Index

_

__init__() (gsnn.gsnn.interpret.ContrastiveIGExplainer method) (gsnn.gsnn.interpret.ContrastiveOcclusionExplainer method) (gsnn.gsnn.interpret.CounterfactualExplainer method) (gsnn.gsnn.interpret.GSNNExplainer method) (gsnn.gsnn.interpret.IGExplainer method) (gsnn.gsnn.interpret.NoiseTunnel method) (gsnn.gsnn.interpret.OcclusionExplainer method) (gsnn.gsnn.models.ChannelEMANorm method) (gsnn.gsnn.models.GroupBatchNorm method) (gsnn.gsnn.models.GroupEMANorm method) (gsnn.gsnn.models.GroupLayerNorm method) (gsnn.gsnn.models.GroupRMSNorm method) (gsnn.gsnn.models.GSNN method) (gsnn.gsnn.models.NN method) (gsnn.gsnn.models.NodeAttention method) (gsnn.gsnn.models.NodeMLP method) (gsnn.gsnn.models.PathwayLatentRegularizer method) (gsnn.gsnn.models.ResBlock method) (gsnn.gsnn.models.SignedMessagePassing method) (gsnn.gsnn.models.SoftmaxGroupNorm method) (gsnn.gsnn.models.SparseLinear method) (gsnn.gsnn.optim.TrainingDiagnostics method) (gsnn.interpret.ContrastiveIGExplainer method) (gsnn.interpret.ContrastiveOcclusionExplainer method) (gsnn.interpret.CounterfactualExplainer method) (gsnn.interpret.GSNNExplainer method) (gsnn.interpret.IGExplainer method) (gsnn.interpret.NoiseTunnel method) (gsnn.interpret.OcclusionExplainer method) (gsnn.models.ChannelEMANorm method) (gsnn.models.GroupBatchNorm method) (gsnn.models.GroupEMANorm method) (gsnn.models.GroupLayerNorm method) (gsnn.models.GroupRMSNorm method) (gsnn.models.GSNN method) (gsnn.models.NN method) (gsnn.models.NodeAttention method) (gsnn.models.NodeMLP method) (gsnn.models.PathwayLatentRegularizer method) (gsnn.models.ResBlock method) (gsnn.models.SignedMessagePassing method) (gsnn.models.SoftmaxGroupNorm method) (gsnn.models.SparseLinear method) (gsnn.optim.TrainingDiagnostics method)

A

adjust_label_positions() (in module gsnn.gsnn.interpret.plot_explanation_graph) (in module gsnn.interpret.plot_explanation_graph) analyze() (gsnn.gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.optim.GradDiagnostics.GradDiagnostics method) apply_norm_and_nonlin() (in module gsnn.gsnn.models.utils) (in module gsnn.models.utils)

arm_retained_grads() (gsnn.gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) (gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) augment_edge_index() (gsnn.gsnn.optim.Environment.Environment method) (gsnn.optim.Environment.Environment method) aux_step() (gsnn.gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) (gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method)

B

bfs_distance() (in module gsnn.gsnn.proc.subset) (in module gsnn.proc.subset) bounding_box_overlap() (in module gsnn.gsnn.interpret.plot_explanation_graph) (in module gsnn.interpret.plot_explanation_graph) build() (gsnn.gsnn.proc.construct.GSNNNetworkConstructor method) (gsnn.proc.construct.GSNNNetworkConstructor method)

build_nx() (in module gsnn.gsnn.proc.subset) (in module gsnn.proc.subset) build_uniprot_symbol_map() (in module gsnn.gsnn.proc.bio) (in module gsnn.proc.bio)

C

ChannelEMANorm (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] compute_ECE() (in module gsnn.gsnn.optim.utils) (in module gsnn.optim.utils) compute_picp() (in module gsnn.gsnn.optim.utils) (in module gsnn.optim.utils) compute_scalar_mmd() (in module gsnn.gsnn.external.mmd) (in module gsnn.gsnn.ot.mmd) ContrastiveGSNNExplainer (class in gsnn.gsnn.interpret.ContrastiveGSNNExplainer) (class in gsnn.interpret.ContrastiveGSNNExplainer)

