Bayesian variable selection for the Cox regression model with missing covariates

In this paper, we develop Bayesian methodology and computational algorithms for variable subset selection in Cox proportional hazards models with missing covariate data. A new joint semi-conjugate prior for the piecewise exponential model is proposed in the presence of missing covariates and its properties are examined. The covariates are assumed to be missing at random (MAR). Under this new prior, a version of the Deviance Information Criterion (DIC) is proposed for Bayesian variable subset selection in the presence of missing covariates. Monte Carlo methods are developed for computing the DICs for all possible subset models in the model space. A Bone Marrow Transplant (BMT) dataset is used to illustrate the proposed methodology.

[1]  Dean Phillips Foster,et al.  Calibration and empirical Bayes variable selection , 2000 .

[2]  Roderick J. A. Little,et al.  Statistical Analysis with Missing Data: Little/Statistical Analysis with Missing Data , 2002 .

[3]  Joseph G. Ibrahim,et al.  A conditional model for incomplete covariates in parametric regression models , 1996 .

[4]  C. McCulloch,et al.  Generalized Linear Mixed Models , 2005 .

[5]  P. Dellaportas,et al.  Bayesian variable and link determination for generalised linear models , 2003 .

[6]  J. Ibrahim,et al.  Prior elicitation, variable selection and Bayesian computation for logistic regression models , 1999 .

[7]  G. Schwarz Estimating the Dimension of a Model , 1978 .

[8]  Joseph G. Ibrahim,et al.  Missing covariates in generalized linear models when the missing data mechanism is non‐ignorable , 1999 .

[9]  Bradley P. Carlin,et al.  Bayesian measures of model complexity and fit , 2002 .

[10]  Joseph G. Ibrahim,et al.  Prior elicitation for model selection and estimation in generalized linear mixed models , 2003 .

[11]  C. Robert,et al.  Deviance information criteria for missing data models , 2006 .

[12]  S. MacEachern,et al.  Bayesian variable selection for proportional hazards models , 1999 .

[13]  J. Ibrahim,et al.  Conjugate priors for generalized linear models , 2003 .

[14]  A. Raftery Approximate Bayes factors and accounting for model uncertainty in generalised linear models , 1996 .

[15]  D. Rubin INFERENCE AND MISSING DATA , 1975 .

[16]  K. Chaloner,et al.  Bayesian analysis in statistics and econometrics : essays in honor of Arnold Zellner , 1996 .

[17]  Edward I. George,et al.  Two Approaches to Bayesian Model Selection with Applications , 1996 .

[18]  S. Lipsitz,et al.  Missing-Data Methods for Generalized Linear Models , 2005 .

[19]  E. George The Variable Selection Problem , 2000 .

[20]  Xiao-Li Meng,et al.  POSTERIOR PREDICTIVE ASSESSMENT OF MODEL FITNESS VIA REALIZED DISCREPANCIES , 1996 .

[21]  J. Ibrahim,et al.  Power prior distributions for regression models , 2000 .

[22]  Dani Gamerman,et al.  Bayesian dynamic models for survival data with a cure fraction , 2007, Lifetime data analysis.

[23]  H. Akaike,et al.  Information Theory and an Extension of the Maximum Likelihood Principle , 1973 .

[24]  T. Fearn,et al.  Bayes model averaging with selection of regressors , 2002 .

[25]  Hong Chang,et al.  Bayesian Approach for Nonlinear Random Effects Models , 1997 .

[26]  H. Chipman,et al.  Bayesian CART Model Search , 1998 .

[27]  Joseph G. Ibrahim,et al.  BAYESIAN VARIABLE SELECTION FOR TIME SERIES COUNT DATA , 2000 .

[28]  Joseph G. Ibrahim,et al.  Bayesian Survival Analysis , 2004 .

[29]  Bradley P. Carlin,et al.  Markov Chain Monte Carlo conver-gence diagnostics: a comparative review , 1996 .

[30]  T. Hanson Inference for Mixtures of Finite Polya Tree Models , 2006 .

[31]  P. Dellaportas,et al.  Markov chain Monte Carlo model determination for hierarchical and graphical log-linear models , 1999 .

[32]  Alan E. Gelfand,et al.  Model choice: A minimum posterior predictive loss approach , 1998, AISTATS.

[33]  Joseph G. Ibrahim,et al.  Criterion-based methods for Bayesian model assessment , 2001 .

[34]  D. Rubin,et al.  Statistical Analysis with Missing Data. , 1989 .

[35]  T. Fearn,et al.  Multivariate Bayesian variable selection and prediction , 1998 .

[36]  Joseph G Ibrahim,et al.  Bayesian Variable Selection and Computation for Generalized Linear Models with Conjugate Priors. , 2008, Bayesian analysis.

[37]  D. Madigan,et al.  Bayesian Model Averaging for Linear Regression Models , 1997 .

[38]  S. Geisser,et al.  A Predictive Approach to Model Selection , 1979 .

[39]  Purushottam W. Laud,et al.  Predictive Model Selection , 1995 .

[40]  E. George,et al.  APPROACHES FOR BAYESIAN VARIABLE SELECTION , 1997 .

[41]  R. Kohn,et al.  Nonparametric regression using Bayesian variable selection , 1996 .

[42]  D. Dey,et al.  Bayesian criterion based model assessment for categorical data , 2004 .

[43]  A. Gelfand,et al.  Bayesian Model Choice: Asymptotics and Exact Calculations , 1994 .

[44]  E. George,et al.  Journal of the American Statistical Association is currently published by American Statistical Association. , 2007 .

[45]  Purushottam W. Laud,et al.  A Predictive Approach to the Analysis of Designed Experiments , 1994 .

[46]  W. Gilks,et al.  Adaptive Rejection Sampling for Gibbs Sampling , 1992 .

[47]  Joseph G Ibrahim,et al.  Bayesian Analysis for Generalized Linear Models with Nonignorably Missing Covariates , 2005, Biometrics.