Index

_

__init__() (AbstractEvaluator method), [1], [2] (AbstractFeatureEncoder method), [1], [2], [3] (AbstractLifting method), [1], [2] (AbstractLoader method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] (AbstractLoss method), [1], [2], [3], [4] (AbstractWrapper method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] (AbstractZeroCellReadOut method), [1], [2], [3] (AddLaplacianEigenvectorPE method) (AllCellFeatureEncoder method), [1] (AlphaComplexLifting method), [1] (AQSOL method) (BaseEncoder method), [1] (BestEpochMetricsCallback method), [1] (CalculateSimplicialCurvature method), [1] (CCCN method), [1], [2] (CellComplex method), [1], [2] (CellComplexLifting method), [1] (CellCycleLifting method), [1] (CitationHypergraphDataset method), [1], [2] (CitationHypergraphDatasetLoader method), [1], [2] (CofaceCCLifting method), [1] (CombinatorialComplex method), [1], [2], [3], [4] (CombinatorialLifting method), [1] (CombinedPSEs method), [1] (Compose method) (Concatenation method), [1] (customMLP method), [1], [2] (CW method), [1], [2] (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] (DataloadDataset method), [1], [2], [3], [4], [5] (DataLoader method) (Dataset method), [1], [2], [3], [4], [5] (DatasetLoss method), [1], [2] (DataTransform method), [1] (defaultdict method), [1] (DGM_d method), [1] (DGMLoss method), [1] (DGMStructureFeatureEncoder method), [1] (DiagLaplacianBuilder method), [1] (DictConfig method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] (DiscreteConfigurationComplexLifting method), [1] (EDGNN method), [1], [2] (EqualGausFeatures method), [1] (EquivSetConv method), [1], [2] (ExampleRegressionMetric method), [1] (ExpanderGraphLifting method), [1] (FlatEncoder method), [1] (GaussianMixture method) (GCNConv method) (GeneralLaplacianBuilder method), [1] (GeometricShapes method) (GeometricShapesDatasetLoader method), [1], [2] (GINConv method) (GPSConv method) (GPSEncoder method), [1], [2] (Graph2CellLifting method), [1], [2], [3] (Graph2CombinatorialLifting method), [1], [2] (Graph2HypergraphLifting method), [1], [2], [3], [4], [5], [6], [7], [8] (Graph2SimplicialLifting method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] (GraphLifting method), [1], [2], [3], [4], [5] (GraphMLP method), [1], [2] (GraphMLPLoss method), [1] (GraphNorm method) (GraphTriangleInducedCC method), [1] (GroupCombinatorialHomophily method), [1] (HeterophilousGraphDataset method) (HeterophilousGraphDatasetLoader method), [1], [2] (HydraConfig method) (HyperEdge method) (Hypergraph2CombinatorialLifting method), [1], [2] (HypergraphDataset method), [1], [2] (HypergraphDatasetLoader method), [1], [2] (HypergraphFormanRicciCurvatureLifting method), [1] (HypergraphKernelLifting method), [1] (HypergraphKHopLifting method), [1] (HypergraphKNNLifting method), [1] (HypergraphLifting method), [1], [2] (Identity method), [1] (IdentityGAT method), [1], [2] (IdentityGCN method), [1], [2] (IdentityGIN method), [1], [2] (IdentitySAGE method), [1], [2] (IdentityTransform method), [1] (InductiveDiscreteBundleSheafDiffusion method), [1] (InductiveDiscreteDiagSheafDiffusion method), [1] (InductiveDiscreteGeneralSheafDiffusion method), [1] (InfereKNNConnectivity method), [1] (InfereRadiusConnectivity method), [1] (InMemoryDataset method), [1], [2], [3] (JumpLinkConv method), [1], [2] (KeepOnlyConnectedComponent method), [1] (KeepSelectedDataFields method), [1] (LaplacianBuilder method) (LapPE method), [1] (LargestConnectedComponents method) (LatentCliqueLifting method), [1] (LayerNorm method) (LightningDataModule method) (LightningModule method), [1] (Linear method) (LocalConcatSheafLearner method), [1] (MantraDataset method), [1], [2], [3] (MantraSimplicialDatasetLoader method), [1], [2], [3], [4] (ManualGraphDatasetLoader method), [1], [2] (MapperCover method) (MapperLifting method), [1] (MeanDegConv method), [1], [2] (MeanMetric method) (MessagePassingHomophily method), [1] (Metric method) (MetricCollection method) (MLP method), [1], [2] (Mlp method), [1], [2] (MLPReadout method), [1] (ModelCheckpoint method) (ModularityMaximizationLifting method), [1] (Module method) (MoGMSTLifting method), [1] (MoleculeDatasetLoader method), [1], [2] (NeighborhoodComplexLifting method), [1] (NodeDegrees method), [1] (NodeFeaturesToFloat method), [1] (NoReadOut method), [1] (NormConnectionLaplacianBuilder method), [1] (NSDEncoder method), [1], [2] (OGBGDatasetLoader method), [1], [2] (OmegaConf method), [1], [2] (OneHotDegreeFeatures method), [1] (Orthogonal method), [1] (PerformerAttention method) (PipelineTimer method), [1] (PlainMLP method), [1], [2] (Planetoid method) (PlanetoidDatasetLoader method), [1], [2] (PNAConv method) (PointCloud2HypergraphLifting method), [1], [2], [3], [4] (PointCloud2SimplicialLifting method), [1], [2], [3] (PointCloudLifting method), [1], [2], [3] (PointNetLifting method), [1] (PreProcessor method), [1], [2] (ProjectionSum method), [1] (PropagateSignalDown method), [1] (PygGraphPropPredDataset method) (RandomFlagComplexLifting method), [1] (RankedLogger method), [1], [2] (RedefineSimplicialNeighbourhoods method), [1] (RedrawProjection method), [1], [2] (RWSE method), [1] (SCCNNCustom method), [1], [2] (SCCNNLayer method), [1], [2] (Set method), [1] (SheafDiffusion method), [1] (SheafLearner method) (Simplicial2CombinatorialLifting method), [1], [2] (SimplicialCliqueLifting method), [1], [2] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] (SimplicialDnDLifting method), [1] (SimplicialEccentricityLifting method), [1] (SimplicialGraphInducedLifting method), [1] (SimplicialKHopLifting method), [1] (SimplicialLifting method), [1], [2] (SimplicialLineLifting method), [1] (SimplicialVietorisRipsLifting method), [1] (SparseTensor method) (StratifiedKFold method) (SVDFeatureReduction method) (TBDataloader method), [1], [2] (TBEvaluator method), [1] (TBLoss method), [1] (TBModel method), [1] (TBOptimizer method), [1] (TopoTune method), [1], [2] (TopoTune_OneHasse method), [1], [2] (ToUndirected method) (tqdm method), [1], [2] (Trainer method) (TUDataset method) (TUDatasetLoader method), [1], [2] (UniversalStrictLifting method), [1] (USCountyDemosDataset method), [1], [2] (USCountyDemosDatasetLoader method), [1], [2] (VoronoiLifting method), [1] (ZINC method)

A

ABC (class in topobench.data.loaders.base) (class in topobench.evaluator.base) (class in topobench.loss.base) (class in topobench.nn.wrappers.base) (class in topobench.optimizer.base) absolute() (Path method), [1], [2], [3], [4], [5] AbstractEvaluator (class in topobench.evaluator) (class in topobench.evaluator.base) (class in topobench.evaluator.evaluator) AbstractFeatureEncoder (class in topobench.nn.encoders.all_cell_encoder) (class in topobench.nn.encoders.base) (class in topobench.nn.encoders.dgm_encoder) (class in topobench.nn.encoders.flat_encoder) AbstractLifting (class in topobench.transforms.liftings) (class in topobench.transforms.liftings.base) (class in topobench.transforms.liftings.liftings) AbstractLoader (class in topobench.data.loaders) (class in topobench.data.loaders.base) (class in topobench.data.loaders.graph.hetero_datasets) (class in topobench.data.loaders.graph.mantra_dataset) (class in topobench.data.loaders.graph.manual_graph_dataset_loader) (class in topobench.data.loaders.graph.modecule_datasets) (class in topobench.data.loaders.graph.ogbg_datasets) (class in topobench.data.loaders.graph.planetoid_datasets) (class in topobench.data.loaders.graph.tu_datasets) (class in topobench.data.loaders.graph.us_county_demos_dataset_loader) (class in topobench.data.loaders.hypergraph.citation_hypergraph_dataset_loader) (class in topobench.data.loaders.hypergraph.hypergraph_dataset_loader) (class in topobench.data.loaders.pointcloud.geometric_shapes) (class in topobench.data.loaders.simplicial.mantra_dataset_loader) AbstractLoss (class in topobench.loss.base) (class in topobench.loss.dataset.DatasetLoss) (class in topobench.loss.loss) (class in topobench.loss.model.DGMLoss) (class in topobench.loss.model.GraphMLPLoss) abstractmethod() (in module topobench.data.loaders.base) (in module topobench.evaluator.base) (in module topobench.loss.base) (in module topobench.nn.backbones.graph.nsd_utils.sheaf_models) (in module topobench.nn.encoders.base) (in module topobench.nn.readouts.base) (in module topobench.nn.wrappers.base) (in module topobench.optimizer.base) (in module topobench.transforms.liftings.base) AbstractOptimizer (class in topobench.optimizer.base) (class in topobench.optimizer.optimizer) AbstractWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.base) (class in topobench.nn.wrappers.cell.can_wrapper) (class in topobench.nn.wrappers.cell.cccn_wrapper) (class in topobench.nn.wrappers.cell.ccxn_wrapper) (class in topobench.nn.wrappers.cell.cwn_wrapper) (class in topobench.nn.wrappers.combinatorial.tune_wrapper) (class in topobench.nn.wrappers.graph.gnn_wrapper) (class in topobench.nn.wrappers.graph.graph_mlp_wrapper) (class in topobench.nn.wrappers.hypergraph.hypergraph_wrapper) (class in topobench.nn.wrappers.pointcloud.pointcloud_wrapper) (class in topobench.nn.wrappers.simplicial.san_wrapper) (class in topobench.nn.wrappers.simplicial.sccn_wrapper) (class in topobench.nn.wrappers.simplicial.sccnn_wrapper) (class in topobench.nn.wrappers.simplicial.scn_wrapper) AbstractZeroCellReadOut (class in topobench.nn.readouts) (class in topobench.nn.readouts.base) (class in topobench.nn.readouts.identical) (class in topobench.nn.readouts.propagate_signal_down)

accelerator (Trainer property) activation_resolver() (in module topobench.nn.backbones.non_relational.mlp) add() (SparseTensor method) add_() (SparseTensor method) add_cell() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] add_cells_from() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] add_edge() (CellComplex method), [1], [2] add_edges_from() (CellComplex method), [1], [2] add_elements_from_nx_graph() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] add_metrics() (MetricCollection method) add_module() (Module method) add_nnz() (SparseTensor method) add_nnz_() (SparseTensor method) add_node() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] add_simplex() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] add_simplices_from() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] add_state() (Metric method) AddLaplacianEigenvectorPE (class in topobench.transforms.liftings.graph2hypergraph.mapper_lifting) adjacency_matrix() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] after_save_checkpoint() (Logger method), [1] aggr_norm_func() (SCCNNLayer method), [1], [2] aggregate_inter_nbhd() (TopoTune method), [1], [2] (TopoTune_OneHasse method), [1], [2] aic() (GaussianMixture method) all_cell_to_node_coadjacency_matrix() (CellComplex method), [1], [2] all_gather() (LightningModule method), [1] all_nbhds_expand() (TopoTune_OneHasse method), [1], [2] all_nbhds_gnn_forward() (TopoTune_OneHasse method), [1], [2] AllCellFeatureEncoder (class in topobench.nn.encoders) (class in topobench.nn.encoders.all_cell_encoder) allow_zero_length_dataloader_with_multiple_devices (LightningDataModule attribute) (LightningModule attribute) (TBDataloader attribute), [1], [2] AlphaComplexLifting (class in topobench.transforms.liftings.pointcloud2simplicial) (class in topobench.transforms.liftings.pointcloud2simplicial.alpha_complex_lifting) Any (class in topobench.data.loaders.graph.manual_graph_dataset_loader) (class in topobench.dataloader.dataloader) (class in topobench.dataloader.utils) (class in topobench.evaluator.metrics.example) (class in topobench.model.model) (class in topobench.nn.backbones.graph.gps) (class in topobench.optimizer.optimizer) (class in topobench.run) (class in topobench.transforms.liftings.graph2simplicial.clique_lifting) (class in topobench.transforms.liftings.graph2simplicial.khop_lifting) (class in topobench.transforms.liftings.graph2simplicial.line_lifting) (class in topobench.transforms.liftings.graph2simplicial.neighborhood_complex_lifting) (class in topobench.utils.logging_utils) (class in topobench.utils.utils) apply() (Module method) AQSOL (class in topobench.data.loaders.graph.modecule_datasets) assign_train_val_test_mask_to_graphs() (in module topobench.data.utils.split_utils) atoms() (AQSOL method) automatic_optimization (LightningModule property), [1] avg_bandwidth() (SparseTensor method) avg_col_length() (SparseTensor method) avg_row_length() (SparseTensor method)

B

backward() (LightningModule method), [1] bandwidth() (SparseTensor method) bandwidth_proportion() (SparseTensor method) BaseEncoder (class in topobench.nn.encoders.all_cell_encoder) (class in topobench.nn.encoders.dgm_encoder) BaseTransform (class in topobench.transforms.data_manipulations.laplacian_encodings) (class in topobench.transforms.data_manipulations.positional_and_structural_encodings) (class in topobench.transforms.data_manipulations.random_walk_encodings) batch (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] batch_size (DataLoader attribute) BestEpochMetricsCallback (class in topobench.callbacks) (class in topobench.callbacks.best_epoch_metrics)

bfloat16() (Module method) (SparseTensor method) bias (LayerNorm attribute) (Linear attribute) bic() (GaussianMixture method) bonds() (AQSOL method) bool() (SparseTensor method) buffers() (Module method) build_mlp_layers() (MLP method), [1], [2] build_norm_layers() (MLP method), [1], [2] build_paths() (in module topobench.transforms.liftings.graph2combinatorial.graph_induced_cc) byte() (SparseTensor method)

