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BELXTR: Biomedical Entity Linking via Contextualized Token Retrieval

arXiv · AI, language, vision and robotics · article · Sep 22, 2026 · UTC

Biomedical Entity Linking disambiguates mentions to entities in a knowledge base (KB), making it the cornerstone of information extraction pipelines. While embedding-based models are a popular approach for the task, they suffer from a key limitation. They compress mentions (and entities) into a single vector, forcing the model to average away crucial fine-grained differences. We present BELXTR, a novel embedding model based on the multi-vector (a.k.a. late interaction) architecture, which allows to leverage token-level matching information. BELXTR extends the original XTR model to biomedical e

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