Index

A

AbstractEvaluator (class in topobenchmark.evaluator.base) AbstractFeatureEncoder (class in topobenchmark.nn.encoders.base) AbstractLifting (class in topobenchmark.transforms.liftings) (class in topobenchmark.transforms.liftings.base) AbstractLoader (class in topobenchmark.data.loaders.base) AbstractLoss (class in topobenchmark.loss.base)

AbstractOptimizer (class in topobenchmark.optimizer.base) AbstractWrapper (class in topobenchmark.nn.wrappers.base) AbstractZeroCellReadOut (class in topobenchmark.nn.readouts.base) aggr_norm_func() (topobenchmark.nn.backbones.simplicial.sccnn.SCCNNLayer method) AllCellFeatureEncoder (class in topobenchmark.nn.encoders.all_cell_encoder) assign_train_val_test_mask_to_graphs() (in module topobenchmark.data.utils.split_utils)

B

BaseEncoder (class in topobenchmark.nn.encoders.all_cell_encoder)

C

calculate_node_degrees() (topobenchmark.transforms.data_manipulations.node_degrees.NodeDegrees method) CalculateSimplicialCurvature (class in topobenchmark.transforms.data_manipulations.calculate_simplicial_curvature) CANWrapper (class in topobenchmark.nn.wrappers.cell.can_wrapper) CCCN (class in topobenchmark.nn.backbones.cell.cccn) CCCNWrapper (class in topobenchmark.nn.wrappers.cell.cccn_wrapper) CCXNWrapper (class in topobenchmark.nn.wrappers.cell.ccxn_wrapper) CellComplexLifting (class in topobenchmark.transforms.liftings) CellCycleLifting (class in topobenchmark.transforms.liftings.graph2cell.cycle) chebyshev_conv() (topobenchmark.nn.backbones.simplicial.sccnn.SCCNNLayer method) collate_fn() (in module topobenchmark.dataloader.utils)

CombinatorialLifting (class in topobenchmark.transforms.liftings) compute() (topobenchmark.evaluator.base.AbstractEvaluator method) (topobenchmark.evaluator.evaluator.TBEvaluator method) compute_logits() (topobenchmark.nn.readouts.base.AbstractZeroCellReadOut method) Concatenation (class in topobenchmark.transforms.feature_liftings.concatenation) configure_optimizer() (topobenchmark.optimizer.base.AbstractOptimizer method) (topobenchmark.optimizer.optimizer.TBOptimizer method) configure_optimizers() (topobenchmark.model.model.TBModel method) CW (class in topobenchmark.nn.backbones.cell.cccn) CWNWrapper (class in topobenchmark.nn.wrappers.cell.cwn_wrapper)

D

DataloadDataset (class in topobenchmark.dataloader.dataload_dataset) DataTransform (class in topobenchmark.transforms.data_transform) DomainData (class in topobenchmark.dataloader.utils)

download() (topobenchmark.data.datasets.us_county_demos_dataset.USCountyDemosDataset method) download_file_from_drive() (in module topobenchmark.data.utils.io_utils) download_file_from_link() (in module topobenchmark.data.utils.io_utils)

E

EDGNN (class in topobenchmark.nn.backbones.hypergraph.edgnn) enforce_tags() (in module topobenchmark.utils.rich_utils) ensure_serializable() (in module topobenchmark.data.utils.utils)

EqualGausFeatures (class in topobenchmark.transforms.data_manipulations.equal_gaus_features) EquivSetConv (class in topobenchmark.nn.backbones.hypergraph.edgnn) extras() (in module topobenchmark.utils.utils)

