Extracting chemical-protein relations with ensembles of SVM and deep learning models

Database : the Journal of Biological Databases and Curation
Yifan PengZhiyong Lu

Abstract

Mining relations between chemicals and proteins from the biomedical literature is an increasingly important task. The CHEMPROT track at BioCreative VI aims to promote the development and evaluation of systems that can automatically detect the chemical-protein relations in running text (PubMed abstracts). This work describes our CHEMPROT track entry, which is an ensemble of three systems, including a support vector machine, a convolutional neural network, and a recurrent neural network. Their output is combined using majority voting or stacking for final predictions. Our CHEMPROT system obtained 0.7266 in precision and 0.5735 in recall for an F-score of 0.6410 during the challenge, demonstrating the effectiveness of machine learning-based approaches for automatic relation extraction from biomedical literature and achieving the highest performance in the task during the 2017 challenge.Database URL: http://www.biocreative.org/tasks/biocreative-vi/track-5/.

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Citations

Aug 2, 2018·BMC Medical Informatics and Decision Making·Kaixian YuJinfeng Zhang
Oct 18, 2019·Database : the Journal of Biological Databases and Curation·Rui Antunes, Sérgio Matos
Jan 10, 2019·Database : the Journal of Biological Databases and Curation·Pei-Yau LungJinfeng Zhang
May 28, 2019·Database : the Journal of Biological Databases and Curation·Yijia ZhangYuanyuan Sun
Jan 30, 2020·BMC Bioinformatics·Jin-Woo ChungJong C Park
Jul 9, 2020·Computational and Structural Biotechnology Journal·David N Nicholson, Casey S Greene
Jan 24, 2021·Journal of the American Medical Informatics Association : JAMIA·Brandon Lwowski, Anthony Rios
Feb 12, 2021·Database : the Journal of Biological Databases and Curation·Yifan ShaoGuodong Zhou
Feb 19, 2020·Journal of Biomedical Informatics·Cong SunJian Wang
Apr 20, 2021·Frontiers in Research Metrics and Analytics·Jiayuan HeKarin Verspoor
Sep 9, 2019··Gillian ReynoldsMorteza Pourreza Shahri

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