L1 penalized estimation in the Cox proportional hazards model

Biometrical Journal. Biometrische Zeitschrift
Jelle J Goeman

Abstract

This article presents a novel algorithm that efficiently computes L(1) penalized (lasso) estimates of parameters in high-dimensional models. The lasso has the property that it simultaneously performs variable selection and shrinkage, which makes it very useful for finding interpretable prediction rules in high-dimensional data. The new algorithm is based on a combination of gradient ascent optimization with the Newton-Raphson algorithm. It is described for a general likelihood function and can be applied in generalized linear models and other models with an L(1) penalty. The algorithm is demonstrated in the Cox proportional hazards model, predicting survival of breast cancer patients using gene expression data, and its performance is compared with competing approaches. An R package, penalized, that implements the method, is available on CRAN.

References

Dec 30, 1993·Statistics in Medicine·P J Verweij, H C Van Houwelingen
Feb 28, 1997·Statistics in Medicine·R Tibshirani
Feb 2, 2002·Nature·Laura J van 't VeerStephen H Friend
Jun 21, 2002·The New England Journal of Medicine·Andreas RosenwaldUNKNOWN Lymphoma/Leukemia Molecular Profiling Project
Jul 16, 2002·Nature Medicine·David G BeerSamir Hanash
Dec 20, 2002·The New England Journal of Medicine·Marc J van de VijverRené Bernards
Jan 11, 2003·Ecotoxicology·Waldo J De BoerCajo F Ter Braak
Jan 20, 2005·Bioinformatics·Jelle J GoemanHans C van Houwelingen
Sep 7, 2005·Statistics in Medicine·Hans C van HouwelingenLodewyk F A Wessels
Jun 8, 2007·Bioinformatics·H M BøvelstadO C Lingjaerde

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Citations

Dec 14, 2011·Bioinformatics·Levi WaldronIgor Jurisica
Oct 27, 2011·Cardiovascular Research·Anna ZampetakiManuel Mayr
Jun 23, 2012·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Hanno MatthaeiAnirban Maitra
Feb 23, 2012·BMC Medical Research Methodology·Ralf StroblUlrich Mansmann
Feb 22, 2012·PloS One·Ander MuniateguiAngel Rubio
Aug 27, 2013·PloS One·Julie A WallaceMichael C Ostrowski
Apr 21, 2010·The International Journal of Biostatistics·Josue G MartinezNilanjan Chatterjee
Apr 22, 2014·PloS One·Vanessa SochatDaniel L Rubin
Jun 17, 2014·Bioinformatics·Christoph BernauLorenzo Trippa
Jul 24, 2015·Breast Cancer Research and Treatment·Sarah A AndresJames L Wittliff
Jul 7, 2015·Computational and Mathematical Methods in Medicine·Shuhei KanekoChikuma Hamada
Jun 24, 2014·American Heart Journal·Anika A M VaarhorstP Eline Slagboom
Jul 10, 2012·American Journal of Human Genetics·Xiayi Ke
Jan 29, 2019·Acta Oto-laryngologica·Rebecca Tosca KarstenMichiel Wilhelmus Maria van den Brekel
Nov 26, 2010·Genetic Epidemiology·Kristin L Ayers, Heather J Cordell
Nov 13, 2018·Journal of Cellular Physiology·Liang ChenYu Xiao
Sep 2, 2016·Statistics in Medicine·Leonhard HeldDaniel Sabanés Bové
Apr 4, 2017·Bioinformatics·Weijia ZhangJiuyong Li

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