topobench package#
TopoBench: A library for benchmarking of topological models.
- initialize_hydra()#
Initialize Hydra when main is not an option (e.g. tests).
- Returns:
- DictConfig
A DictConfig object containing the config tree.
Subpackages#
- topobench.callbacks package
- topobench.data package
- Subpackages
- topobench.data.datasets package
- topobench.data.loaders package
AbstractLoaderCitationHypergraphDatasetLoaderGeometricShapesDatasetLoaderHeterophilousGraphDatasetLoaderHypergraphDatasetLoaderMantraSimplicialDatasetLoaderManualGraphDatasetLoaderMoleculeDatasetLoaderOGBGDatasetLoaderPlanetoidDatasetLoaderTUDatasetLoaderUSCountyDemosDatasetLoader- Subpackages
- Submodules
- topobench.data.preprocessor package
- topobench.data.utils package
data2simplicial()download_file_from_drive()ensure_serializable()generate_zero_sparse_connectivity()get_combinatorial_complex_connectivity()get_complex_connectivity()get_routes_from_neighborhoods()load_cell_complex_dataset()load_coauthorship_hypergraph_splits()load_hypergraph_content_dataset()load_hypergraph_pickle_dataset()load_inductive_splits()load_manual_graph()load_simplicial_dataset()load_transductive_splits()make_hash()read_us_county_demos()select_neighborhoods_of_interest()- Submodules
- Subpackages
- topobench.dataloader package
- topobench.evaluator package
- topobench.loss package
- topobench.model package
TBModelTBModel.__init__()TBModel.configure_optimizers()TBModel.forward()TBModel.log_metrics()TBModel.model_step()TBModel.on_test_epoch_end()TBModel.on_test_epoch_start()TBModel.on_train_epoch_end()TBModel.on_train_epoch_start()TBModel.on_val_epoch_start()TBModel.on_validation_epoch_end()TBModel.on_validation_epoch_start()TBModel.process_outputs()TBModel.setup()TBModel.test_step()TBModel.training_step()TBModel.validation_step()
- Submodules
- topobench.nn package
- topobench.optimizer package
- topobench.transforms package
- Subpackages
- topobench.transforms.data_manipulations package
CalculateSimplicialCurvatureCombinedPSEsEqualGausFeaturesGroupCombinatorialHomophilyIdentityTransformInfereKNNConnectivityInfereRadiusConnectivityKeepOnlyConnectedComponentKeepSelectedDataFieldsLapPEMessagePassingHomophilyNodeDegreesNodeFeaturesToFloatOneHotDegreeFeaturesRWSERedefineSimplicialNeighbourhoods- Submodules
- topobench.transforms.feature_liftings package
- topobench.transforms.liftings package
- topobench.transforms.data_manipulations package
- Submodules
- Subpackages
- topobench.utils package
RankedLoggerenforce_tags()extras()get_metric_value()instantiate_callbacks()instantiate_loggers()log_hyperparameters()print_config_tree()task_wrapper()- Submodules
- topobench.utils.config_resolvers module
check_pses_in_transforms()get_default_metrics()get_default_trainer()get_default_transform()get_flattened_channels()get_monitor_metric()get_monitor_mode()get_non_relational_out_channels()get_required_lifting()infer_in_channels()infer_num_cell_dimensions()infer_topotune_num_cell_dimensions()
- topobench.utils.instantiators module
- topobench.utils.logging_utils module
- topobench.utils.pylogger module
- topobench.utils.rich_utils module
- topobench.utils.utils module
- topobench.utils.config_resolvers module
Submodules#
- topobench.run module
AnyCallbackCallback.load_state_dict()Callback.on_after_backward()Callback.on_before_backward()Callback.on_before_optimizer_step()Callback.on_before_zero_grad()Callback.on_exception()Callback.on_fit_end()Callback.on_fit_start()Callback.on_load_checkpoint()Callback.on_predict_batch_end()Callback.on_predict_batch_start()Callback.on_predict_end()Callback.on_predict_epoch_end()Callback.on_predict_epoch_start()Callback.on_predict_start()Callback.on_sanity_check_end()Callback.on_sanity_check_start()Callback.on_save_checkpoint()Callback.on_test_batch_end()Callback.on_test_batch_start()Callback.on_test_end()Callback.on_test_epoch_end()Callback.on_test_epoch_start()Callback.on_test_start()Callback.on_train_batch_end()Callback.on_train_batch_start()Callback.on_train_end()Callback.on_train_epoch_end()Callback.on_train_epoch_start()Callback.on_train_start()Callback.on_validation_batch_end()Callback.on_validation_batch_start()Callback.on_validation_end()Callback.on_validation_epoch_end()Callback.on_validation_epoch_start()Callback.on_validation_start()Callback.setup()Callback.state_dict()Callback.teardown()Callback.state_key
