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arXiv2024

Sparse higher order partial least squares for simultaneous variable selection, dimension reduction, and tensor denoising

Partial Least Squares (PLS) regression emerged as an alternative to ordinary least squares for addressing multicollinearity in a wide range of scientific applications. As multidimensional tensor data is becoming more widespread, tensor adaptations of PLS have been developed. In this paper, we first establish the statistical behavior of Higher Order PLS (HOPLS) of Zhao et al. (2012), by showing that the consistency of the HOPLS estimator cannot be guaranteed as the tensor dimensions and the number of features increase faster than the sample size. To tackle this issue, we propose Sparse Higher Order Partial Least Squares (SHOPS) regression and an accompanying algorithm. SHOPS simultaneously accommodates variable selection, dimension reduction, and tensor response denoising. We further establish the asymptotic results of the SHOPS algorithm under a high-dimensional regime. The results also complete the unknown theoretic properties of SPLS algorithm (Chun and Keleş, 2010). We verify these findings through comprehensive simulation experiments, and application to an emerging high-dimensional biological data analysis.

stat.ME↗

arXiv2008

Multiple tests of association with biological annotation metadata

We propose a general and formal statistical framework for multiple tests of association between known fixed features of a genome and unknown parameters of the distribution of variable features of this genome in a population of interest. The known gene-annotation profiles, corresponding to the fixed features of the genome, may concern Gene Ontology (GO) annotation, pathway membership, regulation by particular transcription factors, nucleotide sequences, or protein sequences. The unknown gene-parameter profiles, corresponding to the variable features of the genome, may be, for example, regression coefficients relating possibly censored biological and clinical outcomes to genome-wide transcript levels, DNA copy numbers, and other covariates. A generic question of great interest in current genomic research regards the detection of associations between biological annotation metadata and genome-wide expression measures. This biological question may be translated as the test of multiple hypotheses concerning association measures between gene-annotation profiles and gene-parameter profiles. A general and rigorous formulation of the statistical inference question allows us to apply the multiple hypothesis testing methodology developed in [Multiple Testing Procedures with Applications to Genomics (2008) Springer, New York] and related articles, to control a broad class of Type I error rates, defined as generalized tail probabilities and expected values for arbitrary functions of the numbers of Type I errors and rejected hypotheses. The resampling-based single-step and stepwise multiple testing procedures of [Multiple Testing Procedures with Applications to Genomics (2008) Springer, New York] take into account the joint distribution of the test statistics and provide Type I error control in testing problems involving general data generating distributions (with arbitrary dependence structures among variables), null hypotheses, and test statistics.

stat.AP↗