Self-optimizing Single-cell Clustering with Contrastive Learning and Graph Neural Network
CSTR:
Author:
  • Article
  • | |
  • Metrics
  • |
  • Reference
  • |
  • Related
  • |
  • Cited by
  • | |
  • Comments
    Abstract:

    Single-cell RNA sequencing (scRNA-seq) performs high-throughput sequencing analysis of the transcriptomes at the level of individual cells. Its primary application is to identify cell subpopulations with distinct functions, usually based on cell clustering. However, the high dimensionality, noise, and sparsity of scRNA-seq data make clustering challenging. Traditional clustering methods are inadequate, and most existing single-cell clustering approaches only consider gene expression patterns while ignoring relationships between cells. To address these issues, a self-optimizing single-cell clustering method with contrastive learning and graph neural network (scCLG) is proposed. This method employs an autoencoder to learn cellular feature distribution. First, it begins by constructing a cell-gene graph, which is encoded using a graph neural network to effectively harness information on intercellular relationships. Subgraph sampling and feature masking create augmented views for contrastive learning, further optimizing feature representation. Finally, a self-optimizing strategy is utilized to jointly train the clustering and feature modules, continually refining feature representation and clustering centers for more accurate clustering. Experiments on 10 real scRNA-seq datasets demonstrate that scCLG can learn robust representations of cell features, significantly surpassing other methods in clustering accuracy.

    Reference
    Related
    Cited by
Get Citation

蒋维康,王劲贤.联合对比学习与图神经网络的自优化单细胞聚类.计算机系统应用,2024,33(9):1-13

Copy
Related Videos

Share
Article Metrics
  • Abstract:
  • PDF:
  • HTML:
  • Cited by:
History
  • Received:March 28,2024
  • Revised:April 23,2024
  • Online: July 26,2024
Article QR Code
You are the firstVisitors
Copyright: Institute of Software, Chinese Academy of Sciences Beijing ICP No. 05046678-3
Address:4# South Fourth Street, Zhongguancun,Haidian, Beijing,Postal Code:100190
Phone:010-62661041 Fax: Email:csa (a) iscas.ac.cn
Technical Support:Beijing Qinyun Technology Development Co., Ltd.

Beijing Public Network Security No. 11040202500063