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pretrain_gmpt_sup.py
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pretrain_gmpt_sup.py
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import argparse
import os
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch_geometric.nn import global_mean_pool
from tqdm import tqdm
from graph_matching import AdaGMNConv
from splitters import random_split, species_split
from dataloader import DataLoaderAE
class GMPT_Sup(nn.Module):
def __init__(self, args, num_tasks, gnn):
super(GMPT_Sup, self).__init__()
self.mode = args.mode
self.gnn = gnn
self.sgmn = AdaGMNConv(args.emb_dim, args.mode)
self.num_tasks = num_tasks
self.criterion = nn.MSELoss()
self.mask = ~torch.eye(args.batch_size, dtype=torch.bool)
def from_pretrained(self, input_model_file):
print(f'loading pre-trained model from {input_model_file}')
self.gnn.load_state_dict(torch.load(input_model_file, map_location=lambda storage, loc: storage))
def calcu_loss(self, gid, batch_graph):
x, edge_index, edge_attr, batch = batch_graph.x, batch_graph.edge_index, batch_graph.edge_attr, batch_graph.batch
x = self.gnn(x, edge_index, edge_attr)
out_multi, out_single = self.sgmn(gid, x, edge_index, edge_attr, batch)
g_pool1 = global_mean_pool(out_multi, batch) # (batch_size, emb_dim)
g_pool2 = torch.mean(out_single, dim=1) # (batch_size, emb_dim)
g_pool1 = F.normalize(g_pool1)
g_pool2 = F.normalize(g_pool2)
g_sim = (g_pool1 * g_pool2).sum(dim=-1) # (batch_size)
g_sim = g_sim[self.mask[gid]]
if self.mode == 'bio':
batch_y = batch_graph.go_target_pretrain.view(-1, self.num_tasks)
elif self.mode == 'chem':
y = batch_graph.y.view(-1, self.num_tasks).float()
is_valid = (y**2 > 0)
batch_y = torch.where(is_valid, (y+1)/2, torch.randint(2, y.shape, device=y.device).float())
g_y = batch_y[gid]
batch_y = batch_y[self.mask[gid]].float()
g_y = g_y.expand_as(batch_y).float()
batch_y = F.normalize(batch_y)
g_y = F.normalize(g_y)
y_sim = (batch_y * g_y).sum(dim=-1)
loss = self.criterion(y_sim, g_sim)
return loss
def train(args, model, device, loader, optimizer):
model.train()
loss_accum = 0
num_graph = args.batch_size
for step, batch in enumerate(tqdm(loader, desc="Iteration")):
batch = batch.to(device)
g_ids = np.random.permutation(num_graph)[:args.sample_num]
for g_i in g_ids:
loss = model.calcu_loss(g_i, batch) / args.sample_num
optimizer.zero_grad()
loss.backward()
optimizer.step()
loss_accum += float(loss.detach().cpu().item())
return loss_accum / (step + 1)
def main():
# Training settings
parser = argparse.ArgumentParser(description='PyTorch implementation of pre-training of graph neural networks')
parser.add_argument('--mode', type=str, default='bio')
parser.add_argument('--device', type=int, default=0,
help='which gpu to use if any (default: 0)')
parser.add_argument('--batch_size', type=int, default=32,
help='input batch size for training (default: 32)')
parser.add_argument('--epochs', type=int, default=100,
help='number of epochs to train (default: 100)')
parser.add_argument('--lr', type=float, default=0.001,
help='learning rate (default: 0.001)')
parser.add_argument('--decay', type=float, default=0,
help='weight decay (default: 0)')
parser.add_argument('--num_layer', type=int, default=5,
help='number of GNN message passing layers (default: 5).')
parser.add_argument('--emb_dim', type=int, default=300,
help='embedding dimensions (default: 300)')
parser.add_argument('--dropout_ratio', type=float, default=0.2,
help='dropout ratio (default: 0.2)')
parser.add_argument('--graph_pooling', type=str, default="mean",
help='graph level pooling (sum, mean, max, set2set, attention)')
parser.add_argument('--JK', type=str, default="last",
help='how the node features across layers are combined. last, sum, max or concat')
parser.add_argument('--input_model_file', type=str, default = '', help='filename to read the model (if there is any)')
parser.add_argument('--model_file', type = str, default = '', help='filename to output the pre-trained model')
parser.add_argument('--dataset_path', type=str, default='./', help='root path to the dataset')
parser.add_argument('--gnn_type', type=str, default="gin")
parser.add_argument('--num_workers', type=int, default = 0, help='number of workers for dataset loading')
parser.add_argument('--sample_num', type=int, default=1, help='number of sample graph in one batch')
parser.add_argument('--seed', type=int, default=42, help = "Seed for splitting dataset.")
parser.add_argument('--split', type=str, default = "species", help='Random or species split')
args = parser.parse_args()
print(args)
torch.manual_seed(0)
np.random.seed(0)
device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu")
if torch.cuda.is_available():
torch.cuda.manual_seed_all(0)
args.device = device
if args.mode == 'bio':
def combine_dataset(AdaDataset, dataset1, dataset2, root_supervised):
data_list = [data for data in dataset1]
data_list.extend([data for data in dataset2])
dataset = AdaDataset(root_supervised, data_type='supervised', empty = True)
dataset.data, dataset.slices = dataset.collate(data_list)
return dataset
from bio_loader import BioDataset
from bio_model import GNN
root_supervised = os.path.join(args.dataset_path, 'dataset/supervised')
dataset = BioDataset(root_supervised, data_type='supervised')
assert args.split == "species"
print("species splitting")
trainval_dataset, test_dataset = species_split(dataset)
test_dataset_broad, test_dataset_none, _ = random_split(test_dataset, seed = args.seed, frac_train=0.5, frac_valid=0.5, frac_test=0)
print(trainval_dataset)
print(test_dataset_broad)
pretrain_dataset = combine_dataset(BioDataset, trainval_dataset, test_dataset_broad, root_supervised)
print(pretrain_dataset)
num_tasks = len(pretrain_dataset[0].go_target_pretrain)
elif args.mode == 'chem':
from chem_loader import MoleculeDataset
from chem_model import GNN, GNN_graphpred
pretrain_dataset = MoleculeDataset(os.path.join(args.dataset_path, "dataset/chembl_filtered"), dataset='chembl_filtered')
num_tasks = 1310
train_loader = DataLoaderAE(pretrain_dataset, batch_size=args.batch_size, shuffle=True, num_workers = args.num_workers, drop_last=True)
#set up model
gnn = GNN(args.num_layer, args.emb_dim, JK=args.JK, drop_ratio=args.dropout_ratio, gnn_type=args.gnn_type)
model = GMPT_Sup(args, num_tasks, gnn)
if not args.input_model_file == "":
model.from_pretrained(args.input_model_file)
model = model.to(device)
#set up optimizer
optimizer = optim.Adam(model.parameters(), lr=args.lr, weight_decay=args.decay)
print(optimizer)
for epoch in range(1, args.epochs+1):
print("====epoch " + str(epoch))
train_loss = train(args, model, device, train_loader, optimizer)
print(train_loss)
if epoch == 1 or epoch % 20 == 0:
torch.save(model.gnn.state_dict(), args.model_file + f'.pth.{epoch}')
if __name__ == "__main__":
main()