F

flops() (topobenchmark.nn.backbones.hypergraph.edgnn.MLP method) forward() (topobenchmark.loss.base.AbstractLoss method) (topobenchmark.loss.loss.TBLoss method) (topobenchmark.model.model.TBModel method) (topobenchmark.nn.backbones.cell.cccn.CCCN method) (topobenchmark.nn.backbones.cell.cccn.CW method) (topobenchmark.nn.backbones.hypergraph.edgnn.EDGNN method) (topobenchmark.nn.backbones.hypergraph.edgnn.EquivSetConv method) (topobenchmark.nn.backbones.hypergraph.edgnn.JumpLinkConv method) (topobenchmark.nn.backbones.hypergraph.edgnn.MeanDegConv method) (topobenchmark.nn.backbones.hypergraph.edgnn.MLP method) (topobenchmark.nn.backbones.hypergraph.edgnn.PlainMLP method) (topobenchmark.nn.backbones.simplicial.sccnn.SCCNNCustom method) (topobenchmark.nn.backbones.simplicial.sccnn.SCCNNLayer method) (topobenchmark.nn.encoders.all_cell_encoder.AllCellFeatureEncoder method) (topobenchmark.nn.encoders.all_cell_encoder.BaseEncoder method) (topobenchmark.nn.encoders.base.AbstractFeatureEncoder method) (topobenchmark.nn.readouts.base.AbstractZeroCellReadOut method) (topobenchmark.nn.readouts.identical.NoReadOut method) (topobenchmark.nn.readouts.propagate_signal_down.PropagateSignalDown method) (topobenchmark.nn.wrappers.base.AbstractWrapper method) (topobenchmark.nn.wrappers.cell.can_wrapper.CANWrapper method) (topobenchmark.nn.wrappers.cell.cccn_wrapper.CCCNWrapper method) (topobenchmark.nn.wrappers.cell.ccxn_wrapper.CCXNWrapper method) (topobenchmark.nn.wrappers.cell.cwn_wrapper.CWNWrapper method) (topobenchmark.nn.wrappers.graph.gnn_wrapper.GNNWrapper method) (topobenchmark.nn.wrappers.hypergraph.hypergraph_wrapper.HypergraphWrapper method) (topobenchmark.nn.wrappers.simplicial.san_wrapper.SANWrapper method) (topobenchmark.nn.wrappers.simplicial.sccn_wrapper.SCCNWrapper method) (topobenchmark.nn.wrappers.simplicial.sccnn_wrapper.SCCNNWrapper method) (topobenchmark.nn.wrappers.simplicial.scn_wrapper.SCNWrapper method) (topobenchmark.transforms.data_manipulations.calculate_simplicial_curvature.CalculateSimplicialCurvature method) (topobenchmark.transforms.data_manipulations.equal_gaus_features.EqualGausFeatures method) (topobenchmark.transforms.data_manipulations.identity_transform.IdentityTransform method) (topobenchmark.transforms.data_manipulations.keep_only_connected_component.KeepOnlyConnectedComponent method) (topobenchmark.transforms.data_manipulations.keep_selected_data_fields.KeepSelectedDataFields method) (topobenchmark.transforms.data_manipulations.node_degrees.NodeDegrees method) (topobenchmark.transforms.data_manipulations.node_features_to_float.NodeFeaturesToFloat method) (topobenchmark.transforms.data_manipulations.one_hot_degree_features.OneHotDegreeFeatures method) (topobenchmark.transforms.data_transform.DataTransform method) (topobenchmark.transforms.feature_liftings.concatenation.Concatenation method) (topobenchmark.transforms.feature_liftings.identity.Identity method) (topobenchmark.transforms.feature_liftings.projection_sum.ProjectionSum method) (topobenchmark.transforms.feature_liftings.set.Set method) (topobenchmark.transforms.liftings.AbstractLifting method) (topobenchmark.transforms.liftings.base.AbstractLifting method)

G

generate_zero_sparse_connectivity() (in module topobenchmark.data.utils.utils) get() (topobenchmark.dataloader.dataload_dataset.DataloadDataset method) get_complex_connectivity() (in module topobenchmark.data.utils.utils) get_data_dir() (topobenchmark.data.loaders.base.AbstractLoader method) get_default_metrics() (in module topobenchmark.utils.config_resolvers) get_default_transform() (in module topobenchmark.utils.config_resolvers) get_file_id_from_url() (in module topobenchmark.data.utils.io_utils) get_metric_value() (in module topobenchmark.utils.utils)

get_monitor_metric() (in module topobenchmark.utils.config_resolvers) get_monitor_mode() (in module topobenchmark.utils.config_resolvers) get_required_lifting() (in module topobenchmark.utils.config_resolvers) get_routes_from_neighborhoods() (in module topobenchmark.data.utils.utils) GNNWrapper (class in topobenchmark.nn.wrappers.graph.gnn_wrapper) Graph2CellLifting (class in topobenchmark.transforms.liftings.graph2cell.base) Graph2HypergraphLifting (class in topobenchmark.transforms.liftings.graph2hypergraph.base) Graph2SimplicialLifting (class in topobenchmark.transforms.liftings.graph2simplicial.base) GraphLifting (class in topobenchmark.transforms.liftings)

