MethPriorGCN: a deep learning tool for inferring DNA methylation prior knowledge and guiding personalized medicine.

Journal: Briefings in bioinformatics
PMID: 40131311

Abstract

DNA methylation plays a crucial role in human diseases pathogenesis. Substantial experimental evidence from clinical and biological studies has confirmed numerous methylation-disease associations, which provide valuable prior knowledge for advancing precision medicine through biomarker discovery and disease subtyping. To systematically mine reliable methylation prior knowledge from known DNA methylation-disease associations and develop robust computational methods for precision medicine applications, we propose MethPriorGCN. By integrating layer attention mechanisms and feature weighting mechanisms, MethPriorGCN not only identified reliable methylation digital biomarkers but also achieved superior disease subtype classification accuracy.

Authors

  • Jie Ni
    School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, China.
  • Bin Li
    Department of Magnetic Resonance Imaging (MRI), Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
  • Shumei Miao
    Department of Information, The First Affiliated Hospital of Nanjing Medical University & Jiangsu Province Hospital, Nanjing, Jiangsu, China; Institute of Medical Informatics and Management, Nanjing Medical University, Nanjing, Jiangsu, China.
  • Xinting Zhang
    Institute for Molecular Medical Technology, State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, No. 2, Southeast University Road, Jiangning District, Nanjing, Jiangsu 211102, China.
  • Donghui Yan
  • Shengqi Jing
    Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, No. 101, Longmian Avenue, Jiangning District, Nanjing, Jiangsu 211166, China.
  • Shan Lu
    The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
  • Zhuoying Xie
  • Xin Zhang
    First Department of Infectious Diseases, The First Affiliated Hospital of China Medical University, Shenyang, China.
  • Yun Liu
    Google Health, Palo Alto, CA USA.

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