Ensemble pretrained language models to extract biomedical knowledge from literature.

Journal: Journal of the American Medical Informatics Association : JAMIA
Published Date: Sep 1, 2024

Abstract

OBJECTIVES: The rapid expansion of biomedical literature necessitates automated techniques to discern relationships between biomedical concepts from extensive free text. Such techniques facilitate the development of detailed knowledge bases and highlight research deficiencies. The LitCoin Natural Language Processing (NLP) challenge, organized by the National Center for Advancing Translational Science, aims to evaluate such potential and provides a manually annotated corpus for methodology development and benchmarking.

Authors

  • Zhao Li
    Research Center for Data Hub and Security, Zhejiang Lab, Hangzhou, China. lzjoey@gmail.com.
  • Qiang Wei
    School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.
  • Liang-Chin Huang
    School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.
  • Jianfu Li
    Mayo Clinic.
  • Yan Hu
    Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
  • Yao-Shun Chuang
    McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States.
  • Jianping He
    McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, United States.
  • Avisha Das
    Arizona Advanced AI & Innovation (A3I) Hub, Mayo Clinic Arizona, Phoenix, AZ, USA.
  • Vipina Kuttichi Keloth
    Section of Biomedical Informatics and Data Science, School of Medicine, Yale University, New Haven, CT 06510, United States.
  • Yuntao Yang
    School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA.
  • Chiamaka S Diala
    McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, United States.
  • Kirk E Roberts
    McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, United States.
  • Cui Tao
    The University of Texas Health Science Center at Houston, USA.
  • Xiaoqian Jiang
    School of Biomedical Informatics, University of Texas Health, Science Center at Houston, Houston, TX, USA.
  • W Jim Zheng
    McWilliams School of Biomedical Informatics, University of Texas Health Science at Houston, Houston, TX, USA.
  • Hua Xu
    Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

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