ContrastiveIGExplainer (class in gsnn.gsnn.interpret), [1] (class in gsnn.interpret), [1] ContrastiveOcclusionExplainer (class in gsnn.gsnn.interpret), [1] (class in gsnn.interpret), [1] corr_score() (in module gsnn.gsnn.models.utils) (in module gsnn.models.utils) CounterfactualExplainer (class in gsnn.gsnn.interpret), [1] (class in gsnn.interpret), [1]

D

dbscan_silhouette_score() (in module gsnn.gsnn.optim.utils) (in module gsnn.optim.utils) dense_func_node (class in gsnn.gsnn.interpret.extract_entity_function) (class in gsnn.interpret.extract_entity_function) diff_equivalence() (in module gsnn.gsnn.proc.coarsen) (in module gsnn.proc.coarsen)

diff_io_equivalence() (in module gsnn.gsnn.proc.coarsen) (in module gsnn.proc.coarsen) disable() (gsnn.gsnn.models.PathwayLatentRegularizer method), [1] (gsnn.models.PathwayLatentRegularizer method), [1]

E

early_stop() (gsnn.gsnn.optim.EarlyStopper.EarlyStopper method) (gsnn.optim.EarlyStopper.EarlyStopper method) EarlyStopper (class in gsnn.gsnn.optim.EarlyStopper) (class in gsnn.optim.EarlyStopper) edge2node() (in module gsnn.gsnn.models.utils) (in module gsnn.models.utils) edw() (in module gsnn.gsnn.optim.RewardScaler) (in module gsnn.optim.RewardScaler) ema() (in module gsnn.gsnn.optim.Environment) (in module gsnn.optim.Environment) enable() (gsnn.gsnn.models.PathwayLatentRegularizer method), [1] (gsnn.models.PathwayLatentRegularizer method), [1] ensg2symbol() (in module gsnn.gsnn.proc.bio) (in module gsnn.proc.bio) Environment (class in gsnn.gsnn.optim.Environment) (class in gsnn.optim.Environment) evaluate() (gsnn.gsnn.optim.MagnitudeEdgeInferer.MagnitudeEdgeInferer method) (gsnn.gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) (gsnn.gsnn.optim.OutputEdgeInferer.OutputEdgeInferer method) (gsnn.optim.MagnitudeEdgeInferer.MagnitudeEdgeInferer method) (gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) (gsnn.optim.OutputEdgeInferer.OutputEdgeInferer method) evaluate_against() (gsnn.gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) (gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method)

evaluate_target_ranking() (gsnn.gsnn.optim.MagnitudeEdgeInferer.MagnitudeEdgeInferer static method) (gsnn.gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE static method) (gsnn.gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor static method) (gsnn.optim.MagnitudeEdgeInferer.MagnitudeEdgeInferer static method) (gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE static method) (gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor static method) explain() (gsnn.gsnn.interpret.ContrastiveGSNNExplainer.ContrastiveGSNNExplainer method) (gsnn.gsnn.interpret.ContrastiveIGExplainer method), [1] (gsnn.gsnn.interpret.ContrastiveOcclusionExplainer method), [1] (gsnn.gsnn.interpret.CounterfactualExplainer method), [1] (gsnn.gsnn.interpret.GSNNExplainer method), [1] (gsnn.gsnn.interpret.IGExplainer method), [1] (gsnn.gsnn.interpret.NoiseTunnel method), [1] (gsnn.gsnn.interpret.OcclusionExplainer method), [1] (gsnn.interpret.ContrastiveGSNNExplainer.ContrastiveGSNNExplainer method) (gsnn.interpret.ContrastiveIGExplainer method), [1] (gsnn.interpret.ContrastiveOcclusionExplainer method), [1] (gsnn.interpret.CounterfactualExplainer method), [1] (gsnn.interpret.GSNNExplainer method), [1] (gsnn.interpret.IGExplainer method), [1] (gsnn.interpret.NoiseTunnel method), [1] (gsnn.interpret.OcclusionExplainer method), [1] extract_entity_function() (in module gsnn.gsnn.interpret.extract_entity_function) (in module gsnn.interpret.extract_entity_function)

