Source code for dgllife.data.pcba

# -*- coding: utf-8 -*-
#
# Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: Apache-2.0
#
# PCBA from MoleculeNet for the prediction of biological activities

import pandas as pd

from dgl.data.utils import get_download_dir, download, _get_dgl_url, extract_archive

from .csv_dataset import MoleculeCSVDataset
from ..utils.mol_to_graph import smiles_to_bigraph

__all__ = ['PCBA']

[docs]class PCBA(MoleculeCSVDataset): r"""PCBA from MoleculeNet for the prediction of biological activities PubChem BioAssay (PCBA) is a database consisting of biological activities of small molecules generated by high-throughput screening. This dataset is a subset of PCBA, containing 128 bioassays measured over 400 thousand compounds. References: * [1] MoleculeNet: A Benchmark for Molecular Machine Learning. * [2] Massively Multitask Networks for Drug Discovery. Parameters ---------- smiles_to_graph: callable, str -> DGLGraph A function turning a SMILES string into a DGLGraph. Default to :func:`dgllife.utils.smiles_to_bigraph`. node_featurizer : callable, rdkit.Chem.rdchem.Mol -> dict Featurization for nodes like atoms in a molecule, which can be used to update ndata for a DGLGraph. Default to None. edge_featurizer : callable, rdkit.Chem.rdchem.Mol -> dict Featurization for edges like bonds in a molecule, which can be used to update edata for a DGLGraph. Default to None. load : bool Whether to load the previously pre-processed dataset or pre-process from scratch. ``load`` should be False when we want to try different graph construction and featurization methods and need to preprocess from scratch. Default to False. log_every : bool Print a message every time ``log_every`` molecules are processed. Default to 1000. cache_file_path : str Path to the cached DGLGraphs, default to 'pcba_dglgraph.bin'. n_jobs : int The maximum number of concurrently running jobs for graph construction and featurization, using joblib backend. Default to 1. Examples -------- >>> import torch >>> from dgllife.data import PCBA >>> from dgllife.utils import smiles_to_bigraph, CanonicalAtomFeaturizer >>> dataset = PCBA(smiles_to_bigraph, CanonicalAtomFeaturizer()) >>> # Get size of the dataset >>> len(dataset) 437929 >>> # Get the 0th datapoint, consisting of SMILES, DGLGraph, labels, and masks >>> dataset[0] ('CC(=O)N1CCC2(CC1)NC(=O)N(c1ccccc1)N2', DGLGraph(num_nodes=20, num_edges=44, ndata_schemes={'h': Scheme(shape=(74,), dtype=torch.float32)} edata_schemes={}), tensor([0., ..., 0.]), tensor([1., ..., 0.])) The dataset instance also contains information about molecule ids. >>> dataset.ids[i] We can also get the id along with SMILES, DGLGraph, labels, and masks at once. >>> dataset.load_full = True >>> dataset[0] ('CC(=O)N1CCC2(CC1)NC(=O)N(c1ccccc1)N2', DGLGraph(num_nodes=20, num_edges=44, ndata_schemes={'h': Scheme(shape=(74,), dtype=torch.float32)} edata_schemes={}), tensor([0., ..., 0.]), tensor([1., ..., 0.]), 'CID1511280') To address the imbalance between positive and negative samples, we can re-weight positive samples for each task based on the training datapoints. >>> train_ids = torch.arange(1000) >>> dataset.task_pos_weights(train_ids) tensor([7.3400, 489.0000, ..., 1.0000]) """ def __init__(self, smiles_to_graph=smiles_to_bigraph, node_featurizer=None, edge_featurizer=None, load=False, log_every=1000, cache_file_path='./pcba_dglgraph.bin', n_jobs=1): self._url = 'dataset/pcba.zip' data_path = get_download_dir() + '/pcba.zip' dir_path = get_download_dir() + '/pcba' download(_get_dgl_url(self._url), path=data_path, overwrite=False) extract_archive(data_path, dir_path) df = pd.read_csv(dir_path + '/pcba.csv') self.ids = df['mol_id'].tolist() self.load_full = False df = df.drop(columns=['mol_id']) super(PCBA, self).__init__(df=df, smiles_to_graph=smiles_to_graph, node_featurizer=node_featurizer, edge_featurizer=edge_featurizer, smiles_column='smiles', cache_file_path=cache_file_path, load=load, log_every=log_every, init_mask=True, n_jobs=n_jobs) self.ids = [self.ids[i] for i in self.valid_ids]
[docs] def __getitem__(self, item): """Get datapoint with index Parameters ---------- item : int Datapoint index Returns ------- str SMILES for the ith datapoint DGLGraph DGLGraph for the ith datapoint Tensor of dtype float32 and shape (T) Labels of the ith datapoint for all tasks. T for the number of tasks. Tensor of dtype float32 and shape (T) Binary masks of the ith datapoint indicating the existence of labels for all tasks. str, optional Id for the ith datapoint, returned only when ``self.load_full`` is True. """ if self.load_full: return self.smiles[item], self.graphs[item], self.labels[item], \ self.mask[item], self.ids[item] else: return self.smiles[item], self.graphs[item], self.labels[item], self.mask[item]