app.py

import torch
import gradio as gr
import numpy as np
from transformers import T5Tokenizer, T5EncoderModel
import esm
from inference import load_models, predict_ensemble

# 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 ESM model
esm_model, alphabet = esm.pretrained.esm2_t33_650M_UR50D()
batch_converter = alphabet.get_batch_converter()
esm_model.eval()


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)


def extract_esm_embedding(sequence):
    batch_labels, batch_strs, batch_tokens = batch_converter([("protein1", sequence)])
    with torch.no_grad():
        results = esm_model(batch_tokens, repr_layers=[33], return_contacts=False)
    token_representations = results["representations"][33]
    return torch.mean(token_representations[0, 1:len(sequence)+1], dim=0).unsqueeze(0)


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 "Allergen" if pred.item() == 1 else "Non-Allergen"


demo = gr.Interface(fn=classify,
                    inputs=gr.Textbox(lines=3, placeholder="Enter protein sequence..."),
                    outputs=gr.Label(label="Prediction"))

if __name__ == "__main__":
    demo.launch()