H

HypergraphKHopLifting (class in topobenchmark.transforms.liftings.graph2hypergraph.khop) HypergraphKNNLifting (class in topobenchmark.transforms.liftings.graph2hypergraph.knn)

HypergraphLifting (class in topobenchmark.transforms.liftings) HypergraphWrapper (class in topobenchmark.nn.wrappers.hypergraph.hypergraph_wrapper)

I

Identity (class in topobenchmark.transforms.feature_liftings.identity) IdentityTransform (class in topobenchmark.transforms.data_manipulations.identity_transform) infer_in_channels() (in module topobenchmark.utils.config_resolvers) infer_num_cell_dimensions() (in module topobenchmark.utils.config_resolvers)

instantiate_callbacks() (in module topobenchmark.utils.instantiators) instantiate_loggers() (in module topobenchmark.utils.instantiators) instantiate_pre_transform() (topobenchmark.data.preprocessor.preprocessor.PreProcessor method) is_valid() (topobenchmark.dataloader.utils.DomainData method)

J

JumpLinkConv (class in topobenchmark.nn.backbones.hypergraph.edgnn)

K

k_fold_split() (in module topobenchmark.data.utils.split_utils)

KeepOnlyConnectedComponent (class in topobenchmark.transforms.data_manipulations.keep_only_connected_component) KeepSelectedDataFields (class in topobenchmark.transforms.data_manipulations.keep_selected_data_fields)

L

len() (topobenchmark.dataloader.dataload_dataset.DataloadDataset method) lift_features() (topobenchmark.transforms.feature_liftings.concatenation.Concatenation method) (topobenchmark.transforms.feature_liftings.projection_sum.ProjectionSum method) (topobenchmark.transforms.feature_liftings.set.Set method) lift_topology() (topobenchmark.transforms.liftings.AbstractLifting method) (topobenchmark.transforms.liftings.base.AbstractLifting method) (topobenchmark.transforms.liftings.graph2cell.cycle.CellCycleLifting method) (topobenchmark.transforms.liftings.graph2hypergraph.khop.HypergraphKHopLifting method) (topobenchmark.transforms.liftings.graph2hypergraph.knn.HypergraphKNNLifting method) (topobenchmark.transforms.liftings.graph2simplicial.clique.SimplicialCliqueLifting method) (topobenchmark.transforms.liftings.graph2simplicial.khop.SimplicialKHopLifting method) load() (topobenchmark.data.loaders.base.AbstractLoader method) (topobenchmark.data.preprocessor.preprocessor.PreProcessor method)

load_cell_complex_dataset() (in module topobenchmark.data.utils.utils) load_coauthorship_hypergraph_splits() (in module topobenchmark.data.utils.split_utils) load_dataset() (topobenchmark.data.loaders.base.AbstractLoader method) load_dataset_splits() (topobenchmark.data.preprocessor.preprocessor.PreProcessor method) load_hypergraph_pickle_dataset() (in module topobenchmark.data.utils.io_utils) load_inductive_splits() (in module topobenchmark.data.utils.split_utils) load_manual_graph() (in module topobenchmark.data.utils.utils) load_simplicial_dataset() (in module topobenchmark.data.utils.utils) load_transductive_splits() (in module topobenchmark.data.utils.split_utils) log() (topobenchmark.utils.pylogger.RankedLogger method) log_hyperparameters() (in module topobenchmark.utils.logging_utils) log_metrics() (topobenchmark.model.model.TBModel method)

