CBEx: A Hybrid Approach for Cancer Biomarker Extraction

Xiangyu Gao, Jinhe Shi, Wenjin Chen, Nancy Sazo, Huiqi Chu, Evita Sadimin, David J. Foran, Yi Chen

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

This paper presents a novel hybrid approach for extracting cancer biomarkers from pathology reports and a prototype system, CBEx (Cancer Biomarker Extractor). It integrates a Long Short-Time Memory Neural Network that identifies biomarker-containing sentences and a dictionary-based method to extract biomarker mentions from those sentences. Preliminary results show that CBEx outperforms existing methods.

Original languageEnglish (US)
Title of host publicationProceedings - 2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020
EditorsTaesung Park, Young-Rae Cho, Xiaohua Tony Hu, Illhoi Yoo, Hyun Goo Woo, Jianxin Wang, Julio Facelli, Seungyoon Nam, Mingon Kang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages2958
Number of pages1
ISBN (Electronic)9781728162157
DOIs
StatePublished - Dec 16 2020
Event2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020 - Virtual, Seoul, Korea, Republic of
Duration: Dec 16 2020Dec 19 2020

Publication series

NameProceedings - 2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020

Conference

Conference2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020
CountryKorea, Republic of
CityVirtual, Seoul
Period12/16/2012/19/20

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Information Systems and Management
  • Medicine (miscellaneous)
  • Health Informatics

Keywords

  • Cancer Biomarkers
  • Information Extraction
  • Natural Language Processing
  • Neural Networks

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