decagon-pytorch/experiments/decagon_run/decagon_run.py

#!/usr/bin/env python3

from icosagon.data import Data
from icosagon.trainprep import TrainValTest, \
    prepare_training
from icosagon.model import Model
from icosagon.trainloop import TrainLoop
import os
import pandas as pd
from bisect import bisect_left
import torch
import sys


def index(a, x):
    i = bisect_left(a, x)
    if i != len(a) and a[i] == x:
        return i
    raise ValueError


def load_data():
    path = '/pstore/data/data_science/ref/decagon'
    df_combo = pd.read_csv(os.path.join(path, 'bio-decagon-combo.csv'))
    df_effcat = pd.read_csv(os.path.join(path, 'bio-decagon-effectcategories.csv'))
    df_mono = pd.read_csv(os.path.join(path, 'bio-decagon-mono.csv'))
    df_ppi = pd.read_csv(os.path.join(path, 'bio-decagon-ppi.csv'))
    df_tgtall = pd.read_csv(os.path.join(path, 'bio-decagon-targets-all.csv'))
    df_tgt = pd.read_csv(os.path.join(path, 'bio-decagon-targets.csv'))
    lst = [ 'df_combo', 'df_effcat', 'df_mono', 'df_ppi', 'df_tgtall', 'df_tgt' ]
    for nam in lst:
        print(f'len({nam}): {len(locals()[nam])}')
        print(f'{nam}.columns: {locals()[nam].columns}')

    genes = set()
    genes = genes.union(df_ppi['Gene 1']).union(df_ppi['Gene 2']) \
        .union(df_tgtall['Gene']).union(df_tgt['Gene'])
    genes = sorted(genes)
    print('len(genes):', len(genes))

    drugs = set()
    drugs = drugs.union(df_combo['STITCH 1']).union(df_combo['STITCH 2']) \
        .union(df_mono['STITCH']).union(df_tgtall['STITCH']).union(df_tgt['STITCH'])
    drugs = sorted(drugs)
    print('len(drugs):', len(drugs))

    data = Data()
    data.add_node_type('Gene', len(genes))
    data.add_node_type('Drug', len(drugs))

    print('Preparing PPI...')
    print('Indexing rows...')
    rows = [index(genes, g) for g in df_ppi['Gene 1']]
    print('Indexing cols...')
    cols = [index(genes, g) for g in df_ppi['Gene 2']]
    indices = list(zip(rows, cols))
    indices = torch.tensor(indices).transpose(0, 1)
    values = torch.ones(len(rows))
    print('indices.shape:', indices.shape, 'values.shape:', values.shape)
    adj_mat = torch.sparse_coo_tensor(indices, values, size=(len(genes),) * 2)
    adj_mat = (adj_mat + adj_mat.transpose(0, 1)) / 2
    print('adj_mat created')
    fam = data.add_relation_family('PPI', 0, 0, True)
    rel = fam.add_relation_type('PPI', adj_mat)
    print('OK')

    print('Preparing Drug-Gene (Target) edges...')
    rows = [index(drugs, d) for d in df_tgtall['STITCH']]
    cols = [index(genes, g) for g in df_tgtall['Gene']]
    indices = list(zip(rows, cols))
    indices = torch.tensor(indices).transpose(0, 1)
    values = torch.ones(len(rows))
    adj_mat = torch.sparse_coo_tensor(indices, values, size=(len(drugs), len(genes)))
    fam = data.add_relation_family('Drug-Gene (Target)', 1, 0, True)
    rel = fam.add_relation_type('Drug-Gene (Target)', adj_mat)
    print('OK')

    print('Preparing Drug-Drug (Side Effect) edges...')
    fam = data.add_relation_family('Drug-Drug (Side Effect)', 1, 1, True)
    print('# of side effects:', len(df_combo), 'unique:', len(df_combo['Polypharmacy Side Effect'].unique()))
    for eff, df in df_combo.groupby('Polypharmacy Side Effect'):
        sys.stdout.write('.') # print(eff, '...')
        sys.stdout.flush()
        rows = [index(drugs, d) for d in df['STITCH 1']]
        cols = [index(drugs, d) for d in df['STITCH 2']]
        indices = list(zip(rows, cols))
        indices = torch.tensor(indices).transpose(0, 1)
        values = torch.ones(len(rows))
        adj_mat = torch.sparse_coo_tensor(indices, values, size=(len(drugs), len(drugs)))
        adj_mat = (adj_mat + adj_mat.transpose(0, 1)) / 2
        rel = fam.add_relation_type(df['Polypharmacy Side Effect'], adj_mat)
    print()
    print('OK')

    return data


def _wrap(obj, method_name):
    orig_fn = getattr(obj, method_name)
    def fn(*args, **kwargs):
        print(f'{method_name}() :: ENTER')
        res = orig_fn(*args, **kwargs)
        print(f'{method_name}() :: EXIT')
        return res
    setattr(obj, method_name, fn)


def main():
    data = load_data()
    prep_d = prepare_training(data, TrainValTest(.8, .1, .1))
    _wrap(Model, 'build')
    model = Model(prep_d)
    _wrap(TrainLoop, 'build')
    _wrap(TrainLoop, 'run_epoch')
    loop = TrainLoop(model, batch_size=1000000)
    loop.run_epoch()


if __name__ == '__main__':
    main()