SynCABEL: Synthetic Contextualized Augmentation for Biomedical Entity Linking

SynCABEL: Synthetic Contextualized Augmentation for Biomedical Entity Linking

Adam Remaki, Christel Gérardin, Eulàlia Farré-Maduell, Martin Krallinger, Xavier Tannier

Proceedings of the Thirty-Fifth International Joint Conference on Artificial Intelligence
AI and Health. Pages 6859-6867. https://doi.org/10.24963/ijcai.2026/763

We present SynCABEL (Synthetic Contextualized Augmentation for Biomedical Entity Linking), a framework that addresses a central bottleneck in supervised biomedical entity linking (BEL): the scarcity of expert-annotated training data. SynCABEL leverages large language models to generate context-rich synthetic training examples for all candidate concepts in a target knowledge base, providing broad supervision without manual annotation. We demonstrate that SynCABEL, when combined with decoder-only models and guided inference establish new state-of-the-art results across three widely used multilingual benchmarks: MedMentions for English, QUAERO for French, and SPACCC for Spanish. Evaluating data efficiency, we show that SynCABEL reaches the performance of full human supervision using up to 60% less annotated data, substantially reducing reliance on labor-intensive and costly expert labeling. Finally, acknowledging that standard evaluation based on exact code matching often underestimates clinically valid predictions due to ontology redundancy, we introduce an LLM-as-a-judge protocol. This analysis reveals that SynCABEL significantly improves the rate of clinically valid predictions. Our synthetic datasets, models, and code are released to support reproducibility and future research. • HuggingFace Datasets & Models • GitHub Repository
Keywords:
Health data mining: Health data mining
EHR analysis: EHR analysis
Biomedical NLP: Biomedical NLP
LLM in medicine: LLM in medicine
Medical knowledge representation: Medical knowledge representation