BioELX: Cross-lingual Biomedical Entity Linking via Alias-based Retrieval and LLM Ranking
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arXiv
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| Autores principales: | , , , |
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| Formato: | Preprint |
| Publicado: |
2026
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| _version_ | 1866917536777371648 |
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| author | Wang, Yi Dima, Corina Zhong, Liangyu Staab, Steffen |
| author_facet | Wang, Yi Dima, Corina Zhong, Liangyu Staab, Steffen |
| contents | Cross-lingual biomedical entity linking (BEL) maps mentions in any language to unique identifiers in a biomedical knowledge base (KB), supporting clinical and biomedical NLP applications. However, expert-annotated training data for BEL are costly, especially for low-resource languages. Moreover, many cross-lingual BEL systems rely on SapBERT-based retrievers trained on predominantly English aliases in the KB, leading to poor generalization to unseen non-English mentions and limited context-aware disambiguation. We propose BioELX, a two-stage cross-lingual BEL framework that requires no task-specific annotated training corpora. In Stage~1, we enrich SapBERT training with Wikidata-derived multilingual aliases and use the resulting retriever to improve cross-lingual candidate retrieval. In Stage~2, we perform context-aware disambiguation with a pre-trained LLM ranker that jointly considers the mention context and candidate, eliminating the need for supervised training. Experiments on five benchmarks (XL-BEL, EMEA, Patent, WikiMed-DE, and MedMentions) show that BioELX achieves new state-of-the-art performance. It improves average Recall@1 on XL-BEL by +19.2, with especially large gains for low-resource languages, e.g., +21.6 on Turkish, +22.1 on Korean, +30.8 on Thai, and delivers consistent improvements on EMEA (+6.2), Patent (+5.4), and WikiMed-DE (+12.8). Code and resources will be released upon publication. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2605_27380 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | BioELX: Cross-lingual Biomedical Entity Linking via Alias-based Retrieval and LLM Ranking Wang, Yi Dima, Corina Zhong, Liangyu Staab, Steffen Computation and Language Artificial Intelligence Cross-lingual biomedical entity linking (BEL) maps mentions in any language to unique identifiers in a biomedical knowledge base (KB), supporting clinical and biomedical NLP applications. However, expert-annotated training data for BEL are costly, especially for low-resource languages. Moreover, many cross-lingual BEL systems rely on SapBERT-based retrievers trained on predominantly English aliases in the KB, leading to poor generalization to unseen non-English mentions and limited context-aware disambiguation. We propose BioELX, a two-stage cross-lingual BEL framework that requires no task-specific annotated training corpora. In Stage~1, we enrich SapBERT training with Wikidata-derived multilingual aliases and use the resulting retriever to improve cross-lingual candidate retrieval. In Stage~2, we perform context-aware disambiguation with a pre-trained LLM ranker that jointly considers the mention context and candidate, eliminating the need for supervised training. Experiments on five benchmarks (XL-BEL, EMEA, Patent, WikiMed-DE, and MedMentions) show that BioELX achieves new state-of-the-art performance. It improves average Recall@1 on XL-BEL by +19.2, with especially large gains for low-resource languages, e.g., +21.6 on Turkish, +22.1 on Korean, +30.8 on Thai, and delivers consistent improvements on EMEA (+6.2), Patent (+5.4), and WikiMed-DE (+12.8). Code and resources will be released upon publication. |
| title | BioELX: Cross-lingual Biomedical Entity Linking via Alias-based Retrieval and LLM Ranking |
| topic | Computation and Language Artificial Intelligence |
| url | https://arxiv.org/abs/2605.27380 |