fix: fix fetching protein embeddings in the dataset.py

Floto-Lab · Feb 1, 2025 · e20ea14 · e20ea14
1 parent 306e38e
commit e20ea14
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/bactgraph/modeling/model.py b/bactgraph/modeling/model.py
@@ -133,7 +133,7 @@ def forward(self, x: torch.Tensor, edge_index: torch.Tensor):
     def training_step(self, batch, batch_idx):
         """Training step."""
         x_batch, edge_index_batch, y = batch
-        x, edge_index = batch_into_single_graph(x_batch, edge_index_batch)
+        x, edge_index, _ = batch_into_single_graph(x_batch, edge_index_batch)
         print(x.shape, edge_index.shape, y.shape)
         preds = self.forward(x, edge_index)
         # Squeeze if your output_dim=1 to match target shape
@@ -144,7 +144,7 @@ def training_step(self, batch, batch_idx):
     def validation_step(self, batch, batch_idx):
         """Validation step"""
         x_batch, edge_index_batch, y = batch
-        x, edge_index = batch_into_single_graph(x_batch, edge_index_batch)
+        x, edge_index, _ = batch_into_single_graph(x_batch, edge_index_batch)
         print(x.shape, edge_index.shape, y.shape)
         preds = self.forward(x, edge_index)
 
@@ -160,7 +160,7 @@ def validation_step(self, batch, batch_idx):
     def test_step(self, batch, batch_idx) -> dict:
         """Test step."""
         x_batch, edge_index_batch, y = batch
-        x, edge_index = batch_into_single_graph(x_batch, edge_index_batch)
+        x, edge_index, _ = batch_into_single_graph(x_batch, edge_index_batch)
         preds = self.forward(x, edge_index)
 
         loss = F.mse_loss(preds.squeeze(), y.view(-1))