A Multilevel NER Framework for Automatic Clinical Name Entity Recognition

Thoai Man LUU; Rob PHAN; Rachel DAVEY; Girija CHETTY

doi:10.1109/ICDMW.2017.161

A Multilevel NER Framework for Automatic Clinical Name Entity Recognition

Thoai Man LUU, Rob PHAN, Rachel DAVEY, Girija CHETTY

Research output: A Conference proceeding or a Chapter in Book › Conference contribution › peer-review

6 Citations (Scopus)

Abstract

In this paper, we propose a novel multilevel NER framework, for addressing the challenges of clinical name entity recognition, based on different machine learning and text mining algorithms. The proposed framework, with multiple levels, allows models for increasingly complex NER tasks to be built. The experimental evaluation on two different publicly available datasets, corresponding to different application contexts - the CLEF 2016 challenge shared task 1A for nursing handover context, and the BIONLP/NLPBPA 2004 challenge shared task on GENIA corpus for recognizing entities in microbiology, has validated the proposed framework.

Original language	English
Title of host publication	2017 IEEE International Conference on Data Mining Workshops
Editors	Raju Gottumukkala, George Karypis, Vijay Raghavan, Xindong Wu, Lucio Miele, Srinivas Aluru, Xia Ning, Guozhu Dong
Place of Publication	New Orleans
Publisher	IEEE, Institute of Electrical and Electronics Engineers
Pages	1135-1143
Number of pages	8
ISBN (Electronic)	9781538638002
ISBN (Print)	9781538638019
DOIs	https://doi.org/10.1109/ICDMW.2017.161
Publication status	Published - 18 Nov 2017
Event	2017 IEEE International Conference on Data Mining Workshops (ICDMW) - New Orleans, New Orleans, United States Duration: 18 Nov 2017 → 21 Nov 2017

Publication series

Name	IEEE INTERNATIONAL CONFERENCE ON DATA MINING WORKSHOPS
ISSN (Electronic)	2375-9259

Conference

Conference	2017 IEEE International Conference on Data Mining Workshops (ICDMW)
Abbreviated title	ICDMW 2017
Country/Territory	United States
City	New Orleans
Period	18/11/17 → 21/11/17

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10.1109/ICDMW.2017.161

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LUU, T. M., PHAN, R., DAVEY, R., & CHETTY, G. (2017). A Multilevel NER Framework for Automatic Clinical Name Entity Recognition. In R. Gottumukkala, G. Karypis, V. Raghavan, X. Wu, L. Miele, S. Aluru, X. Ning, & G. Dong (Eds.), 2017 IEEE International Conference on Data Mining Workshops (pp. 1135-1143). (IEEE INTERNATIONAL CONFERENCE ON DATA MINING WORKSHOPS). IEEE, Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/ICDMW.2017.161

LUU, Thoai Man ; PHAN, Rob ; DAVEY, Rachel et al. / A Multilevel NER Framework for Automatic Clinical Name Entity Recognition. 2017 IEEE International Conference on Data Mining Workshops. editor / Raju Gottumukkala ; George Karypis ; Vijay Raghavan ; Xindong Wu ; Lucio Miele ; Srinivas Aluru ; Xia Ning ; Guozhu Dong. New Orleans : IEEE, Institute of Electrical and Electronics Engineers, 2017. pp. 1135-1143 (IEEE INTERNATIONAL CONFERENCE ON DATA MINING WORKSHOPS).

@inproceedings{fd5aaa293f364ef597906263124c72d5,

title = "A Multilevel NER Framework for Automatic Clinical Name Entity Recognition",

abstract = "In this paper, we propose a novel multilevel NER framework, for addressing the challenges of clinical name entity recognition, based on different machine learning and text mining algorithms. The proposed framework, with multiple levels, allows models for increasingly complex NER tasks to be built. The experimental evaluation on two different publicly available datasets, corresponding to different application contexts - the CLEF 2016 challenge shared task 1A for nursing handover context, and the BIONLP/NLPBPA 2004 challenge shared task on GENIA corpus for recognizing entities in microbiology, has validated the proposed framework.",

keywords = "Name Entity Recognition, Clinical decision support software, Machine Learning",

author = "LUU, {Thoai Man} and Rob PHAN and Rachel DAVEY and Girija CHETTY",

note = "Funding Information: This work was supported by the National Natural Science Foundation of China (61673290). Publisher Copyright: {\textcopyright} 2017 IEEE.; 2017 IEEE International Conference on Data Mining Workshops (ICDMW), ICDMW 2017 ; Conference date: 18-11-2017 Through 21-11-2017",

