import os import torch from torch_geometric.data import DataLoader import torch.nn.functional as F from Model.GCN import mol2graph from Model.GCN.callbacks import EarlyStopping from Model.GCN.network import MolecularGCN from Model.GCN.utils import get_data import hydra import datetime from config.config import cs from omegaconf import DictConfig, OmegaConf from tqdm.auto import tqdm device = torch.device('cuda' if torch.cuda.is_available() else 'cpu') date = datetime.datetime.now().strftime('%Y%m%d') def train(model, optimizer, loader): model.train() loss_all = 0 for data in loader: optimizer.zero_grad() data = data.to(device) output = model.forward(data.x, data.edge_index, data.batch).squeeze(1) loss = F.cross_entropy(output, data.y) loss.backward() loss_all += loss.item() * data.num_graphs optimizer.step() return loss_all / len(loader) def eval(model, loader, ks=None): model.eval() score_list = [] with torch.no_grad(): loss_all = 0 for data in loader: data = data.to(device) output = model.forward(data.x, data.edge_index, data.batch) # output.shape = (batch_size, vocab_size) loss = F.cross_entropy(output, data.y) loss_all += loss.item() * data.num_graphs if ks is not None: for k in ks: score_list.append(topk_accuracy(data, output, k)) return loss_all/len(loader), score_list def topk_accuracy(data, output, k: int): _, pred = output.topk(k, 1, True, True) # (k, dim=1, largest=True, sorted=True) pred = pred.t() # (batch, maxk) -> (maxk, batch) correct = pred.eq(data.y.unsqueeze(0).expand_as(pred)) # target:(batch,) -> (1, batch) -> (maxk, batch) # Tensor.eq: compute element-wise equality, correct: bool matrix score = correct.float().sum() / len(data) score = score.detach().item() return score @hydra.main(config_path=None, config_name='config', version_base=None) def main(cfg: DictConfig): print('Loading data...') train_path = cfg['GCN_train']['train'] valid_path = cfg['GCN_train']['valid'] test_path = cfg['GCN_train']['test'] batch_size = cfg['GCN_train']['batch_size'] dim = cfg['GCN_train']['dim'] n_conv_hidden = cfg['GCN_train']['n_conv_hidden'] n_mlp_hidden = cfg['GCN_train']['n_mlp_hidden'] dropout = cfg['GCN_train']['dropout'] lr = cfg['GCN_train']['lr'] epochs = cfg['GCN_train']['epochs'] patience = cfg['GCN_train']['patience'] save_path = cfg['GCN_train']['save_path'] ks = [1, 3, 5, 10] mols_train, y_train = get_data(hydra.utils.get_original_cwd() + train_path) mols_valid, y_valid = get_data(hydra.utils.get_original_cwd() + valid_path) print('-'*100) print('Training: ', mols_train.shape) print('Validation: ', mols_valid.shape) print('-'*100) labels = y_train.tolist() + y_valid.tolist() # Mol to Graph print('Converting mol to graph...') X_train = [mol2graph.mol2vec(m) for m in tqdm(mols_train.tolist())] for i, data in enumerate(X_train): data.y = torch.LongTensor([y_train[i]]).to(device) X_valid = [mol2graph.mol2vec(m) for m in tqdm(mols_valid.tolist())] for i, data in enumerate(X_valid): data.y = torch.LongTensor([y_valid[i]]).to(device) train_loader = DataLoader(X_train, batch_size=batch_size, shuffle=True, drop_last=True) valid_loader = DataLoader(X_valid, batch_size=batch_size, shuffle=True, drop_last=True) print('completed.') print('-'*100) num = 1 while True: ckpt_dir = hydra.utils.get_original_cwd()+f'{save_path}/checkpoints_{date}_{num}' try: if any(os.scandir(ckpt_dir)): num +=1 continue else: break except: os.makedirs(ckpt_dir, exist_ok=True) break train_path = cfg['GCN_train']['train'] valid_path = cfg['GCN_train']['valid'] test_path = cfg['GCN_train']['test'] batch_size = cfg['GCN_train']['batch_size'] dim = cfg['GCN_train']['dim'] n_conv_hidden = cfg['GCN_train']['n_conv_hidden'] n_mlp_hidden = cfg['GCN_train']['n_mlp_hidden'] dropout = cfg['GCN_train']['dropout'] lr = cfg['GCN_train']['lr'] epochs = cfg['GCN_train']['epochs'] patience = cfg['GCN_train']['patience'] # Model instance construction print('Model instance construction') model = MolecularGCN( dim = dim, n_conv_hidden = n_conv_hidden, n_mlp_hidden = n_mlp_hidden, dropout = dropout ).to(device) print(model) print('-'*100) # Training optimizer = torch.optim.Adam(model.parameters(), lr=lr) earlystopping = EarlyStopping(patience=patience, path=ckpt_dir + '/ckpt.pth', verbose=True) for epoch in range(1, epochs+1): # training train_loss = train(model, optimizer, train_loader) # performance evaluation loss_train, _ = eval(model, train_loader) loss_valid, score_list = eval(model, valid_loader, ks=ks) top1acc = score_list[0] top3acc = score_list[1] top5acc = score_list[2] top10acc = score_list[3] print(f'Epoch: {epoch}/{epochs}, loss_train: {loss_train:.5}, loss_valid: {loss_valid:.5}') print(f'top k accuracy: top1={top1acc:.2}, top3={top3acc:.2}, top5={top5acc:.2}, top10={top10acc:.2}') # early stopping detection earlystopping(loss_valid, model) if earlystopping.early_stop: print('Early Stopping!') print('-'*100) break if __name__ == '__main__': main()