Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning
This work addresses the challenge of fine-grained biomedical entity linking for natural language understanding, representing an incremental improvement by adapting generative methods to the biomedical domain.
The authors tackled biomedical entity linking by proposing a generative method that incorporates synonyms from knowledge bases through pre-training and fine-tuning, achieving state-of-the-art results on several tasks without candidate selection.
Entities lie in the heart of biomedical natural language understanding, and the biomedical entity linking (EL) task remains challenging due to the fine-grained and diversiform concept names. Generative methods achieve remarkable performances in general domain EL with less memory usage while requiring expensive pre-training. Previous biomedical EL methods leverage synonyms from knowledge bases (KB) which is not trivial to inject into a generative method. In this work, we use a generative approach to model biomedical EL and propose to inject synonyms knowledge in it. We propose KB-guided pre-training by constructing synthetic samples with synonyms and definitions from KB and require the model to recover concept names. We also propose synonyms-aware fine-tuning to select concept names for training, and propose decoder prompt and multi-synonyms constrained prefix tree for inference. Our method achieves state-of-the-art results on several biomedical EL tasks without candidate selection which displays the effectiveness of proposed pre-training and fine-tuning strategies.