C

calculate_affinity_score() (GroupCombinatorialHomophily method), [1] calculate_baseline_matrix() (GroupCombinatorialHomophily method), [1] calculate_D_matrix() (GroupCombinatorialHomophily method), [1] calculate_node_degrees() (NodeDegrees method), [1] CalculateSimplicialCurvature (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.calculate_simplicial_curvature) call_super_init (Module attribute) Callable (class in topobench.utils.utils) Callback (class in topobench.callbacks.best_epoch_metrics) (class in topobench.run) (class in topobench.utils.instantiators) callback_metrics (Trainer property) CANWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.cell) (class in topobench.nn.wrappers.cell.can_wrapper) CCCN (class in topobench.nn.backbones) (class in topobench.nn.backbones.cell) (class in topobench.nn.backbones.cell.cccn) CCCNWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.cell) (class in topobench.nn.wrappers.cell.cccn_wrapper) CCXNWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.cell) (class in topobench.nn.wrappers.cell.ccxn_wrapper) cell_neighbors() (CellComplex method), [1], [2] CellComplex (class in topobench.transforms.liftings.graph2cell.base) (class in topobench.transforms.liftings.graph2cell.cycle_lifting) (class in topobench.transforms.liftings.graph2cell.discrete_configuration_complex_lifting) CellComplexLifting (class in topobench.transforms.liftings) (class in topobench.transforms.liftings.liftings) CellCycleLifting (class in topobench.transforms.liftings.graph2cell) (class in topobench.transforms.liftings.graph2cell.cycle_lifting) cells (CellComplex property), [1], [2] (CombinatorialComplex property), [1], [2], [3], [4] char() (SparseTensor method) chebyshev_conv() (SCCNNLayer method), [1], [2] check_monitor_top_k() (ModelCheckpoint method) check_pses_in_transforms() (in module topobench.utils.config_resolvers) check_worker_number_rationality() (DataLoader method) checkpoint_callback (Trainer property) checkpoint_callbacks (Trainer property) CHECKPOINT_EQUALS_CHAR (ModelCheckpoint attribute) CHECKPOINT_HYPER_PARAMS_KEY (LightningDataModule attribute) (LightningModule attribute), [1] CHECKPOINT_HYPER_PARAMS_NAME (LightningDataModule attribute) (LightningModule attribute), [1] CHECKPOINT_HYPER_PARAMS_TYPE (LightningDataModule attribute) (LightningModule attribute), [1] CHECKPOINT_JOIN_CHAR (ModelCheckpoint attribute) CHECKPOINT_NAME_LAST (ModelCheckpoint attribute) children() (Module method) chmod() (Path method), [1], [2], [3], [4], [5] CitationHypergraphDataset (class in topobench.data.datasets) (class in topobench.data.datasets.citation_hypergraph_dataset) (class in topobench.data.loaders.hypergraph.citation_hypergraph_dataset_loader) CitationHypergraphDatasetLoader (class in topobench.data.loaders) (class in topobench.data.loaders.hypergraph) (class in topobench.data.loaders.hypergraph.citation_hypergraph_dataset_loader) ckpt_path (Trainer property) cleaned_url (TUDataset attribute) clear() (CellComplex method), [1], [2] (tqdm method), [1], [2] clear_cache() (OmegaConf static method), [1], [2] clear_cache_() (SparseTensor method) clear_resolver() (OmegaConf class method), [1], [2] clear_resolvers() (OmegaConf static method), [1], [2] clip_gradients() (LightningModule method), [1] clone() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] (Metric method) (MetricCollection method) (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] (SparseTensor method) close() (tqdm method), [1], [2] coadjacency_matrix() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] coalesce() (in module topobench.data.utils.io_utils) (SparseTensor method)

CofaceCCLifting (class in topobench.transforms.liftings.simplicial2combinatorial) (class in topobench.transforms.liftings.simplicial2combinatorial.coface_cc_lifting) coincidence_matrix() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] collate() (InMemoryDataset static method), [1], [2], [3] collate_fn() (in module topobench.dataloader.dataloader) (in module topobench.dataloader.utils) comb() (in module topobench.transforms.data_manipulations.group_homophily) combinations (class in topobench.transforms.liftings.graph2combinatorial.graph_induced_cc) (class in topobench.transforms.liftings.graph2simplicial.clique_lifting) (class in topobench.transforms.liftings.graph2simplicial.dnd_lifting) (class in topobench.transforms.liftings.graph2simplicial.eccentricity_lifting) (class in topobench.transforms.liftings.graph2simplicial.graph_induced_lifting) (class in topobench.transforms.liftings.graph2simplicial.khop_lifting) (class in topobench.transforms.liftings.graph2simplicial.line_lifting) (class in topobench.transforms.liftings.graph2simplicial.neighborhood_complex_lifting) (class in topobench.transforms.liftings.pointcloud2simplicial.random_flag_complex) CombinatorialComplex (class in topobench.transforms.liftings.graph2combinatorial.base) (class in topobench.transforms.liftings.graph2combinatorial.graph_induced_cc) (class in topobench.transforms.liftings.hypergraph2combinatorial.base) (class in topobench.transforms.liftings.hypergraph2combinatorial.universal_strict_lifting) (class in topobench.transforms.liftings.simplicial2combinatorial.coface_cc_lifting) CombinatorialLifting (class in topobench.transforms.liftings) (class in topobench.transforms.liftings.liftings) CombinedPSEs (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.positional_and_structural_encodings) compile() (Module method) Compose (class in topobench.transforms.liftings.graph2hypergraph.mapper_lifting) compute() (AbstractEvaluator method), [1], [2] (ExampleRegressionMetric method), [1] (MeanMetric method) (Metric method) (MetricCollection method) (TBEvaluator method), [1] compute_groups (MetricCollection property) compute_learnable_diag_laplacian_indices() (in module topobench.nn.backbones.graph.nsd_utils.laplace) (in module topobench.nn.backbones.graph.nsd_utils.laplacian_builders) compute_learnable_laplacian_indices() (in module topobench.nn.backbones.graph.nsd_utils.laplace) (in module topobench.nn.backbones.graph.nsd_utils.laplacian_builders) compute_left_right_map_index() (in module topobench.nn.backbones.graph.nsd_utils.laplace) (in module topobench.nn.backbones.graph.nsd_utils.laplacian_builders) compute_logits() (AbstractZeroCellReadOut method), [1], [2], [3] Concatenation (class in topobench.transforms.feature_liftings) (class in topobench.transforms.feature_liftings.concatenation) configure_callbacks() (LightningModule method), [1] configure_gradient_clipping() (LightningModule method), [1] configure_optimizer() (AbstractOptimizer method), [1] (TBOptimizer method), [1] configure_optimizers() (LightningModule method), [1] (TBModel method), [1] connected_components() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] coo() (SparseTensor method) copy() (defaultdict method), [1] (DictConfig method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] (InMemoryDataset method), [1], [2], [3] (SparseTensor method) copy_cache() (OmegaConf static method), [1], [2] count() (Sequence method) count_number_of_parameters() (in module topobench.run) cpu() (InMemoryDataset method), [1], [2], [3] (Module method) (SparseTensor method) create() (OmegaConf static method), [1], [2] csc() (SparseTensor method) csr() (SparseTensor method) cuda() (InMemoryDataset method), [1], [2], [3] (Module method) (SparseTensor method) current_epoch (LightningModule property), [1] (Trainer property) customMLP (class in topobench.nn.backbones) (class in topobench.nn.backbones.hypergraph) (class in topobench.nn.backbones.hypergraph.edgnn) CW (class in topobench.nn.backbones) (class in topobench.nn.backbones.cell) (class in topobench.nn.backbones.cell.cccn) cwd() (Path class method), [1], [2], [3], [4], [5] CWNWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.cell) (class in topobench.nn.wrappers.cell.cwn_wrapper)

D

Data (class in topobench.data.datasets.citation_hypergraph_dataset) (class in topobench.data.datasets.hypergraph_datasets) (class in topobench.data.datasets.mantra_dataset) (class in topobench.data.datasets.us_county_demos_dataset) (class in topobench.data.utils.io_utils) (class in topobench.model.model) (class in topobench.nn.backbones.combinatorial.gccn) (class in topobench.nn.backbones.combinatorial.gccn_onehasse) (class in topobench.transforms.data_manipulations.laplacian_encodings) (class in topobench.transforms.data_manipulations.positional_and_structural_encodings) (class in topobench.transforms.data_manipulations.random_walk_encodings) (class in topobench.transforms.liftings.graph2simplicial.dnd_lifting) (class in topobench.transforms.liftings.graph2simplicial.neighborhood_complex_lifting) (class in topobench.transforms.liftings.pointcloud2simplicial.random_flag_complex) (class in topobench.transforms.liftings.simplicial2combinatorial.coface_cc_lifting) data (InMemoryDataset property), [1], [2], [3] data2simplicial() (in module topobench.data.utils) (in module topobench.data.utils.utils) (in module topobench.transforms.data_manipulations.redefine_simplicial_neighbourhoods) DataloadDataset (class in topobench.data.loaders.graph.manual_graph_dataset_loader) (class in topobench.data.preprocessor.preprocessor) (class in topobench.data.utils.split_utils) (class in topobench.dataloader) (class in topobench.dataloader.dataload_dataset) (class in topobench.dataloader.dataloader) DataLoader (class in topobench.dataloader.dataloader) Dataset (class in topobench.data.loaders.graph.hetero_datasets) (class in topobench.data.loaders.graph.modecule_datasets) (class in topobench.data.loaders.graph.ogbg_datasets) (class in topobench.data.loaders.graph.planetoid_datasets) (class in topobench.data.loaders.graph.tu_datasets) (class in topobench.data.loaders.pointcloud.geometric_shapes) dataset (DataLoader attribute) DatasetLoss (class in topobench.loss.dataset) (class in topobench.loss.dataset.DatasetLoss) (class in topobench.loss.loss) DataTransform (class in topobench.data.preprocessor.preprocessor) (class in topobench.transforms.data_transform) debug() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] default_factory (defaultdict attribute), [1] default_root_dir (Trainer property) defaultdict (class in topobench.dataloader.utils) (class in topobench.transforms.liftings.graph2combinatorial.graph_induced_cc) degree() (CellComplex method), [1], [2] (in module topobench.nn.backbones.graph.nsd_utils.laplacian_builders) (in module topobench.transforms.data_manipulations.random_walk_encodings) density() (SparseTensor method) detach() (SparseTensor method) detach_() (SparseTensor method) detect_communities() (ModularityMaximizationLifting method), [1] device (Metric property) device() (SparseTensor method) device_as() (SparseTensor method) device_ids (Trainer property) device_mesh (LightningModule property), [1] DGM_d (class in topobench.nn.encoders.dgm_encoder) (class in topobench.nn.encoders.kdgm) DGMLoss (class in topobench.loss.model) (class in topobench.loss.model.DGMLoss) DGMStructureFeatureEncoder (class in topobench.nn.encoders) (class in topobench.nn.encoders.dgm_encoder) DiagLaplacianBuilder (class in topobench.nn.backbones.graph.nsd_utils.inductive_discrete_models) (class in topobench.nn.backbones.graph.nsd_utils.laplacian_builders)

DictConfig (class in topobench.data.datasets.citation_hypergraph_dataset) (class in topobench.data.datasets.hypergraph_datasets) (class in topobench.data.datasets.mantra_dataset) (class in topobench.data.datasets.us_county_demos_dataset) (class in topobench.data.loaders.base) (class in topobench.data.loaders.graph.hetero_datasets) (class in topobench.data.loaders.graph.mantra_dataset) (class in topobench.data.loaders.graph.manual_graph_dataset_loader) (class in topobench.data.loaders.graph.modecule_datasets) (class in topobench.data.loaders.graph.ogbg_datasets) (class in topobench.data.loaders.graph.planetoid_datasets) (class in topobench.data.loaders.graph.tu_datasets) (class in topobench.data.loaders.graph.us_county_demos_dataset_loader) (class in topobench.data.loaders.hypergraph.citation_hypergraph_dataset_loader) (class in topobench.data.loaders.hypergraph.hypergraph_dataset_loader) (class in topobench.data.loaders.pointcloud.geometric_shapes) (class in topobench.data.loaders.simplicial.mantra_dataset_loader) (class in topobench.run) (class in topobench.utils.instantiators) (class in topobench.utils.rich_utils) (class in topobench.utils.utils) dim (CellComplex property), [1], [2] (SimplicialComplex property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] dim() (SparseTensor method) dirac_operator_matrix() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] DiscreteConfigurationComplexLifting (class in topobench.transforms.liftings.graph2cell) (class in topobench.transforms.liftings.graph2cell.discrete_configuration_complex_lifting) display() (tqdm method), [1], [2] distributed_sampler_kwargs (Trainer property) DomainData (class in topobench.dataloader.utils) double() (Metric method) (Module method) (SparseTensor method) down_laplacian_matrix() (CellComplex method), [1], [2] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] download() (AQSOL method) (CitationHypergraphDataset method), [1], [2] (Dataset method), [1], [2], [3], [4], [5] (GeometricShapes method) (HeterophilousGraphDataset method) (HypergraphDataset method), [1], [2] (MantraDataset method), [1], [2], [3] (Planetoid method) (PygGraphPropPredDataset method) (TUDataset method) (USCountyDemosDataset method), [1], [2] (ZINC method) download_file_from_drive() (in module topobench.data.datasets.citation_hypergraph_dataset) (in module topobench.data.datasets.hypergraph_datasets) (in module topobench.data.datasets.us_county_demos_dataset) (in module topobench.data.utils) (in module topobench.data.utils.io_utils) download_file_from_link() (in module topobench.data.datasets.mantra_dataset) (in module topobench.data.utils.io_utils) drop_last (DataLoader attribute) Dropout (class in topobench.nn.backbones.graph.graph_mlp) dtype (Metric property) dtype() (SparseTensor method) dump_patches (Module attribute)

