Neighborhood-Aware Dual Biomedical Entity Linking

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.

Biomedical entity linking maps textual mentions to concepts in structured knowledge bases such as UMLS or SNOMED CT. Most existing systems link each mention independently, using only the mention or its surrounding sentence. This ignores dependencies between mentions in the same document and can lead to inconsistent predictions, especially when the same concept appears under different surface forms. We introduce LongBEL, a document-level generative framework that combines full-document context with a memory of previous predictions. To make this memory robust, LongBEL is trained with cross-validated predictions rather than gold labels, reducing the mismatch between training and inference and limiting cascading errors. Experiments on five biomedical benchmarks across English, French, and Spanish show that LongBEL improves over sentence-level generative baselines, with the largest gains on datasets where concepts frequently recur within documents. An ensemble of local, global, and memory-based variants achieves the best results across all benchmarks. Further analysis shows that the largest gains occur on recurring concepts, suggesting that LongBEL mainly improves document-level consistency rather than isolated mention disambiguation.

We introduce OntologyBench, a tiered biomedical retrieval benchmark comprising 471,854 training and 125,744 evaluation query-document relevance pairs across concept grounding, relational retrieval, and compositional phenotype-based retrieval. Although these tasks can be tractable using ontology-aware reference methods, across task tiers, embedding performance is generally lower on relational and compositional tasks than on concept-grounding tasks. Fine-tuning on ontology-derived supervision improves performance on several relational and compositional tasks, whereas the evaluated reranking and LLM-based candidate-scoring methods provide little or no end-to-end improvement. Errors frequently reflect diseases matching only subsets of the phenotype evidence. These findings indicate that the evaluated embedding and reranking configurations do not reliably recover the compatibility encoded by the selected ontology relations and phenotype combinations and motivate retrieval systems that better integrate learned representations with structured biomedical knowledge.