Update input sequence description

app.py

@@ -1,81 +1,84 @@
-import torch
-import gradio as gr
-import numpy as np
-from transformers import T5Tokenizer, T5EncoderModel
-import esm
-from inference import load_models, predict_ensemble
-from transformers import AutoTokenizer, AutoModel
-import spaces
-
-# Load trained models
-model_protT5, model_cat = load_models()
-
-# Load ProtT5 model
-tokenizer_t5 = T5Tokenizer.from_pretrained("Rostlab/prot_t5_xl_uniref50", do_lower_case=False)
-model_t5 = T5EncoderModel.from_pretrained("Rostlab/prot_t5_xl_uniref50")
-model_t5 = model_t5.eval()
-
-# Load the tokenizer and model
-model_name = "facebook/esm2_t33_650M_UR50D"
-tokenizer_esm = AutoTokenizer.from_pretrained(model_name)
-esm_model = AutoModel.from_pretrained(model_name)
-
-def extract_prott5_embedding(sequence):
-    sequence = sequence.replace(" ", "")
-    seq = " ".join(list(sequence))
-    ids = tokenizer_t5(seq, return_tensors="pt", padding=True)
-    with torch.no_grad():
-        embedding = model_t5(**ids).last_hidden_state
-    return torch.mean(embedding, dim=1)
-
-
-# Extract ESM2 embedding
-def extract_esm_embedding(sequence):
-    # Tokenize the sequence
-    inputs = tokenizer_esm(sequence, return_tensors="pt", padding=True, truncation=True)
-    
-    # Forward pass through the model
-    with torch.no_grad():
-        outputs = esm_model(**inputs)
-    
-    # Extract the embeddings from the 33rd layer (ESM2 layer)
-    token_representations = outputs.last_hidden_state  # This is the default layer
-    return torch.mean(token_representations[0, 1:len(sequence)+1], dim=0).unsqueeze(0)
-
-def estimate_duration(sequence):
-    # Estimate duration based on sequence length
-    base_time = 30  # Base time in seconds
-    time_per_residue = 0.5  # Estimated time per residue
-    estimated_time = base_time + len(sequence) * time_per_residue
-    return min(int(estimated_time), 300)  # Cap at 300 seconds
-
-@spaces.GPU(duration=120)
-def classify(sequence):
-    protT5_emb = extract_prott5_embedding(sequence)
-    esm_emb = extract_esm_embedding(sequence)
-    concat = torch.cat((esm_emb, protT5_emb), dim=1)
-    pred = predict_ensemble(protT5_emb, concat, model_protT5, model_cat)
-    return "Potential Allergen" if pred.item() == 1 else "Non-Allergen"
-
-description_md = """
-## 📌 **About AllerTrans – A Powerful Tool for Predicting the Allergenicity of Protein Sequences**
-
-**🧬 Input Format – FASTA Sequences:** This tool accepts protein sequences in FASTA format.
-
-**🧾 Output Explanation** – AllerTrans classifies your input sequence into one of the following categories:
-###### **🟢 Non-Allergen:** The protein is unlikely to cause an allergic reaction and can be considered safe regarding allergenicity.
-###### **🔴 Potential Allergen:** The protein has the potential to trigger an allergic response or exhibit cross-reactivity in some individuals.
-
-**🔎 Caution & Disclaimer:**
-###### Our model has demonstrated promising performance on the AlgPred 2.0 validation set, which includes a wide range of allergenic and non-allergenic sequences from diverse sources. AllerTrans is also capable of handling recombinant proteins, as supported by additional evaluation using a recombinant protein dataset from UniProt. However, **we advise caution when using this tool on all constructs and modifications of recombinant proteins**. The model's generalizability across various recombinant scenarios has yet to be fully explored.
-
-###### 🚨 Remember, AllerTrans is designed as a reliable screening tool. However, for clinical or regulatory decisions, always confirm the prediction results through experimental validation.
