An Adaptive Sparse Subspace Clustering for Cell Type Identification

• Main Authors: Ruiqing Zheng, Zhenlan Liang, Xiang Chen, Yu Tian, Chen Cao, Min Li
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2020-04-01
• Series: Frontiers in Genetics
• Subjects: single cell RNA-seq; subspace clustering; adaptive sparse strategy; similarity learning; visualization
• Online Access: https://www.frontiersin.org/article/10.3389/fgene.2020.00407/full

The rapid development of single-cell transcriptome sequencing technology has provided us with a cell-level perspective to study biological problems. Identification of cell types is one of the fundamental issues in computational analysis of single-cell data. Due to the large amount of noise from single-cell technologies and high dimension of expression profiles, traditional clustering methods are not so applicable to solve it. To address the problem, we have designed an adaptive sparse subspace clustering method, called AdaptiveSSC, to identify cell types. AdaptiveSSC is based on the assumption that the expression of cells with the same type lies in the same subspace; one cell can be expressed as a linear combination of the other cells. Moreover, it uses a data-driven adaptive sparse constraint to construct the similarity matrix. The comparison results of 10 scRNA-seq datasets show that AdaptiveSSC outperforms original subspace clustering and other state-of-art methods in most cases. Moreover, the learned similarity matrix can also be integrated with a modified t-SNE to obtain an improved visualization result.