Enlarging drug dictionary with semi-supervised learning for Drug Entity Recognition

Donghuo Zeng; Chengjie Sun; Lei Lin; Bingquan Liu

doi:10.1109/BIBM.2016.7822818

Enlarging drug dictionary with semi-supervised learning for Drug Entity Recognition

Donghuo Zeng
, Chengjie Sun
, Lei Lin
, Bingquan Liu

School of Computer Science and Technology, Harbin Institute of Technology

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

5 Scopus citations

Abstract

Drug Entity Recognition (DER) is a crucial task for information extraction in biomedical text. Much of previous work for DER using known drugs to build features, however, the known drug resources are limited. In this paper, we proposed a semi-supervised learning to extend an existing drug dictionary. With the extended dictionary, the features for DER can be enriched. Using Conditional Random Fields (CRF) model with the enriched features, an F-measure of 89.26% is achieved on DDIExtraction2013 challenge data set, which outperforms the best system of the DDIExtraction 2013 challenge.

Original language	English
Title of host publication	Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
Editors	Kevin Burrage, Qian Zhu, Yunlong Liu, Tianhai Tian, Yadong Wang, Xiaohua Tony Hu, Qinghua Jiang, Jiangning Song, Shinichi Morishita, Kevin Burrage, Guohua Wang
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1929-1931
Number of pages	3
ISBN (Electronic)	9781509016105
DOIs	https://doi.org/10.1109/BIBM.2016.7822818
State	Published - 17 Jan 2017
Externally published	Yes
Event	2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 - Shenzhen, China Duration: 15 Dec 2016 → 18 Dec 2016

Publication series

Name	Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

Conference

Conference	2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
Country/Territory	China
City	Shenzhen
Period	15/12/16 → 18/12/16

Keywords

Context pattern
Information extraction
Named entity recognition

Access to Document

10.1109/BIBM.2016.7822818

Cite this

Zeng, D., Sun, C., Lin, L., & Liu, B. (2017). Enlarging drug dictionary with semi-supervised learning for Drug Entity Recognition. In K. Burrage, Q. Zhu, Y. Liu, T. Tian, Y. Wang, X. T. Hu, Q. Jiang, J. Song, S. Morishita, K. Burrage, & G. Wang (Eds.), Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 (pp. 1929-1931). Article 7822818 (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2016.7822818

Zeng, Donghuo ; Sun, Chengjie ; Lin, Lei et al. / Enlarging drug dictionary with semi-supervised learning for Drug Entity Recognition. Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. editor / Kevin Burrage ; Qian Zhu ; Yunlong Liu ; Tianhai Tian ; Yadong Wang ; Xiaohua Tony Hu ; Qinghua Jiang ; Jiangning Song ; Shinichi Morishita ; Kevin Burrage ; Guohua Wang. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 1929-1931 (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016).

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title = "Enlarging drug dictionary with semi-supervised learning for Drug Entity Recognition",

abstract = "Drug Entity Recognition (DER) is a crucial task for information extraction in biomedical text. Much of previous work for DER using known drugs to build features, however, the known drug resources are limited. In this paper, we proposed a semi-supervised learning to extend an existing drug dictionary. With the extended dictionary, the features for DER can be enriched. Using Conditional Random Fields (CRF) model with the enriched features, an F-measure of 89.26\% is achieved on DDIExtraction2013 challenge data set, which outperforms the best system of the DDIExtraction 2013 challenge.",

keywords = "Context pattern, Information extraction, Named entity recognition",

author = "Donghuo Zeng and Chengjie Sun and Lei Lin and Bingquan Liu",

note = "Publisher Copyright: {\textcopyright} 2016 IEEE.; 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 ; Conference date: 15-12-2016 Through 18-12-2016",

year = "2017",

month = jan,

day = "17",

doi = "10.1109/BIBM.2016.7822818",

language = "英语",

series = "Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "1929--1931",

editor = "Kevin Burrage and Qian Zhu and Yunlong Liu and Tianhai Tian and Yadong Wang and Hu, \{Xiaohua Tony\} and Qinghua Jiang and Jiangning Song and Shinichi Morishita and Kevin Burrage and Guohua Wang",

booktitle = "Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016",

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}

Zeng, D, Sun, C , Lin, L & Liu, B 2017, Enlarging drug dictionary with semi-supervised learning for Drug Entity Recognition. in K Burrage, Q Zhu, Y Liu, T Tian, Y Wang, XT Hu, Q Jiang, J Song, S Morishita, K Burrage & G Wang (eds), Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016., 7822818, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Institute of Electrical and Electronics Engineers Inc., pp. 1929-1931, 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Shenzhen, China, 15/12/16. https://doi.org/10.1109/BIBM.2016.7822818

Enlarging drug dictionary with semi-supervised learning for Drug Entity Recognition. / Zeng, Donghuo; Sun, Chengjie ; Lin, Lei et al.
Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. ed. / Kevin Burrage; Qian Zhu; Yunlong Liu; Tianhai Tian; Yadong Wang; Xiaohua Tony Hu; Qinghua Jiang; Jiangning Song; Shinichi Morishita; Kevin Burrage; Guohua Wang. Institute of Electrical and Electronics Engineers Inc., 2017. p. 1929-1931 7822818 (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Enlarging drug dictionary with semi-supervised learning for Drug Entity Recognition

AU - Zeng, Donghuo

AU - Sun, Chengjie

AU - Lin, Lei

AU - Liu, Bingquan

PY - 2017/1/17

Y1 - 2017/1/17

N2 - Drug Entity Recognition (DER) is a crucial task for information extraction in biomedical text. Much of previous work for DER using known drugs to build features, however, the known drug resources are limited. In this paper, we proposed a semi-supervised learning to extend an existing drug dictionary. With the extended dictionary, the features for DER can be enriched. Using Conditional Random Fields (CRF) model with the enriched features, an F-measure of 89.26% is achieved on DDIExtraction2013 challenge data set, which outperforms the best system of the DDIExtraction 2013 challenge.

AB - Drug Entity Recognition (DER) is a crucial task for information extraction in biomedical text. Much of previous work for DER using known drugs to build features, however, the known drug resources are limited. In this paper, we proposed a semi-supervised learning to extend an existing drug dictionary. With the extended dictionary, the features for DER can be enriched. Using Conditional Random Fields (CRF) model with the enriched features, an F-measure of 89.26% is achieved on DDIExtraction2013 challenge data set, which outperforms the best system of the DDIExtraction 2013 challenge.

KW - Context pattern

KW - Information extraction

KW - Named entity recognition

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BT - Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

A2 - Burrage, Kevin

A2 - Zhu, Qian

A2 - Liu, Yunlong

A2 - Tian, Tianhai

A2 - Wang, Yadong

A2 - Hu, Xiaohua Tony

A2 - Jiang, Qinghua

A2 - Song, Jiangning

A2 - Morishita, Shinichi

A2 - Burrage, Kevin

A2 - Wang, Guohua

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

Y2 - 15 December 2016 through 18 December 2016

ER -

Zeng D, Sun C , Lin L , Liu B. Enlarging drug dictionary with semi-supervised learning for Drug Entity Recognition. In Burrage K, Zhu Q, Liu Y, Tian T, Wang Y, Hu XT, Jiang Q, Song J, Morishita S, Burrage K, Wang G, editors, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Institute of Electrical and Electronics Engineers Inc. 2017. p. 1929-1931. 7822818. (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016). doi: 10.1109/BIBM.2016.7822818

Enlarging drug dictionary with semi-supervised learning for Drug Entity Recognition

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