M

make_hash() (in module topobenchmark.data.utils.utils) MeanDegConv (class in topobenchmark.nn.backbones.hypergraph.edgnn) MLP (class in topobenchmark.nn.backbones.hypergraph.edgnn) model_step() (topobenchmark.model.model.TBModel method) module topobenchmark.data.datasets.us_county_demos_dataset topobenchmark.data.loaders.base topobenchmark.data.preprocessor.preprocessor topobenchmark.data.utils.io_utils topobenchmark.data.utils.split_utils topobenchmark.data.utils.utils topobenchmark.dataloader.dataload_dataset topobenchmark.dataloader.dataloader topobenchmark.dataloader.utils topobenchmark.evaluator.base topobenchmark.evaluator.evaluator topobenchmark.loss.base topobenchmark.loss.loss topobenchmark.model.model topobenchmark.nn.backbones.cell.cccn topobenchmark.nn.backbones.hypergraph.edgnn topobenchmark.nn.backbones.simplicial.sccnn topobenchmark.nn.encoders.all_cell_encoder topobenchmark.nn.encoders.base topobenchmark.nn.readouts.base topobenchmark.nn.readouts.identical topobenchmark.nn.readouts.propagate_signal_down topobenchmark.nn.wrappers.base topobenchmark.nn.wrappers.cell.can_wrapper topobenchmark.nn.wrappers.cell.cccn_wrapper topobenchmark.nn.wrappers.cell.ccxn_wrapper topobenchmark.nn.wrappers.cell.cwn_wrapper topobenchmark.nn.wrappers.graph.gnn_wrapper topobenchmark.nn.wrappers.hypergraph.hypergraph_wrapper topobenchmark.nn.wrappers.simplicial.san_wrapper topobenchmark.nn.wrappers.simplicial.sccn_wrapper topobenchmark.nn.wrappers.simplicial.sccnn_wrapper topobenchmark.nn.wrappers.simplicial.scn_wrapper topobenchmark.optimizer.base topobenchmark.optimizer.optimizer topobenchmark.transforms.data_manipulations.calculate_simplicial_curvature topobenchmark.transforms.data_manipulations.equal_gaus_features topobenchmark.transforms.data_manipulations.identity_transform topobenchmark.transforms.data_manipulations.keep_only_connected_component topobenchmark.transforms.data_manipulations.keep_selected_data_fields topobenchmark.transforms.data_manipulations.node_degrees topobenchmark.transforms.data_manipulations.node_features_to_float topobenchmark.transforms.data_manipulations.one_hot_degree_features topobenchmark.transforms.data_transform topobenchmark.transforms.feature_liftings.concatenation topobenchmark.transforms.feature_liftings.identity topobenchmark.transforms.feature_liftings.projection_sum topobenchmark.transforms.feature_liftings.set topobenchmark.transforms.liftings topobenchmark.transforms.liftings.base topobenchmark.transforms.liftings.graph2cell.base topobenchmark.transforms.liftings.graph2cell.cycle topobenchmark.transforms.liftings.graph2hypergraph.base topobenchmark.transforms.liftings.graph2hypergraph.khop topobenchmark.transforms.liftings.graph2hypergraph.knn topobenchmark.transforms.liftings.graph2simplicial.base topobenchmark.transforms.liftings.graph2simplicial.clique topobenchmark.transforms.liftings.graph2simplicial.khop topobenchmark.utils.config_resolvers topobenchmark.utils.instantiators topobenchmark.utils.logging_utils topobenchmark.utils.pylogger topobenchmark.utils.rich_utils topobenchmark.utils.utils

N

NodeDegrees (class in topobenchmark.transforms.data_manipulations.node_degrees) NodeFeaturesToFloat (class in topobenchmark.transforms.data_manipulations.node_features_to_float)

NoReadOut (class in topobenchmark.nn.readouts.identical) normalize_matrix() (topobenchmark.nn.wrappers.simplicial.scn_wrapper.SCNWrapper method)

O

on_test_epoch_end() (topobenchmark.model.model.TBModel method) on_test_epoch_start() (topobenchmark.model.model.TBModel method) on_train_epoch_end() (topobenchmark.model.model.TBModel method) on_train_epoch_start() (topobenchmark.model.model.TBModel method)

on_val_epoch_start() (topobenchmark.model.model.TBModel method) on_validation_epoch_end() (topobenchmark.model.model.TBModel method) on_validation_epoch_start() (topobenchmark.model.model.TBModel method) one_cell_curvature() (topobenchmark.transforms.data_manipulations.calculate_simplicial_curvature.CalculateSimplicialCurvature method) OneHotDegreeFeatures (class in topobenchmark.transforms.data_manipulations.one_hot_degree_features)

