Index

A

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

auto_pysmccnet() (in module bioneuralnet) (in module bioneuralnet.network) (in module bioneuralnet.network.pysmccnet) (in module bioneuralnet.network.pysmccnet.pipeline) AutoEncoder (class in bioneuralnet.downstream_task.dpmon) (class in bioneuralnet.downstream_task.subject_representation)

B

basic_statistics() (bioneuralnet.network.NetworkAnalyzer method) (bioneuralnet.network.tools.NetworkAnalyzer method) best_subgraph (bioneuralnet.clustering.hybrid_louvain.HybridLouvain property) (bioneuralnet.clustering.HybridLouvain property) (bioneuralnet.HybridLouvain property) binary_search() (in module bioneuralnet.network.pysmccnet.math_helpers) bioneuralnet module bioneuralnet.clustering module bioneuralnet.clustering.correlated_louvain module bioneuralnet.clustering.correlated_pagerank module bioneuralnet.clustering.hybrid_louvain module bioneuralnet.clustering.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.external_tools.extract_CVfold module bioneuralnet.metrics module bioneuralnet.metrics.correlation module bioneuralnet.metrics.plot module

bioneuralnet.network module bioneuralnet.network.generate module bioneuralnet.network.pysmccnet module bioneuralnet.network.pysmccnet.analysis module bioneuralnet.network.pysmccnet.core module bioneuralnet.network.pysmccnet.math_helpers module bioneuralnet.network.pysmccnet.pipeline module bioneuralnet.network.pysmccnet.wrappers module bioneuralnet.network.tools 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.feature_selection module bioneuralnet.utils.logger module bioneuralnet.utils.preprocess module bioneuralnet.utils.reproducibility module

C

clean_inf_nan() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) clean_internal() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) clinical_data (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) (bioneuralnet.GNNEmbedding attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) cluster_correlation() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.correlation) cluster_pca_correlation() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.correlation) clustering_coefficient_gpu() (bioneuralnet.network.NetworkAnalyzer method) (bioneuralnet.network.tools.NetworkAnalyzer method) communities (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain property) (bioneuralnet.clustering.CorrelatedLouvain property) (bioneuralnet.clustering.Louvain property) (bioneuralnet.clustering.louvain.Louvain property) (bioneuralnet.CorrelatedLouvain property) compare_clusters() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.plot)

connected_components() (bioneuralnet.network.NetworkAnalyzer method) (bioneuralnet.network.tools.NetworkAnalyzer method) CorrelatedLouvain (class in bioneuralnet) (class in bioneuralnet.clustering) (class in bioneuralnet.clustering.correlated_louvain) CorrelatedPageRank (class in bioneuralnet) (class in bioneuralnet.clustering) (class in bioneuralnet.clustering.correlated_pagerank) correlation_filter() (in module bioneuralnet.utils) (in module bioneuralnet.utils.feature_selection) correlation_network() (in module bioneuralnet.network) (in module bioneuralnet.network.generate) correlation_summary() (in module bioneuralnet.utils) (in module bioneuralnet.utils.data) cross_omics_analysis() (bioneuralnet.network.NetworkAnalyzer method) (bioneuralnet.network.tools.NetworkAnalyzer method) cuda (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) cv (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute)

D

data_preprocess() (in module bioneuralnet.network.pysmccnet.analysis) data_stats() (in module bioneuralnet.utils.data) DatasetLoader (class in bioneuralnet) (class in bioneuralnet.datasets) (class in bioneuralnet.datasets.dataset_loader) degree_distribution() (bioneuralnet.network.NetworkAnalyzer method) (bioneuralnet.network.tools.NetworkAnalyzer method) dim_reduction (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute)

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

E

edge_weight_analysis() (bioneuralnet.network.NetworkAnalyzer method) (bioneuralnet.network.tools.NetworkAnalyzer method) embed() (bioneuralnet.GNNEmbedding method) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding method) (bioneuralnet.network_embedding.GNNEmbedding method) embeddings (bioneuralnet.downstream_task.subject_representation.SubjectRepresentation attribute) (bioneuralnet.downstream_task.SubjectRepresentation attribute) (bioneuralnet.SubjectRepresentation attribute)

expression_summary() (in module bioneuralnet.utils) (in module bioneuralnet.utils.data) extract_and_load_folds() (in module bioneuralnet.external_tools) (in module bioneuralnet.external_tools.extract_CVfold)

