KMS Of Academy of mathematics and systems sciences, CAS
| NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data | |
Xiong, Jiankang1,2; Gong, Fuzhou1,2 ; Wan, Lin1,2; Ma, Liang3
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| 2020-10-06 | |
| Source Publication | FRONTIERS IN GENETICS
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| Volume | 11Pages:8 |
| Abstract | 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. |
| Keyword | single-cell RNA sequencing elastic embedding neural networks large-scale stochastic optimization parametric models generalizable models |
| DOI | 10.3389/fgene.2020.00786 |
| Indexed By | SCI |
| Language | 英语 |
| Funding Project | 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 Research Area | Genetics & Heredity |
| WOS Subject | Genetics & Heredity |
| WOS ID | WOS:000583639900001 |
| Publisher | FRONTIERS MEDIA SA |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/52398 |
| Collection | 应用数学研究所 |
| Corresponding Author | Wan, Lin; Ma, Liang |
| Affiliation | 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 |
| Recommended Citation 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. |
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