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# -*- coding: utf-8 -*-
"""BioGPT-QA-PubMedQA-BioGPT-Large.ipynb
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1grmKyUETABgEsC3hO7CKgnSG1JGBbmHV
"""
from transformers import AutoTokenizer, AutoModelForCausalLM
import gradio as gr
import torch
import re
tokenizer = AutoTokenizer.from_pretrained("microsoft/BioGPT-Large-PubMedQA")
model = AutoModelForCausalLM.from_pretrained("microsoft/BioGPT-Large-PubMedQA")
# Check if GPU is available and move model to GPU
if torch.cuda.is_available():
device = torch.device("cuda")
model.to(device)
print("Using GPU:", torch.cuda.get_device_name(0))
else:
device = torch.device("cpu")
print("Using CPU")
def answer_bio_question(question, context):
"""Answers a biological question using BioGPT-QA-PubMedQA-BioGPT-Large.
Args:
question: The question to be answered.
context: The context or passage containing the answer (concatenated with the question).
Returns:
The answer extracted from the context based on the question.
"""
try:
# Concatenate question and context with a separator
input_ids = tokenizer(question + " [SEP] " + context, return_tensors="pt").to(device)
# Move the input to the chosen device (GPU or CPU)
input_ids = input_ids.to(device)
outputs = model.generate(**input_ids,
max_new_tokens=1024
,
num_beams=1,
early_stopping=False,
do_sample=False,
)
answer = tokenizer.decode(outputs[0], skip_special_tokens=True)
print(answer)
segs = re.search(r"the answer to the question given the context is(.*)", answer)
ans = "unknown"
if segs is not None:
segs = segs.groups()
ans = segs[0].strip()
return "The answer to this question is " + ans
except Exception as e:
print(f"Error during question answering: {e}")
return "An error occurred during question answering. Please try again."
iface = gr.Interface(
fn=answer_bio_question,
inputs=[
gr.Textbox(label="Question", lines=2),
gr.Textbox(label="Context (Passage)", lines=5),
],
outputs="textbox",
title="BioGPT-QA: Answer Biological Questions",
)
# Launch the Gradio interface
iface.launch( debug=True, share=True)
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