Structured, sparse regression with application to HIV drug resistance

DOI10.1214/10-AOAS428MaRDI QIDQ641120zbMATH OpenOpenAlexWikidataFDO

Authors Daniel Percival, Kathryn Roeder, Roni Rosenfeld, Larry Wasserman

Publication date 21 October 2011

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

Full work available at URL https://arxiv.org/abs/1002.3128

zbMATH Keywords

variable selectionregressionsparsitygreedy algorithms

Mathematics Subject Classification ID

Linear regression; mixed models (62J05) Linear inference, regression (62J99) Applications of statistics to biology and medical sciences; meta analysis (62P10) Medical applications (general) (92C50)

Abstract: We introduce a new version of forward stepwise regression. Our modification finds solutions to regression problems where the selected predictors appear in a structured pattern, with respect to a predefined distance measure over the candidate predictors. Our method is motivated by the problem of predicting HIV-1 drug resistance from protein sequences. We find that our method improves the interpretability of drug resistance while producing comparable predictive accuracy to standard methods. We also demonstrate our method in a simulation study and present some theoretical results and connections.

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Cites work

• scientific article; zbMATH DE number 845714 (Why is no real title available?)
• Approximation and learning by greedy algorithms
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• Model Selection and Estimation in Regression with Grouped Variables
• On the consistency of feature selection using greedy least squares regression
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• Semiparametric Regression of Multidimensional Genetic Pathway Data: Least‐Squares Kernel Machines and Linear Mixed Models
• Sparsity and Smoothness Via the Fused Lasso
• Sparsity oracle inequalities for the Lasso

Cited in

(7)

• Super Learning: An Application to the Prediction of HIV-1 Drug Resistance
• Structured, sparse aggregation
• Theoretical properties of the overlapping groups Lasso
• High-dimensional generalized linear models incorporating graphical structure among predictors
• Overlapping group lasso for high-dimensional generalized linear models
• scientific article; zbMATH DE number 2062402 (Why is no real title available?)
• Network-based penalized regression with application to genomic data

Describes a project that uses

Uses Software

• geno2pheno
• glmnet

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