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Fast and precise single-cell data analysis using a hierarchical autoencoder
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DOI：10.1038/s41467-021-21312-2.png)
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Abstract
En 中文
A primary challenge in single-cell RNA sequencing (scRNA-seq) studies comes from the massive amount of data and the excess noise level. To address this challenge, we introduce an analysis framework, named single-cell Decomposition using Hierarchical Autoencoder (scDHA), that reliably extracts representative information of each cell. The scDHA pipeline consists of two core modules. The first module is a non-negative kernel autoencoder able to remove genes or components that have insignificant contributions to the part-based representation of the data. The second module is a stacked Bayesian autoencoder that projects the data onto a low-dimensional space (compressed). To diminish the tendency to overfit of neural networks, we repeatedly perturb the compressed space to learn a more generalized representation of the data. In an extensive analysis, we demonstrate that scDHA outperforms state-of-the-art techniques in many research sub-fields of scRNA-seq analysis, including cell segregation through unsupervised learning, visualization of transcriptome landscape, cell classification, and pseudo-time inference. Accurate analysis of single-cell RNA sequencing (scRNA-seq) data is affected by issues including technical noise and high dropout rate. Here, the authors develop a hierarchical autoencoder, scDHA, which outperforms existing methods in scRNA-seq analyses such as cell segregation and classification.
Keywords:
RNA-SEQ
GENE-EXPRESSION
HETEROGENEITY
TRANSCRIPTOMICS
RECONSTRUCTION
INTEGRATION
DIVERSITY
GENOMICS
STATES
ATLAS
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