Bayesian Analysis
- Bayesian Anal.
- Volume 6, Number 3 (2011), 387-410.
Hyper-$g$ priors for generalized linear models
Daniel Sabanés Bové and Leonhard Held
Full-text: Open access
Abstract
We develop an extension of the classical Zellner's $g$-prior to generalized linear models. Any continuous proper hyperprior $f(g)$ can be used, giving rise to a large class of hyper-$g$ priors. Connections with the literature are described in detail. A fast and accurate integrated Laplace approximation of the marginal likelihood makes inference in large model spaces feasible. For posterior parameter estimation we propose an efficient and tuning-free Metropolis-Hastings sampler. The methodology is illustrated with variable selection and automatic covariate transformation in the Pima Indians diabetes data set.
Article information
Source
Bayesian Anal., Volume 6, Number 3 (2011), 387-410.
Dates
First available in Project Euclid: 13 June 2012
Permanent link to this document
https://projecteuclid.org/euclid.ba/1339616469
Digital Object Identifier
doi:10.1214/11-BA615
Mathematical Reviews number (MathSciNet)
MR2843537
Zentralblatt MATH identifier
1330.62058
Subjects
Primary: 62C12: Empirical decision procedures; empirical Bayes procedures
Secondary: 62F15: Bayesian inference 62J12: Generalized linear models 62P10: Applications to biology and medical sciences
Keywords
$g$-prior generalized linear model integrated Laplace approximation variable selection fractional polynomials
Citation
Sabanés Bové, Daniel; Held, Leonhard. Hyper-$g$ priors for generalized linear models. Bayesian Anal. 6 (2011), no. 3, 387--410. doi:10.1214/11-BA615. https://projecteuclid.org/euclid.ba/1339616469
References
- Barbieri, M. M. and Berger, J. O. (2004). "Optimal predictive model selection." Annals of Statistics, 32(3): 870–897. Mathematical Reviews (MathSciNet): MR2065192
Zentralblatt MATH: 1092.62033
Digital Object Identifier: doi:10.1214/009053604000000238
Project Euclid: euclid.aos/1085408489 - Berger, J. O. and Pericchi, L. R. (2001). "Objective Bayesian methods for model selection: introduction and comparison." Lecture Notes-Monograph Series, 38(1): 135–207.
- Bernardo, J. M. and Smith, A. F. M. (2000). Bayesian Theory. Wiley Series in Probability and Statistics. Chichester: John Wiley & Sons. Mathematical Reviews (MathSciNet): MR1274699
- Box, G. E. P. and Tidwell, P. W. (1962). "Transformation of the independent variables." Technometrics, 4(4): 531–550.
- Breiman, L. and Friedman, J. H. (1985). "Estimating optimal transformations for multiple regression and correlation." Journal of the American Statistical Association, 80(391): 580–598.
- Brent, R. P. (1973). Algorithms for Minimization Without Derivatives. Prentice-Hall series in automatic computation. Englewood Cliffs, NJ: Prentice-Hall. Mathematical Reviews (MathSciNet): MR339493
- Brunsdon, C., Fotheringham, S., and Charlton, M. (1998). "Geographically weighted regression–-modelling spatial non-stationarity." Journal of the Royal Statistical Society. Series D (The Statistician), 47(3): 431–443.
- Buckland, S. T., Burnham, K. P., and Augustin, N. H. (1997). "Model selection: an integral part of inference." Biometrics, 53(2): 603–618. Zentralblatt MATH: 0885.62118
- Chen, M. and Ibrahim, J. (2003). "Conjugate priors for generalized linear models." Statistica Sinica, 13: 461–476.
