DeepAI AI Chat
Log In Sign Up

Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning

by   Hongyi Yuan, et al.
Tsinghua University

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.


Self-alignment Pre-training for Biomedical Entity Representations

Despite the widespread success of self-supervised learning via masked la...

Generative Multimodal Entity Linking

Multimodal Entity Linking (MEL) is the task of mapping mentions with mul...

Knowledge Enhanced Fine-Tuning for Better Handling Unseen Entities in Dialogue Generation

Although pre-training models have achieved great success in dialogue gen...

Benchmarking Diverse-Modal Entity Linking with Generative Models

Entities can be expressed in diverse formats, such as texts, images, or ...

Biomedical Entity Linking with Triple-aware Pre-Training

Linking biomedical entities is an essential aspect in biomedical natural...

A Lightweight Neural Model for Biomedical Entity Linking

Biomedical entity linking aims to map biomedical mentions, such as disea...

Recognising Biomedical Names: Challenges and Solutions

The growth rate in the amount of biomedical documents is staggering. Unl...