P

PlainMLP (class in topobenchmark.nn.backbones.hypergraph.edgnn) PointCloudLifting (class in topobenchmark.transforms.liftings) PreProcessor (class in topobenchmark.data.preprocessor.preprocessor) print_config_tree() (in module topobenchmark.utils.rich_utils) process() (topobenchmark.data.datasets.us_county_demos_dataset.USCountyDemosDataset method) (topobenchmark.data.preprocessor.preprocessor.PreProcessor method)

process_outputs() (topobenchmark.model.model.TBModel method) processed_dir (topobenchmark.data.datasets.us_county_demos_dataset.USCountyDemosDataset property) (topobenchmark.data.preprocessor.preprocessor.PreProcessor property) processed_file_names (topobenchmark.data.datasets.us_county_demos_dataset.USCountyDemosDataset property) (topobenchmark.data.preprocessor.preprocessor.PreProcessor property) ProjectionSum (class in topobenchmark.transforms.feature_liftings.projection_sum) PropagateSignalDown (class in topobenchmark.nn.readouts.propagate_signal_down)

R

random_splitting() (in module topobenchmark.data.utils.split_utils) RankedLogger (class in topobenchmark.utils.pylogger) raw_dir (topobenchmark.data.datasets.us_county_demos_dataset.USCountyDemosDataset property) raw_file_names (topobenchmark.data.datasets.us_county_demos_dataset.USCountyDemosDataset property) read_ndim_manifolds() (in module topobenchmark.data.utils.io_utils) read_us_county_demos() (in module topobenchmark.data.utils.io_utils) reset() (topobenchmark.evaluator.base.AbstractEvaluator method) (topobenchmark.evaluator.evaluator.TBEvaluator method)

reset_parameters() (topobenchmark.nn.backbones.hypergraph.edgnn.EDGNN method) (topobenchmark.nn.backbones.hypergraph.edgnn.EquivSetConv method) (topobenchmark.nn.backbones.hypergraph.edgnn.JumpLinkConv method) (topobenchmark.nn.backbones.hypergraph.edgnn.MeanDegConv method) (topobenchmark.nn.backbones.hypergraph.edgnn.MLP method) (topobenchmark.nn.backbones.hypergraph.edgnn.PlainMLP method) (topobenchmark.nn.backbones.simplicial.sccnn.SCCNNLayer method) residual_connection() (topobenchmark.nn.wrappers.base.AbstractWrapper method)

S

SANWrapper (class in topobenchmark.nn.wrappers.simplicial.san_wrapper) save_transform_parameters() (topobenchmark.data.preprocessor.preprocessor.PreProcessor method) SCCNNCustom (class in topobenchmark.nn.backbones.simplicial.sccnn) SCCNNLayer (class in topobenchmark.nn.backbones.simplicial.sccnn) SCCNNWrapper (class in topobenchmark.nn.wrappers.simplicial.sccnn_wrapper) SCCNWrapper (class in topobenchmark.nn.wrappers.simplicial.sccn_wrapper) SCNWrapper (class in topobenchmark.nn.wrappers.simplicial.scn_wrapper)

select_neighborhoods_of_interest() (in module topobenchmark.data.utils.utils) Set (class in topobenchmark.transforms.feature_liftings.set) set_processed_data_dir() (topobenchmark.data.preprocessor.preprocessor.PreProcessor method) setup() (topobenchmark.model.model.TBModel method) SimplicialCliqueLifting (class in topobenchmark.transforms.liftings.graph2simplicial.clique) SimplicialKHopLifting (class in topobenchmark.transforms.liftings.graph2simplicial.khop) SimplicialLifting (class in topobenchmark.transforms.liftings) state_dict() (topobenchmark.dataloader.dataloader.TBDataloader method)

