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*

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

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

Original languageEnglish
Article number102392
JournalSTAR protocols
Volume4
Issue number3
DOIs
Publication statusPublished - 15 Sept 2023
MoE publication typeA1 Journal article-refereed

Keywords

  • Clinical Protocol
  • Computer Sciences
  • Health Sciences

Fingerprint

Dive into the research topics of 'Protocol for the automatic extraction of epidemiological information via a pre-trained language model'. Together they form a unique fingerprint.

Cite this