-""" 
-
-demo = gr.Interface(fn=classify,
-                    inputs=gr.Textbox(lines=3, placeholder="Enter protein sequence..."),
-                    outputs=gr.Label(label="Prediction"),
-                    description=description_md)
-
-if __name__ == "__main__":
+import torch
+import gradio as gr
+import numpy as np
+from transformers import T5Tokenizer, T5EncoderModel
+import esm
+from inference import load_models, predict_ensemble
+from transformers import AutoTokenizer, AutoModel
+import spaces
+
+# Load trained models
+model_protT5, model_cat = load_models()
+
+# Load ProtT5 model
+tokenizer_t5 = T5Tokenizer.from_pretrained("Rostlab/prot_t5_xl_uniref50", do_lower_case=False)
+model_t5 = T5EncoderModel.from_pretrained("Rostlab/prot_t5_xl_uniref50")
+model_t5 = model_t5.eval()
+
+# Load the tokenizer and model
+model_name = "facebook/esm2_t33_650M_UR50D"
+tokenizer_esm = AutoTokenizer.from_pretrained(model_name)
+esm_model = AutoModel.from_pretrained(model_name)
+
+def extract_prott5_embedding(sequence):
+    sequence = sequence.replace(" ", "")
+    seq = " ".join(list(sequence))
+    ids = tokenizer_t5(seq, return_tensors="pt", padding=True)
+    with torch.no_grad():
+        embedding = model_t5(**ids).last_hidden_state
+    return torch.mean(embedding, dim=1)
+
+
+# Extract ESM2 embedding
+def extract_esm_embedding(sequence):
+    # Tokenize the sequence
+    inputs = tokenizer_esm(sequence, return_tensors="pt", padding=True, truncation=True)
+    
+    # Forward pass through the model
+    with torch.no_grad():
+        outputs = esm_model(**inputs)
+    
+    # Extract the embeddings from the 33rd layer (ESM2 layer)
+    token_representations = outputs.last_hidden_state  # This is the default layer
+    return torch.mean(token_representations[0, 1:len(sequence)+1], dim=0).unsqueeze(0)
+
+def estimate_duration(sequence):
+    # Estimate duration based on sequence length
+    base_time = 30  # Base time in seconds
+    time_per_residue = 0.5  # Estimated time per residue
+    estimated_time = base_time + len(sequence) * time_per_residue
+    return min(int(estimated_time), 300)  # Cap at 300 seconds
+
+@spaces.GPU(duration=120)
+def classify(sequence):
+    protT5_emb = extract_prott5_embedding(sequence)
+    esm_emb = extract_esm_embedding(sequence)
+    concat = torch.cat((esm_emb, protT5_emb), dim=1)
+    pred = predict_ensemble(protT5_emb, concat, model_protT5, model_cat)
+    return "Potential Allergen" if pred.item() == 1 else "Non-Allergen"
+
+description_md = """
+## 📌 **About AllerTrans – A Powerful Tool for Predicting the Allergenicity of Protein Sequences**
+
+**🧬 Input Format – FASTA Sequences:** This tool accepts protein sequences in FASTA format. 
+
+Please provide a single protein sequence at a time.
+For faster predictions, you may enter only the amino acid sequence, without the FASTA header or any additional information.
+
+**🧾 Output Explanation** – AllerTrans classifies your input sequence into one of the following categories:
+###### **🟢 Non-Allergen:** The protein is unlikely to cause an allergic reaction and can be considered safe regarding allergenicity.
+###### **🔴 Potential Allergen:** The protein has the potential to trigger an allergic response or exhibit cross-reactivity in some individuals.
+
+**🔎 Caution & Disclaimer:**
+###### Our model has demonstrated promising performance on the AlgPred 2.0 validation set, which includes a wide range of allergenic and non-allergenic sequences from diverse sources. AllerTrans is also capable of handling recombinant proteins, as supported by additional evaluation using a recombinant protein dataset from UniProt. However, **we advise caution when using this tool on all constructs and modifications of recombinant proteins**. The model's generalizability across various recombinant scenarios has yet to be fully explored.
+
+###### 🚨 Remember, AllerTrans is designed as a reliable screening tool. However, for clinical or regulatory decisions, always confirm the prediction results through experimental validation.
+""" 
+
+demo = gr.Interface(fn=classify,
+                    inputs=gr.Textbox(lines=3, placeholder="Enter protein sequence..."),
+                    outputs=gr.Label(label="Prediction"),
+                    description=description_md)
+
+if __name__ == "__main__":
     demo.launch()