Literature DB >> 21457193

On path restoration for censored outcomes.

Brent A Johnson1, Qi Long, Matthias Chung.   

Abstract

Dimension reduction, model and variable selection are ubiquitous concepts in modern statistical science and deriving new methods beyond the scope of current methodology is noteworthy. This article briefly reviews existing regularization methods for penalized least squares and likelihood for survival data and their extension to a certain class of penalized estimating function. We show that if one's goal is to estimate the entire regularized coefficient path using the observed survival data, then all current strategies fail for the Buckley-James estimating function. We propose a novel two-stage method to estimate and restore the entire Dantzig-regularized coefficient path for censored outcomes in a least-squares framework. We apply our methods to a microarray study of lung andenocarcinoma with sample size n = 200 and p = 1036 gene predictors and find 10 genes that are consistently selected across different criteria and an additional 14 genes that merit further investigation. In simulation studies, we found that the proposed path restoration and variable selection technique has the potential to perform as well as existing methods that begin with a proper convex loss function at the outset.
© 2011, The International Biometric Society.

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Year:  2011        PMID: 21457193      PMCID: PMC3131450          DOI: 10.1111/j.1541-0420.2011.01587.x

Source DB:  PubMed          Journal:  Biometrics        ISSN: 0006-341X            Impact factor:   2.571


  11 in total

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Authors:  E A GEHAN
Journal:  Biometrika       Date:  1965-06       Impact factor: 2.445

2.  Penalized Estimating Functions and Variable Selection in Semiparametric Regression Models.

Authors:  Brent A Johnson; D Y Lin; Donglin Zeng
Journal:  J Am Stat Assoc       Date:  2008-06-01       Impact factor: 5.033

3.  Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data.

Authors:  Jiang Gui; Hongzhe Li
Journal:  Bioinformatics       Date:  2005-04-06       Impact factor: 6.937

4.  Regularized estimation in the accelerated failure time model with high-dimensional covariates.

Authors:  Jian Huang; Shuangge Ma; Huiliang Xie
Journal:  Biometrics       Date:  2006-09       Impact factor: 2.571

5.  Doubly penalized buckley-james method for survival data with high-dimensional covariates.

Authors:  Sijian Wang; Bin Nan; Ji Zhu; David G Beer
Journal:  Biometrics       Date:  2007-08-03       Impact factor: 2.571

6.  Rank-based estimation in the {ell}1-regularized partly linear model for censored outcomes with application to integrated analyses of clinical predictors and gene expression data.

Authors:  Brent A Johnson
Journal:  Biostatistics       Date:  2009-06-24       Impact factor: 5.899

7.  L1 penalized estimation in the Cox proportional hazards model.

Authors:  Jelle J Goeman
Journal:  Biom J       Date:  2010-02       Impact factor: 2.207

8.  Regularization Paths for Generalized Linear Models via Coordinate Descent.

Authors:  Jerome Friedman; Trevor Hastie; Rob Tibshirani
Journal:  J Stat Softw       Date:  2010       Impact factor: 6.440

9.  Survival analysis with high-dimensional covariates: an application in microarray studies.

Authors:  David Engler; Yi Li
Journal:  Stat Appl Genet Mol Biol       Date:  2009-02-11

10.  Predicting patient survival from microarray data by accelerated failure time modeling using partial least squares and LASSO.

Authors:  Susmita Datta; Jennifer Le-Rademacher; Somnath Datta
Journal:  Biometrics       Date:  2007-03       Impact factor: 2.571

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  4 in total

1.  Lasso regularization for left-censored Gaussian outcome and high-dimensional predictors.

Authors:  Perrine Soret; Marta Avalos; Linda Wittkop; Daniel Commenges; Rodolphe Thiébaut
Journal:  BMC Med Res Methodol       Date:  2018-12-04       Impact factor: 4.615

2.  Scalable Bayesian variable selection for structured high-dimensional data.

Authors:  Changgee Chang; Suprateek Kundu; Qi Long
Journal:  Biometrics       Date:  2018-05-08       Impact factor: 2.571

3.  A Tutorial on Rank-based Coefficient Estimation for Censored Data in Small- and Large-Scale Problems.

Authors:  Matthias Chung; Qi Long; Brent A Johnson
Journal:  Stat Comput       Date:  2013-09-01       Impact factor: 2.559

4.  The Dantzig Selector for Censored Linear Regression Models.

Authors:  Yi Li; Lee Dicker; Sihai Dave Zhao
Journal:  Stat Sin       Date:  2014-01-01       Impact factor: 1.261

  4 in total

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