F

fit() (gsnn.gsnn.optim.FunctionEdgeInferer.FunctionEdgeInferer method) (gsnn.gsnn.optim.MagnitudeEdgeInferer.MagnitudeEdgeInferer method) (gsnn.gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.gsnn.optim.OutputEdgeInferer.OutputEdgeInferer method) (gsnn.optim.FunctionEdgeInferer.FunctionEdgeInferer method) (gsnn.optim.MagnitudeEdgeInferer.MagnitudeEdgeInferer method) (gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.optim.OutputEdgeInferer.OutputEdgeInferer method) forward() (gsnn.gsnn.interpret.extract_entity_function.dense_func_node method) (gsnn.gsnn.models.ChannelEMANorm method), [1] (gsnn.gsnn.models.GroupBatchNorm method), [1] (gsnn.gsnn.models.GroupEMANorm method), [1] (gsnn.gsnn.models.GroupLayerNorm method), [1] (gsnn.gsnn.models.GroupRMSNorm method), [1] (gsnn.gsnn.models.GSNN method), [1] (gsnn.gsnn.models.NN method), [1] (gsnn.gsnn.models.NodeActivity.NodeActivity method) (gsnn.gsnn.models.NodeAttention method), [1] (gsnn.gsnn.models.NodeMLP method), [1] (gsnn.gsnn.models.ResBlock method), [1] (gsnn.gsnn.models.SignedMessagePassing method), [1] (gsnn.gsnn.models.SoftmaxGroupNorm method), [1] (gsnn.gsnn.models.SparseLinear method), [1] (gsnn.gsnn.optim.OutputEdgeInferer.OutputEdgeInferer method) (gsnn.interpret.extract_entity_function.dense_func_node method) (gsnn.models.ChannelEMANorm method), [1] (gsnn.models.GroupBatchNorm method), [1] (gsnn.models.GroupEMANorm method), [1] (gsnn.models.GroupLayerNorm method), [1] (gsnn.models.GroupRMSNorm method), [1] (gsnn.models.GSNN method), [1] (gsnn.models.NN method), [1] (gsnn.models.NodeActivity.NodeActivity method) (gsnn.models.NodeAttention method), [1] (gsnn.models.NodeMLP method), [1] (gsnn.models.ResBlock method), [1] (gsnn.models.SignedMessagePassing method), [1] (gsnn.models.SoftmaxGroupNorm method), [1] (gsnn.models.SparseLinear method), [1] (gsnn.optim.OutputEdgeInferer.OutputEdgeInferer method)

FunctionEdgeInferer (class in gsnn.gsnn.optim.FunctionEdgeInferer) (class in gsnn.optim.FunctionEdgeInferer)