DictConfigLightningModuleLightningModule.__init__()LightningModule.all_gather()LightningModule.backward()LightningModule.clip_gradients()LightningModule.configure_callbacks()LightningModule.configure_gradient_clipping()LightningModule.configure_optimizers()LightningModule.forward()LightningModule.freeze()LightningModule.load_from_checkpoint()LightningModule.log()LightningModule.log_dict()LightningModule.lr_scheduler_step()LightningModule.lr_schedulers()LightningModule.manual_backward()LightningModule.optimizer_step()LightningModule.optimizer_zero_grad()LightningModule.optimizers()LightningModule.predict_step()LightningModule.print()LightningModule.test_step()LightningModule.to_onnx()LightningModule.to_torchscript()LightningModule.toggle_optimizer()LightningModule.training_step()LightningModule.unfreeze()LightningModule.untoggle_optimizer()LightningModule.validation_step()LightningModule.CHECKPOINT_HYPER_PARAMS_KEYLightningModule.CHECKPOINT_HYPER_PARAMS_NAMELightningModule.CHECKPOINT_HYPER_PARAMS_TYPELightningModule.allow_zero_length_dataloader_with_multiple_devicesLightningModule.automatic_optimizationLightningModule.current_epochLightningModule.device_meshLightningModule.example_input_arrayLightningModule.fabricLightningModule.global_rankLightningModule.global_stepLightningModule.local_rankLightningModule.loggerLightningModule.loggersLightningModule.on_gpuLightningModule.prepare_data_per_nodeLightningModule.strict_loadingLightningModule.trainerLightningModule.training
LoggerOmegaConfOmegaConf.__init__()OmegaConf.clear_cache()OmegaConf.clear_resolver()OmegaConf.clear_resolvers()OmegaConf.copy_cache()OmegaConf.create()OmegaConf.from_cli()OmegaConf.from_dotlist()OmegaConf.get_cache()OmegaConf.get_type()OmegaConf.has_resolver()OmegaConf.is_config()OmegaConf.is_dict()OmegaConf.is_interpolation()OmegaConf.is_list()OmegaConf.is_missing()OmegaConf.is_readonly()OmegaConf.is_struct()OmegaConf.legacy_register_resolver()OmegaConf.load()OmegaConf.masked_copy()OmegaConf.merge()OmegaConf.missing_keys()OmegaConf.register_new_resolver()OmegaConf.register_resolver()OmegaConf.resolve()OmegaConf.save()OmegaConf.select()OmegaConf.set_cache()OmegaConf.set_readonly()OmegaConf.set_struct()OmegaConf.structured()OmegaConf.to_container()OmegaConf.to_object()OmegaConf.to_yaml()OmegaConf.unsafe_merge()OmegaConf.update()
PreProcessorRankedLoggerTBDataloaderTrainerTrainer.__init__()Trainer.fit()Trainer.init_module()Trainer.predict()Trainer.print()Trainer.save_checkpoint()Trainer.test()Trainer.validate()Trainer.acceleratorTrainer.callback_metricsTrainer.checkpoint_callbackTrainer.checkpoint_callbacksTrainer.ckpt_pathTrainer.current_epochTrainer.default_root_dirTrainer.device_idsTrainer.distributed_sampler_kwargsTrainer.early_stopping_callbackTrainer.early_stopping_callbacksTrainer.enable_validationTrainer.estimated_stepping_batchesTrainer.evaluatingTrainer.global_rankTrainer.global_stepTrainer.interruptedTrainer.is_global_zeroTrainer.is_last_batchTrainer.lightning_moduleTrainer.local_rankTrainer.log_dirTrainer.logged_metricsTrainer.loggerTrainer.loggersTrainer.lr_scheduler_configsTrainer.max_epochsTrainer.max_stepsTrainer.min_epochsTrainer.min_stepsTrainer.modelTrainer.node_rankTrainer.num_devicesTrainer.num_nodesTrainer.num_predict_batchesTrainer.num_sanity_val_batchesTrainer.num_test_batchesTrainer.num_training_batchesTrainer.num_val_batchesTrainer.optimizersTrainer.precisionTrainer.precision_pluginTrainer.predict_dataloadersTrainer.predictingTrainer.progress_bar_callbackTrainer.progress_bar_metricsTrainer.received_sigtermTrainer.sanity_checkingTrainer.scalerTrainer.strategyTrainer.test_dataloadersTrainer.testingTrainer.train_dataloaderTrainer.trainingTrainer.val_dataloadersTrainer.validatingTrainer.world_size
count_number_of_parameters()extras()get_default_metrics()get_default_trainer()get_default_transform()get_flattened_channels()get_metric_value()get_monitor_metric()get_monitor_mode()get_non_relational_out_channels()get_required_lifting()infer_in_channels()infer_num_cell_dimensions()infer_topotune_num_cell_dimensions()initialize_hydra()instantiate_callbacks()instantiate_loggers()log_hyperparameters()main()run()task_wrapper()