GENIE: Generative Note Information Extraction model for structuring EHR data

• URL: http://arxiv.org/abs/2501.18435v1
• Date: Thu, 30 Jan 2025 15:42:24 GMT
• Title: GENIE: Generative Note Information Extraction model for structuring EHR data
• Authors: Huaiyuan Ying, Hongyi Yuan, Jinsen Lu, Zitian Qu, Yang Zhao, Zhengyun Zhao, Isaac Kohane, Tianxi Cai, Sheng Yu,
• Abstract summary: We introduce GENIE, a Generative Note Information Extraction system. GENIE processes entire paragraphs in a single pass, extracting entities, assertion statuses, locations, modifier, values, and purposes with high accuracy. Using a robust data preparation pipeline and fine-tuned small scale LLMs, GENIE achieves competitive performance across multiple information extraction tasks.
• Score: 14.057531175321113
• License:
• Abstract: Electronic Health Records (EHRs) hold immense potential for advancing healthcare, offering rich, longitudinal data that combines structured information with valuable insights from unstructured clinical notes. However, the unstructured nature of clinical text poses significant challenges for secondary applications. Traditional methods for structuring EHR free-text data, such as rule-based systems and multi-stage pipelines, are often limited by their time-consuming configurations and inability to adapt across clinical notes from diverse healthcare settings. Few systems provide a comprehensive attribute extraction for terminologies. While giant large language models (LLMs) like GPT-4 and LLaMA 405B excel at structuring tasks, they are slow, costly, and impractical for large-scale use. To overcome these limitations, we introduce GENIE, a Generative Note Information Extraction system that leverages LLMs to streamline the structuring of unstructured clinical text into usable data with standardized format. GENIE processes entire paragraphs in a single pass, extracting entities, assertion statuses, locations, modifiers, values, and purposes with high accuracy. Its unified, end-to-end approach simplifies workflows, reduces errors, and eliminates the need for extensive manual intervention. Using a robust data preparation pipeline and fine-tuned small scale LLMs, GENIE achieves competitive performance across multiple information extraction tasks, outperforming traditional tools like cTAKES and MetaMap and can handle extra attributes to be extracted. GENIE strongly enhances real-world applicability and scalability in healthcare systems. By open-sourcing the model and test data, we aim to encourage collaboration and drive further advancements in EHR structurization.

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