A kernel non-negative matrix factorization framework for single cell clustering

doi:10.1016/j.apm.2020.08.065

CSpace > 应用数学研究所

	A kernel non-negative matrix factorization framework for single cell clustering
	Jiang, Hao 1; Yi, Ming 2; Zhang, Shihua3
	2021-02-01
发表期刊	APPLIED MATHEMATICAL MODELLING
ISSN	0307-904X
卷号	90 页码:875-888
摘要	The emergence of single-cell RNA-sequencing is ideally placed to unravel cellular het-erogeneity in biological systems, an extremely challenging problem in single cell RNA sequencing studies. However, most current computational approaches lack the sensitivity to reliably detect nonlinear gene-gene relationships masked by dropout events. We proposed a kernel non-negative matrix factorization framework for detecting nonlinear relationships among genes, where the new kernel is developed using kernel tricks on cellular differentiability correlation. The newly constructed kernel not only provides a description on the gene-gene relationship, but also helps to build a new low-dimensional representation on the original data. Besides, we developed an efficient method for determining the optimal cluster number within each data set with the usage of Diffusion Maps. The proposed algorithm is further compared with representative algorithms: SC3 and several other state-of-the-art clustering methods, on several benchmark or real scRNA-Seq datasets using internal criteria (clustering number accuracy) and external criteria (Adjusted rand index and Normalized mutual information) to show effectiveness of our method. (c) 2020 Elsevier Inc. All rights reserved.
关键词	Single cell RNA-sequencing Kernel non-negative matrix factorization Cellular heterogeneity
DOI	10.1016/j.apm.2020.08.065
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[11901575] ; National Natural Science Foundation of China[91730301] ; National Natural Science Foundation of China[11675060]
WOS研究方向	Engineering ; Mathematics ; Mechanics
WOS类目	Engineering, Multidisciplinary ; Mathematics, Interdisciplinary Applications ; Mechanics
WOS记录号	WOS:000590968700001
出版者	ELSEVIER SCIENCE INC
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/57829
专题	应用数学研究所
通讯作者	Jiang, Hao
作者单位	1.Renmin Univ China, Sch Math, Beijing 100872, Peoples R China 2.China Univ Geosci, Sch Math & Phys, Wuhan, Peoples R China 3.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Jiang, Hao,Yi, Ming,Zhang, Shihua. A kernel non-negative matrix factorization framework for single cell clustering[J]. APPLIED MATHEMATICAL MODELLING,2021,90:875-888.
APA	Jiang, Hao,Yi, Ming,&Zhang, Shihua.(2021).A kernel non-negative matrix factorization framework for single cell clustering.APPLIED MATHEMATICAL MODELLING,90,875-888.
MLA	Jiang, Hao,et al."A kernel non-negative matrix factorization framework for single cell clustering".APPLIED MATHEMATICAL MODELLING 90(2021):875-888.