Elucidating transcriptomic profiles from single-cell RNA sequencing data using nature-inspired compressed sensing

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

5 Scopus Citations
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Author(s)

  • Zhuohan Yu
  • Chuang Bian
  • Genggeng Liu
  • Xiangtao Li

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Detail(s)

Original languageEnglish
Article numberbbab125
Journal / PublicationBriefings in Bioinformatics
Volume22
Issue number5
Online published14 Apr 2021
Publication statusPublished - Sept 2021

Abstract

Gene-expression profiling can define the cell state and gene-expression pattern of cells at the genetic level in a high-throughput manner. With the development of transcriptome techniques, processing high-dimensional genetic data has become a major challenge in expression profiling. Thanks to the recent widespread use of matrix decomposition methods in bioinformatics, a computational framework based on compressed sensing was adopted to reduce dimensionality. However, compressed sensing requires an optimization strategy to learn the modular dictionaries and activity levels from the low-dimensional random composite measurements to reconstruct the high-dimensional gene-expression data. Considering this, here we introduce and compare four compressed sensing frameworks coming from nature-inspired optimization algorithms (CSCS, ABCCS, BACS and FACS) to improve the quality of the decompression process. Several experiments establish that the three proposed methods outperform benchmark methods on nine different datasets, especially the FACS method. We illustrate therefore, the robustness and convergence of FACS in various aspects; notably, time complexity and parameter analyses highlight properties of our proposed FACS. Furthermore, differential gene-expression analysis, cell-type clustering, gene ontology enrichment and pathology analysis are conducted, which bring novel insights into cell-type identification and characterization mechanisms from different perspectives. All algorithms are written in Python and available at https://github.com/Philyzh8/Nature-inspired-CS.

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