NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data

doi:10.3389/fgene.2020.00786

CSpace > 应用数学研究所

	NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data
	Xiong, Jiankang 1,2; Gong, Fuzhou1,2 ; Wan, Lin 1,2; Ma, Liang 3
	2020-10-06
发表期刊	FRONTIERS IN GENETICS
卷号	11 页码:8
摘要	The dramatic increase in amount and size of single-cell RNA sequencing data calls for more efficient and scalable dimensional reduction and visualization tools. Here, we design a GPU-accelerated method, NeuralEE, which aggregates the advantages of elastic embedding and neural network. We show that NeuralEE is both scalable and generalizable in dimensional reduction and visualization of large-scale scRNA-seq data. In addition, the GPU-based implementation of NeuralEE makes it applicable to limited computational resources while maintains high performance, as it takes only half an hour to visualize 1.3 million mice brain cells, and NeuralEE has generalizability for integrating newly generated data.
关键词	single-cell RNA sequencing elastic embedding neural networks large-scale stochastic optimization parametric models generalizable models
DOI	10.3389/fgene.2020.00786
收录类别	SCI
语种	英语
资助项目	National Key R&D Program of China[2019YFA0709501] ; National Key R&D Program of China[2018YFB0704304] ; NSFC[81673833] ; NSFC[11971459] ; NSFC[12071466] ; NCMIS of CAS ; LSC of CAS ; Youth Innovation Promotion Association of CAS
WOS研究方向	Genetics & Heredity
WOS类目	Genetics & Heredity
WOS记录号	WOS:000583639900001
出版者	FRONTIERS MEDIA SA
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/52398
专题	应用数学研究所
通讯作者	Wan, Lin; Ma, Liang
作者单位	1.Chinese Acad Sci, Natl Ctr Math & Interdisciplinary Sci, Acad Math & Syst Sci, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Sch Math Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Xiong, Jiankang,Gong, Fuzhou,Wan, Lin,et al. NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data[J]. FRONTIERS IN GENETICS,2020,11:8.
APA	Xiong, Jiankang,Gong, Fuzhou,Wan, Lin,&Ma, Liang.(2020).NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data.FRONTIERS IN GENETICS,11,8.
MLA	Xiong, Jiankang,et al."NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data".FRONTIERS IN GENETICS 11(2020):8.