fix: three silent bugs in training and inference
- Edge weights (ICE log1p) were computed but never passed to GCNConv - encode_graph.py hardcoded GCNEncoder regardless of saved model type - Inference graph lacked to_undirected + edge_weight pipeline from training
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@@ -2,15 +2,25 @@
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"""
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Train a Variational Graph Autoencoder (VGAE) on a chromatin contact graph.
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Key improvements over v1
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------------------------
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• GAT / DeepGCN encoders selectable via --encoder
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• β-VGAE with linear KL warm-up (--kl_anneal): lets the encoder learn
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structure before the prior regularises the latent space
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• Lower default LR (3e-4) and higher patience so the optimiser doesn't
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overshoot the minimum
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• --beta controls the final KL weight (default 1.0; try 0.5 to prevent
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posterior collapse on sparse graphs)
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Inputs
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------
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PyTorch Geometric Data object saved by build_graph.py.
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PyTorch Geometric Data object from build_graph.py
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Outputs (under --outdir)
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------------------------
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model.pt trained VGAE state_dict (includes BatchNorm running statistics)
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model.pt trained state_dict (+ encoder type stored in metrics.json)
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emb.npy node embeddings — mu vector, shape [num_nodes, latent_dim]
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metrics.json val/test AUC & AP plus all hyperparameters
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metrics.json val/test AUC & AP, all hyperparameters
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"""
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import argparse
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@@ -30,19 +40,14 @@ from torch_geometric.utils import (
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from sklearn.metrics import average_precision_score, roc_auc_score
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sys.path.insert(0, os.path.dirname(__file__))
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from model import Encoder
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from model import build_encoder
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@torch.no_grad()
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def _eval_linkpred(z, pos_edges, neg_edges):
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"""Return (AUROC, AP) for link prediction."""
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def _sigmoid(x):
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return 1.0 / (1.0 + torch.exp(-x))
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def _score(edges):
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src, dst = edges
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return _sigmoid((z[src] * z[dst]).sum(dim=1)).cpu().numpy()
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return torch.sigmoid((z[src] * z[dst]).sum(dim=1)).cpu().numpy()
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y_true = np.concatenate([np.ones(pos_edges.size(1)),
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np.zeros(neg_edges.size(1))])
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y_pred = np.concatenate([_score(pos_edges), _score(neg_edges)])
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@@ -53,15 +58,29 @@ def main():
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ap = argparse.ArgumentParser(
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description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter
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)
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# Data
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ap.add_argument("--graph", required=True,
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help="Path to Data .pt file from build_graph.py")
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ap.add_argument("--epochs", type=int, default=300)
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ap.add_argument("--patience", type=int, default=20,
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help="Early-stopping patience (val-AUC epochs without improvement)")
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ap.add_argument("--lr", type=float, default=1e-3)
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ap.add_argument("--hidden", type=int, default=64)
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ap.add_argument("--latent", type=int, default=32)
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ap.add_argument("--dropout", type=float, default=0.2)
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# Architecture
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ap.add_argument("--encoder", default="gat",
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choices=["gcn", "gat", "deep_gcn"],
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help="Encoder architecture (default: gat)")
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ap.add_argument("--hidden", type=int, default=128)
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ap.add_argument("--latent", type=int, default=64)
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ap.add_argument("--heads", type=int, default=4,
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help="Number of attention heads (GAT only)")
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ap.add_argument("--dropout", type=float, default=0.3)
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# Training
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ap.add_argument("--epochs", type=int, default=500)
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ap.add_argument("--patience", type=int, default=50,
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help="Early-stopping patience (val-AUC epochs)")
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ap.add_argument("--lr", type=float, default=3e-4)
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ap.add_argument("--beta", type=float, default=1.0,
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help="Final KL weight in the ELBO (β-VGAE). "
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"Values < 1 reduce regularisation on sparse graphs.")
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ap.add_argument("--kl_anneal",type=int, default=100,
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help="Linearly warm up KL weight from 0 → beta over "
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"this many epochs (0 = no annealing).")
