Sparse matrix linear models for structured high-throughput data

DOI10.1214/21-AOAS1444MaRDI QIDQ2135347zbMATH OpenWikidataFDO

Authors Jane W. Liang, Śaunak Sen

Publication date 6 May 2022

Published in The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1712.05767

zbMATH Keywords

LassoADMMJuliagradient descentFISTAproximal gradient algorithms

Mathematics Subject Classification ID

Computational methods for problems pertaining to statistics (62-08) Linear regression; mixed models (62J05) Applications of statistics to biology and medical sciences; meta analysis (62P10) Convex programming (90C25) Ridge regression; shrinkage estimators (Lasso) (62J07)

Abstract: Recent technological advancements have led to the rapid generation of high-throughput biological data, which can be used to address novel scientific questions in broad areas of research. These data can be thought of as a large matrix with covariates annotating both rows and columns of this matrix. Matrix linear models provide a convenient way for modeling such data. In many situations, sparse estimation of these models is desired. We present fast, general methods for fitting sparse matrix linear models to structured high-throughput data. We induce model sparsity using an L${}_1$ penalty and consider the case when the response matrix and the covariate matrices are large. Due to data size, standard methods for estimation of these penalized regression models fail if the problem is converted to the corresponding univariate regression scenario. By leveraging matrix properties in the structure of our model, we develop several fast estimation algorithms (coordinate descent, FISTA, and ADMM) and discuss their trade-offs. We evaluate our method's performance on simulated data, E. coli chemical genetic screening data, and two Arabidopsis genetic datasets with multivariate responses. Our algorithms have been implemented in the Julia programming language and are available at https://github.com/senresearch/MatrixLMnet.jl.

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Cited in

(4)

• ANOVA Model Fitting via Sparse Matrix Computations: A Fast Direct Method
• MatrixLMnet
• Independent Component Analysis and Blind Signal Separation
• Streamlined solutions to multilevel sparse matrix problems

Describes a project that uses

Uses Software

• sma
• GitHub
• R/qtl
• selectiveInference
• Julia
• Mutoss
• hglasso
• limma
• MESS
• data.table
• glmnet
• fda (R)
• R

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