G

get_all_possible_paths_set() (in module gsnn.gsnn.proc.subset) (in module gsnn.proc.subset) get_alpha_mean() (gsnn.gsnn.models.NodeActivity.NodeActivity method) (gsnn.models.NodeActivity.NodeActivity method) get_batch_params() (gsnn.gsnn.models.GSNN method), [1] (gsnn.models.GSNN method), [1] get_bio_interactions() (in module gsnn.gsnn.proc.bio) (in module gsnn.proc.bio) get_conv_indices() (in module gsnn.gsnn.models.utils) (in module gsnn.models.utils) get_dependency_details() (gsnn.gsnn.simulate.graph_comparison.GraphComparison method) (gsnn.simulate.graph_comparison.GraphComparison method) get_edge_probs() (gsnn.gsnn.optim.REINFORCE.REINFORCE method) (gsnn.optim.REINFORCE.REINFORCE method) get_gradient_histogram_data() (gsnn.gsnn.optim.TrainingDiagnostics method), [1] (gsnn.optim.TrainingDiagnostics method), [1] get_node_activations() (gsnn.gsnn.models.GSNN method), [1] (gsnn.models.GSNN method), [1] get_node_attention() (gsnn.gsnn.models.GSNN method), [1] (gsnn.models.GSNN method), [1] get_params() (gsnn.gsnn.optim.RewardScaler.RewardScaler method) (gsnn.optim.RewardScaler.RewardScaler method) get_reward_params() (gsnn.gsnn.optim.REINFORCE.REINFORCE method) (gsnn.optim.REINFORCE.REINFORCE method) get_summary() (gsnn.gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.gsnn.optim.TrainingDiagnostics method), [1] (gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.optim.TrainingDiagnostics method), [1] get_Win_indices() (in module gsnn.gsnn.models.utils) (in module gsnn.models.utils) get_Wout_indices() (in module gsnn.gsnn.models.utils) (in module gsnn.models.utils) GradDiagnostics (class in gsnn.gsnn.optim.GradDiagnostics) (class in gsnn.optim.GradDiagnostics) GraphComparison (class in gsnn.gsnn.simulate.graph_comparison) (class in gsnn.simulate.graph_comparison) GroupBatchNorm (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] GroupEMANorm (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] GroupLayerNorm (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] GroupRMSNorm (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] GSNN (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] gsnn.gsnn module gsnn.gsnn.external module gsnn.gsnn.external.mmd module gsnn.gsnn.interpret module gsnn.gsnn.interpret.ContrastiveGSNNExplainer module gsnn.gsnn.interpret.extract_entity_function module gsnn.gsnn.interpret.plot_explanation_graph module gsnn.gsnn.interpret.utils module gsnn.gsnn.models module gsnn.gsnn.models.NodeActivity module gsnn.gsnn.models.utils module gsnn.gsnn.optim module gsnn.gsnn.optim.EarlyStopper module gsnn.gsnn.optim.Environment module gsnn.gsnn.optim.FunctionEdgeInferer module gsnn.gsnn.optim.GradDiagnostics module gsnn.gsnn.optim.MagnitudeEdgeInferer module gsnn.gsnn.optim.MagnitudeEdgeKGE module gsnn.gsnn.optim.MagnitudeEdgeRegressor module gsnn.gsnn.optim.OutputEdgeInferer module gsnn.gsnn.optim.REINFORCE module gsnn.gsnn.optim.RewardScaler module gsnn.gsnn.optim.utils module gsnn.gsnn.ot module gsnn.gsnn.ot.mmd module gsnn.gsnn.proc module gsnn.gsnn.proc.bio module gsnn.gsnn.proc.coarsen module gsnn.gsnn.proc.construct module

