topobench.data.loaders package

Subpackages

• topobench.data.loaders.graph package
  • Submodules
  • topobench.data.loaders.graph.hetero_datasets module
    • HeterophilousGraphDatasetLoader
      • HeterophilousGraphDatasetLoader.load_dataset()
  • topobench.data.loaders.graph.mantra_dataset module
    • MantraSimplicialDatasetLoader
      • MantraSimplicialDatasetLoader.load_dataset()
  • topobench.data.loaders.graph.manual_graph_dataset_loader module
    • ManualGraphDatasetLoader
      • ManualGraphDatasetLoader.get_data_dir()
      • ManualGraphDatasetLoader.load_dataset()
  • topobench.data.loaders.graph.modecule_datasets module
    • MoleculeDatasetLoader
      • MoleculeDatasetLoader.get_data_dir()
      • MoleculeDatasetLoader.load_dataset()
  • topobench.data.loaders.graph.ogbg_datasets module
    • OGBGDatasetLoader
      • OGBGDatasetLoader.get_data_dir()
      • OGBGDatasetLoader.load_dataset()
  • topobench.data.loaders.graph.planetoid_datasets module
    • PlanetoidDatasetLoader
      • PlanetoidDatasetLoader.load_dataset()
  • topobench.data.loaders.graph.tu_datasets module
    • TUDatasetLoader
      • TUDatasetLoader.load_dataset()
  • topobench.data.loaders.graph.us_county_demos_dataset_loader module
    • USCountyDemosDatasetLoader
      • USCountyDemosDatasetLoader.load_dataset()
  • Module contents
    • HeterophilousGraphDatasetLoader
      • HeterophilousGraphDatasetLoader.load_dataset()
    • MantraSimplicialDatasetLoader
      • MantraSimplicialDatasetLoader.load_dataset()
    • ManualGraphDatasetLoader
      • ManualGraphDatasetLoader.get_data_dir()
      • ManualGraphDatasetLoader.load_dataset()
    • MoleculeDatasetLoader
      • MoleculeDatasetLoader.get_data_dir()
      • MoleculeDatasetLoader.load_dataset()
    • OGBGDatasetLoader
      • OGBGDatasetLoader.get_data_dir()
      • OGBGDatasetLoader.load_dataset()
    • PlanetoidDatasetLoader
      • PlanetoidDatasetLoader.load_dataset()
    • TUDatasetLoader
      • TUDatasetLoader.load_dataset()
    • USCountyDemosDatasetLoader
      • USCountyDemosDatasetLoader.load_dataset()
• topobench.data.loaders.hypergraph package
  • Submodules
  • topobench.data.loaders.hypergraph.citation_hypergraph_dataset_loader module
    • CitationHypergraphDatasetLoader
      • CitationHypergraphDatasetLoader.load_dataset()
  • Module contents
    • CitationHypergraphDatasetLoader
      • CitationHypergraphDatasetLoader.load_dataset()
    • HypergraphDatasetLoader
      • HypergraphDatasetLoader.load_dataset()
• topobench.data.loaders.pointcloud package
  • Submodules
  • topobench.data.loaders.pointcloud.geometric_shapes module
    • GeometricShapesDatasetLoader
      • GeometricShapesDatasetLoader.load_dataset()
    • rename_pos_to_x()
  • Module contents
    • GeometricShapesDatasetLoader
      • GeometricShapesDatasetLoader.load_dataset()
• topobench.data.loaders.simplicial package
  • Submodules
  • topobench.data.loaders.simplicial.mantra_dataset_loader module
    • MantraSimplicialDatasetLoader
      • MantraSimplicialDatasetLoader.load_dataset()
  • Module contents
    • MantraSimplicialDatasetLoader
      • MantraSimplicialDatasetLoader.load_dataset()

Submodules

topobench.data.loaders.base module

Abstract Loader class.

class topobench.data.loaders.base.AbstractLoader(parameters: DictConfig)

Bases: ABC

Abstract class that provides an interface to load data.

