import os import json import tqdm import argparse from openai import OpenAI # ----------------------------- # CONFIGURATION # ----------------------------- # Ensure this matches the model path used in your run_vllm.sh script MODEL_NAME = "/home/mshahidul/readctrl_model/full_model/qwen3-32B_subclaims_BF16_merged" API_URL = "http://localhost:8015/v1" API_KEY = "EMPTY" # vLLM requires a key, but it can be anything if not set on server # Initialize Client client = OpenAI(base_url=API_URL, api_key=API_KEY) # ----------------------------- # SUBCLAIM EXTRACTION PROMPT # ----------------------------- def extraction_prompt(medical_text: str) -> str: prompt = f""" You are an expert medical annotator. Your task is to extract granular, factual subclaims from medical text. A subclaim is the smallest standalone factual unit that can be independently verified. Instructions: 1. Read the provided medical text. 2. Break it into clear, objective, atomic subclaims. 3. Each subclaim must come directly from the text. 4. Do not add, guess, or infer information. 5. Each subclaim should be short, specific, and verifiable. 6. Return ONLY a Python-style list of strings. Medical Text: {medical_text} Return your output in JSON list format, like: [ "subclaim 1", "subclaim 2", ... ] """ return prompt # ----------------------------- # INFERENCE FUNCTION (vLLM) # ----------------------------- def infer_subclaims(medical_text: str, temperature: float = 0.2) -> str: """Sends prompt to vLLM server and returns generated text.""" # 1. Prepare the prompt final_prompt = extraction_prompt(medical_text) # 2. Call the vLLM Server via OpenAI API try: response = client.chat.completions.create( model=MODEL_NAME, messages=[ {"role": "user", "content": final_prompt} ], max_tokens=1000, # Limit generation length temperature=temperature, top_p=0.9, frequency_penalty=0.0, presence_penalty=0.0, ) res = response.choices[0].message.content.strip() res=res.split("")[-1].strip() return res except Exception as e: print(f"Error during API call: {e}") return None # ----------------------------- # MAIN EXECUTION # ----------------------------- if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument("--input_file", type=str, required=True, help="Path to the input JSON file containing medical texts.") args = parser.parse_args() INPUT_FILE = args.input_file file_name = os.path.basename(INPUT_FILE).split(".json")[0] SAVE_FOLDER = "/home/mshahidul/readctrl/data/extracting_subclaim" os.makedirs(SAVE_FOLDER, exist_ok=True) OUTPUT_FILE = os.path.join(SAVE_FOLDER, f"extracted_subclaims_{file_name}.json") # Load input dataset with open(INPUT_FILE, "r") as f: data = json.load(f) # Load existing results (resume mode) result = [] if os.path.exists(OUTPUT_FILE): with open(OUTPUT_FILE, "r") as f: try: result = json.load(f) except json.JSONDecodeError: result = [] existing_ids = {item["id"] for item in result} print(f"Starting inference on {len(data)} items using vLLM server...") save=False # -------------------------------------------------------- # PROCESS EACH MEDICAL TEXT # -------------------------------------------------------- for item in tqdm.tqdm(data): if item["id"] in existing_ids: continue medical_text = item.get("fulltext", "") # Call the vLLM inference function extracted = infer_subclaims(medical_text) result.append({ "id": item["id"], "medical_text": medical_text, "subclaims": extracted, "summary": item.get("summary", "") }) # Save every 20 entries if len(result) % 20 == 0: with open(OUTPUT_FILE, "w") as f: if save: json.dump(result, f, indent=4, ensure_ascii=False) # Final save with open(OUTPUT_FILE, "w") as f: if save: json.dump(result, f, indent=4, ensure_ascii=False) print(f"Extraction completed. Saved to {OUTPUT_FILE}")