[Dataset] Tox21 (#760)

* tox21

* fix ci

* fix ci

* fix urls to url

* add doc

* remove binary

python/dgl/data/__init__.py

@@ -11,6 +11,7 @@ from .reddit import RedditDataset
 from .ppi import PPIDataset
 from .tu import TUDataset
 from .gindt import GINDataset
+from .chem import Tox21
 
 
 def register_data_args(parser):

python/dgl/data/chem/__init__.py

+from .tox21 import Tox21
\ No newline at end of file

python/dgl/data/chem/csv_dataset.py

+from __future__ import absolute_import
+
+import dgl.backend as F
+import numpy as np
+import os
+import pickle
+import sys
+
+from dgl import DGLGraph
+from .utils import smile2graph
+from ..utils import download, get_download_dir, _get_dgl_url, Subset
+
+class CSVDataset(object):
+    """CSVDataset
+
+    This is a general class for loading data from csv or pd.DataFrame.
+
+    In data pre-processing, we set non-existing labels to be 0, and returning mask with 1 where label exists.
+
+    All molecules are converted into DGLGraphs. After the first-time construction, the
+    DGLGraphs will be saved for reloading so that we do not need to reconstruct them every time.
+
+    Parameters
+    ----------
+    df: pandas.DataFrame
+    Dataframe including smiles and labels. Can be loaded by pandas.read_csv(file_path).
+    One column includes smiles and other columns for labels.
+    Column names other than smiles column would be considered as task names.
+
+    smile2graph: callable, str -> DGLGraph
+    A function turns smiles into a DGLGraph. Default one can be found 
+    at python/dgl/data/chem/utils.py named with smile2graph.
+
+    smile_column: str
+    Column name that including smiles
+
+    cache_file_path: str
+    Path to store the preprocessed data
+    """
+    
+    def __init__(self, df, smile2graph=smile2graph, smile_column='smiles', cache_file_path="csvdata_dglgraph.pkl"):
+        if 'rdkit' not in sys.modules:
+            from ...base import dgl_warning
+            dgl_warning("Please install RDKit (Recommended Version is 2018.09.3)")
+        self.df = df
+        self.smiles = self.df[smile_column].tolist()
+        self.task_names = self.df.columns.drop([smile_column]).tolist()
+        self.cache_file_path = cache_file_path
+        self._pre_process(smile2graph)
+
+    def _pre_process(self, smile2graph):
+        """Pre-process the dataset
+
+        * Convert molecules from smiles format into DGLGraphs
+          and featurize their atoms
+        * Set missing labels to be 0 and use a binary masking
+          matrix to mask them
+        """
+        if os.path.exists(self.cache_file_path):
+            # DGLGraphs have been constructed before, reload them
+            print('Loading previously saved dgl graphs...')
+            with open(self.cache_file_path, 'rb') as f:
+                self.graphs = pickle.load(f)
+        else:
+            self.graphs = []
+            for id, s in enumerate(self.smiles):
+                self.graphs.append(smile2graph(s))
+
+            with open(self.cache_file_path, 'wb') as f:
+                pickle.dump(self.graphs, f)
+
+        _label_values = self.df[self.task_names].values
+        # np.nan_to_num will also turn inf into a very large number
+        self.labels =  F.zerocopy_from_numpy(np.nan_to_num(_label_values))
+        self.mask =  F.zerocopy_from_numpy(~np.isnan(_label_values).astype(np.float32))
+
+    def __getitem__(self, item):
+        """Get the ith datapoint
+
+        Returns
+        -------
+        str
+            SMILES for the ith datapoint
+        DGLGraph
+            DGLGraph for the ith datapoint
+        Tensor of dtype float32
+            Labels of the datapoint for all tasks
+        Tensor of dtype float32
+            Weights of the datapoint for all tasks
+        """
+        return self.smiles[item], self.graphs[item], self.labels[item], self.mask[item]
+
+    def __len__(self):
+        """Length of Dataset
+        
+        Return
+        ------
+        int
+            Length of Dataset
+        """
+        return len(self.smiles)