F

find_omics_modality() (in module bioneuralnet.metrics.plot) find_strongest_edges() (bioneuralnet.network.NetworkAnalyzer method) (bioneuralnet.network.tools.NetworkAnalyzer method) fit() (bioneuralnet.GNNEmbedding method) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding method) (bioneuralnet.network_embedding.GNNEmbedding method) forward() (bioneuralnet.downstream_task.dpmon.AutoEncoder method) (bioneuralnet.downstream_task.dpmon.DownstreamTaskNN method) (bioneuralnet.downstream_task.dpmon.MLPProjection method) (bioneuralnet.downstream_task.dpmon.NeuralNetwork method) (bioneuralnet.downstream_task.dpmon.ScalarProjection 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

GAT (class in bioneuralnet.network_embedding) (class in bioneuralnet.network_embedding.gnn_models) gaussian_knn_network() (in module bioneuralnet.network) (in module bioneuralnet.network.generate) GCN (class in bioneuralnet.network_embedding) (class in bioneuralnet.network_embedding.gnn_models) generate_hidden_dims() (in module bioneuralnet.downstream_task.subject_representation) generate_weighted_personalization() (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank method) (bioneuralnet.clustering.CorrelatedPageRank method) (bioneuralnet.CorrelatedPageRank method) get_abar() (in module bioneuralnet.network.pysmccnet.analysis) get_activation() (in module bioneuralnet.downstream_task.subject_representation) (in module bioneuralnet.network_embedding.gnn_models) get_can_cor_multi() (in module bioneuralnet.network.pysmccnet.analysis) get_can_weights_multi() (in module bioneuralnet.network.pysmccnet.wrappers) get_combined_quality() (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain method) (bioneuralnet.clustering.CorrelatedLouvain method) (bioneuralnet.CorrelatedLouvain method) 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) (in module bioneuralnet.utils) (in module bioneuralnet.utils.logger)

get_omics_modules() (in module bioneuralnet.network.pysmccnet.analysis) get_robust_weights_multi() (in module bioneuralnet.network.pysmccnet.wrappers) get_robust_weights_multi_binary() (in module bioneuralnet.network.pysmccnet.wrappers) get_robust_weights_single_binary() (in module bioneuralnet.network.pysmccnet.wrappers) get_top_communities() (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain method) (bioneuralnet.clustering.CorrelatedLouvain method) (bioneuralnet.CorrelatedLouvain method) GIN (class in bioneuralnet.network_embedding) (class in bioneuralnet.network_embedding.gnn_models) gnn_activation (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) gnn_dropout (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) gnn_hidden_dim (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) gnn_layer_num (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) GNNEmbedding (class in bioneuralnet) (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.DPMON attribute) (bioneuralnet.GNNEmbedding attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute)

H

hidden_dim (bioneuralnet.GNNEmbedding attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) history (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain property) (bioneuralnet.clustering.CorrelatedLouvain property) (bioneuralnet.clustering.Louvain property) (bioneuralnet.clustering.louvain.Louvain property) (bioneuralnet.CorrelatedLouvain property)

hub_analysis() (bioneuralnet.network.NetworkAnalyzer method) (bioneuralnet.network.tools.NetworkAnalyzer method) HybridLouvain (class in bioneuralnet) (class in bioneuralnet.clustering) (class in bioneuralnet.clustering.hybrid_louvain)

I

importance_rf() (in module bioneuralnet.utils) (in module bioneuralnet.utils.feature_selection) impute_knn() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess)

impute_simple() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) iterations (bioneuralnet.clustering.hybrid_louvain.HybridLouvain property) (bioneuralnet.clustering.HybridLouvain property) (bioneuralnet.HybridLouvain property)

L

l2n() (in module bioneuralnet.network.pysmccnet.math_helpers) laplacian_score() (in module bioneuralnet.utils) (in module bioneuralnet.utils.feature_selection) layer_num (bioneuralnet.GNNEmbedding attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) load_brca() (in module bioneuralnet) (in module bioneuralnet.datasets) load_example() (in module bioneuralnet) (in module bioneuralnet.datasets) load_kipan() (in module bioneuralnet) (in module bioneuralnet.datasets) load_lgg() (in module bioneuralnet) (in module bioneuralnet.datasets)

load_monet() (in module bioneuralnet) (in module bioneuralnet.datasets) load_r_export_folds() (in module bioneuralnet.external_tools) (in module bioneuralnet.external_tools.extract_CVfold) Louvain (class in bioneuralnet.clustering) (class in bioneuralnet.clustering.louvain) lr (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) (bioneuralnet.GNNEmbedding attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute)

