SuRF: A new method for sparse variable selection, with application in microbiome data analysis.

Statistics in Medicine
Lihui LiuToby Kenney

Abstract

In this article, we present a new variable selection method for regression and classification purposes, particularly for microbiome analysis. Our method, called subsampling ranking forward selection (SuRF), is based on LASSO penalized regression, subsampling and forward-selection methods. SuRF offers major advantages over existing variable selection methods in terms of both sparsity of selected models and model inference. We provide an R package that can implement our method for generalized linear models. We apply our method to classification problems from microbiome data, using a novel agglomeration approach to deal with the special tree-like correlation structure of the variables. Existing methods arbitrarily choose a taxonomic level a priori before performing the analysis, whereas by combining SuRF with these aggregated variables, we are able to identify the key biomarkers at the appropriate taxonomic level, as suggested by the data. We present simulations in multiple sparse settings to demonstrate that our approach performs better than several other popularly used existing approaches in recovering the true variables. We apply SuRF to two microbiome datasets: one about prediction of pouchitis and another for identifying samp...Continue Reading

References

Mar 17, 2010·Proceedings of the National Academy of Sciences of the United States of America·Noah FiererRob Knight
Jun 1, 2011·Genome Biology·J Gregory CaporasoRob Knight
Dec 16, 2011·Inflammatory Bowel Diseases·Sonia MichailEytan Wine
Apr 23, 2013·Clinical Gastroenterology and Hepatology : the Official Clinical Practice Journal of the American Gastroenterological Association·Bo Shen
Jun 24, 2014·The British Journal of Nutrition·Linda V ThomasKaori Suzuki
Jan 13, 2015·Annals of Statistics·Richard LockhartRobert Tibshirani
Apr 19, 2015·Genome Biology·Anita Y VoigtPeer Bork
Jun 1, 2015·Gastroenterology·Leah ReshefIris Dotan
May 8, 2016·Cell·Julia OhJulia A Segre

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Citations

Jul 4, 2021·Computers in Biology and Medicine·Vartika BishtGeorgios V Gkoutos

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