T

task_wrapper() (in module topobenchmark.utils.utils) TBDataloader (class in topobenchmark.dataloader.dataloader) TBEvaluator (class in topobenchmark.evaluator.evaluator) TBLoss (class in topobenchmark.loss.loss) TBModel (class in topobenchmark.model.model) TBOptimizer (class in topobenchmark.optimizer.optimizer) teardown() (topobenchmark.dataloader.dataloader.TBDataloader method) test_dataloader() (topobenchmark.dataloader.dataloader.TBDataloader method) test_step() (topobenchmark.model.model.TBModel method) to_data_list() (in module topobenchmark.dataloader.utils) topobenchmark.data.datasets.us_county_demos_dataset module topobenchmark.data.loaders.base module topobenchmark.data.preprocessor.preprocessor module topobenchmark.data.utils.io_utils module topobenchmark.data.utils.split_utils module topobenchmark.data.utils.utils module topobenchmark.dataloader.dataload_dataset module topobenchmark.dataloader.dataloader module topobenchmark.dataloader.utils module topobenchmark.evaluator.base module topobenchmark.evaluator.evaluator module topobenchmark.loss.base module topobenchmark.loss.loss module topobenchmark.model.model module topobenchmark.nn.backbones.cell.cccn module topobenchmark.nn.backbones.hypergraph.edgnn module topobenchmark.nn.backbones.simplicial.sccnn module topobenchmark.nn.encoders.all_cell_encoder module topobenchmark.nn.encoders.base module topobenchmark.nn.readouts.base module topobenchmark.nn.readouts.identical module topobenchmark.nn.readouts.propagate_signal_down module topobenchmark.nn.wrappers.base module topobenchmark.nn.wrappers.cell.can_wrapper module topobenchmark.nn.wrappers.cell.cccn_wrapper module topobenchmark.nn.wrappers.cell.ccxn_wrapper module topobenchmark.nn.wrappers.cell.cwn_wrapper module topobenchmark.nn.wrappers.graph.gnn_wrapper module topobenchmark.nn.wrappers.hypergraph.hypergraph_wrapper module topobenchmark.nn.wrappers.simplicial.san_wrapper module

topobenchmark.nn.wrappers.simplicial.sccn_wrapper module topobenchmark.nn.wrappers.simplicial.sccnn_wrapper module topobenchmark.nn.wrappers.simplicial.scn_wrapper module topobenchmark.optimizer.base module topobenchmark.optimizer.optimizer module topobenchmark.transforms.data_manipulations.calculate_simplicial_curvature module topobenchmark.transforms.data_manipulations.equal_gaus_features module topobenchmark.transforms.data_manipulations.identity_transform module topobenchmark.transforms.data_manipulations.keep_only_connected_component module topobenchmark.transforms.data_manipulations.keep_selected_data_fields module topobenchmark.transforms.data_manipulations.node_degrees module topobenchmark.transforms.data_manipulations.node_features_to_float module topobenchmark.transforms.data_manipulations.one_hot_degree_features module topobenchmark.transforms.data_transform module topobenchmark.transforms.feature_liftings.concatenation module topobenchmark.transforms.feature_liftings.identity module topobenchmark.transforms.feature_liftings.projection_sum module topobenchmark.transforms.feature_liftings.set module topobenchmark.transforms.liftings module topobenchmark.transforms.liftings.base module topobenchmark.transforms.liftings.graph2cell.base module topobenchmark.transforms.liftings.graph2cell.cycle module topobenchmark.transforms.liftings.graph2hypergraph.base module topobenchmark.transforms.liftings.graph2hypergraph.khop module topobenchmark.transforms.liftings.graph2hypergraph.knn module topobenchmark.transforms.liftings.graph2simplicial.base module topobenchmark.transforms.liftings.graph2simplicial.clique module topobenchmark.transforms.liftings.graph2simplicial.khop module topobenchmark.utils.config_resolvers module topobenchmark.utils.instantiators module topobenchmark.utils.logging_utils module topobenchmark.utils.pylogger module topobenchmark.utils.rich_utils module topobenchmark.utils.utils module train_dataloader() (topobenchmark.dataloader.dataloader.TBDataloader method) training_step() (topobenchmark.model.model.TBModel method) two_cell_curvature() (topobenchmark.transforms.data_manipulations.calculate_simplicial_curvature.CalculateSimplicialCurvature method)

U

update() (topobenchmark.evaluator.base.AbstractEvaluator method) (topobenchmark.evaluator.evaluator.TBEvaluator method) (topobenchmark.nn.backbones.simplicial.sccnn.SCCNNLayer method)

USCountyDemosDataset (class in topobenchmark.data.datasets.us_county_demos_dataset)

V

val_dataloader() (topobenchmark.dataloader.dataloader.TBDataloader method)

validation_step() (topobenchmark.model.model.TBModel method)

Z

zero_cell_curvature() (topobenchmark.transforms.data_manipulations.calculate_simplicial_curvature.CalculateSimplicialCurvature method)