year = "2017",

month = nov,

day = "18",

doi = "10.1109/ICDMW.2017.161",

language = "English",

isbn = "9781538638019",

series = "IEEE INTERNATIONAL CONFERENCE ON DATA MINING WORKSHOPS",

publisher = "IEEE, Institute of Electrical and Electronics Engineers",

pages = "1135--1143",

editor = "Raju Gottumukkala and George Karypis and Vijay Raghavan and Xindong Wu and Lucio Miele and Srinivas Aluru and Xia Ning and Guozhu Dong",

booktitle = "2017 IEEE International Conference on Data Mining Workshops",

address = "United States",

}

LUU, TM, PHAN, R, DAVEY, R & CHETTY, G 2017, A Multilevel NER Framework for Automatic Clinical Name Entity Recognition. in R Gottumukkala, G Karypis, V Raghavan, X Wu, L Miele, S Aluru, X Ning & G Dong (eds), 2017 IEEE International Conference on Data Mining Workshops. IEEE INTERNATIONAL CONFERENCE ON DATA MINING WORKSHOPS, IEEE, Institute of Electrical and Electronics Engineers, New Orleans, pp. 1135-1143, 2017 IEEE International Conference on Data Mining Workshops (ICDMW), New Orleans, Louisiana, United States, 18/11/17. https://doi.org/10.1109/ICDMW.2017.161

A Multilevel NER Framework for Automatic Clinical Name Entity Recognition. / LUU, Thoai Man; PHAN, Rob; DAVEY, Rachel et al.
2017 IEEE International Conference on Data Mining Workshops. ed. / Raju Gottumukkala; George Karypis; Vijay Raghavan; Xindong Wu; Lucio Miele; Srinivas Aluru; Xia Ning; Guozhu Dong. New Orleans: IEEE, Institute of Electrical and Electronics Engineers, 2017. p. 1135-1143 (IEEE INTERNATIONAL CONFERENCE ON DATA MINING WORKSHOPS).

Research output: A Conference proceeding or a Chapter in Book › Conference contribution › peer-review

TY - GEN

T1 - A Multilevel NER Framework for Automatic Clinical Name Entity Recognition

AU - LUU, Thoai Man

AU - PHAN, Rob

AU - DAVEY, Rachel

AU - CHETTY, Girija

PY - 2017/11/18

Y1 - 2017/11/18

N2 - In this paper, we propose a novel multilevel NER framework, for addressing the challenges of clinical name entity recognition, based on different machine learning and text mining algorithms. The proposed framework, with multiple levels, allows models for increasingly complex NER tasks to be built. The experimental evaluation on two different publicly available datasets, corresponding to different application contexts - the CLEF 2016 challenge shared task 1A for nursing handover context, and the BIONLP/NLPBPA 2004 challenge shared task on GENIA corpus for recognizing entities in microbiology, has validated the proposed framework.

AB - In this paper, we propose a novel multilevel NER framework, for addressing the challenges of clinical name entity recognition, based on different machine learning and text mining algorithms. The proposed framework, with multiple levels, allows models for increasingly complex NER tasks to be built. The experimental evaluation on two different publicly available datasets, corresponding to different application contexts - the CLEF 2016 challenge shared task 1A for nursing handover context, and the BIONLP/NLPBPA 2004 challenge shared task on GENIA corpus for recognizing entities in microbiology, has validated the proposed framework.

KW - Name Entity Recognition

KW - Clinical decision support software

KW - Machine Learning

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DO - 10.1109/ICDMW.2017.161

M3 - Conference contribution

SN - 9781538638019

T3 - IEEE INTERNATIONAL CONFERENCE ON DATA MINING WORKSHOPS

SP - 1135

EP - 1143

BT - 2017 IEEE International Conference on Data Mining Workshops

A2 - Gottumukkala, Raju

A2 - Karypis, George

A2 - Raghavan, Vijay

A2 - Wu, Xindong

A2 - Miele, Lucio

A2 - Aluru, Srinivas

A2 - Ning, Xia

A2 - Dong, Guozhu

PB - IEEE, Institute of Electrical and Electronics Engineers

CY - New Orleans

T2 - 2017 IEEE International Conference on Data Mining Workshops (ICDMW)

Y2 - 18 November 2017 through 21 November 2017

ER -

LUU TM, PHAN R, DAVEY R , CHETTY G. A Multilevel NER Framework for Automatic Clinical Name Entity Recognition. In Gottumukkala R, Karypis G, Raghavan V, Wu X, Miele L, Aluru S, Ning X, Dong G, editors, 2017 IEEE International Conference on Data Mining Workshops. New Orleans: IEEE, Institute of Electrical and Electronics Engineers. 2017. p. 1135-1143. (IEEE INTERNATIONAL CONFERENCE ON DATA MINING WORKSHOPS). doi: 10.1109/ICDMW.2017.161

A Multilevel NER Framework for Automatic Clinical Name Entity Recognition

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