Protocol for the automatic extraction of epidemiological information via a pre-trained language model

Zhizheng Wang; Xiao Fan Liu; Zhanwei Du; Lin Wang; Ye Wu; Petter Holme; Michael Lachmann; Hongfei Lin; Zhuoyue Wang; Yu Cao; Zoie S.Y. Wong; Xiao-Ke Xu; Yuanyuan Sun

doi:10.1016/j.xpro.2023.102392

Author(s)

Zhizheng Wang
Zhanwei Du
Lin Wang
Ye Wu
Petter Holme
Michael Lachmann
Hongfei Lin
Zhuoyue Wang
Yu Cao
Zoie S.Y. Wong
Xiao-Ke Xu
Yuanyuan Sun

Related Research Unit(s)

Department of Media and Communication

Detail(s)

Original language	English
Article number	102392
Journal / Publication	STAR Protocols
Volume	4
Issue number	3
Online published	1 Jul 2023
Publication status	Published - 15 Sept 2023

Link(s)

DOI	DOI https://doi.org/10.1016/j.xpro.2023.102392 Final Published version
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Attachment(s)	Documents 162000990.pdf Final Published version, 6.12 MB, PDF Publisher's Copyright Statement This full text is made available under CC-BY-NC-ND 4.0. https://creativecommons.org/licenses/by-nc-nd/4.0/
Link to Scopus	https://www.scopus.com/record/display.uri?eid=2-s2.0-85164021849&origin=recordpage
Permanent Link	https://scholars.cityu.edu.hk/en/publications/publication(1c60e242-aeba-4145-82d8-12c213ce6968).html

Abstract

The lack of systems to automatically extract epidemiological fields from open-access COVID-19 cases restricts the timeliness of formulating prevention measures. Here we present a protocol for using CCIE, a COVID-19 Cases Information Extraction system based on the pre-trained language model.¹ We describe steps for preparing supervised training data and executing python scripts for named entity recognition and text category classification. We then detail the use of machine evaluation and manual validation to illustrate the effectiveness of CCIE. For complete details on the use and execution of this protocol, please refer to Wang et al.² © 2023 The Authors.

Research Area(s)

Clinical Protocol, Computer Sciences, Health Sciences

Citation Format(s)

[ RIS ] [ BibTeX ]

Protocol for the automatic extraction of epidemiological information via a pre-trained language model. / Wang, Zhizheng; Liu, Xiao Fan; Du, Zhanwei et al.
In: STAR Protocols, Vol. 4, No. 3, 102392, 15.09.2023.

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Wang, Z, Liu, XF, Du, Z, Wang, L, Wu, Y, Holme, P, Lachmann, M, Lin, H, Wang, Z, Cao, Y, Wong, ZSY, Xu, X-K & Sun, Y 2023, 'Protocol for the automatic extraction of epidemiological information via a pre-trained language model', STAR Protocols, vol. 4, no. 3, 102392. https://doi.org/10.1016/j.xpro.2023.102392

Wang, Z., Liu, X. F., Du, Z., Wang, L., Wu, Y., Holme, P., Lachmann, M., Lin, H., Wang, Z., Cao, Y., Wong, Z. S. Y., Xu, X.-K., & Sun, Y. (2023). Protocol for the automatic extraction of epidemiological information via a pre-trained language model. STAR Protocols, 4(3), Article 102392. https://doi.org/10.1016/j.xpro.2023.102392

Wang Z, Liu XF, Du Z, Wang L, Wu Y, Holme P et al. Protocol for the automatic extraction of epidemiological information via a pre-trained language model. STAR Protocols. 2023 Sept 15;4(3):102392. Epub 2023 Jul 1. doi: 10.1016/j.xpro.2023.102392

Wang, Zhizheng ; Liu, Xiao Fan ; Du, Zhanwei et al. / Protocol for the automatic extraction of epidemiological information via a pre-trained language model. In: STAR Protocols. 2023 ; Vol. 4, No. 3.

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