Search arXiv⌕ Search
Home/Archive/arXiv

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
View original source ↗Read source document ↗Export metadata ↓

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.

Explore related subjects

cs.CLcs.AI

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Victoria Blake, Jamie Novak, Mathew Miller, Sze-yuan Ooi, Blanca Gallego. 2026-05-14. CUICurate: A GraphRAG-based Framework for Automated Clinical Concept Curation for NLP applications. https://doi.org/10.1093/jamia%2Focag110

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

What is the Role of Small Models in the LLM Era: A Survey

Large Language Models (LLMs) have demonstrated remarkable capabilities in various reasoning tasks, which leads to the development of increasingly large models. However, scaling up model sizes results in significantly higher computational costs and energy consumption, which makes these models impractical for academic researchers and businesses with limited resources. At the same time, Small Models (SMs) are frequently used in practical settings, although their significance is currently underestimated. This raises important questions about the role of small models in the era of LLMs, a topic that has received limited attention in prior surveys. In this work, we systematically examine the relationship between LLMs and SMs from two key perspectives: Collaboration and Competition (or Complementarity). We hope this survey provides valuable insights for practitioners, fostering a deeper understanding of the contribution of small models and promoting more efficient use of computational resources.

cs.CL↗
arXiv2026

SG-FSM: A Self-Guiding Zero-Shot Prompting Paradigm for Multi-Hop Question Answering Based on Finite State Machine

Large Language Models with chain-of-thought prompting, such as OpenAI-o1, have shown impressive capabilities in natural language inference tasks. However, Multi-hop Question Answering (MHQA) remains challenging for many existing models due to issues like hallucination, error propagation, and limited context length. To address these challenges and enhance LLMs' performance on MHQA, we propose the Self-Guiding prompting Finite State Machine (SG-FSM), designed to strengthen multi-hop reasoning abilities. Unlike traditional chain-of-thought methods, SG-FSM tackles MHQA by iteratively breaking down complex questions into sub-questions, correcting itself to improve accuracy. It processes one sub-question at a time, dynamically deciding the next step based on the current context and results, functioning much like an automaton. Experiments across various benchmarks demonstrate the effectiveness of our approach, outperforming strong baselines on challenging datasets such as Musique. SG-FSM reduces hallucination, enabling recovery of the correct final answer despite intermediate errors. It also improves adherence to specified output formats, simplifying evaluation significantly.

cs.CL↗
arXiv2026

A Course Intelligence Platform for Higher Education: Lessons from AI-Assisted Course Evaluation

The rapid adoption of generative AI has created new opportunities for teaching, learning, and quality assurance. Existing applications, however, remain largely student-facing, with comparatively limited attention to institution-level needs. This paper presents a course intelligence platform deployed across more than 100 universities and serving over 10,000 instructors in China. By linking competency requirements, knowledge structures, teaching activities, and assessment evidence, it establishes a shared foundation for knowledge organization, instructional design, learning assessment, and quality evaluation. The course evaluation module is examined as a representative institution-facing application of the platform, which integrates national evaluation standards, structured educational evidence, customized prompting strategies, and domain-adapted LLMs to generate quantitative scores and qualitative feedback. A case study involving 100 authentic university courses is conducted to evaluate its alignment with expert judgments and the interpretability of its outputs. Statistical analyses show substantial agreement between AI-generated assessments and expert ratings, while qualitative results highlight the credibility of the feedback. The findings further suggest that AI-assisted evaluation requires not only capable models but also structured domain knowledge and transparent criteria. In this context, human ratings should be treated as an informative reference rather than an error-free gold standard, and the objective is to achieve consistent, interpretable, and defensible judgments instead of merely replicating expert scores.

cs.CL↗