Identification of membrane protein types via deep residual hypergraph neural network.

Journal: Mathematical biosciences and engineering : MBE
PMID: 38052642

Abstract

A membrane protein's functions are significantly associated with its type, so it is crucial to identify the types of membrane proteins. Conventional computational methods for identifying the species of membrane proteins tend to ignore two issues: High-order correlation among membrane proteins and the scenarios of multi-modal representations of membrane proteins, which leads to information loss. To tackle those two issues, we proposed a deep residual hypergraph neural network (DRHGNN), which enhances the hypergraph neural network (HGNN) with initial residual and identity mapping in this paper. We carried out extensive experiments on four benchmark datasets of membrane proteins. In the meantime, we compared the DRHGNN with recently developed advanced methods. Experimental results showed the better performance of DRHGNN on the membrane protein classification task on four datasets. Experiments also showed that DRHGNN can handle the over-smoothing issue with the increase of the number of model layers compared with HGNN. The code is available at https://github.com/yunfighting/Identification-of-Membrane-Protein-Types-via-deep-residual-hypergraph-neural-network.

Authors

  • Jiyun Shen
    School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou 215009, China.
  • Yiyi Xia
    Tianping College of Suzhou University of Science and Technology, Suzhou, China.
  • Yiming Lu
    Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China. Electronic address: luym@bmi.ac.cn.
  • Weizhong Lu
    School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China.
  • Meiling Qian
    School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou 215009, China.
  • Hongjie Wu
    School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China.
  • Qiming Fu
    School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China.
  • Jing Chen
    Department of Vascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China.

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