python/dgl/data/chem/tox21.py

+import numpy as np
+import sys
+
+from .csv_dataset import CSVDataset
+from .utils import smile2graph
+from ..utils import get_download_dir, download, _get_dgl_url, Subset
+
+       
+try:
+    import pandas as pd
+except ImportError:
+    pass
+
+
+class Tox21(CSVDataset):
+    
+    _url = 'dataset/tox21.csv.gz'
+
+    """Tox21 dataset.
+
+    The Toxicology in the 21st Century (https://tripod.nih.gov/tox21/challenge/)
+    initiative created a public database measuring toxicity of compounds, which
+    has been used in the 2014 Tox21 Data Challenge. The dataset contains qualitative
+    toxicity measurements for 8014 compounds on 12 different targets, including nuclear
+    receptors and stress response pathways. Each target results in a binary label.
+
+    A common issue for multi-task prediction is that some datapoints are not labeled for
+    all tasks. This is also the case for Tox21. In data pre-processing, we set non-existing
+    labels to be 0 so that they can be placed in tensors and used for masking in loss computation.
+    See examples below for more details.
+
+    All molecules are converted into DGLGraphs. After the first-time construction,
+    the DGLGraphs will be saved for reloading so that we do not need to reconstruct them everytime.
+
+    Parameters
+    ----------
+    smile2graph: callable, str -> DGLGraph
+    A function turns smiles into a DGLGraph. Default one can be found 
+    at python/dgl/data/chem/utils.py named with smile2graph.
+    """
+    def __init__(self, smile2graph=smile2graph):
+        if 'pandas' not in sys.modules:
+            from ...base import dgl_warning
+            dgl_warning("Please install pandas")
+
+        data_path = get_download_dir() + '/tox21.csv.gz'
+        download(_get_dgl_url(self._url), path=data_path)
+        df = pd.read_csv(data_path)
+        self.id = df['mol_id']
+
+        df = df.drop(columns=['mol_id'])
+        super().__init__(df, smile2graph, cache_file_path="tox21_dglgraph.pkl")
+        self._weight_balancing()
+
+    
+    def _weight_balancing(self):
+        """Perform re-balancing for each task.
+
+        It's quite common that the number of positive samples and the
+        number of negative samples are significantly different. To compensate
+        for the class imbalance issue, we can weight each datapoint in
+        loss computation.
+
+        In particular, for each task we will set the weight of negative samples
+        to be 1 and the weight of positive samples to be the number of negative
+        samples divided by the number of positive samples.
+
+        If weight balancing is performed, one attribute will be affected:
+
+        * self._task_pos_weights is set, which is a list of positive sample weights
+          for each task.
+        """
+        num_pos = np.sum(self.labels, axis=0)
+        num_indices = np.sum(self.mask, axis=0)
+        self._task_pos_weights = (num_indices - num_pos) / num_pos
+    
+
+    @property
+    def task_pos_weights(self):
+        """Get weights for positive samples on each task
+
+        Returns
+        -------
+        list
+            numpy array gives the weight of positive samples on all tasks
+        """
+        return self._task_pos_weights

