Biomedical named entity recognition using BERT in the machine reading comprehension framework

Paper

Biomedical named entity recognition using BERT in the machine reading comprehension framework

Model structure

Tested environments

• Ubuntu 16.04
• python 3.6.9
• transformers 2.5.1
• torch 1.6.0
• numpy 1.19.4
• pandas 1.2.3
• scipy 1.4.1

BERT weights

biobert_v1.1_v2.5.1

Run models

002-BERT_MRC_BC4CHEM.ipynb

Cite

@article{SUN2021103799,
title = {Biomedical named entity recognition using BERT in the machine reading comprehension framework},
journal = {Journal of Biomedical Informatics},
volume = {118},
pages = {103799},
year = {2021},
issn = {1532-0464},
doi = {https://doi.org/10.1016/j.jbi.2021.103799},
url = {https://www.sciencedirect.com/science/article/pii/S1532046421001283},
author = {Cong Sun and Zhihao Yang and Lei Wang and Yin Zhang and Hongfei Lin and Jian Wang},
}