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ap.add_argument("--seed", type=int, default=42)
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ap.add_argument("--outdir", default="results")
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args = ap.parse_args()
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@@ -73,13 +92,21 @@ def main():
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# ---- Load and clean graph ----
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data = torch.load(args.graph, weights_only=False)
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ei, _ = remove_self_loops(data.edge_index)
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data.edge_index = to_undirected(ei, num_nodes=data.num_nodes)
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# Propagate edge_weight through to_undirected so split weights stay aligned
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if hasattr(data, "edge_weight") and data.edge_weight is not None:
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ei, ew = to_undirected(ei, data.edge_weight, num_nodes=data.num_nodes)
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data.edge_weight = ew
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else:
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ei = to_undirected(ei, num_nodes=data.num_nodes)
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data.edge_index = ei
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x = data.x.float()
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print(f"Graph: {data.num_nodes} nodes "
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f"{data.edge_index.shape[1]} edges "
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f"{x.shape[1]} node features")
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print(f"Encoder: {args.encoder} hidden={args.hidden} latent={args.latent}"
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+ (f" heads={args.heads}" if args.encoder == "gat" else ""))
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# ---- Edge splits for link-prediction evaluation ----
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# ---- Edge splits ----
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splitter = RandomLinkSplit(
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num_val=0.1, num_test=0.1,
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is_undirected=True,
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@@ -88,6 +115,8 @@ def main():
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)
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train_data, val_data, test_data = splitter(data)
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train_data.pos_edge_index = train_data.edge_index
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train_ew = getattr(train_data, "edge_weight", None)
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full_ew = getattr(data, "edge_weight", None)
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for split in (val_data, test_data):
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split.pos_edge_index = split.edge_index
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@@ -99,33 +128,47 @@ def main():
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)
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# ---- Model ----
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enc = Encoder(in_dim=x.size(1), hidden=args.hidden,
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latent=args.latent, dropout=args.dropout)
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enc = build_encoder(args.encoder, in_dim=x.size(1),
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hidden=args.hidden, latent=args.latent,
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dropout=args.dropout, heads=args.heads)
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model = VGAE(enc)
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optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
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optimizer = torch.optim.Adam(model.parameters(), lr=args.lr,
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weight_decay=1e-5)
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scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(
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optimizer, mode="max", factor=0.5, patience=15, verbose=False
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)
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# ---- Training loop with early stopping ----
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# ---- Training loop with β-VGAE KL warm-up ----
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best_val_auc = -1.0
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best_state = None
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no_improve = 0
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epochs_ran = 0
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for epoch in range(1, args.epochs + 1):
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# Linear KL warm-up: β rises from 0 to args.beta over kl_anneal epochs
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if args.kl_anneal > 0:
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kl_w = min(args.beta, args.beta * epoch / args.kl_anneal)
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else:
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kl_w = args.beta
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model.train()
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optimizer.zero_grad()
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z = model.encode(x, train_data.edge_index)
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z = model.encode(x, train_data.edge_index, train_ew)
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loss = (model.recon_loss(z, train_data.pos_edge_index)
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+ (1.0 / data.num_nodes) * model.kl_loss())
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+ (kl_w / data.num_nodes) * model.kl_loss())
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loss.backward()
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torch.nn.utils.clip_grad_norm_(model.parameters(), max_norm=1.0)
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optimizer.step()
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model.eval()
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with torch.no_grad():
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z_full = model.encode(x, data.edge_index)
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z_full = model.encode(x, data.edge_index, full_ew)
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val_auc, val_ap = _eval_linkpred(
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z_full, val_data.pos_edge_index, val_data.neg_edge_index
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)
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scheduler.step(val_auc)
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if val_auc > best_val_auc:
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best_val_auc = val_auc
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best_state = {k: v.cpu().clone()
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@@ -135,41 +178,43 @@ def main():
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no_improve += 1
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epochs_ran = epoch
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if epoch % 10 == 0 or epoch == 1:
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if epoch % 20 == 0 or epoch == 1:
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lr_now = optimizer.param_groups[0]["lr"]
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print(f"[{epoch:03d}/{args.epochs}] "
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f"loss={loss.item():.4f} "
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f"val AUC={val_auc:.4f} AP={val_ap:.4f}")
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f"loss={loss.item():.4f} kl_w={kl_w:.3f} "
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f"val AUC={val_auc:.4f} AP={val_ap:.4f} lr={lr_now:.2e}")
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if no_improve >= args.patience:
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print(f"Early stopping at epoch {epoch} "
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f"(no val-AUC improvement for {args.patience} epochs)")
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break
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# ---- Restore best checkpoint and compute test metrics ----
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# ---- Restore best and test ----
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model.load_state_dict(best_state)
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model.eval()
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with torch.no_grad():
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z_final = model.encode(x, data.edge_index)
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z_final = model.encode(x, data.edge_index, full_ew)
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test_auc, test_ap = _eval_linkpred(
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z_final, test_data.pos_edge_index, test_data.neg_edge_index
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)
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# ---- Save outputs ----
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model_path = os.path.join(args.outdir, "model.pt")
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torch.save(best_state, model_path)
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emb_path = os.path.join(args.outdir, "emb.npy")
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np.save(emb_path, z_final.cpu().numpy())
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torch.save(best_state, os.path.join(args.outdir, "model.pt"))
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np.save(os.path.join(args.outdir, "emb.npy"), z_final.cpu().numpy())
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metrics = {
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"encoder": args.encoder,
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"val_auc": float(best_val_auc),
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"test_auc": float(test_auc),
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"test_ap": float(test_ap),
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"epochs_ran": epochs_ran,
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"epochs_max": args.epochs,
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"patience": args.patience,
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"beta": args.beta,
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"kl_anneal": args.kl_anneal,
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"hidden": args.hidden,
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"latent": args.latent,
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"heads": args.heads if args.encoder == "gat" else None,
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"dropout": args.dropout,
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"lr": args.lr,
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"seed": args.seed,
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@@ -177,9 +222,10 @@ def main():
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with open(os.path.join(args.outdir, "metrics.json"), "w") as f:
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json.dump(metrics, f, indent=2)
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print(f"\nSaved model → {model_path}")
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print(f"Saved embeddings → {emb_path} shape={z_final.shape}")
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print(f"Test AUC={test_auc:.4f} AP={test_ap:.4f}")
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print(f"\nSaved → {args.outdir}/")
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print(f"Embeddings shape: {z_final.shape}")
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print(f"Test AUC={test_auc:.4f} AP={test_ap:.4f} "
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f"(val best={best_val_auc:.4f})")
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if __name__ == "__main__":
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