Journal
BRIEFINGS IN BIOINFORMATICS
Volume 22, Issue 6, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbab282
Keywords
biomedical named entity recognition; deep learning; benchmark
Funding
- National Natural Science Foundation of China [61872309, 61972138]
- Fundamental Research Funds for the Central Universities [531118010355, 531118010626]
- Hunan Provincial Natural Science Foundation of China [2020JJ4215]
- Key Research and Development Program of Changsha [kq2004016]
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Deep learning methods have achieved state-of-the-art performance in biomedical named entity recognition, and can be applied to BioNER in various domains based on dataset size and type. These methods are classified into four categories, including single neural network-based, multitask learning-based, transfer learning-based, and hybrid models.
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.
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