- Chen, M.-H., Huang, L., Ibrahim, J. G., and Kim, S. (2008). "Bayesian variable selection and computation for generalized linear models with conjugate priors." Bayesian Analysis, 3(3): 585–614. Mathematical Reviews (MathSciNet): MR2434404
Digital Object Identifier: doi:10.1214/08-BA323
Zentralblatt MATH: 1330.62298 - Chib, S. and Jeliazkov, I. (2001). "Marginal likelihood from the Metropolis-Hastings output." Journal of the American Statistical Association, 96(453): 270–281. Mathematical Reviews (MathSciNet): MR1952737
Zentralblatt MATH: 1015.62020
Digital Object Identifier: doi:10.1198/016214501750332848 - Clyde, M. and George, E. I. (2004). "Model uncertainty." Statistical Science, 19(1): 81–94. Mathematical Reviews (MathSciNet): MR2082148
Digital Object Identifier: doi:10.1214/088342304000000035
Project Euclid: euclid.ss/1089808274
Zentralblatt MATH: 1062.62044 - Cottet, R., Kohn, R. J., and Nott, D. J. (2008). "Variable selection and model averaging in semiparametric overdispersed generalized linear models." Journal of the American Statistical Association, 103(482): 661–671. Mathematical Reviews (MathSciNet): MR2524000
Zentralblatt MATH: 05564519
Digital Object Identifier: doi:10.1198/016214508000000346 - Cui, W. and George, E. I. (2008). "Empirical Bayes vs. fully Bayes variable selection." Journal of Statistical Planning and Inference, 138(4): 888–900. Mathematical Reviews (MathSciNet): MR2416869
Zentralblatt MATH: 1130.62007
Digital Object Identifier: doi:10.1016/j.jspi.2007.02.011 - Dobra, A. (2009). "Variable selection and dependency networks for genomewide data." Biostatistics, 10(4): 621–639.
- Fernández, C., Ley, E., and Steel, M. F. J. (2001). "Benchmark priors for Bayesian model averaging." Journal of Econometrics, 100(2): 381–427. Mathematical Reviews (MathSciNet): MR1820410
Zentralblatt MATH: 1091.62507
Digital Object Identifier: doi:10.1016/S0304-4076(00)00076-2 - Frank, A. and Asuncion, A. (2010). UCI Machine Learning Repository. http://archive.ics.uci.edu/ml URL: Link to item
- Gamerman, D. (1997). "Sampling from the posterior distribution in generalized linear mixed models." Statistics and Computing, 7(1): 57–68.
- George, E. I. and Foster, D. P. (2000). "Calibration and empirical Bayes variable selection." Biometrika, 87(4): 731–747. Mathematical Reviews (MathSciNet): MR1813972
Zentralblatt MATH: 1029.62008
Digital Object Identifier: doi:10.1093/biomet/87.4.731 - George, E. I. and McCulloch, R. E. (1993). "Variable selection via Gibbs sampling." Journal of the American Statistical Association, 88(423): 881–889.
- Golub, G. and Welsch, J. (1969). "Calculation of Gauss quadrature rules." Mathematics of Computation, 23(106): 221–230. Mathematical Reviews (MathSciNet): MR245201
Zentralblatt MATH: 0179.21901
Digital Object Identifier: doi:10.1090/S0025-5718-69-99647-1 - Gupta, M. and Ibrahim, J. (2009). "An information matrix prior for Bayesian analysis in generalized linear models with high dimensional data." Statistica Sinica, 19(4): 1641–1663.
- Han, C. and Carlin, B. (2001). "Markov chain Monte Carlo methods for computing Bayes factors: A comparative review." Journal of the American Statistical Association, 96(455): 1122–1132.
- Hans, C., Dobra, A., and West, M. (2007). "Shotgun stochastic search for ”large p” regression." Journal of the American Statistical Association, 102(478): 507–516. Mathematical Reviews (MathSciNet): MR2370849
Digital Object Identifier: doi:10.1198/016214507000000121
Zentralblatt MATH: 1134.62398 - Hansen, M. H. and Yu, B. (2001). "Model selection and the principle of minimum description length." Journal of the American Statistical Association, 96(454): 746–774. Mathematical Reviews (MathSciNet): MR1939352
Zentralblatt MATH: 1017.62004
Digital Object Identifier: doi:10.1198/016214501753168398 - –- (2003). "Minimum description length model selection criteria for generalized linear models." Lecture Notes-Monograph Series, 40(1): 145–163. Statistics and Science: A Festschrift for Terry Speed.
- Holmes, C. C. and Held, L. (2006). "Bayesian auxiliary variable models for binary and multinomial regression." Bayesian Analysis, 1(1): 145–168. Mathematical Reviews (MathSciNet): MR2227368
Digital Object Identifier: doi:10.1214/06-BA105
Zentralblatt MATH: 1331.62142 - Jeffreys, H. (1961). Theory of Probability. Oxford: Oxford University Press, third edition.