python/dgl/data/chem/utils.py

+import dgl.backend as F
+import numpy as np
+import os
+import pickle
+
+from dgl import DGLGraph
+
+try:
+    from rdkit import Chem
+    from rdkit.Chem import rdmolfiles, rdmolops
+except ImportError:
+    pass
+
+def one_hot_encoding(x, allowable_set):
+    """One-hot encoding.
+
+    Parameters
+    ----------
+    x : str, int or Chem.rdchem.HybridizationType
+    allowable_set : list
+        The elements of the allowable_set should be of the
+        same type as x.
+
+    Returns
+    -------
+    list
+        List of boolean values where at most one value is True.
+        If the i-th value is True, then we must have
+        x == allowable_set[i].
+    """
+    return list(map(lambda s: x == s, allowable_set))
+
+
+class BaseAtomFeaturizer(object):
+    """An abstract class for atom featurizers
+
+    All atom featurizers that map a molecule to atom features should subclass it.
+    All subclasses should overwrite ``_featurize_atom``, which featurizes a single
+    atom and ``__call__``, which featurizes all atoms in a molecule.
+    """
+
+    def _featurize_atom(self, atom):
+        return NotImplementedError
+
+    def __call__(self, mol):
+        return NotImplementedError
+
+
+class DefaultAtomFeaturizer(BaseAtomFeaturizer):
+    """A default featurizer for atoms.
+
+    The atom features include:
+
+    * **One hot encoding of the atom type**. The supported atom types include
+      ``C``, ``N``, ``O``, ``S``, ``F``, ``Si``, ``P``, ``Cl``, ``Br``, ``Mg``,
+      ``Na``, ``Ca``, ``Fe``, ``As``, ``Al``, ``I``, ``B``, ``V``, ``K``, ``Tl``,
+      ``Yb``, ``Sb``, ``Sn``, ``Ag``, ``Pd``, ``Co``, ``Se``, ``Ti``, ``Zn``,
+      ``H``, ``Li``, ``Ge``, ``Cu``, ``Au``, ``Ni``, ``Cd``, ``In``, ``Mn``, ``Zr``,
+      ``Cr``, ``Pt``, ``Hg``, ``Pb``.
+    * **One hot encoding of the atom degree**. The supported possibilities
+      include ``0 - 10``.
+    * **One hot encoding of the number of implicit Hs on the atom**. The supported
+      possibilities include ``0 - 6``.
+    * **Formal charge of the atom**.
+    * **Number of radical electrons of the atom**.
+    * **One hot encoding of the atom hybridization**. The supported possibilities include
+      ``SP``, ``SP2``, ``SP3``, ``SP3D``, ``SP3D2``.
+    * **Whether the atom is aromatic**.
+    * **One hot encoding of the number of total Hs on the atom**. The supported possibilities
+      include ``0 - 4``.
+
+    Parameters
+    ----------
+    atom_data_field : str
+        Name for storing atom features in DGLGraphs, default to be 'h'.
+    """
+
+    def __init__(self, atom_data_field='h'):
+        super(DefaultAtomFeaturizer, self).__init__()
+        self.atom_data_field = atom_data_field
+
+    @property
+    def feat_size(self):
+        """Returns feature size"""
+        return 74
+
+    def _featurize_atom(self, atom):
+        """Featurize an atom
+
+        Parameters
+        ----------
+        atom : rdkit.Chem.rdchem.Atom
+
+        Returns
+        -------
+        results : list
+            List of feature values, including boolean values and numbers
+        """
+        atom_types = ['C', 'N', 'O', 'S', 'F', 'Si', 'P', 'Cl', 'Br',
+                      'Mg', 'Na', 'Ca', 'Fe', 'As', 'Al', 'I', 'B', 'V',
+                      'K', 'Tl', 'Yb', 'Sb', 'Sn', 'Ag', 'Pd', 'Co', 'Se',
+                      'Ti', 'Zn', 'H', 'Li', 'Ge', 'Cu', 'Au', 'Ni', 'Cd',
+                      'In', 'Mn', 'Zr', 'Cr', 'Pt', 'Hg', 'Pb']
+        results = one_hot_encoding(atom.GetSymbol(), atom_types) + \