E

early_stopping_callback (Trainer property) early_stopping_callbacks (Trainer property) edge_attr (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] edge_cycle_to_vertex_cycle() (in module topobench.transforms.liftings.graph2cell.discrete_configuration_complex_lifting) edge_index (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] edge_stores (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] edge_subgraph() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] edge_weight (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] edges (CellComplex property), [1], [2] EDGNN (class in topobench.nn.backbones) (class in topobench.nn.backbones.hypergraph) (class in topobench.nn.backbones.hypergraph.edgnn) eigsh() (in module topobench.transforms.data_manipulations.laplacian_encodings) elementwise_affine (LayerNorm attribute) enable_validation (Trainer property) enforce_tags() (in module topobench.utils) (in module topobench.utils.rich_utils) ensure_serializable() (in module topobench.data.preprocessor.preprocessor) (in module topobench.data.utils) (in module topobench.data.utils.utils) eps (LayerNorm attribute) EqualGausFeatures (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.equal_gaus_features) EquivSetConv (class in topobench.nn.backbones) (class in topobench.nn.backbones.hypergraph) (class in topobench.nn.backbones.hypergraph.edgnn)

estimated_stepping_batches (Trainer property) euler_characterisitics() (CellComplex method), [1], [2] eval() (Module method) evaluating (Trainer property) every_n_epochs (ModelCheckpoint property) example_input_array (LightningModule property), [1] ExampleRegressionMetric (class in topobench.evaluator.metrics) (class in topobench.evaluator.metrics.example) exists() (Path method), [1], [2], [3], [4], [5] ExpanderGraphLifting (class in topobench.transforms.liftings.graph2hypergraph) (class in topobench.transforms.liftings.graph2hypergraph.expander_graph_lifting) expanduser() (Path method), [1], [2], [3], [4], [5] external_write_mode() (tqdm class method), [1], [2] extra_repr() (LayerNorm method) (Linear method) (Module method) extract_gz() (in module topobench.data.datasets.mantra_dataset) extract_zip() (in module topobench.data.datasets.citation_hypergraph_dataset) (in module topobench.data.datasets.hypergraph_datasets) (in module topobench.data.datasets.us_county_demos_dataset) extras() (in module topobench.run) (in module topobench.utils) (in module topobench.utils.utils) eye() (SparseTensor class method)

F

fabric (LightningModule property), [1] face (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] file_exists() (ModelCheckpoint method) FILE_EXTENSION (ModelCheckpoint attribute) FILE_FORMAT (CitationHypergraphDataset attribute), [1], [2] (HypergraphDataset attribute), [1], [2] (MantraDataset attribute), [1], [2], [3] (USCountyDemosDataset attribute), [1], [2] fill_cache_() (SparseTensor method) fill_diag() (SparseTensor method) fill_value() (SparseTensor method) fill_value_() (SparseTensor method) find_mog() (MoGMSTLifting method), [1] find_overlapping_paths() (in module topobench.transforms.liftings.graph2combinatorial.graph_induced_cc) find_spec() (in module topobench.utils.utils) find_tetrahedrons() (in module topobench.data.utils.utils) find_triangles() (in module topobench.data.utils.utils) fit() (Trainer method) fit_transform() (MapperCover method) FlatEncoder (class in topobench.nn.encoders) (class in topobench.nn.encoders.flat_encoder) float() (Metric method) (Module method) (SparseTensor method) flops() (customMLP method), [1], [2] fmp() (in module topobench.transforms.liftings.graph2hypergraph.kernel_lifting) format_checkpoint_name() (ModelCheckpoint method) format_dict (tqdm property), [1], [2] format_interval() (tqdm static method), [1], [2] format_meter() (tqdm static method), [1], [2] format_num() (tqdm static method), [1], [2] format_sizeof() (tqdm static method), [1], [2] forward() (AbstractFeatureEncoder method), [1], [2], [3] (AbstractLifting method), [1], [2] (AbstractLoss method), [1], [2], [3], [4] (AbstractWrapper method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] (AbstractZeroCellReadOut method), [1], [2], [3] (AddLaplacianEigenvectorPE method) (AllCellFeatureEncoder method), [1] (BaseEncoder method), [1] (BaseTransform method), [1], [2] (CalculateSimplicialCurvature method), [1] (CANWrapper method), [1], [2] (CCCN method), [1], [2] (CCCNWrapper method), [1], [2] (CCXNWrapper method), [1], [2] (CofaceCCLifting method), [1] (CombinedPSEs method), [1] (Compose method) (Concatenation method), [1] (customMLP method), [1], [2] (CW method), [1], [2] (CWNWrapper method), [1], [2] (DatasetLoss method), [1], [2] (DataTransform method), [1] (DGM_d method), [1] (DGMLoss method), [1] (DGMStructureFeatureEncoder method), [1] (DiagLaplacianBuilder method), [1] (DiscreteConfigurationComplexLifting method), [1] (Dropout method) (EDGNN method), [1], [2] (EqualGausFeatures method), [1] (EquivSetConv method), [1], [2] (FlatEncoder method), [1] (GCNConv method) (GeneralLaplacianBuilder method), [1] (GINConv method) (GNNWrapper method), [1], [2] (GPSConv method) (GPSEncoder method), [1], [2] (GraphMLP method), [1], [2] (GraphMLPLoss method), [1] (GraphMLPWrapper method), [1], [2] (GraphNorm method) (GroupCombinatorialHomophily method), [1] (HypergraphWrapper method), [1], [2] (Identity method), [1] (IdentityGAT method), [1], [2] (IdentityGCN method), [1], [2] (IdentityGIN method), [1], [2] (IdentitySAGE method), [1], [2] (IdentityTransform method), [1] (InductiveDiscreteBundleSheafDiffusion method), [1] (InductiveDiscreteDiagSheafDiffusion method), [1] (InductiveDiscreteGeneralSheafDiffusion method), [1] (InfereKNNConnectivity method), [1] (InfereRadiusConnectivity method), [1] (JumpLinkConv method), [1], [2] (KeepOnlyConnectedComponent method), [1] (KeepSelectedDataFields method), [1] (LapPE method), [1] (LargestConnectedComponents method) (LayerNorm method) (LightningModule method), [1] (Linear method) (LocalConcatSheafLearner method), [1] (MeanDegConv method), [1], [2] (MessagePassingHomophily method), [1] (Metric method) (MetricCollection method) (MLP method), [1], [2] (Mlp method), [1], [2] (MLPReadout method), [1] (Module method) (NodeDegrees method), [1] (NodeFeaturesToFloat method), [1] (NoReadOut method), [1] (NormConnectionLaplacianBuilder method), [1] (NSDEncoder method), [1], [2] (OneHotDegreeFeatures method), [1] (Orthogonal method), [1] (PerformerAttention method) (PlainMLP method), [1], [2] (PNAConv method) (PointcloudWrapper method), [1], [2] (ProjectionSum method), [1] (PropagateSignalDown method), [1] (RedefineSimplicialNeighbourhoods method), [1] (RWSE method), [1] (SANWrapper method), [1], [2] (SCCNNCustom method), [1], [2] (SCCNNLayer method), [1], [2] (SCCNNWrapper method), [1], [2] (SCCNWrapper method), [1], [2] (SCNWrapper method), [1], [2] (Set method), [1] (SheafLearner method) (SVDFeatureReduction method) (TBLoss method), [1] (TBModel method), [1] (TopoTune method), [1], [2] (TopoTune_OneHasse method), [1], [2] (ToUndirected method) (TuneWrapper method), [1], [2]

forward_criterion() (DatasetLoss method), [1], [2] fps() (in module topobench.transforms.liftings.pointcloud2hypergraph.pointnet_lifting) (in module topobench.transforms.liftings.pointcloud2hypergraph.voronoi_lifting) freeze() (LightningModule method), [1] from_cli() (OmegaConf static method), [1], [2] from_datasets() (LightningDataModule class method) from_dense() (SparseTensor class method) from_dict() (Data class method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] from_dotlist() (OmegaConf static method), [1], [2] from_edge_index() (SparseTensor class method) from_gudhi() (SimplicialComplex class method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] from_networkx_graph() (CellComplex method), [1], [2] from_numpy_array() (in module topobench.transforms.liftings.pointcloud2hypergraph.mogmst_lifting) from_nx() (SimplicialComplex class method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] from_scipy() (SparseTensor method) from_sparse() (in module topobench.data.utils.utils) from_spharapy() (SimplicialComplex class method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] from_spharpy() (SimplicialComplex class method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] from_storage() (SparseTensor class method) from_torch_sparse_coo_tensor() (SparseTensor class method) from_torch_sparse_csr_tensor() (SparseTensor class method) from_trimesh() (CellComplex class method), [1], [2] (SimplicialComplex class method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] full_state_update (ExampleRegressionMetric attribute), [1] (Metric attribute)

G

GAT (class in topobench.nn.backbones.graph.identity_gnn) GaussianMixture (class in topobench.transforms.liftings.pointcloud2hypergraph.mogmst_lifting) GCN (class in topobench.nn.backbones.graph.identity_gnn) GCNConv (class in topobench.nn.backbones.cell.cccn) GeneralLaplacianBuilder (class in topobench.nn.backbones.graph.nsd_utils.inductive_discrete_models) (class in topobench.nn.backbones.graph.nsd_utils.laplacian_builders) generate_configuration_class() (in module topobench.transforms.liftings.graph2cell.discrete_configuration_complex_lifting) generate_membership_vectors() (TopoTune method), [1], [2] (TopoTune_OneHasse method), [1], [2] generate_zero_sparse_connectivity() (in module topobench.data.utils) (in module topobench.data.utils.utils) geom_gcn_url (Planetoid attribute) GeometricShapes (class in topobench.data.loaders.pointcloud.geometric_shapes) GeometricShapesDatasetLoader (class in topobench.data.loaders) (class in topobench.data.loaders.pointcloud) (class in topobench.data.loaders.pointcloud.geometric_shapes) get() (DataloadDataset method), [1], [2], [3], [4], [5] (Dataset method), [1], [2], [3], [4], [5] (DictConfig method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] (HydraConfig static method) (InMemoryDataset method), [1], [2], [3] (Mapping method) get_activation() (in module topobench.nn.backbones.combinatorial.gccn) (in module topobench.nn.backbones.combinatorial.gccn_onehasse) get_all_edge_attrs() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] get_all_maximal_simplices() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] get_all_tensor_attrs() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] get_boundaries() (SimplicialComplex static method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] get_buffer() (Module method) get_cache() (OmegaConf static method), [1], [2] get_cell_attributes() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] get_cell_data() (CellComplex method), [1], [2] get_cofaces() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] get_combination() (in module topobench.transforms.liftings.graph2hypergraph.kernel_lifting) get_combinatorial_complex_connectivity() (in module topobench.data.utils) (in module topobench.data.utils.utils) (in module topobench.transforms.liftings.graph2combinatorial.base) (in module topobench.transforms.liftings.hypergraph2combinatorial.base) (in module topobench.transforms.liftings.simplicial2combinatorial.coface_cc_lifting) get_complex_connectivity() (in module topobench.data.utils) (in module topobench.data.utils.io_utils) (in module topobench.data.utils.utils) (in module topobench.transforms.data_manipulations.redefine_simplicial_neighbourhoods) (in module topobench.transforms.liftings.graph2cell.base) (in module topobench.transforms.liftings.graph2simplicial.base) (in module topobench.transforms.liftings.pointcloud2simplicial.base) (in module topobench.transforms.liftings.pointcloud2simplicial.random_flag_complex) get_data_dir() (AbstractLoader method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] (ManualGraphDatasetLoader method), [1], [2] (MoleculeDatasetLoader method), [1], [2] (OGBGDatasetLoader method), [1], [2] get_default_metrics() (in module topobench.run) (in module topobench.utils.config_resolvers) get_default_trainer() (in module topobench.run) (in module topobench.utils.config_resolvers) get_default_transform() (in module topobench.run) (in module topobench.utils.config_resolvers) get_degree_histogram() (PNAConv static method) get_diag() (SparseTensor method) get_edge_attributes() (CellComplex method), [1], [2] get_edges_from_matrix() (SimplicialComplex static method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] get_extra_state() (Module method) get_feat_kernel() (in module topobench.transforms.liftings.graph2hypergraph.kernel_lifting) get_feature_dis() (in module topobench.nn.backbones.graph.graph_mlp) get_file_id_from_url() (in module topobench.data.utils.io_utils) get_filtration() (CellComplex method), [1], [2] get_flattened_channels() (in module topobench.run) (in module topobench.utils.config_resolvers) get_graph_kernel() (in module topobench.transforms.liftings.graph2hypergraph.kernel_lifting) get_idx_split() (PygGraphPropPredDataset method) get_laplacian() (in module topobench.transforms.data_manipulations.laplacian_encodings) get_linegraph() (CellComplex method), [1], [2] get_lock() (tqdm class method), [1], [2] get_lower_cells() (CofaceCCLifting method), [1] get_maximal_simplices_of_simplex() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] get_metric_value() (in module topobench.run) (in module topobench.utils) (in module topobench.utils.utils) get_monitor_metric() (in module topobench.run) (in module topobench.utils.config_resolvers) get_monitor_mode() (in module topobench.run) (in module topobench.utils.config_resolvers) get_nbhd_cache() (TopoTune method), [1], [2] get_node_attributes() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13]

