BioELX: Context-Aware Cross-lingual Biomedical Entity Linking without Task-Specific Supervision

arXiv:2605.27380v2 Announce Type: replace-cross Abstract: Cross-lingual biomedical entity linking (BEL) maps mentions in any language to unique identifiers in a biomedical knowledge base, supporting clinical and biomedical NLP applications.

We identify two issues affecting current systems.

First, the UMLS (Bodenreider,2004) aliases used to train cross-lingual BEL retrievers are heavily skewed toward English, so retrievers generalize poorly to non-English mentions. Second, although context is often necessary for disambiguation, naively injecting context into retrievers trained only to align aliases severely degrades retrieval. We propose BioELX, a retrieve-rerank framework that addresses both issues.

For retrieval, we continue training SapBERT_multi (Liu et al., 2021b) using Wikidata-derived cross-lingual alias supervision, forming shared concept neighborhoods across languages.

For reranking, we adapt pretrained LLM rerankers to entity linking through mention-anchored prompting, which marks the target mention so that rerankers score candidates with respect to the intended mention rather than other salient tokens in the context.

Experiments show that BioELX achieves new state-of-the-art results on four cross-lingual BEL benchmarks, improving Recall@1 by 4.8 to 18.2 percentage points over prior best results, without any task-specific BEL annotations. Our code and resources are available at https://github.com/AI4MedCode/BioELX.