Literature DB >> 27065756

Regularization Paths for Cox's Proportional Hazards Model via Coordinate Descent.

Noah Simon1, Jerome Friedman1, Trevor Hastie1, Rob Tibshirani1.   

Abstract

We introduce a pathwise algorithm for the Cox proportional hazards model, regularized by convex combinations of ℓ1 and ℓ2 penalties (elastic net). Our algorithm fits via cyclical coordinate descent, and employs warm starts to find a solution along a regularization path. We demonstrate the efficacy of our algorithm on real and simulated data sets, and find considerable speedup between our algorithm and competing methods.

Entities:  

Keywords:  Cox model; elastic net; lasso; survival

Year:  2011        PMID： 27065756      PMCID： PMC4824408          DOI： 10.18637/jss.v039.i05

Source DB:  PubMed          Journal:  J Stat Softw        ISSN： 1548-7660            Impact factor:   6.440


  6 in total

1.  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

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

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

3.  The lasso method for variable selection in the Cox model.

Authors:  R Tibshirani
Journal:  Stat Med       Date:  1997-02-28       Impact factor: 2.373

4.  Cross-validated Cox regression on microarray gene expression data.

Authors:  Hans C van Houwelingen; Tako Bruinsma; Augustinus A M Hart; Laura J Van't Veer; Lodewyk F A Wessels
Journal:  Stat Med       Date:  2006-09-30       Impact factor: 2.373

5.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.

Authors:  A A Alizadeh; M B Eisen; R E Davis; C Ma; I S Lossos; A Rosenwald; J C Boldrick; H Sabet; T Tran; X Yu; J I Powell; L Yang; G E Marti; T Moore; J Hudson; L Lu; D B Lewis; R Tibshirani; G Sherlock; W C Chan; T C Greiner; D D Weisenburger; J O Armitage; R Warnke; R Levy; W Wilson; M R Grever; J C Byrd; D Botstein; P O Brown; L M Staudt
Journal:  Nature       Date:  2000-02-03       Impact factor: 49.962

6.  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
  6 in total
  484 in total

Review 1.  Overview of LASSO-related penalized regression methods for quantitative trait mapping and genomic selection.

Authors:  Zitong Li; Mikko J Sillanpää
Journal:  Theor Appl Genet       Date:  2012-05-24       Impact factor: 5.699

2.  Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates.

Authors:  Kevin He; Yanming Li; Ji Zhu; Hongliang Liu; Jeffrey E Lee; Christopher I Amos; Terry Hyslop; Jiashun Jin; Huazhen Lin; Qinyi Wei; Yi Li
Journal:  Bioinformatics       Date:  2015-09-17       Impact factor: 6.937

3.  Selection of effects in Cox frailty models by regularization methods.

Authors:  Andreas Groll; Trevor Hastie; Gerhard Tutz
Journal:  Biometrics       Date:  2017-01-13       Impact factor: 2.571

4.  SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.

Authors:  Siwen Hu-Lieskovan; Srabani Bhaumik; Kavita Dhodapkar; Jean-Charles J B Grivel; Sumati Gupta; Brent A Hanks; Sylvia Janetzki; Thomas O Kleen; Yoshinobu Koguchi; Amanda W Lund; Cristina Maccalli; Yolanda D Mahnke; Ruslan D Novosiadly; Senthamil R Selvan; Tasha Sims; Yingdong Zhao; Holden T Maecker
Journal:  J Immunother Cancer       Date:  2020-12       Impact factor: 13.751

5.  Pathway-structured predictive modeling for multi-level drug response in multiple myeloma.

Authors:  Xinyan Zhang; Bingzong Li; Huiying Han; Sha Song; Hongxia Xu; Zixuan Yi; Yating Hong; Wenzhuo Zhuang; Nengjun Yi
Journal:  Bioinformatics       Date:  2018-11-01       Impact factor: 6.937

6.  Efficient ℓ0 -norm feature selection based on augmented and penalized minimization.

Authors:  Xiang Li; Shanghong Xie; Donglin Zeng; Yuanjia Wang
Journal:  Stat Med       Date:  2017-10-30       Impact factor: 2.373

7.  A clinical prediction model for cancer-associated venous thromboembolism: a development and validation study in two independent prospective cohorts.

Authors:  Ingrid Pabinger; Nick van Es; Georg Heinze; Florian Posch; Julia Riedl; Eva-Maria Reitter; Marcello Di Nisio; Gabriela Cesarman-Maus; Noémie Kraaijpoel; Christoph Carl Zielinski; Harry Roger Büller; Cihan Ay
Journal:  Lancet Haematol       Date:  2018-06-07       Impact factor: 18.959

8.  A LASSO Method to Identify Protein Signature Predicting Post-transplant Renal Graft Survival.

Authors:  Ling Zhou; Lu Tang; Angela T Song; Diane M Cibrik; Peter X-K Song
Journal:  Stat Biosci       Date:  2016-10-03

9.  Metastatic melanoma: pretreatment contrast-enhanced CT texture parameters as predictive biomarkers of survival in patients treated with pembrolizumab.

Authors:  Carole Durot; Sébastien Mulé; Philippe Soyer; Aude Marchal; Florent Grange; Christine Hoeffel
Journal:  Eur Radiol       Date:  2019-01-15       Impact factor: 5.315

10.  A fast divide-and-conquer sparse Cox regression.

Authors:  Yan Wang; Chuan Hong; Nathan Palmer; Qian Di; Joel Schwartz; Isaac Kohane; Tianxi Cai
Journal:  Biostatistics       Date:  2021-04-10       Impact factor: 5.899
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