get_non_relational_out_channels() (in module topobench.run) (in module topobench.utils.config_resolvers) get_param_size() (InductiveDiscreteBundleSheafDiffusion method), [1] get_parameter() (Module method) get_power_adj() (GraphMLPLoss method), [1] get_required_lifting() (in module topobench.run) (in module topobench.utils.config_resolvers) get_routes_from_neighborhoods() (in module topobench.data.utils) (in module topobench.data.utils.utils) (in module topobench.nn.backbones.combinatorial.gccn) (in module topobench.nn.backbones.combinatorial.gccn_onehasse) get_sheaf_model() (NSDEncoder method), [1], [2] get_simplex_attributes() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] get_star() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] get_submodule() (Module method) get_summary() (Dataset method), [1], [2], [3], [4], [5] get_type() (OmegaConf static method), [1], [2] GIN (class in topobench.nn.backbones.graph.identity_gnn) GINConv (class in topobench.nn.backbones.graph.gps) glob() (Path method), [1], [2], [3], [4], [5] global_rank (LightningModule property), [1] (Trainer property) global_step (LightningModule property), [1] (Trainer property) GNNWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.graph) (class in topobench.nn.wrappers.graph.gnn_wrapper) GPSConv (class in topobench.nn.backbones.graph.gps) GPSEncoder (class in topobench.nn.backbones) (class in topobench.nn.backbones.graph) (class in topobench.nn.backbones.graph.gps) Graph2CellLifting (class in topobench.transforms.liftings.graph2cell) (class in topobench.transforms.liftings.graph2cell.base) (class in topobench.transforms.liftings.graph2cell.cycle_lifting) (class in topobench.transforms.liftings.graph2cell.discrete_configuration_complex_lifting) Graph2CombinatorialLifting (class in topobench.transforms.liftings.graph2combinatorial) (class in topobench.transforms.liftings.graph2combinatorial.base) (class in topobench.transforms.liftings.graph2combinatorial.graph_induced_cc) Graph2HypergraphLifting (class in topobench.transforms.liftings.graph2hypergraph) (class in topobench.transforms.liftings.graph2hypergraph.base) (class in topobench.transforms.liftings.graph2hypergraph.expander_graph_lifting) (class in topobench.transforms.liftings.graph2hypergraph.forman_ricci_curvature_lifting) (class in topobench.transforms.liftings.graph2hypergraph.kernel_lifting) (class in topobench.transforms.liftings.graph2hypergraph.khop_lifting) (class in topobench.transforms.liftings.graph2hypergraph.knn_lifting) (class in topobench.transforms.liftings.graph2hypergraph.mapper_lifting) (class in topobench.transforms.liftings.graph2hypergraph.modularity_maximization_lifting) Graph2SimplicialLifting (class in topobench.transforms.liftings.graph2simplicial) (class in topobench.transforms.liftings.graph2simplicial.base) (class in topobench.transforms.liftings.graph2simplicial.clique_lifting) (class in topobench.transforms.liftings.graph2simplicial.dnd_lifting) (class in topobench.transforms.liftings.graph2simplicial.eccentricity_lifting) (class in topobench.transforms.liftings.graph2simplicial.graph_induced_lifting) (class in topobench.transforms.liftings.graph2simplicial.khop_lifting) (class in topobench.transforms.liftings.graph2simplicial.latentclique_lifting) (class in topobench.transforms.liftings.graph2simplicial.line_lifting) (class in topobench.transforms.liftings.graph2simplicial.neighborhood_complex_lifting) (class in topobench.transforms.liftings.graph2simplicial.vietoris_rips_lifting) graph_heat_kernel() (in module topobench.transforms.liftings.graph2hypergraph.kernel_lifting) graph_matern_kernel() (in module topobench.transforms.liftings.graph2hypergraph.kernel_lifting) graph_mlp_contrast_loss() (GraphMLPLoss method), [1] graph_skeleton() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] GraphLifting (class in topobench.transforms.liftings) (class in topobench.transforms.liftings.graph2cell.base) (class in topobench.transforms.liftings.graph2combinatorial.base) (class in topobench.transforms.liftings.graph2hypergraph.base) (class in topobench.transforms.liftings.graph2simplicial.base) (class in topobench.transforms.liftings.liftings) GraphMLP (class in topobench.nn.backbones) (class in topobench.nn.backbones.graph) (class in topobench.nn.backbones.graph.graph_mlp) GraphMLPLoss (class in topobench.loss.model) (class in topobench.loss.model.GraphMLPLoss) GraphMLPWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.graph) (class in topobench.nn.wrappers.graph.graph_mlp_wrapper) GraphNorm (class in topobench.nn.encoders.all_cell_encoder) GraphSAGE (class in topobench.nn.backbones.graph.identity_gnn) GraphTriangleInducedCC (class in topobench.transforms.liftings.graph2combinatorial) (class in topobench.transforms.liftings.graph2combinatorial.graph_induced_cc) group() (Path method), [1], [2], [3], [4], [5] GroupCombinatorialHomophily (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.group_homophily)

H

half() (Metric method) (Module method) (SparseTensor method) hardlink_to() (Path method), [1], [2], [3], [4], [5] has_download (Dataset property), [1], [2], [3], [4], [5] has_process (Dataset property), [1], [2], [3], [4], [5] has_resolver() (OmegaConf class method), [1], [2] has_value() (SparseTensor method) HeterophilousGraphDataset (class in topobench.data.loaders.graph.hetero_datasets) HeterophilousGraphDatasetLoader (class in topobench.data.loaders) (class in topobench.data.loaders.graph) (class in topobench.data.loaders.graph.hetero_datasets) higher_is_better (ExampleRegressionMetric attribute), [1] (Metric attribute) hodge_laplacian_matrix() (CellComplex method), [1], [2] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] home() (Path class method), [1], [2], [3], [4], [5] HydraConfig (class in topobench.utils.rich_utils) HyperEdge (class in topobench.transforms.liftings.simplicial2combinatorial.coface_cc_lifting) Hypergraph2CombinatorialLifting (class in topobench.transforms.liftings.hypergraph2combinatorial) (class in topobench.transforms.liftings.hypergraph2combinatorial.base) (class in topobench.transforms.liftings.hypergraph2combinatorial.universal_strict_lifting)

HypergraphDataset (class in topobench.data.datasets) (class in topobench.data.datasets.hypergraph_datasets) (class in topobench.data.loaders.hypergraph.hypergraph_dataset_loader) HypergraphDatasetLoader (class in topobench.data.loaders) (class in topobench.data.loaders.hypergraph) (class in topobench.data.loaders.hypergraph.hypergraph_dataset_loader) HypergraphFormanRicciCurvatureLifting (class in topobench.transforms.liftings.graph2hypergraph) (class in topobench.transforms.liftings.graph2hypergraph.forman_ricci_curvature_lifting) HypergraphKernelLifting (class in topobench.transforms.liftings.graph2hypergraph) (class in topobench.transforms.liftings.graph2hypergraph.kernel_lifting) HypergraphKHopLifting (class in topobench.transforms.liftings.graph2hypergraph) (class in topobench.transforms.liftings.graph2hypergraph.khop_lifting) HypergraphKNNLifting (class in topobench.transforms.liftings.graph2hypergraph) (class in topobench.transforms.liftings.graph2hypergraph.knn_lifting) HypergraphLifting (class in topobench.transforms.liftings) (class in topobench.transforms.liftings.hypergraph2combinatorial.base) (class in topobench.transforms.liftings.liftings) HypergraphWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.hypergraph) (class in topobench.nn.wrappers.hypergraph.hypergraph_wrapper)

I

Identity (class in topobench.transforms.feature_liftings) (class in topobench.transforms.feature_liftings.identity) IdentityGAT (class in topobench.nn.backbones) (class in topobench.nn.backbones.graph) (class in topobench.nn.backbones.graph.identity_gnn) IdentityGCN (class in topobench.nn.backbones) (class in topobench.nn.backbones.graph) (class in topobench.nn.backbones.graph.identity_gnn) IdentityGIN (class in topobench.nn.backbones) (class in topobench.nn.backbones.graph) (class in topobench.nn.backbones.graph.identity_gnn) IdentitySAGE (class in topobench.nn.backbones) (class in topobench.nn.backbones.graph) (class in topobench.nn.backbones.graph.identity_gnn) IdentityTransform (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.identity_transform) in_features (Linear attribute) incidence_matrix() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] index() (Sequence method) index_select() (Dataset method), [1], [2], [3], [4], [5] (SparseTensor method) index_select_nnz() (SparseTensor method) indices() (Dataset method), [1], [2], [3], [4], [5] InductiveDiscreteBundleSheafDiffusion (class in topobench.nn.backbones.graph.nsd) (class in topobench.nn.backbones.graph.nsd_utils.inductive_discrete_models) InductiveDiscreteDiagSheafDiffusion (class in topobench.nn.backbones.graph.nsd) (class in topobench.nn.backbones.graph.nsd_utils.inductive_discrete_models) InductiveDiscreteGeneralSheafDiffusion (class in topobench.nn.backbones.graph.nsd) (class in topobench.nn.backbones.graph.nsd_utils.inductive_discrete_models) infer_in_channels() (in module topobench.run) (in module topobench.utils.config_resolvers) infer_num_cell_dimensions() (in module topobench.run) (in module topobench.utils.config_resolvers) infer_topotune_num_cell_dimensions() (in module topobench.run) (in module topobench.utils.config_resolvers) InfereKNNConnectivity (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.infere_knn_connectivity) InfereRadiusConnectivity (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.infere_radius_connectivity) init_conv() (GAT method) (GCN method) (GIN method) (GraphSAGE method) init_module() (Trainer method) initialize_hydra() (in module topobench) (in module topobench.run) initialized() (HydraConfig static method) InMemoryDataset (class in topobench.data.datasets.citation_hypergraph_dataset) (class in topobench.data.datasets.hypergraph_datasets) (class in topobench.data.datasets.mantra_dataset) (class in topobench.data.datasets.us_county_demos_dataset) instance() (HydraConfig static method) instantiate_callbacks() (in module topobench.run) (in module topobench.utils) (in module topobench.utils.instantiators)

instantiate_loggers() (in module topobench.run) (in module topobench.utils) (in module topobench.utils.instantiators) instantiate_pre_transform() (PreProcessor method), [1], [2] int() (SparseTensor method) interrank_boundary_index() (in module topobench.nn.backbones.combinatorial.gccn) interrank_expand() (TopoTune method), [1], [2] interrank_gnn_forward() (TopoTune method), [1], [2] interrupted (Trainer property) intrarank_expand() (TopoTune method), [1], [2] intrarank_gnn_forward() (TopoTune method), [1], [2] ipu() (Module method) is_block_device() (Path method), [1], [2], [3], [4], [5] is_char_device() (Path method), [1], [2], [3], [4], [5] is_coalesced() (SparseTensor method) is_config() (OmegaConf static method), [1], [2] is_connected() (CellComplex method), [1], [2] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] is_cuda() (SparseTensor method) is_dict() (OmegaConf static method), [1], [2] is_differentiable (ExampleRegressionMetric attribute), [1] (Metric attribute) is_dir() (Path method), [1], [2], [3], [4], [5] is_edge_attr() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] is_fifo() (Path method), [1], [2], [3], [4], [5] is_file() (Path method), [1], [2], [3], [4], [5] is_floating_point() (SparseTensor method) is_global_zero (Trainer property) is_insertable_cycle() (CellComplex method), [1], [2] is_interpolation() (OmegaConf static method), [1], [2] is_last_batch (Trainer property) is_list() (OmegaConf static method), [1], [2] is_maximal() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] is_missing() (OmegaConf static method), [1], [2] is_mount() (Path method), [1], [2], [3], [4], [5] is_node_attr() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] is_pinned() (SparseTensor method) is_quadratic() (SparseTensor method) is_readonly() (OmegaConf static method), [1], [2] is_regular (CellComplex property), [1], [2] is_shared() (SparseTensor method) is_socket() (Path method), [1], [2], [3], [4], [5] is_struct() (OmegaConf static method), [1], [2] is_symlink() (Path method), [1], [2], [3], [4], [5] is_symmetric() (SparseTensor method) is_triangular_mesh() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] is_undirected() (in module topobench.transforms.liftings.liftings) is_valid() (DomainData method) items() (DictConfig method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] (Mapping method) (MetricCollection method) items_ex() (DictConfig method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] iterdir() (Path method), [1], [2], [3], [4], [5]

J

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

K

k_fold_split() (in module topobench.data.utils.split_utils) KeepOnlyConnectedComponent (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.keep_only_connected_component) KeepSelectedDataFields (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.keep_selected_data_fields)

keys() (DictConfig method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] (Mapping method) (MetricCollection method) kmeans() (ModularityMaximizationLifting method), [1] knn() (in module topobench.transforms.liftings.pointcloud2hypergraph.voronoi_lifting) knn_graph() (in module topobench.transforms.data_manipulations.infere_knn_connectivity)

L

laplace_beltrami_operator() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] LaplacianBuilder (class in topobench.nn.backbones.graph.nsd_utils.laplacian_builders) LapPE (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.laplacian_encodings) LargestConnectedComponents (class in topobench.transforms.data_manipulations.keep_only_connected_component) LatentCliqueLifting (class in topobench.transforms.liftings.graph2simplicial) (class in topobench.transforms.liftings.graph2simplicial.latentclique_lifting) LayerNorm (class in topobench.nn.backbones.graph.graph_mlp) lchmod() (Path method), [1], [2], [3], [4], [5] left_right_linear() (InductiveDiscreteBundleSheafDiffusion method), [1] (InductiveDiscreteGeneralSheafDiffusion method), [1] legacy_register_resolver() (OmegaConf static method), [1], [2] len() (DataloadDataset method), [1], [2], [3], [4], [5] (Dataset method), [1], [2], [3], [4], [5] (InMemoryDataset method), [1], [2], [3] lift_features() (Concatenation method), [1] (ProjectionSum method), [1] (Set method), [1] lift_topology() (AbstractLifting method), [1], [2] (AlphaComplexLifting method), [1] (CellCycleLifting method), [1] (CofaceCCLifting method), [1] (DiscreteConfigurationComplexLifting method), [1] (ExpanderGraphLifting method), [1] (GraphTriangleInducedCC method), [1] (HypergraphFormanRicciCurvatureLifting method), [1] (HypergraphKernelLifting method), [1] (HypergraphKHopLifting method), [1] (HypergraphKNNLifting method), [1] (LatentCliqueLifting method), [1] (MapperLifting method), [1] (ModularityMaximizationLifting method), [1] (MoGMSTLifting method), [1] (NeighborhoodComplexLifting method), [1] (PointNetLifting method), [1] (RandomFlagComplexLifting method), [1] (SimplicialCliqueLifting method), [1], [2] (SimplicialDnDLifting method), [1] (SimplicialEccentricityLifting method), [1] (SimplicialGraphInducedLifting method), [1] (SimplicialKHopLifting method), [1] (SimplicialLineLifting method), [1] (SimplicialVietorisRipsLifting method), [1] (UniversalStrictLifting method), [1] (VoronoiLifting method), [1] lightning_module (Trainer property) LightningDataModule (class in topobench.dataloader.dataloader) LightningModule (class in topobench.model.model) (class in topobench.run) Linear (class in topobench.nn.backbones.graph.graph_mlp) link_to() (Path method), [1], [2], [3], [4], [5] load() (AbstractLoader method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] (InMemoryDataset method), [1], [2], [3] (OmegaConf static method), [1], [2] (PreProcessor method), [1], [2] load_cell_complex_dataset() (in module topobench.data.utils) (in module topobench.data.utils.utils) load_coauthorship_hypergraph_splits() (in module topobench.data.utils) (in module topobench.data.utils.split_utils) load_dataset() (AbstractLoader method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] (CitationHypergraphDatasetLoader method), [1], [2] (GeometricShapesDatasetLoader method), [1], [2] (HeterophilousGraphDatasetLoader method), [1], [2] (HypergraphDatasetLoader method), [1], [2] (MantraSimplicialDatasetLoader method), [1], [2], [3], [4] (ManualGraphDatasetLoader method), [1], [2] (MoleculeDatasetLoader method), [1], [2] (OGBGDatasetLoader method), [1], [2] (PlanetoidDatasetLoader method), [1], [2] (TUDatasetLoader method), [1], [2] (USCountyDemosDatasetLoader method), [1], [2]

