Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison

Abstract

The biomedical literature is growing rapidly, and the extraction of meaningful information from the large amount of literature is increasingly important. Biomedical named entity (BioNE) identification is one of the critical and fundamental tasks in biomedical text mining. Accurate identification of entities in the literature facilitates the performance of other tasks. Given that an end-to-end neural network can automatically extract features, several deep learning-based methods have been proposed for BioNE recognition (BioNER), yielding state-of-the-art performance. In this review, we comprehensively summarize deep learning-based methods for BioNER and datasets used in training and testing. The deep learning methods are classified into four categories: single neural network-based, multitask learning-based, transfer learning-based and hybrid model-based methods. They can be applied to BioNER in multiple domains, and the results are determined by the dataset size and type. Lastly, we discuss the future development and opportunities of BioNER methods.

Keywords: benchmark; biomedical named entity recognition; deep learning.