- Kass, R. E. and Raftery, A. E. (1995). "Bayes factors." Journal of the American Statistical Association, 90(430): 773–795. Mathematical Reviews (MathSciNet): MR3363402
Zentralblatt MATH: 0846.62028
Digital Object Identifier: doi:10.1080/01621459.1995.10476572 - Kass, R. E. and Wasserman, L. (1995). "A reference Bayesian test for nested hypotheses and its relationship to the Schwarz criterion." Journal of the American Statistical Association, 90(431): 928–934.
- Liang, F., Paulo, R., Molina, G., Clyde, M. A., and Berger, J. O. (2008). "Mixtures of $g$ priors for Bayesian variable selection." Journal of the American Statistical Association, 103(481): 410–423. Mathematical Reviews (MathSciNet): MR2420243
Zentralblatt MATH: 05564499
Digital Object Identifier: doi:10.1198/016214507000001337 - Lindley, D. V. (1957). "A statistical paradox." Biometrika, 44(1–2): 187–192.
- –- (1980). "Approximate Bayesian methods." In Bernardo, J. M., DeGroot, M. H., Lindley, D. V., and Smith, A. F. M. (eds.), Bayesian Statistics: Proceedings of the First International Meeting Held in Valencia, 223–245. Valencia: University of Valencia Press.
- Madigan, D. and York, J. (1995). "Bayesian graphical models for discrete data." International Statistical Review, 63(2): 215–232. Zentralblatt MATH: 0834.62003
- Marin, J.-M. and Robert, C. P. (2007). Bayesian Core: A Practical Approach to Computational Bayesian Statistics. Springer texts in Statistics. New York: Springer.
- Maruyama, Y. and George, E. I. (2010). "gBF": A Fully Bayes Factor with a Generalized g-prior. Technical report, Center for Spatial Information Science, University of Tokyo. http://arxiv.org/abs/0801.4410 URL: Link to item
Mathematical Reviews (MathSciNet): MR2906885
Zentralblatt MATH: 1231.62036
Digital Object Identifier: doi:10.1214/11-AOS917
Project Euclid: euclid.aos/1324563354 - McCullagh, P. and Nelder, J. A. (1989). Generalized Linear Models. Number 37 in Monographs on Statistics and Applied Probability. Chapman and Hall, second edition.
- Naylor, J. C. and Smith, A. F. M. (1982). "Applications of a method for the efficient computation of posterior distributions." Journal of the Royal Statistical Society. Series C (Applied Statistics), 31(3): 214–225. Mathematical Reviews (MathSciNet): MR694917
Digital Object Identifier: doi:10.2307/2347995
Zentralblatt MATH: 0521.65017 - Nott, D. J., Kohn, R. J., and Fielding, M. (2008). "Approximating the marginal likelihood using copula." Technical report, Department of Statistics and Applied Probability, National University of Singapore. http://arxiv.org/abs/0810.5474 URL: Link to item
- Ntzoufras, I., Dellaportas, P., and Forster, J. J. (2003). "Bayesian variable and link determination for generalised linear models." Journal of Statistical Planning and Inference, 111(1-2): 165–180. Mathematical Reviews (MathSciNet): MR1955879
Zentralblatt MATH: 1033.62026
Digital Object Identifier: doi:10.1016/S0378-3758(02)00298-7 - Overstall, A. M. and Forster, J. J. (2010). "Default Bayesian model determination methods for generalised linear mixed models." Computational Statistics and Data Analysis, 54(12): 3269–3288.
- Pfeffermann, D. (1993). "The role of sampling weights when modeling survey data." International Statistical Review, 61(2): 317–337. Zentralblatt MATH: 0779.62009
- Press, W. H., Teukolsky, S. A., Vetterling, W. T., and Flannery, B. P. (2007). Numerical Recipes: The Art of Scientific Computing. Cambridge: Cambridge University Press, 3rd edition.
- R Development Core Team (2010). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
- Raudenbush, S. W., Yang, M.-L., and Yosef, M. (2000). "Maximum likelihood for generalized linear models with nested random effects via high-order, multivariate Laplace approximation." Journal of Computational and Graphical Statistics, 9(1): 141–157. Mathematical Reviews (MathSciNet): MR1826278
- Ripley, B. D. (1996). Pattern Recognition and Neural Networks. Cambridge: Cambridge University Press.
