Improving Biomedical Entity Linking with Cross-Entity Interaction

Abstract

Biomedical entity linking (EL) is the task of linking mentions in a biomedical document to corresponding entities in a knowledge base (KB). The challenge in biomedical EL lies in leveraging mention context to select the most appropriate entity among possible candidates. Although some EL models achieve competitive results by retrieving candidate entities and then exploiting context to re-rank them, these re-ranking models concatenate mention context with one candidate at a time. They lack fine-grained interaction among candidates, and potentially cannot handle ambiguous mentions when facing candidates both with high lexical similarity. We cope with this issue using a re-ranking model based on prompt tuning, which represents mention context and all candidates at once, letting candidates in comparison attend to each other. We also propose a KB-enhanced self-supervised pretraining strategy. Instead of large-scale pretraining on biomedical EL data in previous work, we use masked language modeling with synonyms from KB. Our method achieves state-of-the-art results on 3 biomedical EL datasets: NCBI disease, BC5CDR and COMETA, showing the effectiveness of cross-entity interaction and KB-enhanced pretraining strategy. Code is available at https://github.com/HITsz-TMG/Prompt-BioEL.