BioXP-0.5b-v2 / app.py
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from fastapi import FastAPI, HTTPException
from fastapi.middleware.cors import CORSMiddleware
from pydantic import BaseModel
import torch
from transformers import AutoModelForMultipleChoice, AutoTokenizer
import os
from datasets import load_dataset
import random
from typing import Optional, List
import gradio as gr
app = FastAPI()
# Add CORS middleware for Gradio
app.add_middleware(
CORSMiddleware,
allow_origins=["*"],
allow_credentials=True,
allow_methods=["*"],
allow_headers=["*"],
)
# Define input models
class QuestionRequest(BaseModel):
question: str
options: list[str] # List of 4 options
class DatasetQuestion(BaseModel):
question: str
opa: str
opb: str
opc: str
opd: str
cop: Optional[int] = None # Correct option (0-3)
exp: Optional[str] = None # Explanation if available
# Global variables
model = None
tokenizer = None
dataset = None
def load_model():
global model, tokenizer, dataset
try:
# Load your fine-tuned model and tokenizer
model_name = os.getenv("BioXP-0.5b", "rgb2gbr/GRPO_BioMedmcqa_Qwen2.5-0.5B")
model = AutoModelForMultipleChoice.from_pretrained(model_name)
tokenizer = AutoTokenizer.from_pretrained(model_name)
# Load MedMCQA dataset
dataset = load_dataset("openlifescienceai/medmcqa")
# Move model to GPU if available
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
model = model.to(device)
model.eval()
except Exception as e:
raise Exception(f"Error loading model: {str(e)}")
def predict_gradio(question: str, option_a: str, option_b: str, option_c: str, option_d: str):
"""Gradio interface prediction function"""
try:
options = [option_a, option_b, option_c, option_d]
inputs = []
for option in options:
text = f"{question} {option}"
inputs.append(text)
encodings = tokenizer(
inputs,
padding=True,
truncation=True,
max_length=512,
return_tensors="pt"
)
device = next(model.parameters()).device
encodings = {k: v.to(device) for k, v in encodings.items()}
with torch.no_grad():
outputs = model(**encodings)
logits = outputs.logits
probabilities = torch.softmax(logits, dim=1)[0].tolist()
predicted_class = torch.argmax(logits, dim=1).item()
# Format the output for Gradio
result = f"Predicted Answer: {options[predicted_class]}\n\n"
result += "Confidence Scores:\n"
for i, (opt, prob) in enumerate(zip(options, probabilities)):
result += f"{opt}: {prob:.2%}\n"
return result
except Exception as e:
return f"Error: {str(e)}"
def get_random_question():
"""Get a random question for Gradio interface"""
if dataset is None:
return "Error: Dataset not loaded", "", "", "", ""
index = random.randint(0, len(dataset['train']) - 1)
question_data = dataset['train'][index]
return (
question_data['question'],
question_data['opa'],
question_data['opb'],
question_data['opc'],
question_data['opd']
)
# Create Gradio interface
with gr.Blocks(title="Medical MCQ Predictor") as demo:
gr.Markdown("# Medical MCQ Predictor")
gr.Markdown("Enter a medical question and its options, or get a random question from MedMCQA dataset.")
with gr.Row():
with gr.Column():
question = gr.Textbox(label="Question", lines=3)
option_a = gr.Textbox(label="Option A")
option_b = gr.Textbox(label="Option B")
option_c = gr.Textbox(label="Option C")
option_d = gr.Textbox(label="Option D")
with gr.Row():
predict_btn = gr.Button("Predict")
random_btn = gr.Button("Get Random Question")
output = gr.Textbox(label="Prediction", lines=5)
predict_btn.click(
fn=predict_gradio,
inputs=[question, option_a, option_b, option_c, option_d],
outputs=output
)
random_btn.click(
fn=get_random_question,
inputs=[],
outputs=[question, option_a, option_b, option_c, option_d]
)
# Mount Gradio app to FastAPI
app = gr.mount_gradio_app(app, demo, path="/")
@app.on_event("startup")
async def startup_event():
load_model()
@app.get("/dataset/question")
async def get_dataset_question(index: Optional[int] = None, random_question: bool = False):
"""Get a question from the MedMCQA dataset"""
try:
if dataset is None:
raise HTTPException(status_code=500, detail="Dataset not loaded")
if random_question:
index = random.randint(0, len(dataset['train']) - 1)
elif index is None:
raise HTTPException(status_code=400, detail="Either index or random_question must be provided")
question_data = dataset['train'][index]
question = DatasetQuestion(
question=question_data['question'],
opa=question_data['opa'],
opb=question_data['opb'],
opc=question_data['opc'],
opd=question_data['opd'],
cop=question_data['cop'] if 'cop' in question_data else None,
exp=question_data['exp'] if 'exp' in question_data else None
)
return question
except Exception as e:
raise HTTPException(status_code=500, detail=str(e))
@app.post("/predict")
async def predict(request: QuestionRequest):
if len(request.options) != 4:
raise HTTPException(status_code=400, detail="Exactly 4 options are required")
try:
inputs = []
for option in request.options:
text = f"{request.question} {option}"
inputs.append(text)
encodings = tokenizer(
inputs,
padding=True,
truncation=True,
max_length=512,
return_tensors="pt"
)
device = next(model.parameters()).device
encodings = {k: v.to(device) for k, v in encodings.items()}
with torch.no_grad():
outputs = model(**encodings)
logits = outputs.logits
probabilities = torch.softmax(logits, dim=1)[0].tolist()
predicted_class = torch.argmax(logits, dim=1).item()
response = {
"predicted_option": request.options[predicted_class],
"option_index": predicted_class,
"confidence": probabilities[predicted_class],
"probabilities": {
f"option_{i}": prob for i, prob in enumerate(probabilities)
}
}
return response
except Exception as e:
raise HTTPException(status_code=500, detail=str(e))
@app.get("/health")
async def health_check():
return {
"status": "healthy",
"model_loaded": model is not None,
"dataset_loaded": dataset is not None
}