load_dataset_splits() (PreProcessor method), [1], [2] load_from_checkpoint() (LightningDataModule method) (LightningModule method), [1] load_hypergraph_content_dataset() (in module topobench.data.datasets.hypergraph_datasets) (in module topobench.data.utils) (in module topobench.data.utils.io_utils) load_hypergraph_pickle_dataset() (in module topobench.data.datasets.citation_hypergraph_dataset) (in module topobench.data.utils) (in module topobench.data.utils.io_utils) load_inductive_splits() (in module topobench.data.preprocessor.preprocessor) (in module topobench.data.utils) (in module topobench.data.utils.split_utils) load_manual_graph() (in module topobench.data.loaders.graph.manual_graph_dataset_loader) (in module topobench.data.utils) (in module topobench.data.utils.utils) load_manual_graph_second_structure() (in module topobench.data.utils.utils) load_manual_hypergraph() (in module topobench.data.utils.utils) load_manual_pointcloud() (in module topobench.data.utils.utils) load_manual_points() (in module topobench.data.utils.utils) load_manual_simplicial_complex() (in module topobench.data.utils.utils) load_mesh() (CellComplex class method), [1], [2] (SimplicialComplex class method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] load_simplicial_dataset() (in module topobench.data.utils) (in module topobench.data.utils.utils) load_state_dict() (Callback method), [1], [2] (LightningDataModule method) (ModelCheckpoint method) (Module method) load_transductive_splits() (in module topobench.data.preprocessor.preprocessor) (in module topobench.data.utils) (in module topobench.data.utils.split_utils) local_rank (LightningModule property), [1] (Trainer property) LocalConcatSheafLearner (class in topobench.nn.backbones.graph.nsd_utils.inductive_discrete_models) (class in topobench.nn.backbones.graph.nsd_utils.sheaf_models) log() (LightningModule method), [1] (RankedLogger method), [1], [2] log_dict() (LightningModule method), [1] log_dir (Trainer property) log_hyperparameters() (in module topobench.run) (in module topobench.utils) (in module topobench.utils.logging_utils) log_metrics() (TBModel method), [1] logged_metrics (Trainer property) Logger (class in topobench.run) (class in topobench.utils.instantiators) logger (LightningModule property), [1] (Trainer property) loggers (LightningModule property), [1] (Trainer property) logsumexp() (in module topobench.transforms.liftings.graph2simplicial.latentclique_lifting) long() (SparseTensor method) lr_scheduler_configs (Trainer property) lr_scheduler_step() (LightningModule method), [1] lr_schedulers() (LightningModule method), [1] lstat() (Path method), [1], [2], [3], [4], [5]

M

main() (in module topobench.run) make_hash() (in module topobench.data.preprocessor.preprocessor) (in module topobench.data.utils) (in module topobench.data.utils.utils) MantraDataset (class in topobench.data.datasets) (class in topobench.data.datasets.mantra_dataset) (class in topobench.data.loaders.graph.mantra_dataset) (class in topobench.data.loaders.simplicial.mantra_dataset_loader) MantraSimplicialDatasetLoader (class in topobench.data.loaders) (class in topobench.data.loaders.graph) (class in topobench.data.loaders.graph.mantra_dataset) (class in topobench.data.loaders.simplicial) (class in topobench.data.loaders.simplicial.mantra_dataset_loader) manual_backward() (LightningModule method), [1] ManualGraphDatasetLoader (class in topobench.data.loaders) (class in topobench.data.loaders.graph) (class in topobench.data.loaders.graph.manual_graph_dataset_loader) MapperCover (class in topobench.transforms.liftings.graph2hypergraph.mapper_lifting) MapperLifting (class in topobench.transforms.liftings.graph2hypergraph) (class in topobench.transforms.liftings.graph2hypergraph.mapper_lifting) Mapping (class in topobench.utils.pylogger) masked_copy() (OmegaConf static method), [1], [2] masked_select() (SparseTensor method) masked_select_nnz() (SparseTensor method) matmul() (SparseTensor method) max() (SparseTensor method) max_epochs (Trainer property) max_steps (Trainer property) maxdim (CellComplex property), [1], [2] (SimplicialComplex property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] maybe_regular_expander() (in module topobench.transforms.liftings.graph2hypergraph.expander_graph_lifting) mean() (SparseTensor method) mean_value (MeanMetric attribute) MeanDegConv (class in topobench.nn.backbones) (class in topobench.nn.backbones.hypergraph) (class in topobench.nn.backbones.hypergraph.edgnn) MeanMetric (class in topobench.model.model) merge() (OmegaConf static method), [1], [2] merge_state() (Metric method) mergesp() (in module topobench.nn.backbones.graph.nsd_utils.laplace) (in module topobench.nn.backbones.graph.nsd_utils.laplacian_builders) message() (GCNConv method) (GINConv method) (PNAConv method) message_and_aggregate() (GCNConv method) (GINConv method) MessagePassingHomophily (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.mp_homophily) Metric (class in topobench.evaluator.metrics.example) metric_state (Metric property) (MetricCollection property) MetricCollection (class in topobench.evaluator.evaluator) min() (SparseTensor method) min_epochs (Trainer property) min_steps (Trainer property) minimum_spanning_tree() (in module topobench.transforms.liftings.pointcloud2hypergraph.mogmst_lifting) missing_keys() (OmegaConf static method), [1], [2] mkdir() (Path method), [1], [2], [3], [4], [5] MLP (class in topobench.nn.backbones) Mlp (class in topobench.nn.backbones) (class in topobench.nn.backbones.graph) (class in topobench.nn.backbones.graph.graph_mlp) MLP (class in topobench.nn.backbones.non_relational) (class in topobench.nn.backbones.non_relational.mlp) MLPBackbone (in module topobench.nn.readouts.mlp_readout) MLPReadout (class in topobench.nn.readouts) (class in topobench.nn.readouts.mlp_readout) model (Trainer property) model_step() (TBModel method), [1] ModelCheckpoint (class in topobench.callbacks.best_epoch_metrics) modularity_matrix() (ModularityMaximizationLifting method), [1] ModularityMaximizationLifting (class in topobench.transforms.liftings.graph2hypergraph) (class in topobench.transforms.liftings.graph2hypergraph.modularity_maximization_lifting) module topobench topobench.callbacks topobench.callbacks.best_epoch_metrics topobench.callbacks.timer_callback topobench.data topobench.data.datasets topobench.data.datasets.citation_hypergraph_dataset topobench.data.datasets.hypergraph_datasets topobench.data.datasets.mantra_dataset topobench.data.datasets.us_county_demos_dataset topobench.data.loaders topobench.data.loaders.base topobench.data.loaders.graph topobench.data.loaders.graph.hetero_datasets topobench.data.loaders.graph.mantra_dataset topobench.data.loaders.graph.manual_graph_dataset_loader topobench.data.loaders.graph.modecule_datasets topobench.data.loaders.graph.ogbg_datasets topobench.data.loaders.graph.planetoid_datasets topobench.data.loaders.graph.tu_datasets topobench.data.loaders.graph.us_county_demos_dataset_loader topobench.data.loaders.hypergraph topobench.data.loaders.hypergraph.citation_hypergraph_dataset_loader topobench.data.loaders.hypergraph.hypergraph_dataset_loader topobench.data.loaders.pointcloud topobench.data.loaders.pointcloud.geometric_shapes topobench.data.loaders.simplicial topobench.data.loaders.simplicial.mantra_dataset_loader topobench.data.preprocessor topobench.data.preprocessor.preprocessor topobench.data.utils topobench.data.utils.io_utils topobench.data.utils.split_utils topobench.data.utils.utils topobench.dataloader topobench.dataloader.dataload_dataset topobench.dataloader.dataloader topobench.dataloader.utils topobench.evaluator topobench.evaluator.base topobench.evaluator.evaluator topobench.evaluator.metrics topobench.evaluator.metrics.example topobench.loss topobench.loss.base topobench.loss.dataset topobench.loss.dataset.DatasetLoss topobench.loss.loss topobench.loss.model topobench.loss.model.DGMLoss topobench.loss.model.GraphMLPLoss topobench.model topobench.model.model topobench.nn topobench.nn.backbones topobench.nn.backbones.cell topobench.nn.backbones.cell.cccn topobench.nn.backbones.combinatorial topobench.nn.backbones.combinatorial.gccn topobench.nn.backbones.combinatorial.gccn_onehasse topobench.nn.backbones.graph topobench.nn.backbones.graph.gps topobench.nn.backbones.graph.graph_mlp topobench.nn.backbones.graph.identity_gnn topobench.nn.backbones.graph.nsd topobench.nn.backbones.graph.nsd_utils topobench.nn.backbones.graph.nsd_utils.inductive_discrete_models topobench.nn.backbones.graph.nsd_utils.laplace topobench.nn.backbones.graph.nsd_utils.laplacian_builders topobench.nn.backbones.graph.nsd_utils.orthogonal topobench.nn.backbones.graph.nsd_utils.sheaf_base topobench.nn.backbones.graph.nsd_utils.sheaf_models topobench.nn.backbones.hypergraph topobench.nn.backbones.hypergraph.edgnn topobench.nn.backbones.non_relational topobench.nn.backbones.non_relational.mlp topobench.nn.backbones.simplicial topobench.nn.backbones.simplicial.sccnn topobench.nn.encoders topobench.nn.encoders.all_cell_encoder topobench.nn.encoders.base topobench.nn.encoders.dgm_encoder topobench.nn.encoders.flat_encoder topobench.nn.encoders.kdgm topobench.nn.readouts topobench.nn.readouts.base topobench.nn.readouts.identical topobench.nn.readouts.mlp_readout topobench.nn.readouts.propagate_signal_down topobench.nn.wrappers topobench.nn.wrappers.base topobench.nn.wrappers.cell topobench.nn.wrappers.cell.can_wrapper topobench.nn.wrappers.cell.cccn_wrapper topobench.nn.wrappers.cell.ccxn_wrapper topobench.nn.wrappers.cell.cwn_wrapper topobench.nn.wrappers.combinatorial topobench.nn.wrappers.combinatorial.tune_wrapper topobench.nn.wrappers.graph topobench.nn.wrappers.graph.gnn_wrapper topobench.nn.wrappers.graph.graph_mlp_wrapper topobench.nn.wrappers.hypergraph topobench.nn.wrappers.hypergraph.hypergraph_wrapper topobench.nn.wrappers.pointcloud topobench.nn.wrappers.pointcloud.pointcloud_wrapper topobench.nn.wrappers.simplicial topobench.nn.wrappers.simplicial.san_wrapper topobench.nn.wrappers.simplicial.sccn_wrapper topobench.nn.wrappers.simplicial.sccnn_wrapper topobench.nn.wrappers.simplicial.scn_wrapper topobench.optimizer topobench.optimizer.base topobench.optimizer.optimizer topobench.run topobench.transforms topobench.transforms.data_manipulations topobench.transforms.data_manipulations.calculate_simplicial_curvature topobench.transforms.data_manipulations.equal_gaus_features topobench.transforms.data_manipulations.group_homophily topobench.transforms.data_manipulations.identity_transform topobench.transforms.data_manipulations.infere_knn_connectivity topobench.transforms.data_manipulations.infere_radius_connectivity topobench.transforms.data_manipulations.keep_only_connected_component topobench.transforms.data_manipulations.keep_selected_data_fields topobench.transforms.data_manipulations.laplacian_encodings topobench.transforms.data_manipulations.mp_homophily topobench.transforms.data_manipulations.node_degrees topobench.transforms.data_manipulations.node_features_to_float topobench.transforms.data_manipulations.one_hot_degree_features topobench.transforms.data_manipulations.positional_and_structural_encodings topobench.transforms.data_manipulations.random_walk_encodings topobench.transforms.data_manipulations.redefine_simplicial_neighbourhoods topobench.transforms.data_transform topobench.transforms.feature_liftings topobench.transforms.feature_liftings.concatenation topobench.transforms.feature_liftings.identity topobench.transforms.feature_liftings.projection_sum topobench.transforms.feature_liftings.set topobench.transforms.liftings topobench.transforms.liftings.base topobench.transforms.liftings.graph2cell topobench.transforms.liftings.graph2cell.base topobench.transforms.liftings.graph2cell.cycle_lifting topobench.transforms.liftings.graph2cell.discrete_configuration_complex_lifting topobench.transforms.liftings.graph2combinatorial topobench.transforms.liftings.graph2combinatorial.base topobench.transforms.liftings.graph2combinatorial.graph_induced_cc topobench.transforms.liftings.graph2hypergraph topobench.transforms.liftings.graph2hypergraph.base topobench.transforms.liftings.graph2hypergraph.expander_graph_lifting topobench.transforms.liftings.graph2hypergraph.forman_ricci_curvature_lifting topobench.transforms.liftings.graph2hypergraph.kernel_lifting topobench.transforms.liftings.graph2hypergraph.khop_lifting topobench.transforms.liftings.graph2hypergraph.knn_lifting topobench.transforms.liftings.graph2hypergraph.mapper_lifting topobench.transforms.liftings.graph2hypergraph.modularity_maximization_lifting topobench.transforms.liftings.graph2simplicial topobench.transforms.liftings.graph2simplicial.base topobench.transforms.liftings.graph2simplicial.clique_lifting topobench.transforms.liftings.graph2simplicial.dnd_lifting topobench.transforms.liftings.graph2simplicial.eccentricity_lifting topobench.transforms.liftings.graph2simplicial.graph_induced_lifting topobench.transforms.liftings.graph2simplicial.khop_lifting topobench.transforms.liftings.graph2simplicial.latentclique_lifting topobench.transforms.liftings.graph2simplicial.line_lifting topobench.transforms.liftings.graph2simplicial.neighborhood_complex_lifting topobench.transforms.liftings.graph2simplicial.vietoris_rips_lifting topobench.transforms.liftings.hypergraph2combinatorial topobench.transforms.liftings.hypergraph2combinatorial.base topobench.transforms.liftings.hypergraph2combinatorial.universal_strict_lifting topobench.transforms.liftings.liftings topobench.transforms.liftings.pointcloud2hypergraph topobench.transforms.liftings.pointcloud2hypergraph.base topobench.transforms.liftings.pointcloud2hypergraph.mogmst_lifting topobench.transforms.liftings.pointcloud2hypergraph.pointnet_lifting topobench.transforms.liftings.pointcloud2hypergraph.voronoi_lifting topobench.transforms.liftings.pointcloud2simplicial topobench.transforms.liftings.pointcloud2simplicial.alpha_complex_lifting topobench.transforms.liftings.pointcloud2simplicial.base topobench.transforms.liftings.pointcloud2simplicial.random_flag_complex topobench.transforms.liftings.simplicial2combinatorial topobench.transforms.liftings.simplicial2combinatorial.base topobench.transforms.liftings.simplicial2combinatorial.coface_cc_lifting topobench.utils topobench.utils.config_resolvers topobench.utils.instantiators topobench.utils.logging_utils topobench.utils.pylogger topobench.utils.rich_utils topobench.utils.utils

