Update requirements and make necessary code changes

.ipynb_checkpoints/app-checkpoint.py

@@ -99,6 +99,7 @@ def predict_protein_sequence(test_one_letter_sequence):
     
     device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
     model.to(device)
+    model.eval()
     for batch in test_loader:
         input_ids = batch['input_ids'].to(device)
         attention_mask = batch['attention_mask'].to(device)
@@ -106,13 +107,12 @@ def predict_protein_sequence(test_one_letter_sequence):
     
         outputs = model(input_ids, attention_mask=attention_mask)
         logits = outputs.logits.detach().cpu().numpy()
-    
+
+    logits = logits[:, :-1] #remove for prot_t5 the last element, because it is a special token
     logits=convert_predictions(logits)
-    logits.shape
-    
-    
-    
+      
     normalized_scores = normalize_scores(logits)
+    test_one_letter_sequence = test_one_letter_sequence.replace(" ", "")
     
     result_str = "\n".join([f"{aa}: {score:.2f}" for aa, score in zip(test_one_letter_sequence, normalized_scores)])
 

app.py

@@ -99,6 +99,7 @@ def predict_protein_sequence(test_one_letter_sequence):
     
     device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
     model.to(device)
+    model.eval()
     for batch in test_loader:
         input_ids = batch['input_ids'].to(device)
         attention_mask = batch['attention_mask'].to(device)
@@ -106,13 +107,12 @@ def predict_protein_sequence(test_one_letter_sequence):
     
         outputs = model(input_ids, attention_mask=attention_mask)
         logits = outputs.logits.detach().cpu().numpy()
-    
+
+    logits = logits[:, :-1] #remove for prot_t5 the last element, because it is a special token
     logits=convert_predictions(logits)
-    logits.shape
-    
-    
-    
+      
     normalized_scores = normalize_scores(logits)
+    test_one_letter_sequence = test_one_letter_sequence.replace(" ", "")
     
     result_str = "\n".join([f"{aa}: {score:.2f}" for aa, score in zip(test_one_letter_sequence, normalized_scores)])