Training-Free BioNEL-RAG: Advancing Biomedical Entity Linking through Retrieval-Augmented Generation and Large Language Model

Abstract

Biomedical Named Entity Linking (BioNEL) is the task of mapping mentions extracted from biomedical texts to canonical entities or concepts in the standardized knowledge base. Although existing methods have achieved remarkable performance in mapping accuracy, most rely on training with domain-specific datasets, which fundamentally limits their cross-domain adaptability. To address this limitation, we propose BioNEL-RAG, a novel training-free framework that combines retrieval-augmented generation (RAG) with large language models (LLMs). Within this framework, the RAG module focuses on retrieving candidate entities, while the large language model module plays the role of selecting the most appropriate candidate for entity normalization, which is based on the analysis of the mention's context, with the aid of its remarkable text comprehension capabilities. Experimental results demonstrate that BioNEL-RAG achieves performance comparable to existing methods without requiring training on subdomain datasets, whereas these methods necessitate fine-tuning on specific subdomains such as genes, diseases, or chemical compounds.