+            one_hot_encoding(atom.GetDegree(), [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]) + \
+            one_hot_encoding(atom.GetImplicitValence(), [0, 1, 2, 3, 4, 5, 6]) + \
+            [atom.GetFormalCharge(), atom.GetNumRadicalElectrons()] + \
+            one_hot_encoding(atom.GetHybridization(),
+                             [Chem.rdchem.HybridizationType.SP,
+                              Chem.rdchem.HybridizationType.SP2,
+                              Chem.rdchem.HybridizationType.SP3,
+                              Chem.rdchem.HybridizationType.SP3D,
+                              Chem.rdchem.HybridizationType.SP3D2]) + \
+            [atom.GetIsAromatic()] + \
+            one_hot_encoding(atom.GetTotalNumHs(), [0, 1, 2, 3, 4])
+
+        return results
+
+    def __call__(self, mol):
+        """Featurize a molecule
+
+        Parameters
+        ----------
+        mol : rdkit.Chem.rdchem.Mol
+            RDKit molecule instance.
+
+        Returns
+        -------
+        dict
+            Atom features of shape (N, 74),
+            where N is the number of atoms in the molecule
+        """
+        num_atoms = mol.GetNumAtoms()
+        atom_features = []
+        for i in range(num_atoms):
+            atom = mol.GetAtomWithIdx(i)
+            atom_features.append(self._featurize_atom(atom))
+        atom_features = np.stack(atom_features)
+        atom_features = F.zerocopy_from_numpy(atom_features.astype(np.float32))
+
+        return {self.atom_data_field: atom_features}
+
+
+def smile2graph(smile, add_self_loop=False, atom_featurizer=None, bond_featurizer=None):
+    """Convert SMILES into a DGLGraph.
+
+    The **i** th atom in the molecule, i.e. ``mol.GetAtomWithIdx(i)``, corresponds to the
+    **i** th node in the returned DGLGraph.
+
+    The **i** th bond in the molecule, i.e. ``mol.GetBondWithIdx(i)``, corresponds to the
+    **(2i)**-th and **(2i+1)**-th edges in the returned DGLGraph. The **(2i)**-th and
+    **(2i+1)**-th edges will be separately from **u** to **v** and **v** to **u**, where
+    **u** is ``bond.GetBeginAtomIdx()`` and **v** is ``bond.GetEndAtomIdx()``.
+
+    If self loops are added, the last **n** edges will separately be self loops for
+    atoms ``0, 1, ..., n-1``.
+
+    Parameters
+    ----------
+    smiles : str
+        String of SMILES
+    add_self_loop : bool
+        Whether to add self loops in DGLGraphs.
+    atom_featurizer : callable, rdkit.Chem.rdchem.Mol -> dict
+        Featurization for atoms in a molecule, which can be used to update
+        ndata for a DGLGraph.
+    bond_featurizer : callable, rdkit.Chem.rdchem.Mol -> dict
+        Featurization for bonds in a molecule, which can be used to update
+        edata for a DGLGraph.
+    """
+    mol = Chem.MolFromSmiles(smile)
+    new_order = rdmolfiles.CanonicalRankAtoms(mol)
+    mol = rdmolops.RenumberAtoms(mol, new_order)
+    g = DGLGraph()
+    num_atoms = mol.GetNumAtoms()
+    g.add_nodes(num_atoms)
+
+    src_list = []
+    dst_list = []
+    num_bonds = mol.GetNumBonds()
+    for i in range(num_bonds):
+        bond = mol.GetBondWithIdx(i)
+        u = bond.GetBeginAtomIdx()
+        v = bond.GetEndAtomIdx()
+        src_list.extend([u, v])
+        dst_list.extend([v, u])
+    g.add_edges(src_list, dst_list)
+
+    if add_self_loop:
+        nodes = g.nodes()
+        g.add_edges(nodes, nodes)
+
+    # Featurization
+    if atom_featurizer is not None:
+        g.ndata.update(atom_featurizer(mol))
+
+    if bond_featurizer is not None:
+        g.edata.update(bond_featurizer(mol))
+
+    return g

