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 generated_peptide.replace(' ', '')



# Define the Gradio interface
interface = gr.Interface(
    fn=generate_peptide,
    inputs=[
        gr.Textbox(label="Protein Sequence", info = "Enter protein sequence here", type="text"),
        gr.Slider(3, 50, value=15, label="Peptide Length",
        info='Default value is 15'),
        gr.Slider(1, 10, value=3, label="Top K Value", default="3",
        info='Default value is 3')
        ],
    outputs="textbox",
)

interface.launch()