gsnn.gsnn.proc.subset module gsnn.gsnn.simulate module gsnn.gsnn.simulate.datasets module gsnn.gsnn.simulate.graph_comparison module gsnn.gsnn.simulate.nx2pyg module gsnn.gsnn.simulate.utils module gsnn.gsnn.tests module gsnn.gsnn.tests.helpers module gsnn.gsnn.tests.test_contrastive_explainers module gsnn.gsnn.tests.test_diagnostics module gsnn.gsnn.tests.test_early_stopper module gsnn.gsnn.tests.test_graph_comparison module gsnn.gsnn.tests.test_nn module gsnn.gsnn.tests.test_node_mlp module gsnn.gsnn.tests.test_nx2pyg module gsnn.gsnn.tests.test_optim_utils module gsnn.gsnn.tests.test_proc_coarsen module gsnn.gsnn.tests.test_proc_construct module gsnn.gsnn.tests.test_reward_scaler module gsnn.interpret module gsnn.interpret.ContrastiveGSNNExplainer module gsnn.interpret.extract_entity_function module gsnn.interpret.plot_explanation_graph module gsnn.interpret.utils module gsnn.models module gsnn.models.NodeActivity module gsnn.models.utils module gsnn.optim module gsnn.optim.EarlyStopper module gsnn.optim.Environment module gsnn.optim.FunctionEdgeInferer module gsnn.optim.GradDiagnostics module gsnn.optim.MagnitudeEdgeInferer module gsnn.optim.MagnitudeEdgeKGE module gsnn.optim.MagnitudeEdgeRegressor module gsnn.optim.OutputEdgeInferer module gsnn.optim.REINFORCE module gsnn.optim.RewardScaler module gsnn.optim.utils module gsnn.proc module gsnn.proc.bio module gsnn.proc.coarsen module gsnn.proc.construct module gsnn.proc.subset module gsnn.simulate module gsnn.simulate.datasets module gsnn.simulate.graph_comparison module gsnn.simulate.nx2pyg module gsnn.simulate.utils module GSNNExplainer (class in gsnn.gsnn.interpret), [1] (class in gsnn.interpret), [1] GSNNNetworkConstructor (class in gsnn.gsnn.proc.construct) (class in gsnn.proc.construct)

H

hetero2homo() (in module gsnn.gsnn.models.utils) (in module gsnn.models.utils)

I

IGExplainer (class in gsnn.gsnn.interpret), [1] (class in gsnn.interpret), [1]

io_equivalence() (in module gsnn.gsnn.proc.coarsen) (in module gsnn.proc.coarsen)

L

load_best() (gsnn.gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) (gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method)

loss() (gsnn.gsnn.models.PathwayLatentRegularizer method), [1] (gsnn.models.PathwayLatentRegularizer method), [1]

M

MagnitudeEdgeInferer (class in gsnn.gsnn.optim.MagnitudeEdgeInferer) (class in gsnn.optim.MagnitudeEdgeInferer) MagnitudeEdgeKGE (class in gsnn.gsnn.optim.MagnitudeEdgeKGE) (class in gsnn.optim.MagnitudeEdgeKGE) MagnitudeEdgeRegressor (class in gsnn.gsnn.optim.MagnitudeEdgeRegressor) (class in gsnn.optim.MagnitudeEdgeRegressor) maybe_save_best() (gsnn.gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) (gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) message() (gsnn.gsnn.models.SignedMessagePassing method), [1] (gsnn.models.SignedMessagePassing method), [1] mmd_distance() (in module gsnn.gsnn.external.mmd) (in module gsnn.gsnn.ot.mmd) module gsnn.gsnn gsnn.gsnn.external gsnn.gsnn.external.mmd gsnn.gsnn.interpret gsnn.gsnn.interpret.ContrastiveGSNNExplainer gsnn.gsnn.interpret.extract_entity_function gsnn.gsnn.interpret.plot_explanation_graph gsnn.gsnn.interpret.utils gsnn.gsnn.models gsnn.gsnn.models.NodeActivity gsnn.gsnn.models.utils gsnn.gsnn.optim gsnn.gsnn.optim.EarlyStopper gsnn.gsnn.optim.Environment gsnn.gsnn.optim.FunctionEdgeInferer gsnn.gsnn.optim.GradDiagnostics gsnn.gsnn.optim.MagnitudeEdgeInferer gsnn.gsnn.optim.MagnitudeEdgeKGE gsnn.gsnn.optim.MagnitudeEdgeRegressor gsnn.gsnn.optim.OutputEdgeInferer gsnn.gsnn.optim.REINFORCE gsnn.gsnn.optim.RewardScaler gsnn.gsnn.optim.utils gsnn.gsnn.ot gsnn.gsnn.ot.mmd gsnn.gsnn.proc gsnn.gsnn.proc.bio gsnn.gsnn.proc.coarsen gsnn.gsnn.proc.construct gsnn.gsnn.proc.subset gsnn.gsnn.simulate gsnn.gsnn.simulate.datasets gsnn.gsnn.simulate.graph_comparison gsnn.gsnn.simulate.nx2pyg gsnn.gsnn.simulate.utils gsnn.gsnn.tests gsnn.gsnn.tests.helpers gsnn.gsnn.tests.test_contrastive_explainers gsnn.gsnn.tests.test_diagnostics gsnn.gsnn.tests.test_early_stopper gsnn.gsnn.tests.test_graph_comparison gsnn.gsnn.tests.test_nn gsnn.gsnn.tests.test_node_mlp gsnn.gsnn.tests.test_nx2pyg gsnn.gsnn.tests.test_optim_utils gsnn.gsnn.tests.test_proc_coarsen gsnn.gsnn.tests.test_proc_construct gsnn.gsnn.tests.test_reward_scaler gsnn.interpret gsnn.interpret.ContrastiveGSNNExplainer gsnn.interpret.extract_entity_function gsnn.interpret.plot_explanation_graph gsnn.interpret.utils gsnn.models gsnn.models.NodeActivity gsnn.models.utils gsnn.optim gsnn.optim.EarlyStopper gsnn.optim.Environment gsnn.optim.FunctionEdgeInferer gsnn.optim.GradDiagnostics gsnn.optim.MagnitudeEdgeInferer gsnn.optim.MagnitudeEdgeKGE gsnn.optim.MagnitudeEdgeRegressor gsnn.optim.OutputEdgeInferer gsnn.optim.REINFORCE gsnn.optim.RewardScaler gsnn.optim.utils gsnn.proc gsnn.proc.bio gsnn.proc.coarsen gsnn.proc.construct gsnn.proc.subset gsnn.simulate gsnn.simulate.datasets gsnn.simulate.graph_comparison gsnn.simulate.nx2pyg gsnn.simulate.utils

