add run.py

Graph/GraphMAE_MQ9/run.py

@@ -0,0 +1,94 @@
+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()