Module (class in topobench.nn.backbones.graph.nsd) modules() (Module method) MoGMSTLifting (class in topobench.transforms.liftings.pointcloud2hypergraph) (class in topobench.transforms.liftings.pointcloud2hypergraph.mogmst_lifting) MoleculeDatasetLoader (class in topobench.data.loaders) (class in topobench.data.loaders.graph) (class in topobench.data.loaders.graph.modecule_datasets) monitor (tqdm attribute), [1], [2] monitor_interval (tqdm attribute), [1], [2] moveto() (tqdm method), [1], [2] mul() (SparseTensor method) mul_() (SparseTensor method) mul_nnz() (SparseTensor method) mul_nnz_() (SparseTensor method) multiprocessing_context (DataLoader property)

N

name (LightningDataModule attribute) named_buffers() (Module method) named_children() (Module method) named_modules() (Module method) named_parameters() (Module method) narrow() (SparseTensor method) NeighborhoodComplexLifting (class in topobench.transforms.liftings.graph2simplicial) (class in topobench.transforms.liftings.graph2simplicial.neighborhood_complex_lifting) neighbors() (CellComplex method), [1], [2] nnz() (SparseTensor method) node_rank (Trainer property) node_stores (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] node_to_all_cell_adjacnecy_matrix() (CellComplex method), [1], [2] node_to_all_cell_incidence_matrix() (CellComplex method), [1], [2] NodeDegrees (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.node_degrees) NodeFeaturesToFloat (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.node_features_to_float) nodes (CellComplex property), [1], [2] (CombinatorialComplex property), [1], [2], [3], [4] (SimplicialComplex property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] nodes_search() (in module topobench.transforms.liftings.graph2simplicial.vietoris_rips_lifting) NoReadOut (class in topobench.nn.readouts) (class in topobench.nn.readouts.identical) normalization_resolver() (in module topobench.nn.backbones.non_relational.mlp) normalize_matrix() (SCNWrapper method), [1], [2] normalized_laplacian_matrix() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] normalized_shape (LayerNorm attribute) NormConnectionLaplacianBuilder (class in topobench.nn.backbones.graph.nsd_utils.inductive_discrete_models) (class in topobench.nn.backbones.graph.nsd_utils.laplacian_builders) NSDEncoder (class in topobench.nn.backbones) (class in topobench.nn.backbones.graph) (class in topobench.nn.backbones.graph.nsd)

num_classes (Dataset property), [1], [2], [3], [4], [5] (InMemoryDataset property), [1], [2], [3] (PygGraphPropPredDataset property) num_devices (Trainer property) num_edge_attributes (TUDataset property) num_edge_features (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] (Dataset property), [1], [2], [3], [4], [5] num_edge_labels (TUDataset property) num_edge_types (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] num_faces (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] num_features (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] (Dataset property), [1], [2], [3], [4], [5] num_node_attributes (TUDataset property) num_node_features (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] (Dataset property), [1], [2], [3], [4], [5] num_node_labels (TUDataset property) num_node_types (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] num_nodes (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] (Trainer property) num_predict_batches (Trainer property) num_sanity_val_batches (Trainer property) num_test_batches (Trainer property) num_training_batches (Trainer property) num_val_batches (Trainer property) num_workers (DataLoader attribute) number_of_cells() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] number_of_edges() (CellComplex method), [1], [2] number_of_nodes() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] numel() (SparseTensor method)

O

OGBGDatasetLoader (class in topobench.data.loaders) (class in topobench.data.loaders.graph) (class in topobench.data.loaders.graph.ogbg_datasets) OmegaConf (class in topobench.run) (class in topobench.utils.logging_utils) (class in topobench.utils.rich_utils) on_after_backward() (Callback method), [1], [2] on_before_backward() (Callback method), [1], [2] on_before_optimizer_step() (Callback method), [1], [2] on_before_zero_grad() (Callback method), [1], [2] on_exception() (Callback method), [1], [2] (LightningDataModule method) on_fit_end() (Callback method), [1], [2] on_fit_start() (Callback method), [1], [2] on_gpu (LightningModule property), [1] on_load_checkpoint() (Callback method), [1], [2] on_predict_batch_end() (Callback method), [1], [2] on_predict_batch_start() (Callback method), [1], [2] on_predict_end() (Callback method), [1], [2] on_predict_epoch_end() (Callback method), [1], [2] on_predict_epoch_start() (Callback method), [1], [2] on_predict_start() (Callback method), [1], [2] on_sanity_check_end() (Callback method), [1], [2] on_sanity_check_start() (Callback method), [1], [2] on_save_checkpoint() (Callback method), [1], [2] on_test_batch_end() (Callback method), [1], [2] (PipelineTimer method), [1] on_test_batch_start() (Callback method), [1], [2] (PipelineTimer method), [1] on_test_end() (Callback method), [1], [2] on_test_epoch_end() (Callback method), [1], [2] (PipelineTimer method), [1] (TBModel method), [1] on_test_epoch_start() (Callback method), [1], [2] (PipelineTimer method), [1] (TBModel method), [1] on_test_start() (Callback method), [1], [2] on_train_batch_end() (Callback method), [1], [2] (ModelCheckpoint method) (PipelineTimer method), [1] on_train_batch_start() (Callback method), [1], [2] (PipelineTimer method), [1] on_train_end() (BestEpochMetricsCallback method), [1] (Callback method), [1], [2] (PipelineTimer method), [1]

on_train_epoch_end() (BestEpochMetricsCallback method), [1] (Callback method), [1], [2] (ModelCheckpoint method) (PipelineTimer method), [1] (TBModel method), [1] on_train_epoch_start() (Callback method), [1], [2] (PipelineTimer method), [1] (TBModel method), [1] on_train_start() (BestEpochMetricsCallback method), [1] (Callback method), [1], [2] (ModelCheckpoint method) on_val_epoch_start() (TBModel method), [1] on_validation_batch_end() (Callback method), [1], [2] (PipelineTimer method), [1] on_validation_batch_start() (Callback method), [1], [2] (PipelineTimer method), [1] on_validation_end() (Callback method), [1], [2] (ModelCheckpoint method) on_validation_epoch_end() (BestEpochMetricsCallback method), [1] (Callback method), [1], [2] (PipelineTimer method), [1] (TBModel method), [1] on_validation_epoch_start() (Callback method), [1], [2] (PipelineTimer method), [1] (TBModel method), [1] on_validation_start() (Callback method), [1], [2] one_cell_curvature() (CalculateSimplicialCurvature method), [1] one_hot() (in module topobench.transforms.data_manipulations.one_hot_degree_features) OneHotDegreeFeatures (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.one_hot_degree_features) open() (Path method), [1], [2], [3], [4], [5] open_dict() (in module topobench.utils.rich_utils) optimizer_step() (LightningModule method), [1] optimizer_zero_grad() (LightningModule method), [1] optimizers (Trainer property) optimizers() (LightningModule method), [1] order() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] Orthogonal (class in topobench.nn.backbones.graph.nsd_utils.laplacian_builders) (class in topobench.nn.backbones.graph.nsd_utils.orthogonal) out_features (Linear attribute) owner() (Path method), [1], [2], [3], [4], [5]

P

pairwise_distances() (in module topobench.transforms.liftings.pointcloud2hypergraph.mogmst_lifting) pairwise_euclidean_distances() (in module topobench.nn.encoders.kdgm) pairwise_poincare_distances() (in module topobench.nn.encoders.kdgm) pandas() (tqdm class method), [1], [2] Parameter (class in topobench.nn.backbones.simplicial.sccnn) parameters() (Module method) parse_qs() (in module topobench.data.utils.io_utils) partition() (SparseTensor method) Path (class in topobench.data.loaders.base) (class in topobench.data.loaders.graph.manual_graph_dataset_loader) (class in topobench.data.loaders.graph.modecule_datasets) (class in topobench.data.loaders.graph.ogbg_datasets) (class in topobench.data.loaders.graph.us_county_demos_dataset_loader) (class in topobench.utils.rich_utils) PerformerAttention (class in topobench.nn.backbones.graph.gps) permutations (class in topobench.transforms.liftings.graph2cell.discrete_configuration_complex_lifting) permute() (SparseTensor method) persistent() (Metric method) (MetricCollection method) pin_memory (DataLoader attribute) pin_memory() (SparseTensor method) pin_memory_device (DataLoader attribute) PipelineTimer (class in topobench.callbacks) (class in topobench.callbacks.timer_callback) PlainMLP (class in topobench.nn.backbones) (class in topobench.nn.backbones.hypergraph) (class in topobench.nn.backbones.hypergraph.edgnn) Planetoid (class in topobench.data.loaders.graph.planetoid_datasets) PlanetoidDatasetLoader (class in topobench.data.loaders) (class in topobench.data.loaders.graph) (class in topobench.data.loaders.graph.planetoid_datasets) plot() (MeanMetric method) (Metric method) (MetricCollection method) plot_legend_name (Metric attribute) plot_lower_bound (Metric attribute) plot_upper_bound (Metric attribute) PNAConv (class in topobench.nn.backbones.graph.gps) PointCloud2HypergraphLifting (class in topobench.transforms.liftings.pointcloud2hypergraph) (class in topobench.transforms.liftings.pointcloud2hypergraph.base) (class in topobench.transforms.liftings.pointcloud2hypergraph.mogmst_lifting) (class in topobench.transforms.liftings.pointcloud2hypergraph.pointnet_lifting) (class in topobench.transforms.liftings.pointcloud2hypergraph.voronoi_lifting) PointCloud2SimplicialLifting (class in topobench.transforms.liftings.pointcloud2simplicial) (class in topobench.transforms.liftings.pointcloud2simplicial.alpha_complex_lifting) (class in topobench.transforms.liftings.pointcloud2simplicial.base) (class in topobench.transforms.liftings.pointcloud2simplicial.random_flag_complex) PointCloudLifting (class in topobench.transforms.liftings) (class in topobench.transforms.liftings.liftings) (class in topobench.transforms.liftings.pointcloud2hypergraph.base) (class in topobench.transforms.liftings.pointcloud2simplicial.base) PointcloudWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.pointcloud) (class in topobench.nn.wrappers.pointcloud.pointcloud_wrapper) PointNetLifting (class in topobench.transforms.liftings.pointcloud2hypergraph) (class in topobench.transforms.liftings.pointcloud2hypergraph.pointnet_lifting) pop() (DictConfig method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] pos (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] precision (Trainer property) precision_plugin (Trainer property) predict() (Trainer method) predict_dataloaders (Trainer property)

predict_step() (LightningModule method), [1] predicting (Trainer property) prefetch_factor (DataLoader attribute) prepare_data_per_node (LightningDataModule attribute) (LightningModule attribute) (TBDataloader attribute), [1], [2] PreProcessor (class in topobench.data.preprocessor) (class in topobench.data.preprocessor.preprocessor) (class in topobench.run) print() (LightningModule method), [1] (Trainer method) print_config_tree() (in module topobench.utils) (in module topobench.utils.rich_utils) print_summary() (Dataset method), [1], [2], [3], [4], [5] process() (AQSOL method) (CitationHypergraphDataset method), [1], [2] (Dataset method), [1], [2], [3], [4], [5] (GeometricShapes method) (HeterophilousGraphDataset method) (HypergraphDataset method), [1], [2] (MantraDataset method), [1], [2], [3] (Planetoid method) (PreProcessor method), [1], [2] (PygGraphPropPredDataset method) (TUDataset method) (USCountyDemosDataset method), [1], [2] (ZINC method) process_outputs() (TBModel method), [1] process_set() (GeometricShapes method) processed_dir (CitationHypergraphDataset property), [1], [2] (Dataset property), [1], [2], [3], [4], [5] (HeterophilousGraphDataset property) (HypergraphDataset property), [1], [2] (MantraDataset property), [1], [2], [3] (Planetoid property) (PreProcessor property), [1], [2] (TUDataset property) (USCountyDemosDataset property), [1], [2] (ZINC property) processed_file_names (AQSOL property) (CitationHypergraphDataset property), [1], [2] (Dataset property), [1], [2], [3], [4], [5] (GeometricShapes property) (HeterophilousGraphDataset property) (HypergraphDataset property), [1], [2] (InMemoryDataset property), [1], [2], [3] (MantraDataset property), [1], [2], [3] (Planetoid property) (PreProcessor property), [1], [2] (PygGraphPropPredDataset property) (TUDataset property) (USCountyDemosDataset property), [1], [2] (ZINC property) processed_paths (Dataset property), [1], [2], [3], [4], [5] progress_bar_callback (Trainer property) progress_bar_metrics (Trainer property) ProjectionSum (class in topobench.transforms.feature_liftings) (class in topobench.transforms.feature_liftings.projection_sum) Prompt (class in topobench.utils.rich_utils) PropagateSignalDown (class in topobench.nn.readouts) (class in topobench.nn.readouts.propagate_signal_down) PygGraphPropPredDataset (class in topobench.data.loaders.graph.ogbg_datasets)

