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arXiv · 2602.17949

CUICurate: A GraphRAG-based Framework for Automated Clinical Concept Curation for NLP applications

Victoria Blake·Jamie Novak·Mathew Miller·Sze-yuan Ooi·Blanca Gallego
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Abstract

Background: Clinical named entity recognition tools commonly map free text to Unified Medical Language System (UMLS) Concept Unique Identifiers (CUIs). For many downstream tasks, however, the clinically meaningful unit is not a single CUI but a concept set comprising related synonyms, subtypes, and associated concepts. Constructing these sets is labour-intensive, inconsistently performed, and poorly supported by existing tools. Methods We present CUICurate, a graph-based retrieval-augmented generation (GraphRAG) framework for automated UMLS concept set curation. A UMLS knowledge graph (KG) was constructed and embedded for semantic retrieval. Candidate CUIs were retrieved using graph-based expansion and then filtered and classified using large language models (GPT-5 and Qwen3-32B). The framework was evaluated on five lexically heterogeneous clinical concepts against a manually curated concept sets and gold-standard concept sets. Results CUICurate produced substantially larger and more complete concept sets than the manual benchmarks. A single retrieval configuration across concepts achieved high recall of definitive concepts with manageable candidate sets. GPT-5 outperformed manual curation for all concepts and retained at least 95% of definitive gold-standard CUIs, while Qwen3-32B achieved comparable but slightly lower performance. Many missed concepts were not observed in 10,000 MIMIC-III notes. CUICurate infrastructure and end-to-end processing was inexpensive and stable across runs. Conclusions CUICurate offers a scalable, reproducible and cost-efficient approach for generating clinician-reviewable UMLS concept sets tailored to clinical natural language processing and phenotyping applications.

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Victoria Blake, Jamie Novak, Mathew Miller, Sze-yuan Ooi, Blanca Gallego. 2026-02-20. CUICurate: A GraphRAG-based Framework for Automated Clinical Concept Curation for NLP applications. https://doi.org/10.1093/jamia%2Focag110

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