app.py

import gradio as gr
from transformers import AutoTokenizer, AutoModelForCausalLM
import torch, re

MODEL_ID = "llm-rna-api-rmit/rna-structure-model"  # your uploaded model

tokenizer = AutoTokenizer.from_pretrained(MODEL_ID)
model = AutoModelForCausalLM.from_pretrained(MODEL_ID)

DB_FULL = re.compile(r"^[().]+$")
DB_SCAN = re.compile(r"[().]{5,}")

def _generate(prompt, max_new_tokens=512, temperature=0.0):
    with torch.no_grad():
        inputs = tokenizer(prompt, return_tensors="pt")
        outputs = model.generate(
            **inputs,
            max_new_tokens=max_new_tokens,
            temperature=temperature,
            do_sample=(temperature > 0),
            pad_token_id=tokenizer.eos_token_id,
            eos_token_id=tokenizer.eos_token_id,
        )
    return tokenizer.decode(outputs[0], skip_special_tokens=True)

def _extract_dotbracket(text, length):
    s = text.strip()
    if len(s) == length and DB_FULL.match(s):
        return s
    for m in DB_SCAN.finditer(text):
        cand = m.group(0)
        if len(cand) == length:
            return cand
    return None

def predict(seq):
    seq = (seq or "").strip().upper()
    if not seq or not set(seq) <= {"A","U","C","G"}:
        return "Please enter an RNA sequence (A/U/C/G)."

    n = len(seq)
    prompt = f"RNA: {seq}\nDot-bracket structure:"
    text = _generate(prompt, max_new_tokens=n + 10, temperature=0.0)
    db_chars = [c for c in text if c in "()."]
    db = "".join(db_chars)
    if len(db) == n:
        return db
    for m in DB_SCAN.finditer(text):
        cand = m.group(0)
        if len(cand) == n:
            return cand
    return text.strip()


demo = gr.Interface(
    fn=predict,
    inputs=gr.Textbox(lines=4, label="RNA Sequence (A/U/C/G)"),
    outputs=gr.Textbox(lines=6, label="Predicted Dot-Bracket Structure"),
    title="RNA Structure Predictor",
    description="Uses your fine-tuned model to output RNA secondary structure in dot-bracket notation."
)

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