mrr() (in module gsnn.gsnn.optim.FunctionEdgeInferer) (in module gsnn.optim.FunctionEdgeInferer)

N

neighborhood_preservation_score() (in module gsnn.gsnn.optim.utils) (in module gsnn.optim.utils) NN (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] node2edge() (in module gsnn.gsnn.models.utils) (in module gsnn.models.utils) NodeActivity (class in gsnn.gsnn.models.NodeActivity) (class in gsnn.models.NodeActivity) NodeAttention (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1]

NodeMLP (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] NoiseTunnel (class in gsnn.gsnn.interpret), [1] (class in gsnn.interpret), [1] nx2pyg() (in module gsnn.gsnn.simulate.nx2pyg) (in module gsnn.simulate.nx2pyg) nx_to_pyro_model() (in module gsnn.gsnn.simulate.utils) (in module gsnn.simulate.utils)

O

OcclusionExplainer (class in gsnn.gsnn.interpret), [1] (class in gsnn.interpret), [1]

OutputEdgeInferer (class in gsnn.gsnn.optim.OutputEdgeInferer) (class in gsnn.optim.OutputEdgeInferer)

P

PathwayLatentRegularizer (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] plot_diagnostics() (gsnn.gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.gsnn.optim.TrainingDiagnostics method), [1] (gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.optim.TrainingDiagnostics method), [1] plot_edge_importance() (in module gsnn.gsnn.interpret.utils) (in module gsnn.interpret.utils) plot_explanation_graph() (in module gsnn.gsnn.interpret.plot_explanation_graph) (in module gsnn.interpret.plot_explanation_graph) plot_gradient_magnitude_by_layer() (gsnn.gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.optim.GradDiagnostics.GradDiagnostics method) plot_gradient_ratio_heatmap() (gsnn.gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.optim.GradDiagnostics.GradDiagnostics method) plot_hairball() (in module gsnn.gsnn.interpret.plot_explanation_graph) (in module gsnn.interpret.plot_explanation_graph) plot_node_importance() (in module gsnn.gsnn.interpret.utils) (in module gsnn.interpret.utils)

