Fast and effective biomedical named entity recognition using temporal convolutional network with conditional random field

Abstract

Biomedical named entity recognition (Bio-NER) is the prerequisite for mining knowledge from biomedical texts. The state-of-the-art models for Bio-NER are mostly based on bidirectional long short-term memory (BiLSTM) and bidirectional encoder representations from transformers (BERT) models. However, both BiLSTM and BERT models are extremely computationally intensive. To this end, this paper proposes a temporal convolutional network (TCN) with a conditional random field (TCN-CRF) layer for Bio-NER. The model uses TCN to extract features, which are then decoded by the CRF to obtain the final result. We improve the original TCN model by fusing the features extracted by convolution kernel with different sizes to enhance the performance of Bio-NER. We compared our model with five deep learning models on the GENIA and CoNLL-2003 datasets. The experimental results show that our model can achieve comparative performance with much less training time. The implemented code has been made available to the research community.

Keywords

• biomedical named entity recognition
• temporal convolutional network
• conditional random field