Structured, sparse regression with application to HIV drug resistance

DOI10.1214/10-AOAS428zbMATH Open1223.62164arXiv1002.3128OpenAlexW3105051557WikidataQ35191050 ScholiaQ35191050MaRDI QIDQ641120FDOQ641120

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)

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.

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

Recommendations

• Structured, sparse aggregation
• Super Learning: An Application to the Prediction of HIV-1 Drug Resistance
• scientific article; zbMATH DE number 2062402
• Characterizing the relationship between HIV-1 genotype and phenotype: prediction-based classification
• Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data.

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)

Cites Work

• Title not available (Why is that?)
• Sparsity and Smoothness Via the Fused Lasso
• Model Selection and Estimation in Regression with Grouped Variables
• Persistene in high-dimensional linear predictor-selection and the virtue of overparametrization
• Sparsity oracle inequalities for the Lasso
• Approximation and learning by greedy algorithms
• On the consistency of feature selection using greedy least squares regression
• Learning with Structured Sparsity
• Information-Theoretic Limits on Sparsity Recovery in the High-Dimensional and Noisy Setting
• Semiparametric Regression of Multidimensional Genetic Pathway Data: Least‐Squares Kernel Machines and Linear Mixed Models

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
• Title not available (Why is that?)
• Network-based penalized regression with application to genomic data

Uses Software

• glmnet
• geno2pheno

This page was built for publication: Structured, sparse regression with application to HIV drug resistance

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q641120)