中国科学院机构知识库网格
Chinese Academy of Sciences Institutional Repositories Grid
A kernel non-negative matrix factorization framework for single cell clustering

文献类型:期刊论文

作者Jiang, Hao1; Yi, Ming2; Zhang, Shihua3
刊名APPLIED MATHEMATICAL MODELLING
出版日期2021-02-01
卷号90页码:875-888
关键词Single cell RNA-sequencing Kernel non-negative matrix factorization Cellular heterogeneity
ISSN号0307-904X
DOI10.1016/j.apm.2020.08.065
英文摘要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.
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
语种英语
WOS记录号WOS:000590968700001
出版者ELSEVIER SCIENCE INC
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/57828]  
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.

入库方式: OAI收割

来源:数学与系统科学研究院

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