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D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell data

BACKGROUND: Dimensionality reduction and visualization play vital roles in single-cell RNA sequencing (scRNA-seq) data analysis. While they have been extensively studied, state-of-the-art dimensionality reduction algorithms are often unable to preserve the global structures underlying data. Elastic...

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Autores principales: An, Shaokun, Huang, Jizu, Wan, Lin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7657844/
https://www.ncbi.nlm.nih.gov/pubmed/33179041
http://dx.doi.org/10.1093/gigascience/giaa126
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author An, Shaokun
Huang, Jizu
Wan, Lin
author_facet An, Shaokun
Huang, Jizu
Wan, Lin
author_sort An, Shaokun
collection PubMed
description BACKGROUND: Dimensionality reduction and visualization play vital roles in single-cell RNA sequencing (scRNA-seq) data analysis. While they have been extensively studied, state-of-the-art dimensionality reduction algorithms are often unable to preserve the global structures underlying data. Elastic embedding (EE), a nonlinear dimensionality reduction method, has shown promise in revealing low-dimensional intrinsic local and global data structure. However, the current implementation of the EE algorithm lacks scalability to large-scale scRNA-seq data. RESULTS: We present a distributed optimization implementation of the EE algorithm, termed distributed elastic embedding (D-EE). D-EE reveals the low-dimensional intrinsic structures of data with accuracy equal to that of elastic embedding, and it is scalable to large-scale scRNA-seq data. It leverages distributed storage and distributed computation, achieving memory efficiency and high-performance computing simultaneously. In addition, an extended version of D-EE, termed distributed optimization implementation of time-series elastic embedding (D-TSEE), enables the user to visualize large-scale time-series scRNA-seq data by incorporating experimentally temporal information. Results with large-scale scRNA-seq data indicate that D-TSEE can uncover oscillatory gene expression patterns by using experimentally temporal information. CONCLUSIONS: D-EE is a distributed dimensionality reduction and visualization tool. Its distributed storage and distributed computation technique allow us to efficiently analyze large-scale single-cell data at the cost of constant time speedup. The source code for D-EE algorithm based on C and MPI tailored to a high-performance computing cluster is available at https://github.com/ShaokunAn/D-EE.
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spelling pubmed-76578442020-11-18 D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell data An, Shaokun Huang, Jizu Wan, Lin Gigascience Technical Note BACKGROUND: Dimensionality reduction and visualization play vital roles in single-cell RNA sequencing (scRNA-seq) data analysis. While they have been extensively studied, state-of-the-art dimensionality reduction algorithms are often unable to preserve the global structures underlying data. Elastic embedding (EE), a nonlinear dimensionality reduction method, has shown promise in revealing low-dimensional intrinsic local and global data structure. However, the current implementation of the EE algorithm lacks scalability to large-scale scRNA-seq data. RESULTS: We present a distributed optimization implementation of the EE algorithm, termed distributed elastic embedding (D-EE). D-EE reveals the low-dimensional intrinsic structures of data with accuracy equal to that of elastic embedding, and it is scalable to large-scale scRNA-seq data. It leverages distributed storage and distributed computation, achieving memory efficiency and high-performance computing simultaneously. In addition, an extended version of D-EE, termed distributed optimization implementation of time-series elastic embedding (D-TSEE), enables the user to visualize large-scale time-series scRNA-seq data by incorporating experimentally temporal information. Results with large-scale scRNA-seq data indicate that D-TSEE can uncover oscillatory gene expression patterns by using experimentally temporal information. CONCLUSIONS: D-EE is a distributed dimensionality reduction and visualization tool. Its distributed storage and distributed computation technique allow us to efficiently analyze large-scale single-cell data at the cost of constant time speedup. The source code for D-EE algorithm based on C and MPI tailored to a high-performance computing cluster is available at https://github.com/ShaokunAn/D-EE. Oxford University Press 2020-11-11 /pmc/articles/PMC7657844/ /pubmed/33179041 http://dx.doi.org/10.1093/gigascience/giaa126 Text en © The Author(s) 2020. Published by Oxford University Press GigaScience. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Note
An, Shaokun
Huang, Jizu
Wan, Lin
D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell data
title D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell data
title_full D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell data
title_fullStr D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell data
title_full_unstemmed D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell data
title_short D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell data
title_sort d-ee: distributed software for visualizing intrinsic structure of large-scale single-cell data
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7657844/
https://www.ncbi.nlm.nih.gov/pubmed/33179041
http://dx.doi.org/10.1093/gigascience/giaa126
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