RES E A R C H Open Access
Entity recognition in Chinese clinical text
using attention-based CNN-LSTM-CRF
Buzhou Tang
1
, Xiaolong Wang
1
, Jun Yan
2
and Qingcai Chen
1*
From The Sixth IEEE International Conference on Healthcare Informatics (ICHI 2018)
New York, NY, USA. 4-7 June 2018
Abstract
Background: Clinical entity recognition as a fundamental task of clinical text processing has been attracted a great
deal of attention during the last decade. However, most studies focus on clinical text in English rather than other
languages. Recently, a few researchers have began to study entity recognition in Chinese clinical text.
Methods: In this paper, a novel deep neural network, called attention-based CNN-LSTM-CRF, is proposed to recognize
entities in Chinese clinical text. Attention-based CNN-LSTM-CRF is an extension of LSTM-C RF by introducing a
CNN (convolutional neural network) layer after the input layer to capture local context information of words of
interest and an attention layer before the CRF layer to select relevant words in the same sentence.
Results: In order to evaluate the proposed method, we compare it with other two currently popular methods,
CRF (conditional random field) and LSTM-CRF, on two benchmark datasets. One of the datasets is publically
available and only contains contiguous clinical entities, and the other one is constructed by us and contains
contiguous and discontiguous clinical entities. Experimental resul ts show that attent ion-based CNN- LSTM-CRF
outperforms CRF and LSTM-CRF.
Conclusions: CNN and attention mechanism are in dividually beneficial to LSTM-CRF-based Chinese clinical entity
recognition system, no matter whether contiguous clinical entities are considered. The conribution of attention mechanism
is greater than CNN.
Keywords: Chinese clinical entity recognition, Neural network, Convolutional neural network, Long-short term
memory, Condi tional random field
Introduction
With rapid development of electronic medical information
systems, more and more electronic medical records
(EMRs) are available for medical research and application.
In EMRs, plenty of useful information is embedded in
clinical text. The first step to use clinical text is clinical
entity recognition that finds which words form clinical
entities and which type each entity belongs to.
In the last decades, a large number of methods have
been proposed for clinical entity recognitio n. The
methods includes early rule-based methods, machine
learning methods based on manually-crafted features in
past a few years and recently deep neural networks. The
most popular machine learning method used for clinical
entity recognition is conditional random field (CRF) [1],
and the most popular deep neural network is
LSTM-CRF [2]. However, most studies focus on entity
recognition in English clinical text rather than other
languages. It is necessary to investigate the latest
methods for entity recognition in other languages, for
example Chinese.
To promote de velopment of entity recognition in
Chinese clinical tex t, the organizers of China conference
on knowledge graph and semantic computing
(CCKS) launched a c hallenge was launched in 2017
[3]. The challenge organizer provided a dataset
(called CCKS2017_CNER) with only contiguous clinical
entities following the guideline of i2b2 (Informatics for
* Correspondence: qingcai.chen@gmail.com
1
Key Laboratory of Network Oriented Intelligent Computation, Harbin
Institute of Technology, (Shenzhen), Shenzhen 518055, China
Full list of author information is available at the end of the article
© The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Tang et al. BMC Medical Informatics and Decision Making 2019, 19(Suppl 3):74
https://doi.org/10.1186/s12911-019-0787-y