topobench package

Subpackages

• topobench.callbacks package
  • Submodules
  • topobench.callbacks.timer_callback module
    • PipelineTimer
      • PipelineTimer.on_test_batch_end()
      • PipelineTimer.on_test_batch_start()
      • PipelineTimer.on_test_epoch_end()
      • PipelineTimer.on_test_epoch_start()
      • PipelineTimer.on_train_batch_end()
      • PipelineTimer.on_train_batch_start()
      • PipelineTimer.on_train_end()
      • PipelineTimer.on_train_epoch_end()
      • PipelineTimer.on_train_epoch_start()
      • PipelineTimer.on_validation_batch_end()
      • PipelineTimer.on_validation_batch_start()
      • PipelineTimer.on_validation_epoch_end()
      • PipelineTimer.on_validation_epoch_start()
  • Module contents
• topobench.data package
  • Subpackages
    • topobench.data.datasets package
      • Submodules
      • topobench.data.datasets.citation_hypergaph_dataset module
      • topobench.data.datasets.mantra_dataset module
      • topobench.data.datasets.us_county_demos_dataset module
      • Module contents
    • topobench.data.loaders package
      • Subpackages
      • Submodules
      • topobench.data.loaders.base module
      • Module contents
    • topobench.data.preprocessor package
      • Submodules
      • topobench.data.preprocessor.preprocessor module
      • Module contents
    • topobench.data.utils package
      • Submodules
      • topobench.data.utils.io_utils module
      • topobench.data.utils.split_utils module
      • topobench.data.utils.utils module
      • Module contents
  • Module contents
• topobench.dataloader package
  • Submodules
  • topobench.dataloader.dataload_dataset module
    • DataloadDataset
      • DataloadDataset.get()
      • DataloadDataset.len()
  • topobench.dataloader.dataloader module
    • TBDataloader
      • TBDataloader.state_dict()
      • TBDataloader.teardown()
      • TBDataloader.test_dataloader()
      • TBDataloader.train_dataloader()
      • TBDataloader.val_dataloader()
  • topobench.dataloader.utils module
    • DomainData
      • DomainData.is_valid()
    • collate_fn()
    • to_data_list()
  • Module contents
    • DataloadDataset
      • DataloadDataset.get()
      • DataloadDataset.len()
    • TBDataloader
      • TBDataloader.state_dict()
      • TBDataloader.teardown()
      • TBDataloader.test_dataloader()
      • TBDataloader.train_dataloader()
      • TBDataloader.val_dataloader()
• topobench.evaluator package
  • Subpackages
    • topobench.evaluator.metrics package
      • Submodules
      • topobench.evaluator.metrics.example module
      • Module contents
  • Submodules
  • topobench.evaluator.base module
    • AbstractEvaluator
      • AbstractEvaluator.compute()
      • AbstractEvaluator.reset()
      • AbstractEvaluator.update()
  • topobench.evaluator.evaluator module
    • TBEvaluator
      • TBEvaluator.compute()
      • TBEvaluator.reset()
      • TBEvaluator.update()
  • Module contents
    • AbstractEvaluator
      • AbstractEvaluator.compute()
      • AbstractEvaluator.reset()
      • AbstractEvaluator.update()
    • TBEvaluator
      • TBEvaluator.compute()
      • TBEvaluator.reset()
      • TBEvaluator.update()
• topobench.loss package
  • Subpackages
    • topobench.loss.dataset package
      • Submodules
      • topobench.loss.dataset.DatasetLoss module
      • Module contents
    • topobench.loss.model package
      • Submodules
      • topobench.loss.model.DGMLoss module
      • topobench.loss.model.GraphMLPLoss module
      • Module contents
  • Submodules
  • topobench.loss.base module
    • AbstractLoss
      • AbstractLoss.forward()
  • topobench.loss.loss module
    • TBLoss
      • TBLoss.forward()
  • Module contents
    • TBLoss
      • TBLoss.forward()
• topobench.model package
  • Submodules
  • topobench.model.model module
    • TBModel
      • 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()
  • Module contents
    • TBModel
      • 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()
• topobench.nn package
  • Subpackages
    • topobench.nn.backbones package
      • Subpackages
      • Module contents
