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The power of matrix factorization: methods for deconvoluting genetic heterogeneous data at expression level

Author(s):

Yuan Liu, Zhining Wen and Menglong Li*  

Abstract:


Background: The utilization of genetic data to investigate biological problems has recently become a vital approach. However, it is undeniable that the heterogeneity of original samples at biological level is usually ignored when utilizing genetic data. Different cell-constitutions of a sample could differentiate the expression profile, and set considerable biases for downstream research. Matrix factorization (MF) which originated as a set of mathematical methods, has contributed massively to deconvoluting genetic profiles in silico, especially at expression level.

Objective: With the development of artificial intelligence algorithms and machine learning, the number of computational methods for solving heterogeneous problems are also rapidly abundant. However, a structural view from the angle of using MF to deconvolute genetic data is quite limited. This study was conducted to review the usages of MF methods on heterogeneous problems of genetic data on expression level.

Methods: MF methods involved in deconvolution were reviewed according to their individual strengths. The demonstration is presented separately into five sections following Chou’s 5-steps rule: definition of deconvolution, formulation of the heterogeneous problems, categories of MF algorithms, indicators of validations and summaries of available tools. Additionally, the challenges and opportunities of relative fields are discussed.

Results and conclusion: Based on the investigation, this study aims to present a relatively global picture to assist researchers to achieve a quicker access of deconvoluting genetic data in silico, further to help researchers in selecting suitable MF methods based on the different scenarios.

Keywords:

Matrix factorization, Heterogenization, Gene expression, Deconvolution, Computational method, Cell type

Affiliation:

College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064



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