Literature DB >> 22408278

Principled sure independence screening for Cox models with ultra-high-dimensional covariates.

Sihai Dave Zhao1, Yi Li.   

Abstract

It is rather challenging for current variable selectors to handle situations where the number of covariates under consideration is ultra-high. Consider a motivating clinical trial of the drug bortezomib for the treatment of multiple myeloma, where overall survival and expression levels of 44760 probesets were measured for each of 80 patients with the goal of identifying genes that predict survival after treatment. This dataset defies analysis even with regularized regression. Some remedies have been proposed for the linear model and for generalized linear models, but there are few solutions in the survival setting and, to our knowledge, no theoretical support. Furthermore, existing strategies often involve tuning parameters that are difficult to interpret. In this paper we propose and theoretically justify a principled method for reducing dimensionality in the analysis of censored data by selecting only the important covariates. Our procedure involves a tuning parameter that has a simple interpretation as the desired false positive rate of this selection. We present simulation results and apply the proposed procedure to analyze the aforementioned myeloma study.

Entities:  

Year:  2012        PMID: 22408278      PMCID: PMC3293491          DOI: 10.1016/j.jmva.2011.08.002

Source DB:  PubMed          Journal:  J Multivar Anal        ISSN: 0047-259X            Impact factor:   1.473


  13 in total

1.  Immunoglobulin genes in multiple myeloma: expressed and non-expressed repertoires, heavy and light chain pairings and somatic mutation patterns in a series of 101 cases.

Authors:  Anastasia Hadzidimitriou; Kostas Stamatopoulos; Chrysoula Belessi; Chrysavgi Lalayianni; Niki Stavroyianni; Tatjana Smilevska; Katerina Hatzi; Nikolaos Laoutaris; Achilles Anagnostopoulos; Panagoula Kollia; Athanasios Fassas
Journal:  Haematologica       Date:  2006-06       Impact factor: 9.941

2.  Gene prioritization through genomic data fusion.

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Journal:  Nat Biotechnol       Date:  2006-05       Impact factor: 54.908

3.  Discussion of "Sure Independence Screening for Ultra-High Dimensional Feature Space.

Authors:  Hao Helen Zhang
Journal:  J R Stat Soc Series B Stat Methodol       Date:  2008-11       Impact factor: 4.488

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

Authors:  R Tibshirani
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5.  On the C-statistics for evaluating overall adequacy of risk prediction procedures with censored survival data.

Authors:  Hajime Uno; Tianxi Cai; Michael J Pencina; Ralph B D'Agostino; L J Wei
Journal:  Stat Med       Date:  2011-01-13       Impact factor: 2.373

6.  Gene expression profiling and correlation with outcome in clinical trials of the proteasome inhibitor bortezomib.

Authors:  George Mulligan; Constantine Mitsiades; Barb Bryant; Fenghuang Zhan; Wee J Chng; Steven Roels; Erik Koenig; Andrew Fergus; Yongsheng Huang; Paul Richardson; William L Trepicchio; Annemiek Broyl; Pieter Sonneveld; John D Shaughnessy; P Leif Bergsagel; David Schenkein; Dixie-Lee Esseltine; Anthony Boral; Kenneth C Anderson
Journal:  Blood       Date:  2006-12-21       Impact factor: 22.113

7.  HIGH DIMENSIONAL VARIABLE SELECTION.

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Journal:  Ann Stat       Date:  2009-01-01       Impact factor: 4.028

8.  Univariate shrinkage in the cox model for high dimensional data.

Authors:  Robert J Tibshirani
Journal:  Stat Appl Genet Mol Biol       Date:  2009-04-14

9.  Prediction of survival in multiple myeloma based on gene expression profiles reveals cell cycle and chromosomal instability signatures in high-risk patients and hyperdiploid signatures in low-risk patients: a study of the Intergroupe Francophone du Myélome.

Authors:  Olivier Decaux; Laurence Lodé; Florence Magrangeas; Catherine Charbonnel; Wilfried Gouraud; Pascal Jézéquel; Michel Attal; Jean-Luc Harousseau; Philippe Moreau; Régis Bataille; Loïc Campion; Hervé Avet-Loiseau; Stéphane Minvielle
Journal:  J Clin Oncol       Date:  2008-06-30       Impact factor: 44.544

10.  One-step Sparse Estimates in Nonconcave Penalized Likelihood Models.

Authors:  Hui Zou; Runze Li
Journal:  Ann Stat       Date:  2008-08-01       Impact factor: 4.028

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  49 in total

1.  Exploiting Linkage Disequilibrium for Ultrahigh-Dimensional Genome-Wide Data with an Integrated Statistical Approach.

Authors:  Michelle Carlsen; Guifang Fu; Shaun Bushman; Christopher Corcoran
Journal:  Genetics       Date:  2015-12-12       Impact factor: 4.562

2.  Nonparametric Independence Screening in Sparse Ultra-High Dimensional Additive Models.

Authors:  Jianqing Fan; Yang Feng; Rui Song
Journal:  J Am Stat Assoc       Date:  2011-06       Impact factor: 5.033

3.  Censored Rank Independence Screening for High-dimensional Survival Data.

Authors:  Rui Song; Wenbin Lu; Shuangge Ma; X Jessie Jeng
Journal:  Biometrika       Date:  2014       Impact factor: 2.445

4.  Variance estimation using refitted cross-validation in ultrahigh dimensional regression.

Authors:  Jianqing Fan; Shaojun Guo; Ning Hao
Journal:  J R Stat Soc Series B Stat Methodol       Date:  2012-01-01       Impact factor: 4.488

5.  Survival impact index and ultrahigh-dimensional model-free screening with survival outcomes.

Authors:  Jialiang Li; Qi Zheng; Limin Peng; Zhipeng Huang
Journal:  Biometrics       Date:  2016-02-22       Impact factor: 2.571

6.  Protein-coding and microRNA biomarkers of recurrence of prostate cancer following radical prostatectomy.

Authors:  Qi Long; Brent A Johnson; Adeboye O Osunkoya; Yu-Heng Lai; Wei Zhou; Mark Abramovitz; Mingjing Xia; Mark B Bouzyk; Robert K Nam; Linda Sugar; Aleksandra Stanimirovic; Daron J Williams; Brian R Leyland-Jones; Arun K Seth; John A Petros; Carlos S Moreno
Journal:  Am J Pathol       Date:  2011-05-03       Impact factor: 4.307

7.  Penalized full likelihood approach to variable selection for Cox's regression model under nested case-control sampling.

Authors:  Jie-Huei Wang; Chun-Hao Pan; I-Shou Chang; Chao Agnes Hsiung
Journal:  Lifetime Data Anal       Date:  2019-05-07       Impact factor: 1.588

8.  Censored cumulative residual independent screening for ultrahigh-dimensional survival data.

Authors:  Jing Zhang; Guosheng Yin; Yanyan Liu; Yuanshan Wu
Journal:  Lifetime Data Anal       Date:  2017-05-26       Impact factor: 1.588

9.  Screening group variables in the proportional hazards model.

Authors:  Kwang Woo Ahn; Natasha Sahr; Soyoung Kim
Journal:  Stat Probab Lett       Date:  2017-12-13       Impact factor: 0.870

10.  Ultrahigh dimensional time course feature selection.

Authors:  Peirong Xu; Lixing Zhu; Yi Li
Journal:  Biometrics       Date:  2014-01-19       Impact factor: 2.571

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