Utilizing Large Language Models for Zero-Shot Medical Ontology Extension from Clinical Notes
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arXiv
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| Main Authors: | , , , , , , |
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| Format: | Preprint |
| Published: |
2025
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| _version_ | 1866908667394129920 |
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| author | Wu, Guanchen Xie, Yuzhang Wu, Huanwei He, Zhe Shao, Hui Hu, Xiao Yang, Carl |
| author_facet | Wu, Guanchen Xie, Yuzhang Wu, Huanwei He, Zhe Shao, Hui Hu, Xiao Yang, Carl |
| contents | Integrating novel medical concepts and relationships into existing ontologies can significantly enhance their coverage and utility for both biomedical research and clinical applications. Clinical notes, as unstructured documents rich with detailed patient observations, offer valuable context-specific insights and represent a promising yet underutilized source for ontology extension. Despite this potential, directly leveraging clinical notes for ontology extension remains largely unexplored. To address this gap, we propose CLOZE, a novel framework that uses large language models (LLMs) to automatically extract medical entities from clinical notes and integrate them into hierarchical medical ontologies. By capitalizing on the strong language understanding and extensive biomedical knowledge of pre-trained LLMs, CLOZE effectively identifies disease-related concepts and captures complex hierarchical relationships. The zero-shot framework requires no additional training or labeled data, making it a cost-efficient solution. Furthermore, CLOZE ensures patient privacy through automated removal of protected health information (PHI). Experimental results demonstrate that CLOZE provides an accurate, scalable, and privacy-preserving ontology extension framework, with strong potential to support a wide range of downstream applications in biomedical research and clinical informatics. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2511_16548 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Utilizing Large Language Models for Zero-Shot Medical Ontology Extension from Clinical Notes Wu, Guanchen Xie, Yuzhang Wu, Huanwei He, Zhe Shao, Hui Hu, Xiao Yang, Carl Artificial Intelligence Integrating novel medical concepts and relationships into existing ontologies can significantly enhance their coverage and utility for both biomedical research and clinical applications. Clinical notes, as unstructured documents rich with detailed patient observations, offer valuable context-specific insights and represent a promising yet underutilized source for ontology extension. Despite this potential, directly leveraging clinical notes for ontology extension remains largely unexplored. To address this gap, we propose CLOZE, a novel framework that uses large language models (LLMs) to automatically extract medical entities from clinical notes and integrate them into hierarchical medical ontologies. By capitalizing on the strong language understanding and extensive biomedical knowledge of pre-trained LLMs, CLOZE effectively identifies disease-related concepts and captures complex hierarchical relationships. The zero-shot framework requires no additional training or labeled data, making it a cost-efficient solution. Furthermore, CLOZE ensures patient privacy through automated removal of protected health information (PHI). Experimental results demonstrate that CLOZE provides an accurate, scalable, and privacy-preserving ontology extension framework, with strong potential to support a wide range of downstream applications in biomedical research and clinical informatics. |
| title | Utilizing Large Language Models for Zero-Shot Medical Ontology Extension from Clinical Notes |
| topic | Artificial Intelligence |
| url | https://arxiv.org/abs/2511.16548 |