Parameters:

parametersDictConfig

Configuration parameters.

get_data_dir() → Path

Get the data directory.

Returns:

Path

The path to the dataset directory.

load(**kwargs) → tuple[Data, str]

Load data.

Parameters:

**kwargsdict

Additional keyword arguments.

Returns:

tuple[torch_geometric.data.Data, str]

Tuple containing the loaded data and the data directory.

abstract load_dataset() → Dataset | Dataset

Load data into a dataset.

Returns:

Union[torch_geometric.data.Dataset, torch.utils.data.Dataset]

The loaded dataset, which could be a PyG or PyTorch dataset.

Raises:

NotImplementedError

If the method is not implemented.

Module contents

Init file for load module.

class topobench.data.loaders.AbstractLoader(parameters: DictConfig)

Bases: ABC

Abstract class that provides an interface to load data.

Parameters:

parametersDictConfig

Configuration parameters.

get_data_dir() → Path

Get the data directory.

Returns:

Path

The path to the dataset directory.

load(**kwargs) → tuple[Data, str]

Load data.

Parameters:

**kwargsdict

Additional keyword arguments.

Returns:

tuple[torch_geometric.data.Data, str]

Tuple containing the loaded data and the data directory.

abstract load_dataset() → Dataset | Dataset

Load data into a dataset.

Returns:

Union[torch_geometric.data.Dataset, torch.utils.data.Dataset]

The loaded dataset, which could be a PyG or PyTorch dataset.

Raises:

NotImplementedError

If the method is not implemented.

class topobench.data.loaders.CitationHypergraphDatasetLoader(parameters: DictConfig)

Bases: AbstractLoader

Load Citation Hypergraph dataset with configurable parameters.

Parameters:

parametersDictConfig

Configuration parameters containing:

• data_dir: Root directory for data

• data_name: Name of the dataset

• other relevant parameters

load_dataset() → CitationHypergraphDataset

Load the Citation Hypergraph dataset.

Returns:

CitationHypergraphDataset

The loaded Citation Hypergraph dataset with the appropriate data_dir.

Raises:

RuntimeError

If dataset loading fails.

class topobench.data.loaders.GeometricShapesDatasetLoader(parameters: DictConfig)

Bases: AbstractLoader

Load GeometricShapes dataset.

Parameters:

parametersDictConfig

Configuration parameters containing:

• data_dir: Root directory for data

load_dataset() → Dataset

Load GeometricShapes dataset.

Returns:

Dataset

The loaded GeometricShapes dataset.

Raises:

RuntimeError

If dataset loading fails.

class topobench.data.loaders.HeterophilousGraphDatasetLoader(parameters: DictConfig)

Bases: AbstractLoader

Load Heterophilous Graph datasets.

Parameters:

parametersDictConfig

Configuration parameters containing:

• data_dir: Root directory for data

• data_name: Name of the dataset

• data_type: Type of the dataset (e.g., “heterophilous”)

load_dataset() → Dataset

Load Heterophilous Graph dataset.

Returns:

Dataset

The loaded Heterophilous Graph dataset.

Raises:

RuntimeError

If dataset loading fails.

class topobench.data.loaders.HypergraphDatasetLoader(parameters: DictConfig)

Bases: AbstractLoader

Load Citation Hypergraph dataset with configurable parameters.

Parameters:

parametersDictConfig

Configuration parameters containing:

• data_dir: Root directory for data

• data_name: Name of the dataset

• other relevant parameters

load_dataset() → HypergraphDataset

Load the Citation Hypergraph dataset.

Returns:

HypergraphDataset

The loaded Citation Hypergraph dataset with the appropriate data_dir.

Raises:

RuntimeError

If dataset loading fails.

class topobench.data.loaders.MantraSimplicialDatasetLoader(parameters: DictConfig, **kwargs)

Bases: AbstractLoader

Load Mantra dataset with configurable parameters.

Note: for the simplicial datasets it is necessary to include DatasetLoader into the name of the class!

