diff --git a/models/analysis/multimodal_integrator.py b/models/analysis/multimodal_integrator.py
index a1d5477..465a0f6 100644
--- a/models/analysis/multimodal_integrator.py
+++ b/models/analysis/multimodal_integrator.py
@@ -162,27 +162,43 @@ def forward(
         structure_features: torch.Tensor,
         function_results: Dict[str, torch.Tensor]
     ) -> Dict[str, torch.Tensor]:
+        # Add debug prints for input shapes
+        print(f"Sequence features shape: {sequence_features.shape}")
+        print(f"Structure features shape: {structure_features.shape}")
+        print(f"Function results GO terms shape: {function_results['go_terms'].shape}")
+
         # Transform function features to match dimensions
         function_features = self.function_encoder(function_results['go_terms'])
+        print(f"Transformed function features shape: {function_features.shape}")
 
         # Ensure all features have the same dimensions before combining
         batch_size = sequence_features.size(0)
         seq_len = sequence_features.size(1)
+        feature_dim = sequence_features.size(2)  # Should be 768
+
+        # Reshape features if needed
+        sequence_features = sequence_features.view(batch_size, seq_len, feature_dim)
+        structure_features = structure_features.view(batch_size, seq_len, feature_dim)
+        function_features = function_features.view(batch_size, seq_len, feature_dim)
 
-        # Reshape function features if needed
-        function_features = function_features.view(batch_size, seq_len, -1)
+        print(f"Reshaped sequence features: {sequence_features.shape}")
+        print(f"Reshaped structure features: {structure_features.shape}")
+        print(f"Reshaped function features: {function_features.shape}")
 
         # Combine all features
         combined_features = torch.cat([
             sequence_features,
             structure_features,
             function_features
-        ], dim=-1)
+        ], dim=-1)  # Concatenate along feature dimension
+
+        print(f"Combined features shape: {combined_features.shape}")
 
-        # Generate unified representation
+        # Process through integration network
         unified_features = self.integration_network(combined_features)
+        print(f"Unified features shape: {unified_features.shape}")
 
-        # Estimate prediction confidence
+        # Estimate confidence
         confidence = self.confidence_estimator(unified_features)
 
         return {