Model Card for GENIE
Model Details
Model Size: 7B
Max Tokens: 8192
Base model: Qwen 2.5 7B
Model Description
GENIE (Generative Note Information Extraction, 中文名：病历精灵) is an end-to-end model designed to structure free text from electronic health records (EHRs). It processes EHRs in a single pass, extracting biomedical named entities along with their assertion statuses, body locations, modifiers, values, units, and intended purposes, outputting this information in a structured JSON format. This streamlined approach simplifies traditional natural language processing workflows by replacing all the analysis components with a single model, making the system easier to maintain while leveraging the advanced analytical capabilities of large language models (LLMs). Comparing with general-purpose LLMs, GENIE does not require prompt engineering or few-shot examples. Additionally, it generates all relevant attributes in one pass, significantly reducing both runtime and operational costs. GENIE is co-developed by the groups of Sheng Yu (https://www.stat.tsinghua.edu.cn/teachers/shengyu/), Tianxi Cai (https://dbmi.hms.harvard.edu/people/tianxi-cai), and Isaac Kohane (https://dbmi.hms.harvard.edu/people/isaac-kohane).
Usage
from vllm import LLM, SamplingParams
PROMPT_TEMPLATE = "Human:\n{query}\n\n Assistant:\n"
sampling_params = SamplingParams(temperature=temperature, max_tokens=max_new_token)
EHR = ['xxxxx1','xxxxx2']
texts = [PROMPT_TEMPLATE.format(query=k) for k in EHR]
output = model.generate(texts, sampling_params)
An example
Input:
EHR = ['慢性乙型肝炎病史10余年，曾有肝功能异常，中医治疗后好转；1年余前查HBsAg转阴，但肝脏病理提示病毒性肝炎伴肝纤维化（G1S3-4）']
Output:
res = [
{ "术语": "慢性乙型肝炎",
"语义类型": "疾病、综合征、病理功能",
"叙述状态": "存在",
"身体部位": "无",
"数值": "NA",
"单位": "NA",
"修饰词": "无" },
{ "术语": "肝功能异常",
"语义类型": "症状、体征、临床所见",
"叙述状态": "存在",
"身体部位": "无",
"数值": "NA",
"单位": "NA",
"修饰词": "无" },
{ "术语": "HBsAg",
"语义类型": "化学物质、药物",
"叙述状态": "不存在",
"身体部位": "NA",
"数值": "无",
"单位": "NA",
"修饰词": "NA" },
{ "术语": "肝脏病理",
"语义类型": "诊断操作",
"叙述状态": "存在",
"身体部位": "无",
"数值": "无",
"单位": "NA",
"修饰词": "NA" },
{ "术语": "病毒性肝炎",
"语义类型": "疾病、综合征、病理功能",
"叙述状态": "存在",
"身体部位": "无",
"数值": "NA",
"单位": "NA",
"修饰词": "无" },
{ "术语": "肝纤维化",
"语义类型": "疾病、综合征、病理功能",
"叙述状态": "存在",
"身体部位": "无",
"数值": "NA",
"单位": "NA",
"修饰词": "无" },
]
Citation
If you find our paper or models helpful, please consider cite:
BibTeX:
@misc{ying2025geniegenerativenoteinformation,
title={GENIE: Generative Note Information Extraction model for structuring EHR data},
author={Huaiyuan Ying and Hongyi Yuan and Jinsen Lu and Zitian Qu and Yang Zhao and Zhengyun Zhao and Isaac Kohane and Tianxi Cai and Sheng Yu},
year={2025},
eprint={2501.18435},
archivePrefix={arXiv},
primaryClass={cs.CL},
url={https://arxiv.org/abs/2501.18435},
}