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Detection of gene–gene interactions using multistage sparse and low‐rank regression
Author(s) -
Hung Hung,
Lin YuTing,
Chen Penweng,
Wang ChenChien,
Huang SuYun,
Tzeng JungYing
Publication year - 2016
Publication title -
biometrics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.298
H-Index - 130
eISSN - 1541-0420
pISSN - 0006-341X
DOI - 10.1111/biom.12374
Subject(s) - lasso (programming language) , rank (graph theory) , curse of dimensionality , computer science , covariate , inference , gene interaction , data mining , machine learning , artificial intelligence , mathematics , gene , biology , combinatorics , world wide web , biochemistry
Summary Finding an efficient and computationally feasible approach to deal with the curse of high‐dimensionality is a daunting challenge faced by modern biological science. The problem becomes even more severe when the interactions are the research focus. To improve the performance of statistical analyses, we propose a sparse and low‐rank (SLR) screening based on the combination of a low‐rank interaction model and the Lasso screening. SLR models the interaction effects using a low‐rank matrix to achieve parsimonious parametrization. The low‐rank model increases the efficiency of statistical inference and, hence, SLR screening is able to more accurately detect gene–gene interactions than conventional methods. Incorporation of SLR screening into the Screen‐and‐Clean approach (Wasserman and Roeder, 2009; Wu et al., 2010) is also discussed, which suffers less penalty from Boferroni correction, and is able to assign p‐values for the identified variables in high‐dimensional model. We apply the proposed screening procedure to the Warfarin dosage study and the CoLaus study. The results suggest that the new procedure can identify main and interaction effects that would have been omitted by conventional screening methods.