioneuralnet.downstream_task.subject_representation bioneuralnet.external_tools bioneuralnet.metrics bioneuralnet.metrics.correlation bioneuralnet.metrics.evaluation bioneuralnet.metrics.plot bioneuralnet.network_embedding bioneuralnet.network_embedding.gnn_embedding bioneuralnet.network_embedding.gnn_models bioneuralnet.utils bioneuralnet.utils.data bioneuralnet.utils.graph bioneuralnet.utils.logger bioneuralnet.utils.preprocess bioneuralnet.utils.rdata_convert

N

network_remove_high_zero_fraction() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) network_remove_low_variance() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) NeuralNetwork (class in bioneuralnet.downstream_task.dpmon) nn_hidden_dim1 (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute)

nn_hidden_dim2 (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) num_epochs (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute)

O

omics_correlation() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.correlation) omics_data (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) omics_list (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute)

output_dir (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank attribute) (bioneuralnet.clustering.CorrelatedPageRank attribute) (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute)

P

partition_to_adjacency() (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain method) (bioneuralnet.clustering.CorrelatedLouvain method) phen_omics_corr() (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank method) (bioneuralnet.clustering.CorrelatedPageRank method) phenotype_col (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) phenotype_data (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) plot_embeddings() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.plot) plot_grouped_performance() (in module bioneuralnet.metrics.evaluation) plot_multiple_metrics() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.evaluation) plot_network() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.plot)

plot_performance() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.plot) plot_performance_three() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.plot) plot_variance_by_feature() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.plot) plot_variance_distribution() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.plot) preprocess_clinical() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) process_dropout() (in module bioneuralnet.network_embedding.gnn_models) prune_network() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) prune_network_by_quantile() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess)

R

rdata_to_df() (in module bioneuralnet.utils) (in module bioneuralnet.utils.rdata_convert) repeat_num (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) run() (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain method) (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank method) (bioneuralnet.clustering.CorrelatedLouvain method) (bioneuralnet.clustering.CorrelatedPageRank method) (bioneuralnet.clustering.hybrid_louvain.HybridLouvain method) (bioneuralnet.clustering.HybridLouvain method) (bioneuralnet.downstream_task.DPMON method) (bioneuralnet.downstream_task.dpmon.DPMON method) (bioneuralnet.downstream_task.subject_representation.SubjectRepresentation method) (bioneuralnet.downstream_task.SubjectRepresentation method)

run_gnn_embedding_tuning() (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding method) (bioneuralnet.network_embedding.GNNEmbedding method) run_hyperparameter_tuning() (in module bioneuralnet.downstream_task.dpmon) run_pagerank_clustering() (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank method) (bioneuralnet.clustering.CorrelatedPageRank method) run_standard_training() (in module bioneuralnet.downstream_task.dpmon) run_tuning() (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain method) (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank method) (bioneuralnet.clustering.CorrelatedLouvain method) (bioneuralnet.clustering.CorrelatedPageRank method)

S

SAGE (class in bioneuralnet.network_embedding) (class in bioneuralnet.network_embedding.gnn_models) seed (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) select_top_k_correlation() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) select_top_k_variance() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) select_top_randomforest() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess)

setup_device() (in module bioneuralnet.downstream_task.dpmon) shape (bioneuralnet.datasets.dataset_loader.DatasetLoader property) (bioneuralnet.datasets.DatasetLoader property) slice_omics_datasets() (in module bioneuralnet.downstream_task.dpmon) SubjectRepresentation (class in bioneuralnet.downstream_task) (class in bioneuralnet.downstream_task.subject_representation) sweep_cut() (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank method) (bioneuralnet.clustering.CorrelatedPageRank method)

T

tol (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank attribute) (bioneuralnet.clustering.CorrelatedPageRank attribute) top_anova_f_features() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) train_model() (in module bioneuralnet.downstream_task.dpmon) tune (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain attribute) (bioneuralnet.clustering.CorrelatedLouvain attribute) (bioneuralnet.clustering.hybrid_louvain.HybridLouvain attribute) (bioneuralnet.clustering.HybridLouvain attribute) (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute)

V

variance_summary() (in module bioneuralnet.utils) (in module bioneuralnet.utils.data)

W

weight (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain attribute) (bioneuralnet.clustering.CorrelatedLouvain attribute) (bioneuralnet.clustering.hybrid_louvain.HybridLouvain attribute) (bioneuralnet.clustering.HybridLouvain attribute)

weight_decay (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute)

Y

Y (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain attribute) (bioneuralnet.clustering.CorrelatedLouvain attribute) (bioneuralnet.clustering.hybrid_louvain.HybridLouvain attribute) (bioneuralnet.clustering.HybridLouvain attribute)

Z

zero_fraction_summary() (in module bioneuralnet.utils) (in module bioneuralnet.utils.data)