DeepAI
Log In Sign Up

End-to-end Biomedical Entity Linking with Span-based Dictionary Matching

04/21/2021
by   Shogo Ujiie, et al.
1

Disease name recognition and normalization, which is generally called biomedical entity linking, is a fundamental process in biomedical text mining. Recently, neural joint learning of both tasks has been proposed to utilize the mutual benefits. While this approach achieves high performance, disease concepts that do not appear in the training dataset cannot be accurately predicted. This study introduces a novel end-to-end approach that combines span representations with dictionary-matching features to address this problem. Our model handles unseen concepts by referring to a dictionary while maintaining the performance of neural network-based models, in an end-to-end fashion. Experiments using two major datasets demonstrate that our model achieved competitive results with strong baselines, especially for unseen concepts during training.

READ FULL TEXT

page 1

page 2

page 3

page 4

03/08/2021

Fast and Effective Biomedical Entity Linking Using a Dual Encoder

Biomedical entity linking is the task of identifying mentions of biomedi...
09/17/2020

PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology

Automatic phenotype concept recognition from unstructured text remains a...
08/31/2020

PNEL: Pointer Network based End-To-End Entity Linking over Knowledge Graphs

Question Answering systems are generally modelled as a pipeline consisti...
06/14/2021

Biomedical Entity Linking with Contrastive Context Matching

We introduce BioCoM, a contrastive learning framework for biomedical ent...
08/23/2018

End-to-End Neural Entity Linking

Entity Linking (EL) is an essential task for semantic text understanding...
12/16/2020

A Lightweight Neural Model for Biomedical Entity Linking

Biomedical entity linking aims to map biomedical mentions, such as disea...
10/07/2020

COMETA: A Corpus for Medical Entity Linking in the Social Media

Whilst there has been growing progress in Entity Linking (EL) for genera...