plot_summary_statistics() (gsnn.gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.optim.GradDiagnostics.GradDiagnostics method) plot_vanishing_over_time() (gsnn.gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.optim.GradDiagnostics.GradDiagnostics method) pre_forward() (gsnn.gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) (gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) predict_gsnn() (in module gsnn.gsnn.models.utils) (in module gsnn.models.utils) print_progress_() (gsnn.gsnn.optim.REINFORCE.REINFORCE method) (gsnn.optim.REINFORCE.REINFORCE method) prob_of() (gsnn.gsnn.optim.REINFORCE.REINFORCE method) (gsnn.optim.REINFORCE.REINFORCE method) prune() (gsnn.gsnn.models.GSNN method), [1] (gsnn.gsnn.models.SparseLinear method), [1] (gsnn.models.GSNN method), [1] (gsnn.models.SparseLinear method), [1] pyg2nx() (in module gsnn.gsnn.simulate.nx2pyg) (in module gsnn.simulate.nx2pyg)

R

REINFORCE (class in gsnn.gsnn.optim.REINFORCE) (class in gsnn.optim.REINFORCE) ResBlock (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] reset() (gsnn.gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.gsnn.optim.TrainingDiagnostics method), [1] (gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.optim.TrainingDiagnostics method), [1]

reset_stats() (gsnn.gsnn.optim.MagnitudeEdgeInferer.MagnitudeEdgeInferer method) (gsnn.optim.MagnitudeEdgeInferer.MagnitudeEdgeInferer method) RewardScaler (class in gsnn.gsnn.optim.RewardScaler) (class in gsnn.optim.RewardScaler) root_mean_squared_picp_error() (in module gsnn.gsnn.optim.utils) (in module gsnn.optim.utils) run() (gsnn.gsnn.optim.Environment.Environment method) (gsnn.optim.Environment.Environment method)

S

sample() (gsnn.gsnn.optim.REINFORCE.REINFORCE method) (gsnn.optim.REINFORCE.REINFORCE method) scale() (gsnn.gsnn.optim.REINFORCE.REINFORCE method) (gsnn.gsnn.optim.RewardScaler.RewardScaler method) (gsnn.optim.REINFORCE.REINFORCE method) (gsnn.optim.RewardScaler.RewardScaler method) score_matrix() (gsnn.gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) (gsnn.optim.MagnitudeEdgeKGE.MagnitudeEdgeKGE method) (gsnn.optim.MagnitudeEdgeRegressor.MagnitudeEdgeRegressor method) set_node_mask() (gsnn.gsnn.models.ResBlock method), [1] (gsnn.models.ResBlock method), [1] SignedMessagePassing (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] simulate() (in module gsnn.gsnn.simulate), [1] (in module gsnn.simulate), [1]

simulate_10_in_25_func_10_out_cyclic() (in module gsnn.gsnn.simulate.datasets) (in module gsnn.simulate.datasets) simulate_3_in_3_out() (in module gsnn.gsnn.simulate.datasets) (in module gsnn.simulate.datasets) SoftmaxGroupNorm (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] SparseLinear (class in gsnn.gsnn.models), [1] (class in gsnn.models), [1] step() (gsnn.gsnn.optim.REINFORCE.REINFORCE method) (gsnn.optim.REINFORCE.REINFORCE method) subset_graph() (in module gsnn.gsnn.proc.subset) (in module gsnn.proc.subset) symbol2uniprot() (in module gsnn.gsnn.proc.bio) (in module gsnn.proc.bio)

