UMCR: Universal Medical Concept Recognition through Guideline Integration and Agentic Linking

Fabrice Lamarche, Amal Zouaq

Medical Concept Recognition is the task of extracting and grounding spans in medical text to entries in a standard ontology. Current methods are generally developed towards a single ontology and source text type (clinical notes, drug labels, etc.) The central challenge is therefore to build methods that adapt to any target ontology without requiring ontology-specific retraining. More recent approaches like REAL and AutoPCR make direct use of Large Language Models and can theoretically adapt to any ontology choice but suffer from a lack of generalization. We propose UMCR, a pipeline that allows extraction and linking to any target ontology using any source text variety, utilizing direct guideline integration and an agentic linking module. We evaluate our method on the recent MedPath benchmark, covering a wide variety of medical text types and vocabularies, and show that our method achieves strong performance across these tasks. This ability unlocks interoperability in the healthcare domain, allowing for extraction and alignment between different medical standards. Our method also reduces dependence on parametric LLM memory, thanks to improved interaction with the target ontology…