import argparse import os import dgl import torch.utils.data from dgl.dataloading import GraphDataLoader from torch import optim from tqdm import tqdm from QM9_dataset_class import PreprocessedQM9Dataset from model import SimpleGnn, GMae import torch.nn as nn def train_epoch(epoch, graphLoader: torch.utils.data.DataLoader, model: nn.Module,device, optimizer:torch.optim.Optimizer, save_dir:str ): print(f"epoch {epoch} started!") model.train() model.encoder.train() model.decoder.train() model.to(device) loss_epoch = 0 for batch in tqdm(graphLoader): optimizer.zero_grad() batch_g, _ = batch R = batch_g.ndata["R"].to(device) # Z_index = batch_g.ndata["Z_index"].to(device) Z_index = batch_g.ndata["Z_index"].to(device) Z_emb = model.encode_atom_index(Z_index) feat = torch.cat([R, Z_emb], dim=1) batch_g = batch_g.to(device) loss = model.mask_attr_prediction(batch_g, feat) loss.backward() optimizer.step() loss_epoch += loss.item() return loss_epoch def train_loop(dataset_path, epochs, batch_size,device,save_dir): device = torch.device(device) dataset = PreprocessedQM9Dataset(None) dataset.load_dataset(dataset_path) print("Dataset loaded:", dataset_path, "Total samples:", len(dataset)) print("Initializing dataloader") myGLoader = GraphDataLoader(dataset, batch_size=batch_size, pin_memory=True,shuffle=False) sage_enc = SimpleGnn(in_feats=7, hid_feats=4, out_feats=4) # 7 = R_dim(3)+Z_embedding_dim(4) sage_dec = SimpleGnn(in_feats=4, hid_feats=4, out_feats=7) gmae = GMae(sage_enc, sage_dec, 7, 4, 7, replace_rate=0) optimizer = optim.Adam(gmae.parameters(), lr=1e-3) print("Start training", "epochs:", epochs, "batch_size:", batch_size) for epoch in range(epochs): loss_epoch = train_epoch(epoch, myGLoader,gmae,device,optimizer,save_dir) formatted_loss_epoch = f"{loss_epoch:.3f}" save_path = os.path.join(save_dir,f"epoch_{epoch}",f"gmae_{formatted_loss_epoch}.pt") save_subdir = os.path.dirname(save_path) if not os.path.exists(save_subdir): os.makedirs(save_subdir, exist_ok=True) torch.save(gmae.state_dict(), save_path) print(f"Epoch:{epoch},loss:{loss_epoch},Model saved:{save_path}") with torch.no_grad(): embedded_graphs = [] print(f"Epoch:{epoch},start embedding") gmae.eval() gmae.encoder.eval() for batch in tqdm(myGLoader): batch_g, _ = batch R = batch_g.ndata["R"].to(device) Z_index = batch_g.ndata["Z_index"].to(device) Z_emb = gmae.encode_atom_index(Z_index) feat = torch.cat([R, Z_emb], dim=1) batch_g = batch_g.to(device) batch_g.ndata["embedding"] = gmae.embed(batch_g,feat) unbatched_graphs = dgl.unbatch(batch_g) embedded_graphs.extend(unbatched_graphs) for idx,embedded_graph in enumerate(embedded_graphs): embeddings_save_path = os.path.join(save_dir, f"epoch_{epoch}", f"embedding_{idx}.dgl") dgl.save_graphs(embeddings_save_path, [embedded_graph]) print(f"epoch:{epoch},embedding saved:{embeddings_save_path},total_graphs:{len(embedded_graphs)}") def main(): parser = argparse.ArgumentParser(description="Prepare QM9 dataset") parser.add_argument('--dataset_path', type=str, default='dataset/QM9_dataset_processed.pt') parser.add_argument('--batch_size', type=int, default=4) parser.add_argument('--epochs', type=int, default=10, help='number of epochs') parser.add_argument("--device", type=str, default='cuda:0') parser.add_argument("--save_dir", type=str, default='./model') args = parser.parse_args() train_loop(args.dataset_path, args.epochs, args.batch_size,args.device,args.save_dir) if __name__ == '__main__': main()