    • topobench.nn.encoders package
      • Submodules
      • topobench.nn.encoders.all_cell_encoder module
      • topobench.nn.encoders.base module
      • topobench.nn.encoders.dgm_encoder module
      • topobench.nn.encoders.kdgm module
      • Module contents
    • topobench.nn.readouts package
      • Submodules
      • topobench.nn.readouts.base module
      • topobench.nn.readouts.identical module
      • topobench.nn.readouts.propagate_signal_down module
      • Module contents
    • topobench.nn.wrappers package
      • Subpackages
      • Submodules
      • topobench.nn.wrappers.base module
      • Module contents
  • Module contents
• topobench.optimizer package
  • Submodules
  • topobench.optimizer.base module
    • AbstractOptimizer
      • AbstractOptimizer.configure_optimizer()
  • topobench.optimizer.optimizer module
    • TBOptimizer
      • TBOptimizer.configure_optimizer()
  • Module contents
    • TBOptimizer
      • TBOptimizer.configure_optimizer()
• topobench.transforms package
  • Subpackages
    • topobench.transforms.data_manipulations package
      • Submodules
      • 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.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.redefine_simplicial_neighbourhoods module
      • Module contents
    • topobench.transforms.feature_liftings package
      • Submodules
      • 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
      • Module contents
    • topobench.transforms.liftings package
      • Subpackages
      • Submodules
      • topobench.transforms.liftings.base module
      • topobench.transforms.liftings.liftings module
      • Module contents
  • Submodules
  • topobench.transforms.data_transform module
    • DataTransform
      • DataTransform.forward()
  • Module contents
• topobench.utils package
  • Submodules
  • topobench.utils.config_resolvers module
    • get_default_metrics()
    • get_default_trainer()
    • get_default_transform()
    • get_monitor_metric()
    • get_monitor_mode()
    • get_required_lifting()
    • infer_in_channels()
    • infer_num_cell_dimensions()
  • topobench.utils.instantiators module
    • instantiate_callbacks()
    • instantiate_loggers()
  • topobench.utils.logging_utils module
    • log_hyperparameters()
  • topobench.utils.pylogger module
    • RankedLogger
      • RankedLogger.log()
  • topobench.utils.rich_utils module
    • enforce_tags()
    • print_config_tree()
  • topobench.utils.utils module
    • extras()
    • get_metric_value()
    • task_wrapper()
  • Module contents
    • RankedLogger
      • RankedLogger.log()
    • enforce_tags()
    • extras()
    • get_metric_value()
    • instantiate_callbacks()
    • instantiate_loggers()
    • log_hyperparameters()
    • print_config_tree()
    • task_wrapper()

Submodules

topobench.run module

Main entry point for training and testing models.

topobench.run.count_number_of_parameters(model: Module, only_trainable: bool = True) → int

Count the number of trainable params.

If all params, specify only_trainable = False.

Ref:

• https://discuss.pytorch.org/t/how-do-i-check-the-number-of-parameters-of-a-model/4325/9?u=brando_miranda

• https://stackoverflow.com/questions/49201236/check-the-total-number-of-parameters-in-a-pytorch-model/62764464#62764464

Parameters:

modeltorch.nn.Module

The model.

only_trainablebool, optional

If True, only count trainable parameters (default: True).

Returns:

int

The number of parameters.

topobench.run.initialize_hydra() → DictConfig

Initialize Hydra when main is not an option (e.g. tests).

Returns:

DictConfig

A DictConfig object containing the config tree.

topobench.run.main(cfg: DictConfig) → float | None

Main entry point for training.

Parameters:

cfgDictConfig

Configuration composed by Hydra.

Returns:

float | None

Optional[float] with optimized metric value.

Module contents

TopoBench: A library for benchmarking of topological models.

topobench.initialize_hydra() → DictConfig

Initialize Hydra when main is not an option (e.g. tests).

Returns:

DictConfig

A DictConfig object containing the config tree.