GNODEVAE: a graph-based ODE-VAE enhances clustering for single-cell data.

Journal: BMC genomics
Published Date: Aug 21, 2025

Abstract

BACKGROUND: Single-cell RNA sequencing analysis faces critical challenges including high dimensionality, sparsity, and complex topological relationships between cells. Current methods struggle to simultaneously preserve global structure, model cellular dynamics, and handle technical noise effectively.

Authors

  • Zeyu Fu
    Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
  • Chunlin Chen
    Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
  • Song Wang
    Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, China.
  • Junping Wang
    Foundation Department, Huaibei Vocational and Technical College, Huaibei 23500, China.
  • Shilei Chen
    State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Army Medical University, Chongqing, 400038, China. chen.shilei@foxmail.com.

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