app.py

import gradio as gr
from transformers import AutoTokenizer, AutoModelForMaskedLM
import torch
from torch.distributions.categorical import Categorical

# Load the model and tokenizer
tokenizer = AutoTokenizer.from_pretrained("TianlaiChen/PepMLM-650M")
model = AutoModelForMaskedLM.from_pretrained("TianlaiChen/PepMLM-650M")

def generate_peptide(protein_seq, peptide_length, top_k):
    peptide_length = int(peptide_length)
    top_k = int(top_k)
    
    masked_peptide = '<mask>' * peptide_length
    input_sequence = protein_seq + masked_peptide
    inputs = tokenizer(input_sequence, return_tensors="pt").to(model.device)

    with torch.no_grad():
        logits = model(**inputs).logits
    mask_token_indices = (inputs["input_ids"] == tokenizer.mask_token_id).nonzero(as_tuple=True)[1]
    logits_at_masks = logits[0, mask_token_indices]
    
    # Apply top-k sampling
    top_k_logits, top_k_indices = logits_at_masks.topk(top_k, dim=-1)
    probabilities = torch.nn.functional.softmax(top_k_logits, dim=-1)
    predicted_indices = Categorical(probabilities).sample()
    predicted_token_ids = top_k_indices.gather(-1, predicted_indices.unsqueeze(-1)).squeeze(-1)

    generated_peptide = tokenizer.decode(predicted_token_ids, skip_special_tokens=True)
    return f"Generated Sequence: {generated_peptide.replace(' ', '')}"

# Define the Gradio interface
interface = gr.Interface(
    fn=generate_peptide,
    inputs=[
        gr.inputs.Textbox(label="Protein Sequence", default="Enter protein sequence here", type="text"),
        gr.inputs.Dropdown(choices=[str(i) for i in range(2, 51)], label="Peptide Length", default="15"),
        gr.inputs.Dropdown(choices=[str(i) for i in range(1, 11)], label="Top K Value", default="3")
    ],
    outputs="textbox",
    live=True
)

interface.launch()