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

arXiv: https://arxiv.org/abs/2605.27380 · HTML: https://mlsanity.com/paper/2605.27380/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 22 of its 46 references that are in the map.
- First posted on arXiv 9 Apr 2026.

## Builds on (most cited first, 22 of 22)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Qwen3 Embedding: Advancing Text Embedding and Reranking Through Foundation Models](https://mlsanity.com/paper/2506.05176/) (2025)
- [M3-Embedding: Multi-Linguality, Multi-Functionality, Multi-Granularity Text Embeddings Through Self-Knowledge Distillation](https://mlsanity.com/paper/2402.03216/) (2024)
- [Multilingual Denoising Pre-training for Neural Machine Translation](https://mlsanity.com/paper/2001.08210/) (2020)
- [Multi-Similarity Loss with General Pair Weighting for Deep Metric Learning](https://mlsanity.com/paper/1904.06627/) (2019)
- [Autoregressive Entity Retrieval](https://mlsanity.com/paper/2010.00904/) (2020)
- [Self-Alignment Pretraining for Biomedical Entity Representations](https://mlsanity.com/paper/2010.11784/) (2020)
- [Zero-Shot Entity Linking by Reading Entity Descriptions](https://mlsanity.com/paper/1906.07348/) (2019)
- [MedMentions: A Large Biomedical Corpus Annotated with UMLS Concepts](https://mlsanity.com/paper/1902.09476/) (2019)
- [Biomedical Entity Representations with Synonym Marginalization](https://mlsanity.com/paper/2005.00239/) (2020)
- [CODER: Knowledge infused cross-lingual medical term embedding for term normalization](https://mlsanity.com/paper/2011.02947/) (2020)
- [Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning](https://mlsanity.com/paper/2204.05164/) (2022)
- [Learning Domain-Specialised Representations for Cross-Lingual Biomedical Entity Linking](https://mlsanity.com/paper/2105.14398/) (2021)
- [FOCUS: Internal MLLM Representations for Efficient Fine-Grained Visual Question Answering](https://mlsanity.com/paper/2506.21710/) (2025)
- [LLMAEL: Large Language Models are Good Context Augmenters for Entity Linking](https://mlsanity.com/paper/2407.04020/) (2024)
- [Instructed Language Models with Retrievers Are Powerful Entity Linkers](https://mlsanity.com/paper/2311.03250/) (2023)
- [ReLiK: Retrieve and LinK, Fast and Accurate Entity Linking and Relation Extraction on an Academic Budget](https://mlsanity.com/paper/2408.00103/) (2024)
- [PromptLink: Leveraging Large Language Models for Cross-Source Biomedical Concept Linking](https://mlsanity.com/paper/2405.07500/) (2024)
- [Learning from Negative Samples in Biomedical Generative Entity Linking](https://mlsanity.com/paper/2408.16493/) (2024)
- [xMEN: A Modular Toolkit for Cross-Lingual Medical Entity Normalization](https://mlsanity.com/paper/2310.11275/) (2023)
- [ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish](https://mlsanity.com/paper/2404.06367/) (2024)
- [Biomedical Entity Linking as Multiple Choice Question Answering](https://mlsanity.com/paper/2402.15189/) (2024)

## Abstract (arXiv)

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.