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--- |
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license: apache-2.0 |
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language: |
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- zh |
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base_model: |
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- Qwen/Qwen2.5-7B-Instruct |
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pipeline_tag: feature-extraction |
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tags: |
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- structuring |
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- EHR |
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- medical |
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- IE |
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--- |
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# Model Card for GENIE |
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## Model Details |
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Model Size: 8B (English) / 7B (Chinese) |
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Max Tokens: 8192 |
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Base model: Llama 3.1 8B (English) / Qwen 2.5 7B (Chinese) |
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### Model Description |
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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. |
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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). |
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## Usage |
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```python |
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from vllm import LLM, SamplingParams |
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PROMPT_TEMPLATE = "Human:\n{query}\n\n Assistant:" |
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sampling_params = SamplingParams(temperature=temperature, max_tokens=max_new_token) |
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EHR = ['xxxxx1','xxxxx2'] |
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texts = [PROMPT_TEMPLATE.format(query=k) for k in EHR] |
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output = model.generate(texts, sampling_params) |
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``` |
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# An example |
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Input: |
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```python |
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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）'] |
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``` |
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Output: |
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```python |
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res = [ |
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{ "术语": "慢性乙型肝炎", |
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"语义类型": "疾病、综合征、病理功能", |
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"叙述状态": "存在", |
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"身体部位": "无", |
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"数值": "NA", |
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"单位": "NA", |
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"修饰词": "无" }, |
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{ "术语": "肝功能异常", |
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"语义类型": "症状、体征、临床所见", |
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"叙述状态": "存在", |
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"身体部位": "无", |
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"数值": "NA", |
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"单位": "NA", |
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"修饰词": "无" }, |
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{ "术语": "HBsAg", |
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"语义类型": "化学物质、药物", |
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"叙述状态": "不存在", |
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"身体部位": "NA", |
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"数值": "无", |
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"单位": "NA", |
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"修饰词": "NA" }, |
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{ "术语": "肝脏病理", |
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"语义类型": "诊断操作", |
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"叙述状态": "存在", |
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"身体部位": "无", |
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"数值": "无", |
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"单位": "NA", |
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"修饰词": "NA" }, |
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{ "术语": "病毒性肝炎", |
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"语义类型": "疾病、综合征、病理功能", |
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"叙述状态": "存在", |
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"身体部位": "无", |
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"数值": "NA", |
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"单位": "NA", |
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"修饰词": "无" }, |
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{ "术语": "肝纤维化", |
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"语义类型": "疾病、综合征、病理功能", |
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"叙述状态": "存在", |
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"身体部位": "无", |
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"数值": "NA", |
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"单位": "NA", |
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"修饰词": "无" }, |
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] |
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``` |
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## Citation [optional] |
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If you find our paper or models helpful, please consider cite: (to be released) |
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**BibTeX:** |
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[More Information Needed] |