R

radius() (in module topobench.transforms.liftings.pointcloud2hypergraph.pointnet_lifting) radius_graph() (in module topobench.transforms.data_manipulations.infere_radius_connectivity) random_splitting() (in module topobench.data.utils.split_utils) random_walk() (SparseTensor method) RandomFlagComplexLifting (class in topobench.transforms.liftings.pointcloud2simplicial) (class in topobench.transforms.liftings.pointcloud2simplicial.random_flag_complex) rank (HyperEdge property) rank_prefixed_message() (in module topobench.utils.pylogger) rank_zero_only() (in module topobench.utils.logging_utils) (in module topobench.utils.pylogger) (in module topobench.utils.rich_utils) RankedLogger (class in topobench.run) (class in topobench.utils) (class in topobench.utils.pylogger) raw_dir (CitationHypergraphDataset property), [1], [2] (Dataset property), [1], [2], [3], [4], [5] (HeterophilousGraphDataset property) (HypergraphDataset property), [1], [2] (MantraDataset property), [1], [2], [3] (Planetoid property) (TUDataset property) (USCountyDemosDataset property), [1], [2] raw_file_names (AQSOL property) RAW_FILE_NAMES (CitationHypergraphDataset attribute), [1], [2] raw_file_names (CitationHypergraphDataset property), [1], [2] (Dataset property), [1], [2], [3], [4], [5] (GeometricShapes property) (HeterophilousGraphDataset property) RAW_FILE_NAMES (HypergraphDataset attribute), [1], [2] raw_file_names (HypergraphDataset property), [1], [2] (InMemoryDataset property), [1], [2], [3] RAW_FILE_NAMES (MantraDataset attribute), [1], [2], [3] raw_file_names (MantraDataset property), [1], [2], [3] (Planetoid property) (PygGraphPropPredDataset property) (TUDataset property) RAW_FILE_NAMES (USCountyDemosDataset attribute), [1], [2] raw_file_names (USCountyDemosDataset property), [1], [2] (ZINC property) raw_paths (Dataset property), [1], [2], [3], [4], [5] read_bytes() (Path method), [1], [2], [3], [4], [5] read_ndim_manifolds() (in module topobench.data.datasets.mantra_dataset) (in module topobench.data.utils.io_utils) read_text() (Path method), [1], [2], [3], [4], [5] read_us_county_demos() (in module topobench.data.datasets.us_county_demos_dataset) (in module topobench.data.utils) (in module topobench.data.utils.io_utils) readlink() (Path method), [1], [2], [3], [4], [5] received_sigterm (Trainer property) RedefineSimplicialNeighbourhoods (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.redefine_simplicial_neighbourhoods) redraw_projection_matrix() (PerformerAttention method) redraw_projections() (RedrawProjection method), [1], [2] RedrawProjection (class in topobench.nn.backbones) (class in topobench.nn.backbones.graph) (class in topobench.nn.backbones.graph.gps) refresh() (tqdm method), [1], [2] register_backward_hook() (Module method) register_buffer() (Module method) register_forward_hook() (Module method) register_forward_pre_hook() (Module method)

register_full_backward_hook() (Module method) register_full_backward_pre_hook() (Module method) register_load_state_dict_post_hook() (Module method) register_module() (Module method) register_new_resolver() (OmegaConf static method), [1], [2] register_parameter() (Module method) register_resolver() (OmegaConf static method), [1], [2] register_state_dict_pre_hook() (Module method) remove_cell() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] remove_cells() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] remove_diag() (SparseTensor method) remove_equivalent_cells() (CellComplex method), [1], [2] remove_maximal_simplex() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] remove_node() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] remove_nodes() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] remove_singletons() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] rename() (Path method), [1], [2], [3], [4], [5] rename_pos_to_x() (in module topobench.data.loaders.pointcloud.geometric_shapes) replace() (Path method), [1], [2], [3], [4], [5] requires_grad() (SparseTensor method) requires_grad_() (Module method) (SparseTensor method) reset() (AbstractEvaluator method), [1], [2] (Metric method) (MetricCollection method) (TBEvaluator method), [1] (tqdm method), [1], [2] reset_parameters() (customMLP method), [1], [2] (EDGNN method), [1], [2] (EquivSetConv method), [1], [2] (GCNConv method) (GINConv method) (GPSConv method) (GraphNorm method) (JumpLinkConv method), [1], [2] (LayerNorm method) (Linear method) (MeanDegConv method), [1], [2] (PlainMLP method), [1], [2] (PNAConv method) (SCCNNLayer method), [1], [2] residual_connection() (AbstractWrapper method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] resolve() (OmegaConf static method), [1], [2] (Path method), [1], [2], [3], [4], [5] response_type (Prompt attribute) restrict_to_cells() (CellComplex method), [1], [2] restrict_to_nodes() (CellComplex method), [1], [2] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] restrict_to_simplices() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] reverse_cuthill_mckee() (SparseTensor method) rglob() (Path method), [1], [2], [3], [4], [5] rmdir() (Path method), [1], [2], [3], [4], [5] run() (in module topobench.run) RWSE (class in topobench.transforms.data_manipulations) (class in topobench.transforms.data_manipulations.random_walk_encodings)

S

saint_subgraph() (SparseTensor method) samefile() (Path method), [1], [2], [3], [4], [5] sample() (SparseTensor method) sample_adj() (SparseTensor method) sample_without_replacement() (DGM_d method), [1] sampler (DataLoader attribute) sanity_checking (Trainer property) SANWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.simplicial) (class in topobench.nn.wrappers.simplicial.san_wrapper) save() (InMemoryDataset class method), [1], [2], [3] (OmegaConf static method), [1], [2] save_checkpoint() (Trainer method) save_dir (Logger property), [1] save_transform_parameters() (PreProcessor method), [1], [2] scalar_normalise() (LaplacianBuilder method) scaler (Trainer property) scatter() (in module topobench.nn.readouts.base) (in module topobench.nn.readouts.mlp_readout) scatter_add() (in module topobench.nn.backbones.graph.nsd_utils.laplacian_builders) SCCNNCustom (class in topobench.nn.backbones) (class in topobench.nn.backbones.simplicial) (class in topobench.nn.backbones.simplicial.sccnn) SCCNNLayer (class in topobench.nn.backbones) (class in topobench.nn.backbones.simplicial) (class in topobench.nn.backbones.simplicial.sccnn) SCCNNWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.simplicial) (class in topobench.nn.wrappers.simplicial.sccnn_wrapper) SCCNWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.simplicial) (class in topobench.nn.wrappers.simplicial.sccn_wrapper) SCNWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.simplicial) (class in topobench.nn.wrappers.simplicial.scn_wrapper) select() (OmegaConf static method), [1], [2] (SparseTensor method) select_neighborhoods_of_interest() (in module topobench.data.utils) (in module topobench.data.utils.utils) Sequence (class in topobench.utils.rich_utils) Set (class in topobench.transforms.feature_liftings) (class in topobench.transforms.feature_liftings.set) set_cache() (OmegaConf static method), [1], [2] set_cell_attributes() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] set_cell_data() (CellComplex method), [1], [2] set_config() (HydraConfig method) set_description() (tqdm method), [1], [2] set_description_str() (tqdm method), [1], [2] set_diag() (SparseTensor method) set_dtype() (Metric method) (MetricCollection method) set_edge_attributes() (CellComplex method), [1], [2] set_extra_state() (Module method) set_filtration() (CellComplex method), [1], [2] set_L() (SheafLearner method) set_lock() (tqdm class method), [1], [2] set_node_attributes() (CellComplex method), [1], [2] set_postfix() (tqdm method), [1], [2] set_postfix_str() (tqdm method), [1], [2] set_processed_data_dir() (PreProcessor method), [1], [2] set_readonly() (OmegaConf static method), [1], [2] set_simplex_attributes() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] set_struct() (OmegaConf static method), [1], [2] set_value() (SparseTensor method) set_value_() (SparseTensor method) setdefault() (DictConfig method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] setup() (Callback method), [1], [2] (ModelCheckpoint method) (TBModel method), [1] shape (CellComplex property), [1], [2] (CombinatorialComplex property), [1], [2], [3], [4] (SimplicialComplex property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] share_memory() (Module method) share_memory_() (SparseTensor method) SheafDiffusion (class in topobench.nn.backbones.graph.nsd_utils.inductive_discrete_models) (class in topobench.nn.backbones.graph.nsd_utils.sheaf_base) SheafLearner (class in topobench.nn.backbones.graph.nsd_utils.sheaf_models) short() (SparseTensor method) shuffle() (Dataset method), [1], [2], [3], [4], [5] simplices (SimplicialComplex property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] Simplicial2CombinatorialLifting (class in topobench.transforms.liftings.simplicial2combinatorial) (class in topobench.transforms.liftings.simplicial2combinatorial.base) (class in topobench.transforms.liftings.simplicial2combinatorial.coface_cc_lifting) simplicial_closure_of_hypergraph() (SimplicialComplex class method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] SimplicialCliqueLifting (class in topobench.transforms.liftings.graph2simplicial) (class in topobench.transforms.liftings.graph2simplicial.clique_lifting) (class in topobench.transforms.liftings.graph2simplicial.latentclique_lifting)

SimplicialComplex (class in topobench.data.utils.io_utils) (class in topobench.data.utils.utils) (class in topobench.transforms.liftings.graph2simplicial.base) (class in topobench.transforms.liftings.graph2simplicial.clique_lifting) (class in topobench.transforms.liftings.graph2simplicial.dnd_lifting) (class in topobench.transforms.liftings.graph2simplicial.eccentricity_lifting) (class in topobench.transforms.liftings.graph2simplicial.graph_induced_lifting) (class in topobench.transforms.liftings.graph2simplicial.khop_lifting) (class in topobench.transforms.liftings.graph2simplicial.line_lifting) (class in topobench.transforms.liftings.graph2simplicial.neighborhood_complex_lifting) (class in topobench.transforms.liftings.graph2simplicial.vietoris_rips_lifting) (class in topobench.transforms.liftings.pointcloud2simplicial.alpha_complex_lifting) (class in topobench.transforms.liftings.pointcloud2simplicial.base) (class in topobench.transforms.liftings.pointcloud2simplicial.random_flag_complex) SimplicialDnDLifting (class in topobench.transforms.liftings.graph2simplicial) (class in topobench.transforms.liftings.graph2simplicial.dnd_lifting) SimplicialEccentricityLifting (class in topobench.transforms.liftings.graph2simplicial) (class in topobench.transforms.liftings.graph2simplicial.eccentricity_lifting) SimplicialGraphInducedLifting (class in topobench.transforms.liftings.graph2simplicial) (class in topobench.transforms.liftings.graph2simplicial.graph_induced_lifting) SimplicialKHopLifting (class in topobench.transforms.liftings.graph2simplicial) (class in topobench.transforms.liftings.graph2simplicial.khop_lifting) SimplicialLifting (class in topobench.transforms.liftings) (class in topobench.transforms.liftings.liftings) (class in topobench.transforms.liftings.simplicial2combinatorial.base) SimplicialLineLifting (class in topobench.transforms.liftings.graph2simplicial) (class in topobench.transforms.liftings.graph2simplicial.line_lifting) SimplicialVietorisRipsLifting (class in topobench.transforms.liftings.graph2simplicial) (class in topobench.transforms.liftings.graph2simplicial.vietoris_rips_lifting) singletons() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] size() (CellComplex method), [1], [2] (SparseTensor method) sizes() (SparseTensor method) skeleton() (CellComplex method), [1], [2] (CombinatorialComplex method), [1], [2], [3], [4] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] slices (CitationHypergraphDataset attribute) (HypergraphDataset attribute) (MantraDataset attribute), [1] (USCountyDemosDataset attribute) sparse_reshape() (SparseTensor method) sparse_resize() (SparseTensor method) sparse_size() (SparseTensor method) sparse_sizes() (SparseTensor method) SPARSE_THRESHOLD (AddLaplacianEigenvectorPE attribute) SparseTensor (class in topobench.dataloader.utils) sparsity() (SparseTensor method) split() (StratifiedKFold method) split_url (ZINC attribute) spmm() (SparseTensor method) spspmm() (SparseTensor method) STARTING_VERSION (ModelCheckpoint attribute) stat() (Path method), [1], [2], [3], [4], [5] state_dict() (Callback method), [1], [2] (LightningDataModule method) (Metric method) (ModelCheckpoint method) (Module method) (TBDataloader method), [1], [2] state_key (Callback property), [1], [2] (ModelCheckpoint property) status_printer() (tqdm static method), [1], [2] storage (SparseTensor attribute) stores (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] stores_as() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] strategy (Trainer property) StratifiedKFold (class in topobench.data.utils.split_utils) strict_loading (LightningModule property), [1] structured() (OmegaConf static method), [1], [2] subgraph() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] sum() (SparseTensor method) sum_squared_error (ExampleRegressionMetric attribute), [1] supports_edge_attr (GAT attribute) (GCN attribute) (GIN attribute) (GraphSAGE attribute) supports_edge_weight (GAT attribute) (GCN attribute) (GIN attribute) (GraphSAGE attribute) supports_norm_batch (GAT attribute) (GCN attribute) (GIN attribute) (GraphSAGE attribute) SVDFeatureReduction (class in topobench.transforms.liftings.graph2hypergraph.mapper_lifting) symlink_to() (Path method), [1], [2], [3], [4], [5] sync() (Metric method) sync_context() (Metric method)