T

test_compute_ECE() (in module gsnn.gsnn.tests.test_optim_utils) test_compute_picp() (in module gsnn.gsnn.tests.test_optim_utils) test_constructor_force_include_names() (in module gsnn.gsnn.tests.test_proc_construct) test_constructor_graph_summary() (in module gsnn.gsnn.tests.test_proc_construct) test_constructor_prunes_unreachable() (in module gsnn.gsnn.tests.test_proc_construct) test_contrastive_gsnn_explainer_edges() (in module gsnn.gsnn.tests.test_contrastive_explainers) test_contrastive_gsnn_explainer_nodes() (in module gsnn.gsnn.tests.test_contrastive_explainers) test_contrastive_ig_explainer() (in module gsnn.gsnn.tests.test_contrastive_explainers) test_contrastive_occlusion_explainer() (in module gsnn.gsnn.tests.test_contrastive_explainers) test_diff_equivalence() (in module gsnn.gsnn.tests.test_proc_coarsen) test_diff_io_equivalence() (in module gsnn.gsnn.tests.test_proc_coarsen) test_early_stop_improvement_resets() (in module gsnn.gsnn.tests.test_early_stopper) test_early_stop_min_delta() (in module gsnn.gsnn.tests.test_early_stopper) test_early_stop_triggers() (in module gsnn.gsnn.tests.test_early_stopper) test_edw_weights() (in module gsnn.gsnn.tests.test_reward_scaler) test_get_dependency_details() (in module gsnn.gsnn.tests.test_graph_comparison) test_grad_diagnostics_analyze() (in module gsnn.gsnn.tests.test_diagnostics) test_grad_diagnostics_update_reset() (in module gsnn.gsnn.tests.test_diagnostics) test_graph_comparison_disjoint() (in module gsnn.gsnn.tests.test_graph_comparison) test_graph_comparison_identical() (in module gsnn.gsnn.tests.test_graph_comparison)

test_gsnn_network_constructor_build() (in module gsnn.gsnn.tests.test_proc_construct) test_io_equivalence() (in module gsnn.gsnn.tests.test_proc_coarsen) test_nn_forward_shape() (in module gsnn.gsnn.tests.test_nn) test_nn_layers_depth() (in module gsnn.gsnn.tests.test_nn) test_nn_no_norm() (in module gsnn.gsnn.tests.test_nn) test_node_mlp_dropout_train_eval() (in module gsnn.gsnn.tests.test_node_mlp) test_node_mlp_forward_shape() (in module gsnn.gsnn.tests.test_node_mlp) test_nx2pyg_edge_categorization() (in module gsnn.gsnn.tests.test_nx2pyg) test_nx2pyg_with_weights() (in module gsnn.gsnn.tests.test_nx2pyg) test_pyg2nx_roundtrip() (in module gsnn.gsnn.tests.test_nx2pyg) test_reward_scaler_scale_clip() (in module gsnn.gsnn.tests.test_reward_scaler) test_reward_scaler_warmup() (in module gsnn.gsnn.tests.test_reward_scaler) test_training_diagnostics_smoke() (in module gsnn.gsnn.tests.test_diagnostics) train() (gsnn.gsnn.optim.Environment.Environment method) (gsnn.optim.Environment.Environment method) TrainingDiagnostics (class in gsnn.gsnn.optim), [1] (class in gsnn.optim), [1] tune() (gsnn.gsnn.interpret.ContrastiveGSNNExplainer.ContrastiveGSNNExplainer method) (gsnn.gsnn.interpret.GSNNExplainer method), [1] (gsnn.interpret.ContrastiveGSNNExplainer.ContrastiveGSNNExplainer method) (gsnn.interpret.GSNNExplainer method), [1]

U

uniprot2symbol() (in module gsnn.gsnn.proc.bio) (in module gsnn.proc.bio) update() (gsnn.gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.gsnn.optim.REINFORCE.REINFORCE method) (gsnn.gsnn.optim.RewardScaler.RewardScaler method) (gsnn.gsnn.optim.TrainingDiagnostics method), [1] (gsnn.optim.GradDiagnostics.GradDiagnostics method) (gsnn.optim.REINFORCE.REINFORCE method) (gsnn.optim.RewardScaler.RewardScaler method) (gsnn.optim.TrainingDiagnostics method), [1]

V

validate() (gsnn.gsnn.optim.Environment.Environment method) (gsnn.optim.Environment.Environment method)