M

m_transform() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) mad_filter() (in module bioneuralnet.utils) (in module bioneuralnet.utils.feature_selection) MLPProjection (class in bioneuralnet.downstream_task.dpmon) model (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) model_type (bioneuralnet.GNNEmbedding attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) modularity (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain property) (bioneuralnet.clustering.CorrelatedLouvain property) (bioneuralnet.clustering.Louvain property) (bioneuralnet.clustering.louvain.Louvain property) (bioneuralnet.CorrelatedLouvain property) module bioneuralnet bioneuralnet.clustering bioneuralnet.clustering.correlated_louvain bioneuralnet.clustering.correlated_pagerank bioneuralnet.clustering.hybrid_louvain bioneuralnet.clustering.louvain bioneuralnet.datasets bioneuralnet.datasets.dataset_loader bioneuralnet.downstream_task bioneuralnet.downstream_task.dpmon bioneuralnet.downstream_task.subject_representation bioneuralnet.external_tools bioneuralnet.external_tools.extract_CVfold bioneuralnet.metrics bioneuralnet.metrics.correlation bioneuralnet.metrics.plot bioneuralnet.network bioneuralnet.network.generate bioneuralnet.network.pysmccnet bioneuralnet.network.pysmccnet.analysis bioneuralnet.network.pysmccnet.core bioneuralnet.network.pysmccnet.math_helpers bioneuralnet.network.pysmccnet.pipeline bioneuralnet.network.pysmccnet.wrappers bioneuralnet.network.tools bioneuralnet.network_embedding bioneuralnet.network_embedding.gnn_embedding bioneuralnet.network_embedding.gnn_models bioneuralnet.utils bioneuralnet.utils.data bioneuralnet.utils.feature_selection bioneuralnet.utils.logger bioneuralnet.utils.preprocess bioneuralnet.utils.reproducibility

my_get_cors() (in module bioneuralnet.network.pysmccnet.core) my_get_crit() (in module bioneuralnet.network.pysmccnet.core) my_multi_cca() (in module bioneuralnet.network.pysmccnet.core) my_update_w() (in module bioneuralnet.network.pysmccnet.core)

N

n_folds (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) nan_summary() (in module bioneuralnet.utils) (in module bioneuralnet.utils.data) 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) network_search() (in module bioneuralnet.network) (in module bioneuralnet.network.tools) NetworkAnalyzer (class in bioneuralnet.network) (class in bioneuralnet.network.tools) NeuralNetwork (class in bioneuralnet.downstream_task.dpmon)

nn_hidden_dim1 (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) nn_hidden_dim2 (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) normalize() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) num_epochs (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) (bioneuralnet.GNNEmbedding 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.downstream_task.subject_representation.SubjectRepresentation attribute) (bioneuralnet.downstream_task.SubjectRepresentation attribute) (bioneuralnet.GNNEmbedding attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) (bioneuralnet.SubjectRepresentation attribute)

omics_list (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) output_dir (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.downstream_task.subject_representation.SubjectRepresentation attribute) (bioneuralnet.downstream_task.SubjectRepresentation attribute) (bioneuralnet.DPMON attribute) (bioneuralnet.SubjectRepresentation attribute)

P

partition (bioneuralnet.clustering.correlated_louvain.CorrelatedLouvain property) (bioneuralnet.clustering.CorrelatedLouvain property) (bioneuralnet.clustering.Louvain property) (bioneuralnet.clustering.louvain.Louvain property) (bioneuralnet.CorrelatedLouvain property) pca_loadings() (in module bioneuralnet.utils) (in module bioneuralnet.utils.feature_selection) phen_omics_corr() (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank method) (bioneuralnet.clustering.CorrelatedPageRank method) (bioneuralnet.CorrelatedPageRank method) phenotype_col (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.downstream_task.subject_representation.SubjectRepresentation attribute) (bioneuralnet.downstream_task.SubjectRepresentation attribute) (bioneuralnet.DPMON attribute) (bioneuralnet.GNNEmbedding attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) (bioneuralnet.SubjectRepresentation attribute) phenotype_data (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.downstream_task.subject_representation.SubjectRepresentation attribute) (bioneuralnet.downstream_task.SubjectRepresentation attribute) (bioneuralnet.DPMON attribute) (bioneuralnet.GNNEmbedding attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) (bioneuralnet.SubjectRepresentation attribute)