python/dgl/data/utils.py

 """Dataset utilities."""
 from __future__ import absolute_import
 
-import os, sys
+import os
+import sys
 import hashlib
 import warnings
 import zipfile
 import tarfile
+import numpy as np
 try:
     import requests
 except ImportError:
@@ -13,7 +15,9 @@ except ImportError:
         pass
     requests = requests_failed_to_import
 
-__all__ = ['download', 'check_sha1', 'extract_archive', 'get_download_dir']
+__all__ = ['download', 'check_sha1', 'extract_archive',
+           'get_download_dir', 'Subset', 'split_dataset']
+
 
 def _get_dgl_url(file_url):
     """Get DGL online url for download."""
@@ -24,6 +28,25 @@ def _get_dgl_url(file_url):
     return repo_url + file_url
 
 
+def split_dataset(dataset, frac_list=None, shuffle=False, random_state=None):
+    from itertools import accumulate
+    if frac_list is None:
+        frac_list = [0.8, 0.1, 0.1]
+    frac_list = np.array(frac_list)
+    assert np.allclose(np.sum(frac_list), 1.), \
+        'Expect frac_list sum to 1, got {:.4f}'.format(
+            np.sum(frac_list))
+    num_data = len(dataset)
+    lengths = (num_data * frac_list).astype(int)
+    lengths[-1] = num_data - np.sum(lengths[:-1])
+    if shuffle:
+        indices = np.random.RandomState(
+            seed=random_state).permutation(num_data)
+    else:
+        indices = np.arange(num_data)
+    return [Subset(dataset, indices[offset - length:offset]) for offset, length in zip(accumulate(lengths), lengths)]
+
+
 def download(url, path=None, overwrite=False, sha1_hash=None, retries=5, verify_ssl=True):
     """Download a given URL.
 
@@ -77,18 +100,18 @@ def download(url, path=None, overwrite=False, sha1_hash=None, retries=5, verify_
             # Disable pyling too broad Exception
             # pylint: disable=W0703
             try:
-                print('Downloading %s from %s...'%(fname, url))
+                print('Downloading %s from %s...' % (fname, url))
                 r = requests.get(url, stream=True, verify=verify_ssl)
                 if r.status_code != 200:
-                    raise RuntimeError("Failed downloading url %s"%url)
+                    raise RuntimeError("Failed downloading url %s" % url)
                 with open(fname, 'wb') as f:
                     for chunk in r.iter_content(chunk_size=1024):
-                        if chunk: # filter out keep-alive new chunks
+                        if chunk:  # filter out keep-alive new chunks
                             f.write(chunk)
                 if sha1_hash and not check_sha1(fname, sha1_hash):
-                    raise UserWarning('File {} is downloaded but the content hash does not match.'\
-                                      ' The repo may be outdated or download may be incomplete. '\
-                                      'If the "repo_url" is overridden, consider switching to '\
+                    raise UserWarning('File {} is downloaded but the content hash does not match.'
+                                      ' The repo may be outdated or download may be incomplete. '
+                                      'If the "repo_url" is overridden, consider switching to '
                                       'the default repo.'.format(fname))
                 break
             except Exception as e:
@@ -101,6 +124,7 @@ def download(url, path=None, overwrite=False, sha1_hash=None, retries=5, verify_
 
     return fname
 
+
 def check_sha1(filename, sha1_hash):
     """Check whether the sha1 hash of the file content matches the expected hash.
 
@@ -128,6 +152,7 @@ def check_sha1(filename, sha1_hash):
 
     return sha1.hexdigest() == sha1_hash
 
+
 def extract_archive(file, target_dir):
     """Extract archive file.
 
@@ -150,6 +175,7 @@ def extract_archive(file, target_dir):
     archive.extractall(path=target_dir)
     archive.close()
 
+
 def get_download_dir():
     """Get the absolute path to the download directory.
 
@@ -163,3 +189,41 @@ def get_download_dir():
     if not os.path.exists(dirname):
         os.makedirs(dirname)
     return dirname
+
+
+class Subset(object):
+    """Subset of a dataset at specified indices
+
+    Code adapted from PyTorch.
+
+    Parameters
+    ----------
+    dataset
+        dataset[i] should return the ith datapoint
+    indices : list
+        List of datapoint indices to construct the subset
+    """
+
+    def __init__(self, dataset, indices):
+        self.dataset = dataset
+        self.indices = indices
+
+    def __getitem__(self, item):
+        """Get the datapoint indexed by item
+
+        Returns
+        -------
+        tuple
+            datapoint
+        """
+        return self.dataset[self.indices[item]]
+
+    def __len__(self):
+        """Get subset size
+
+        Returns
+        -------
+        int
+            Number of datapoints in the subset
+        """
+        return len(self.indices)