Utilizing Large Language Models for Zero-Shot Medical Ontology Extension from Clinical Notes

TL;DR

This paper introduces CLOZE, a zero-shot framework utilizing large language models to automatically extract and integrate new medical concepts from clinical notes into existing ontologies, enhancing biomedical data coverage without additional training.

Contribution

CLOZE is a novel zero-shot approach that leverages LLMs for automatic, scalable, and privacy-preserving ontology extension from unstructured clinical notes, without requiring labeled data.

Findings

CLOZE accurately identifies disease concepts from clinical notes.

The framework effectively captures hierarchical relationships in medical ontologies.

CLOZE demonstrates scalability and privacy preservation in ontology extension.

Abstract

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.