{Reference Type}: Journal Article
{Title}: scGAAC: A graph attention autoencoder for clustering single-cell RNA-sequencing data.
{Author}: Zhang L;Xiang H;Wang F;Chen Z;Shen M;Ma J;Liu H;Zheng H;
{Journal}: Methods
{Volume}: 229
{Issue}: 0
{Year}: 2024 Sep 29
{Factor}: 4.647
{DOI}: 10.1016/j.ymeth.2024.06.010
{Abstract}: Single-cell RNA-sequencing (scRNA-seq) enables the investigation of intricate mechanisms governing cell heterogeneity and diversity. Clustering analysis remains a pivotal tool in scRNA-seq for discerning cell types. However, persistent challenges arise from noise, high dimensionality, and dropout in single-cell data. Despite the proliferation of scRNA-seq clustering methods, these often focus on extracting representations from individual cell expression data, neglecting potential intercellular relationships. To overcome this limitation, we introduce scGAAC, a novel clustering method based on an attention-based graph convolutional autoencoder. By leveraging structural information between cells through a graph attention autoencoder, scGAAC uncovers latent relationships while extracting representation information from single-cell gene expression patterns. An attention fusion module amalgamates the learned features of the graph attention autoencoder and the autoencoder through attention weights. Ultimately, a self-supervised learning policy guides model optimization. scGAAC, a hypothesis-free framework, performs better on four real scRNA-seq datasets than most state-of-the-art methods. The scGAAC implementation is publicly available on Github at: https://github.com/labiip/scGAAC.