mirror of
https://github.com/dmlc/dgl.git
synced 2026-06-05 19:54:25 +08:00
237 lines
4.9 KiB
ReStructuredText
237 lines
4.9 KiB
ReStructuredText
.. _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__
|
|
|
|
|
|
Karate Club dataset
|
|
```````````````````````````````````
|
|
|
|
.. autoclass:: KarateClub
|
|
:members: __getitem__, __len__
|
|
|
|
|
|
Citation Network dataset
|
|
```````````````````````````````````
|
|
|
|
.. autoclass:: CitationGraphDataset
|
|
:members: __getitem__, __len__
|
|
|
|
|
|
Cora Citation Network dataset
|
|
```````````````````````````````````
|
|
|
|
.. autoclass:: CoraDataset
|
|
:members: __getitem__, __len__
|
|
|
|
|
|
CoraFull dataset
|
|
```````````````````````````````````
|
|
|
|
.. autoclass:: CoraFull
|
|
:members: __getitem__, __len__
|
|
|
|
|
|
Amazon Co-Purchase dataset
|
|
```````````````````````````````````
|
|
|
|
.. autoclass:: AmazonCoBuy
|
|
:members: __getitem__, __len__
|
|
|
|
|
|
Coauthor dataset
|
|
```````````````````````````````````
|
|
|
|
.. autoclass:: Coauthor
|
|
:members: __getitem__, __len__
|
|
|
|
|
|
BitcoinOTC dataset
|
|
```````````````````````````````````
|
|
|
|
.. autoclass:: BitcoinOTC
|
|
:members: __getitem__, __len__
|
|
|
|
|
|
ICEWS18 dataset
|
|
```````````````````````````````````
|
|
|
|
.. autoclass:: ICEWS18
|
|
:members: __getitem__, __len__
|
|
|
|
|
|
QM7b dataset
|
|
```````````````````````````````````
|
|
|
|
.. autoclass:: QM7b
|
|
:members: __getitem__, __len__
|
|
|
|
|
|
|
|
GDELT dataset
|
|
```````````````````````````````````
|
|
|
|
.. autoclass:: GDELT
|
|
: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 Utils
|
|
```````````````````
|
|
|
|
For the use of graph neural networks, we need to featurize nodes (atoms) and edges (bonds).
|
|
|
|
General utils:
|
|
|
|
.. autosummary::
|
|
:toctree: ../../generated/
|
|
|
|
chem.one_hot_encoding
|
|
chem.ConcatFeaturizer
|
|
chem.ConcatFeaturizer.__call__
|
|
|
|
Utils for atom featurization:
|
|
|
|
.. autosummary::
|
|
:toctree: ../../generated/
|
|
|
|
chem.atom_type_one_hot
|
|
chem.atomic_number_one_hot
|
|
chem.atomic_number
|
|
chem.atom_degree_one_hot
|
|
chem.atom_degree
|
|
chem.atom_total_degree_one_hot
|
|
chem.atom_total_degree
|
|
chem.atom_implicit_valence_one_hot
|
|
chem.atom_implicit_valence
|
|
chem.atom_hybridization_one_hot
|
|
chem.atom_total_num_H_one_hot
|
|
chem.atom_total_num_H
|
|
chem.atom_formal_charge_one_hot
|
|
chem.atom_formal_charge
|
|
chem.atom_num_radical_electrons_one_hot
|
|
chem.atom_num_radical_electrons
|
|
chem.atom_is_aromatic_one_hot
|
|
chem.atom_is_aromatic
|
|
chem.atom_chiral_tag_one_hot
|
|
chem.atom_mass
|
|
chem.BaseAtomFeaturizer
|
|
chem.BaseAtomFeaturizer.feat_size
|
|
chem.BaseAtomFeaturizer.__call__
|
|
chem.CanonicalAtomFeaturizer
|
|
|
|
Utils for bond featurization:
|
|
|
|
.. autosummary::
|
|
:toctree: ../../generated/
|
|
|
|
chem.bond_type_one_hot
|
|
chem.bond_is_conjugated_one_hot
|
|
chem.bond_is_conjugated
|
|
chem.bond_is_in_ring_one_hot
|
|
chem.bond_is_in_ring
|
|
chem.bond_stereo_one_hot
|
|
chem.BaseBondFeaturizer
|
|
chem.BaseBondFeaturizer.feat_size
|
|
chem.BaseBondFeaturizer.__call__
|
|
chem.CanonicalBondFeaturizer
|
|
|
|
Graph Construction
|
|
``````````````````
|
|
|
|
Several methods for constructing DGLGraphs from SMILES/RDKit molecule objects are listed below:
|
|
|
|
.. autosummary::
|
|
:toctree: ../../generated/
|
|
|
|
chem.mol_to_graph
|
|
chem.smiles_to_bigraph
|
|
chem.mol_to_bigraph
|
|
chem.smiles_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
|