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

doi:10.3389/fgene.2020.00786

CORC > 数学与系统科学研究院 > 中国科学院数学与系统科学研究院 > 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 2,3; Gong, Fuzhou 2,3; Wan, Lin 2,3; Ma, Liang 1
刊名	FRONTIERS IN GENETICS
	2020-10-06
卷号	11 页码:8
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
英文摘要	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.
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
语种	英语
出版者	FRONTIERS MEDIA SA
WOS记录号	WOS:000583639900001
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/52397]
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, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Sch Math Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Natl Ctr Math & Interdisciplinary Sci, Acad Math & Syst Sci, 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.