T

t() (SparseTensor method) T_destination (Module attribute) task_wrapper() (in module topobench.run) (in module topobench.utils) (in module topobench.utils.utils) TBDataloader (class in topobench.dataloader) (class in topobench.dataloader.dataloader) (class in topobench.run) TBEvaluator (class in topobench.evaluator) (class in topobench.evaluator.evaluator) TBLoss (class in topobench.loss) (class in topobench.loss.loss) TBModel (class in topobench.model) (class in topobench.model.model) TBOptimizer (class in topobench.optimizer) (class in topobench.optimizer.optimizer) teardown() (Callback method), [1], [2] (TBDataloader method), [1], [2] test() (Trainer method) test_dataloader() (TBDataloader method), [1], [2] test_dataloaders (Trainer property) test_step() (LightningModule method), [1] (TBModel method), [1] testing (Trainer property) time (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] timeout (DataLoader attribute) to() (InMemoryDataset method), [1], [2], [3] (Module method) (SparseTensor method) to_cell_complex() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] to_colored_hypergraph() (CellComplex method), [1], [2] to_combinatorial_complex() (CellComplex method), [1], [2] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] to_container() (OmegaConf static method), [1], [2] to_data_list() (in module topobench.dataloader.utils) to_datapipe() (Dataset method), [1], [2], [3], [4], [5] to_dense() (SparseTensor method) to_device() (SparseTensor method) to_dict() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] to_empty() (Module method) to_hasse_graph() (CellComplex method), [1], [2] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] to_heterogeneous() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] to_hypergraph() (CellComplex method), [1], [2] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] to_namedtuple() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] to_object() (OmegaConf static method), [1], [2] to_on_disk_dataset() (InMemoryDataset method), [1], [2], [3] to_onnx() (LightningModule method), [1] to_scipy() (SparseTensor method) to_scipy_sparse_matrix() (in module topobench.transforms.data_manipulations.laplacian_encodings) to_spharapy() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] to_symmetric() (SparseTensor method) to_torch_sparse_coo_tensor() (SparseTensor method) to_torch_sparse_csc_tensor() (SparseTensor method) to_torch_sparse_csr_tensor() (SparseTensor method) to_torchscript() (LightningModule method), [1] to_trimesh() (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] to_undirected() (in module topobench.nn.backbones.graph.nsd) (in module topobench.transforms.liftings.graph2simplicial.neighborhood_complex_lifting) (in module topobench.transforms.liftings.liftings) to_yaml() (ModelCheckpoint method) (OmegaConf static method), [1], [2] toggle_optimizer() (LightningModule method), [1] topobench module topobench.callbacks module topobench.callbacks.best_epoch_metrics module topobench.callbacks.timer_callback module topobench.data module topobench.data.datasets module topobench.data.datasets.citation_hypergraph_dataset module topobench.data.datasets.hypergraph_datasets module topobench.data.datasets.mantra_dataset module topobench.data.datasets.us_county_demos_dataset module topobench.data.loaders module topobench.data.loaders.base module topobench.data.loaders.graph module topobench.data.loaders.graph.hetero_datasets module topobench.data.loaders.graph.mantra_dataset module topobench.data.loaders.graph.manual_graph_dataset_loader module topobench.data.loaders.graph.modecule_datasets module topobench.data.loaders.graph.ogbg_datasets module topobench.data.loaders.graph.planetoid_datasets module topobench.data.loaders.graph.tu_datasets module topobench.data.loaders.graph.us_county_demos_dataset_loader module topobench.data.loaders.hypergraph module topobench.data.loaders.hypergraph.citation_hypergraph_dataset_loader module topobench.data.loaders.hypergraph.hypergraph_dataset_loader module topobench.data.loaders.pointcloud module topobench.data.loaders.pointcloud.geometric_shapes module topobench.data.loaders.simplicial module topobench.data.loaders.simplicial.mantra_dataset_loader module topobench.data.preprocessor module topobench.data.preprocessor.preprocessor module topobench.data.utils module topobench.data.utils.io_utils module topobench.data.utils.split_utils module topobench.data.utils.utils module topobench.dataloader module topobench.dataloader.dataload_dataset module topobench.dataloader.dataloader module topobench.dataloader.utils module topobench.evaluator module topobench.evaluator.base module topobench.evaluator.evaluator module topobench.evaluator.metrics module topobench.evaluator.metrics.example module topobench.loss module topobench.loss.base module topobench.loss.dataset module topobench.loss.dataset.DatasetLoss module topobench.loss.loss module topobench.loss.model module topobench.loss.model.DGMLoss module topobench.loss.model.GraphMLPLoss module topobench.model module topobench.model.model module topobench.nn module topobench.nn.backbones module topobench.nn.backbones.cell module topobench.nn.backbones.cell.cccn module topobench.nn.backbones.combinatorial module topobench.nn.backbones.combinatorial.gccn module topobench.nn.backbones.combinatorial.gccn_onehasse module topobench.nn.backbones.graph module topobench.nn.backbones.graph.gps module topobench.nn.backbones.graph.graph_mlp module topobench.nn.backbones.graph.identity_gnn module topobench.nn.backbones.graph.nsd module topobench.nn.backbones.graph.nsd_utils module topobench.nn.backbones.graph.nsd_utils.inductive_discrete_models module topobench.nn.backbones.graph.nsd_utils.laplace module topobench.nn.backbones.graph.nsd_utils.laplacian_builders module topobench.nn.backbones.graph.nsd_utils.orthogonal module topobench.nn.backbones.graph.nsd_utils.sheaf_base module topobench.nn.backbones.graph.nsd_utils.sheaf_models module topobench.nn.backbones.hypergraph module topobench.nn.backbones.hypergraph.edgnn module topobench.nn.backbones.non_relational module topobench.nn.backbones.non_relational.mlp module topobench.nn.backbones.simplicial module topobench.nn.backbones.simplicial.sccnn module topobench.nn.encoders module topobench.nn.encoders.all_cell_encoder module topobench.nn.encoders.base module topobench.nn.encoders.dgm_encoder module topobench.nn.encoders.flat_encoder module topobench.nn.encoders.kdgm module topobench.nn.readouts module topobench.nn.readouts.base module topobench.nn.readouts.identical module topobench.nn.readouts.mlp_readout module

topobench.nn.readouts.propagate_signal_down module topobench.nn.wrappers module topobench.nn.wrappers.base module topobench.nn.wrappers.cell module topobench.nn.wrappers.cell.can_wrapper module topobench.nn.wrappers.cell.cccn_wrapper module topobench.nn.wrappers.cell.ccxn_wrapper module topobench.nn.wrappers.cell.cwn_wrapper module topobench.nn.wrappers.combinatorial module topobench.nn.wrappers.combinatorial.tune_wrapper module topobench.nn.wrappers.graph module topobench.nn.wrappers.graph.gnn_wrapper module topobench.nn.wrappers.graph.graph_mlp_wrapper module topobench.nn.wrappers.hypergraph module topobench.nn.wrappers.hypergraph.hypergraph_wrapper module topobench.nn.wrappers.pointcloud module topobench.nn.wrappers.pointcloud.pointcloud_wrapper module topobench.nn.wrappers.simplicial module topobench.nn.wrappers.simplicial.san_wrapper module topobench.nn.wrappers.simplicial.sccn_wrapper module topobench.nn.wrappers.simplicial.sccnn_wrapper module topobench.nn.wrappers.simplicial.scn_wrapper module topobench.optimizer module topobench.optimizer.base module topobench.optimizer.optimizer module topobench.run module topobench.transforms module topobench.transforms.data_manipulations module topobench.transforms.data_manipulations.calculate_simplicial_curvature module topobench.transforms.data_manipulations.equal_gaus_features module topobench.transforms.data_manipulations.group_homophily module topobench.transforms.data_manipulations.identity_transform module topobench.transforms.data_manipulations.infere_knn_connectivity module topobench.transforms.data_manipulations.infere_radius_connectivity module topobench.transforms.data_manipulations.keep_only_connected_component module topobench.transforms.data_manipulations.keep_selected_data_fields module topobench.transforms.data_manipulations.laplacian_encodings module topobench.transforms.data_manipulations.mp_homophily module topobench.transforms.data_manipulations.node_degrees module topobench.transforms.data_manipulations.node_features_to_float module topobench.transforms.data_manipulations.one_hot_degree_features module topobench.transforms.data_manipulations.positional_and_structural_encodings module topobench.transforms.data_manipulations.random_walk_encodings module topobench.transforms.data_manipulations.redefine_simplicial_neighbourhoods module topobench.transforms.data_transform module topobench.transforms.feature_liftings module topobench.transforms.feature_liftings.concatenation module topobench.transforms.feature_liftings.identity module topobench.transforms.feature_liftings.projection_sum module topobench.transforms.feature_liftings.set module topobench.transforms.liftings module topobench.transforms.liftings.base module topobench.transforms.liftings.graph2cell module topobench.transforms.liftings.graph2cell.base module topobench.transforms.liftings.graph2cell.cycle_lifting module topobench.transforms.liftings.graph2cell.discrete_configuration_complex_lifting module topobench.transforms.liftings.graph2combinatorial module topobench.transforms.liftings.graph2combinatorial.base module topobench.transforms.liftings.graph2combinatorial.graph_induced_cc module topobench.transforms.liftings.graph2hypergraph module topobench.transforms.liftings.graph2hypergraph.base module topobench.transforms.liftings.graph2hypergraph.expander_graph_lifting module topobench.transforms.liftings.graph2hypergraph.forman_ricci_curvature_lifting module topobench.transforms.liftings.graph2hypergraph.kernel_lifting module topobench.transforms.liftings.graph2hypergraph.khop_lifting module topobench.transforms.liftings.graph2hypergraph.knn_lifting module topobench.transforms.liftings.graph2hypergraph.mapper_lifting module topobench.transforms.liftings.graph2hypergraph.modularity_maximization_lifting module topobench.transforms.liftings.graph2simplicial module topobench.transforms.liftings.graph2simplicial.base module topobench.transforms.liftings.graph2simplicial.clique_lifting module topobench.transforms.liftings.graph2simplicial.dnd_lifting module topobench.transforms.liftings.graph2simplicial.eccentricity_lifting module topobench.transforms.liftings.graph2simplicial.graph_induced_lifting module topobench.transforms.liftings.graph2simplicial.khop_lifting module topobench.transforms.liftings.graph2simplicial.latentclique_lifting module topobench.transforms.liftings.graph2simplicial.line_lifting module topobench.transforms.liftings.graph2simplicial.neighborhood_complex_lifting module topobench.transforms.liftings.graph2simplicial.vietoris_rips_lifting module topobench.transforms.liftings.hypergraph2combinatorial module topobench.transforms.liftings.hypergraph2combinatorial.base module topobench.transforms.liftings.hypergraph2combinatorial.universal_strict_lifting module topobench.transforms.liftings.liftings module topobench.transforms.liftings.pointcloud2hypergraph module topobench.transforms.liftings.pointcloud2hypergraph.base module topobench.transforms.liftings.pointcloud2hypergraph.mogmst_lifting module topobench.transforms.liftings.pointcloud2hypergraph.pointnet_lifting module topobench.transforms.liftings.pointcloud2hypergraph.voronoi_lifting module topobench.transforms.liftings.pointcloud2simplicial module topobench.transforms.liftings.pointcloud2simplicial.alpha_complex_lifting module topobench.transforms.liftings.pointcloud2simplicial.base module topobench.transforms.liftings.pointcloud2simplicial.random_flag_complex module topobench.transforms.liftings.simplicial2combinatorial module topobench.transforms.liftings.simplicial2combinatorial.base module topobench.transforms.liftings.simplicial2combinatorial.coface_cc_lifting module topobench.utils module topobench.utils.config_resolvers module topobench.utils.instantiators module topobench.utils.logging_utils module topobench.utils.pylogger module topobench.utils.rich_utils module topobench.utils.utils module TopoTune (class in topobench.nn.backbones) (class in topobench.nn.backbones.combinatorial) (class in topobench.nn.backbones.combinatorial.gccn) TopoTune_OneHasse (class in topobench.nn.backbones) (class in topobench.nn.backbones.combinatorial) (class in topobench.nn.backbones.combinatorial.gccn_onehasse) total (ExampleRegressionMetric attribute), [1] touch() (Path method), [1], [2], [3], [4], [5] ToUndirected (class in topobench.transforms.liftings.graph2hypergraph.mapper_lifting) tqdm (class in topobench.transforms.liftings.graph2simplicial.khop_lifting) (class in topobench.transforms.liftings.graph2simplicial.neighborhood_complex_lifting) (class in topobench.transforms.liftings.graph2simplicial.vietoris_rips_lifting) (in module topobench.transforms.liftings.graph2simplicial.latentclique_lifting) train() (Module method) train_dataloader (Trainer property) train_dataloader() (TBDataloader method), [1], [2] Trainer (class in topobench.run) trainer (LightningModule property), [1] training (LightningModule attribute) (Module attribute) (Trainer property) training_step() (LightningModule method), [1] (TBModel method), [1] TUDataset (class in topobench.data.loaders.graph.tu_datasets) TUDatasetLoader (class in topobench.data.loaders) (class in topobench.data.loaders.graph) (class in topobench.data.loaders.graph.tu_datasets) TuneWrapper (class in topobench.nn.wrappers) (class in topobench.nn.wrappers.combinatorial) (class in topobench.nn.wrappers.combinatorial.tune_wrapper) two_cell_curvature() (CalculateSimplicialCurvature method), [1] type() (Metric method) (Module method) (SparseTensor method) type_as() (SparseTensor method)

U

unfreeze() (LightningModule method), [1] UniversalStrictLifting (class in topobench.transforms.liftings.hypergraph2combinatorial) (class in topobench.transforms.liftings.hypergraph2combinatorial.universal_strict_lifting) unlink() (Path method), [1], [2], [3], [4], [5] unpause() (tqdm method), [1], [2] unsafe_merge() (OmegaConf static method), [1], [2] unsync() (Metric method) untoggle_optimizer() (LightningModule method), [1] up_laplacian_matrix() (CellComplex method), [1], [2] (SimplicialComplex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] update() (AbstractEvaluator method), [1], [2] (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] (ExampleRegressionMetric method), [1] (MeanMetric method) (Metric method) (MetricCollection method) (OmegaConf static method), [1], [2] (SCCNNLayer method), [1], [2] (TBEvaluator method), [1] (tqdm method), [1], [2]

update_called (Metric property) update_count (Metric property) url (AQSOL attribute) (GeometricShapes attribute) (HeterophilousGraphDataset attribute) (Planetoid attribute) (TUDataset attribute) (ZINC attribute) urlparse() (in module topobench.data.utils.io_utils) URLS (CitationHypergraphDataset attribute), [1], [2] (HypergraphDataset attribute), [1], [2] (MantraDataset attribute), [1], [2], [3] (USCountyDemosDataset attribute), [1], [2] USCountyDemosDataset (class in topobench.data.datasets) (class in topobench.data.datasets.us_county_demos_dataset) (class in topobench.data.loaders.graph.us_county_demos_dataset_loader) USCountyDemosDatasetLoader (class in topobench.data.loaders) (class in topobench.data.loaders.graph) (class in topobench.data.loaders.graph.us_county_demos_dataset_loader)

V

val_dataloader() (TBDataloader method), [1], [2] val_dataloaders (Trainer property) validate() (Data method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] (Trainer method) validating (Trainer property) validation_step() (LightningModule method), [1] (TBModel method), [1]

values() (Mapping method) (MetricCollection method) Vertex (in module topobench.transforms.liftings.graph2cell.discrete_configuration_complex_lifting) VoronoiLifting (class in topobench.transforms.liftings.pointcloud2hypergraph) (class in topobench.transforms.liftings.pointcloud2hypergraph.voronoi_lifting)

W

weight (LayerNorm attribute) (Linear attribute), [1] (MeanMetric attribute) world_size (Trainer property)

wrapattr() (tqdm class method), [1], [2] write() (tqdm class method), [1], [2] write_bytes() (Path method), [1], [2], [3], [4], [5] write_text() (Path method), [1], [2], [3], [4], [5]

X

x (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14]

xpu() (Module method)

Y

y (Data property), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14]

Z

zero_cell_curvature() (CalculateSimplicialCurvature method), [1]

zero_grad() (Module method) ZINC (class in topobench.data.loaders.graph.modecule_datasets)