plot_embeddings() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.plot) plot_multiple_metrics() (in module bioneuralnet.metrics) (in module bioneuralnet.metrics.plot) 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) prepare_node_features() (in module bioneuralnet.downstream_task.dpmon) preprocess_clinical() (in module bioneuralnet.utils) (in module bioneuralnet.utils.preprocess) process_dropout() (in module bioneuralnet.network_embedding.gnn_models) prune_modules() (in module bioneuralnet.network.pysmccnet.analysis) 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

r_scale() (in module bioneuralnet.network.pysmccnet.math_helpers) r_scale_torch() (in module bioneuralnet.network.pysmccnet.math_helpers) r_vec_mult_sum() (in module bioneuralnet.network.pysmccnet.math_helpers) rdata_to_df() (in module bioneuralnet.external_tools) reduce_method (bioneuralnet.downstream_task.subject_representation.SubjectRepresentation attribute) (bioneuralnet.downstream_task.SubjectRepresentation attribute) (bioneuralnet.SubjectRepresentation attribute) repeat_num (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.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.clustering.Louvain method) (bioneuralnet.clustering.louvain.Louvain method) (bioneuralnet.CorrelatedLouvain method) (bioneuralnet.CorrelatedPageRank method) (bioneuralnet.downstream_task.DPMON method) (bioneuralnet.downstream_task.dpmon.DPMON method) (bioneuralnet.downstream_task.subject_representation.SubjectRepresentation method) (bioneuralnet.downstream_task.SubjectRepresentation method) (bioneuralnet.DPMON method) (bioneuralnet.HybridLouvain method) (bioneuralnet.SubjectRepresentation method)

run_gnn_embedding_tuning() (bioneuralnet.GNNEmbedding method) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding method) (bioneuralnet.network_embedding.GNNEmbedding method) run_hyperparameter_tuning() (in module bioneuralnet.downstream_task.dpmon) run_standard_training() (in module bioneuralnet.downstream_task.dpmon)

S

SAGE (class in bioneuralnet.network_embedding) (class in bioneuralnet.network_embedding.gnn_models) ScalarProjection (class in bioneuralnet.downstream_task.dpmon) seed (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.downstream_task.subject_representation.SubjectRepresentation attribute) (bioneuralnet.downstream_task.SubjectRepresentation attribute) (bioneuralnet.DPMON attribute) (bioneuralnet.GNNEmbedding attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) (bioneuralnet.SubjectRepresentation attribute) seed_trials (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute) set_seed() (in module bioneuralnet) (in module bioneuralnet.utils) (in module bioneuralnet.utils.reproducibility)

setup_device() (in module bioneuralnet.downstream_task.dpmon) shape (bioneuralnet.DatasetLoader property) (bioneuralnet.datasets.dataset_loader.DatasetLoader property) (bioneuralnet.datasets.DatasetLoader property) similarity_network() (in module bioneuralnet.network) (in module bioneuralnet.network.generate) slice_omics_datasets() (in module bioneuralnet.downstream_task.dpmon) soft() (in module bioneuralnet.network.pysmccnet.math_helpers) sparse_filter() (in module bioneuralnet.utils.data) SubjectRepresentation (class in bioneuralnet) (class in bioneuralnet.downstream_task) (class in bioneuralnet.downstream_task.subject_representation) summarize_netshy() (in module bioneuralnet.network.pysmccnet.analysis) sweep_cut() (bioneuralnet.clustering.correlated_pagerank.CorrelatedPageRank method) (bioneuralnet.clustering.CorrelatedPageRank method) (bioneuralnet.CorrelatedPageRank method)

T

threshold_network() (bioneuralnet.network.NetworkAnalyzer method) (bioneuralnet.network.tools.NetworkAnalyzer method) (in module bioneuralnet.network) (in module bioneuralnet.network.generate) top_anova_f_features() (in module bioneuralnet.utils) (in module bioneuralnet.utils.feature_selection) train_model() (in module bioneuralnet.downstream_task.dpmon) tune (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.downstream_task.subject_representation.SubjectRepresentation attribute) (bioneuralnet.downstream_task.SubjectRepresentation attribute) (bioneuralnet.DPMON attribute) (bioneuralnet.GNNEmbedding attribute) (bioneuralnet.network_embedding.gnn_embedding.GNNEmbedding attribute) (bioneuralnet.network_embedding.GNNEmbedding attribute) (bioneuralnet.SubjectRepresentation attribute)

tune_trials (bioneuralnet.downstream_task.DPMON attribute) (bioneuralnet.downstream_task.dpmon.DPMON attribute) (bioneuralnet.DPMON attribute)

V

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

variance_threshold() (in module bioneuralnet.utils) (in module bioneuralnet.utils.feature_selection)

W

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

Z

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