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SCDRHA: A scRNA-Seq Data Dimensionality Reduction Algorithm Based on Hierarchical Autoencoder

Dimensionality reduction of high-dimensional data is crucial for single-cell RNA sequencing (scRNA-seq) visualization and clustering. One prominent challenge in scRNA-seq studies comes from the dropout events, which lead to zero-inflated data. To address this issue, in this paper, we propose a scRNA...

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Autores principales: Zhao, Jianping, Wang, Na, Wang, Haiyun, Zheng, Chunhou, Su, Yansen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8429846/
https://www.ncbi.nlm.nih.gov/pubmed/34512734
http://dx.doi.org/10.3389/fgene.2021.733906
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author Zhao, Jianping
Wang, Na
Wang, Haiyun
Zheng, Chunhou
Su, Yansen
author_facet Zhao, Jianping
Wang, Na
Wang, Haiyun
Zheng, Chunhou
Su, Yansen
author_sort Zhao, Jianping
collection PubMed
description Dimensionality reduction of high-dimensional data is crucial for single-cell RNA sequencing (scRNA-seq) visualization and clustering. One prominent challenge in scRNA-seq studies comes from the dropout events, which lead to zero-inflated data. To address this issue, in this paper, we propose a scRNA-seq data dimensionality reduction algorithm based on a hierarchical autoencoder, termed SCDRHA. The proposed SCDRHA consists of two core modules, where the first module is a deep count autoencoder (DCA) that is used to denoise data, and the second module is a graph autoencoder that projects the data into a low-dimensional space. Experimental results demonstrate that SCDRHA has better performance than existing state-of-the-art algorithms on dimension reduction and noise reduction in five real scRNA-seq datasets. Besides, SCDRHA can also dramatically improve the performance of data visualization and cell clustering.
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spelling pubmed-84298462021-09-11 SCDRHA: A scRNA-Seq Data Dimensionality Reduction Algorithm Based on Hierarchical Autoencoder Zhao, Jianping Wang, Na Wang, Haiyun Zheng, Chunhou Su, Yansen Front Genet Genetics Dimensionality reduction of high-dimensional data is crucial for single-cell RNA sequencing (scRNA-seq) visualization and clustering. One prominent challenge in scRNA-seq studies comes from the dropout events, which lead to zero-inflated data. To address this issue, in this paper, we propose a scRNA-seq data dimensionality reduction algorithm based on a hierarchical autoencoder, termed SCDRHA. The proposed SCDRHA consists of two core modules, where the first module is a deep count autoencoder (DCA) that is used to denoise data, and the second module is a graph autoencoder that projects the data into a low-dimensional space. Experimental results demonstrate that SCDRHA has better performance than existing state-of-the-art algorithms on dimension reduction and noise reduction in five real scRNA-seq datasets. Besides, SCDRHA can also dramatically improve the performance of data visualization and cell clustering. Frontiers Media S.A. 2021-08-27 /pmc/articles/PMC8429846/ /pubmed/34512734 http://dx.doi.org/10.3389/fgene.2021.733906 Text en Copyright © 2021 Zhao, Wang, Wang, Zheng and Su. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Zhao, Jianping
Wang, Na
Wang, Haiyun
Zheng, Chunhou
Su, Yansen
SCDRHA: A scRNA-Seq Data Dimensionality Reduction Algorithm Based on Hierarchical Autoencoder
title SCDRHA: A scRNA-Seq Data Dimensionality Reduction Algorithm Based on Hierarchical Autoencoder
title_full SCDRHA: A scRNA-Seq Data Dimensionality Reduction Algorithm Based on Hierarchical Autoencoder
title_fullStr SCDRHA: A scRNA-Seq Data Dimensionality Reduction Algorithm Based on Hierarchical Autoencoder
title_full_unstemmed SCDRHA: A scRNA-Seq Data Dimensionality Reduction Algorithm Based on Hierarchical Autoencoder
title_short SCDRHA: A scRNA-Seq Data Dimensionality Reduction Algorithm Based on Hierarchical Autoencoder
title_sort scdrha: a scrna-seq data dimensionality reduction algorithm based on hierarchical autoencoder
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8429846/
https://www.ncbi.nlm.nih.gov/pubmed/34512734
http://dx.doi.org/10.3389/fgene.2021.733906
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