Parameters:

parametersDictConfig

Configuration parameters containing:

• data_dir: Root directory for data

• data_name: Name of the dataset

• other relevant parameters

**kwargsdict

Additional keyword arguments.

load_dataset(**kwargs) → MantraDataset

Load the Citation Hypergraph dataset.

Parameters:

**kwargsdict

Additional keyword arguments for dataset initialization.

Returns:

CitationHypergraphDataset

The loaded Citation Hypergraph dataset with the appropriate data_dir.

Raises:

RuntimeError

If dataset loading fails.

class topobench.data.loaders.ManualGraphDatasetLoader(parameters: DictConfig)

Bases: AbstractLoader

Load manually provided graph datasets.

Parameters:

parametersDictConfig

Configuration parameters containing:

• data_name: Name of the dataset

• data_dir: Root directory for data

get_data_dir() → Path

Get the data directory.

Returns:

Path

The path to the dataset directory.

load_dataset() → Any

Load the manual graph dataset.

Returns:

DataloadDataset

The dataset object containing the manually loaded graph.

class topobench.data.loaders.MoleculeDatasetLoader(parameters: DictConfig)

Bases: AbstractLoader

Load molecule datasets (ZINC and AQSOL) with predefined splits.

Parameters:

parametersDictConfig

Configuration parameters containing:

• data_dir: Root directory for data

• data_name: Name of the dataset

• data_type: Type of the dataset (e.g., “molecule”)

get_data_dir() → Path

Get the data directory.

Returns:

Path

The path to the dataset directory.

load_dataset() → Dataset

Load the molecule dataset with predefined splits.

Returns:

Dataset

The combined dataset with predefined splits.

Raises:

RuntimeError

If dataset loading fails.

class topobench.data.loaders.OGBGDatasetLoader(parameters: DictConfig)

Bases: AbstractLoader

Load molecule datasets (molhiv, molpcba, ppa) with predefined splits.

Parameters:

parametersDictConfig

Configuration parameters containing:

• data_dir: Root directory for data

• data_name: Name of the dataset

• data_type: Type of the dataset (e.g., “molecule”)

get_data_dir() → Path

Get the data directory.

Returns:

Path

The path to the dataset directory.

load_dataset() → Dataset

Load the molecule dataset with predefined splits.

Returns:

Dataset

The combined dataset with predefined splits.

Raises:

RuntimeError

If dataset loading fails.

class topobench.data.loaders.PlanetoidDatasetLoader(parameters: DictConfig)

Bases: AbstractLoader

Load PLANETOID datasets.

Parameters:

parametersDictConfig

Configuration parameters containing:

• data_dir: Root directory for data

• data_name: Name of the dataset

• data_type: Type of the dataset (e.g., “cocitation”)

load_dataset() → Dataset

Load Planetoid dataset.

Returns:

Dataset

The loaded Planetoid dataset.

Raises:

RuntimeError

If dataset loading fails.

class topobench.data.loaders.TUDatasetLoader(parameters: DictConfig)

Bases: AbstractLoader

Load TU datasets.

Parameters:

parametersDictConfig

Configuration parameters containing:

• data_dir: Root directory for data

• data_name: Name of the dataset

• data_type: Type of the dataset (e.g., “graph_classification”)

load_dataset() → Dataset

Load TU dataset.

Returns:

Dataset

The loaded TU dataset.

Raises:

RuntimeError

If dataset loading fails.

class topobench.data.loaders.USCountyDemosDatasetLoader(parameters: DictConfig)

Bases: AbstractLoader

Load US County Demos dataset with configurable year and task variable.

Parameters:

parametersDictConfig

Configuration parameters containing:

• data_dir: Root directory for data

• data_name: Name of the dataset

• year: Year of the dataset (if applicable)

• task_variable: Task variable for the dataset

load_dataset() → USCountyDemosDataset

Load the US County Demos dataset.

Returns:

USCountyDemosDataset

The loaded US County Demos dataset with the appropriate data_dir.

Raises:

RuntimeError

If dataset loading fails.