data.rst

.. _apidata:

Dataset
=======

.. currentmodule:: dgl.data

Utils
-----

.. autosummary::
    :toctree: ../../generated/

    utils.get_download_dir
    utils.download
    utils.check_sha1
    utils.extract_archive
    utils.split_dataset
    utils.save_graphs
    utils.load_graphs
    utils.load_labels

.. autoclass:: dgl.data.utils.Subset
    :members: __getitem__, __len__

Dataset Classes
---------------

Stanford sentiment treebank dataset
```````````````````````````````````

For more information about the dataset, see `Sentiment Analysis <https://nlp.stanford.edu/sentiment/index.html>`__.

.. autoclass:: SST
    :members: __getitem__, __len__

Mini graph classification dataset
`````````````````````````````````

.. autoclass:: MiniGCDataset
    :members: __getitem__, __len__, num_classes


Graph kernel dataset
````````````````````

For more information about the dataset, see `Benchmark Data Sets for Graph Kernels <https://ls11-www.cs.tu-dortmund.de/staff/morris/graphkerneldatasets>`__.

.. autoclass:: TUDataset
    :members: __getitem__, __len__


Graph isomorphism network dataset
```````````````````````````````````

A compact subset of graph kernel dataset

.. autoclass:: GINDataset
    :members: __getitem__, __len__


Protein-Protein Interaction dataset
```````````````````````````````````

.. autoclass:: PPIDataset
    :members: __getitem__, __len__

Molecular Graphs
----------------

To work on molecular graphs, make sure you have installed `RDKit 2018.09.3 <https://www.rdkit.org/docs/Install.html>`__.

Featurization
`````````````

For the use of graph neural networks, we need to featurize nodes (atoms) and edges (bonds). Below we list some
featurization methods/utilities:

.. autosummary::
    :toctree: ../../generated/

    chem.one_hot_encoding
    chem.BaseAtomFeaturizer
    chem.CanonicalAtomFeaturizer

Graph Construction
``````````````````

Several methods for constructing DGLGraphs from SMILES/RDKit molecule objects are listed below:

.. autosummary::
    :toctree: ../../generated/

    chem.mol_to_graph
    chem.smile_to_bigraph
    chem.mol_to_bigraph
    chem.smile_to_complete_graph
    chem.mol_to_complete_graph

Dataset Classes
```````````````

If your dataset is stored in a ``.csv`` file, you may find it helpful to use

.. autoclass:: dgl.data.chem.CSVDataset
    :members: __getitem__, __len__

Currently two datasets are supported:

* Tox21
* TencentAlchemyDataset

.. autoclass:: dgl.data.chem.Tox21
    :members: __getitem__, __len__, task_pos_weights

.. autoclass:: dgl.data.chem.TencentAlchemyDataset
    :members: __getitem__, __len__, set_mean_and_std