- Robert, C. P. (2001). The Bayesian Choice. Springer Texts in Statistics. New York: Springer, second edition. Mathematical Reviews (MathSciNet): MR1835885
- Robert, C. P., Chopin, N., and Rousseau, J. (2009). "Harold Jeffreys's Theory of Probability revisited." Statistical Science, 24(2): 141–172. Mathematical Reviews (MathSciNet): MR2655841
Digital Object Identifier: doi:10.1214/09-STS284
Project Euclid: euclid.ss/1263478373
Zentralblatt MATH: 1328.62012 - Robert, C. P. and Saleh, A. K. M. E. (1991). "Point estimation and confidence set estimation in a parallelism model: an empirical Bayes approach." Annales d'Économie et de Statistique, 23: 65–89. Mathematical Reviews (MathSciNet): MR1144848
- Robins, J. M., Hernán, M. A., and Brumback, B. (2000). "Marginal structural models and causal inference in epidemiology." Epidemiology, 11(5): 550–560.
- Royston, P. and Altman, D. G. (1994). "Regression using fractional polynomials of continuous covariates: Parsimonious parametric modelling." Journal of the Royal Statistical Society. Series C (Applied Statistics), 43(3): 429–467.
- Rue, H., Martino, S., and Chopin, N. (2009). "Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations." Journal of the Royal Statistical Society. Series B (Methodological), 71(2): 319–392. Mathematical Reviews (MathSciNet): MR2649602
Digital Object Identifier: doi:10.1111/j.1467-9868.2008.00700.x
Zentralblatt MATH: 1248.62156 - Sabanés Bové, D. and Held, L. (2010). "Bayesian fractional polynomials." Statistics and Computing. Epub ahead of print, DOI: 10.1007/s11222-010-9170-7.
- Scott, J. G. and Berger, J. O. (2010). "Bayes and empirical-Bayes multiplicity adjustment in the variable-selection problem." Annals of Statistics, 38(5): 2587–2619. Mathematical Reviews (MathSciNet): MR2722450
Zentralblatt MATH: 1200.62020
Digital Object Identifier: doi:10.1214/10-AOS792
Project Euclid: euclid.aos/1278861454 - Smyth, G., Hu, Y., and Dunn, P. (2010). statmod: Statistical Modeling. R package version 1.4.8.
- Tierney, L. and Kadane, J. B. (1986). "Accurate approximations for posterior moments and marginal densities." Journal of the American Statistical Association, 81(393): 82–86.
- Wang, X. and George, E. I. (2007). "Adaptive Bayesian criteria in variable selection for generalized linear models." Statistica Sinica, 17(2): 667–690.
- Wedderburn, R. W. M. (1976). "On the existence and uniqueness of the maximum likelihood estimates for certain generalized linear models." Biometrika, 63(1): 27–32. Mathematical Reviews (MathSciNet): MR408092
Zentralblatt MATH: 0329.62027
Digital Object Identifier: doi:10.1093/biomet/63.1.27 - West, M. (1985). "Generalized linear models: scale parameters, outlier accommodation and prior distributions." In Bernardo, J. M., DeGroot, M. H., Lindley, D. V., and Smith, A. F. M. (eds.), Bayesian Statistics 2: Proceedings of the Second Valencia International Meeting, 531–558. Amsterdam: North-Holland. Mathematical Reviews (MathSciNet): MR862501
- –- (2003). "Bayesian factor regression models in the "large p, small n" paradigm." In Bernardo, J., Bayarri, M., Berger, J., Dawid, A., Heckerman, D., Smith, A., and West, M. (eds.), Bayesian Statistics 7: Proceedings of the Seventh Valencia International Meeting, 733–742. Oxford University Press. Mathematical Reviews (MathSciNet): MR2003537
- Zellner, A. (1986). "On assessing prior distributions and Bayesian regression analysis with $g$-prior distributions." In Goel, P. K. and Zellner, A. (eds.), Bayesian Inference and Decision Techniques: Essays in Honor of Bruno de Finetti, volume 6 of Studies in Bayesian Econometrics and Statistics, chapter 5, 233–243. Amsterdam: North-Holland.
- Zellner, A. and Siow, A. (1980). "Posterior odds ratios for selected regression hypotheses." In Bernardo, J. M., DeGroot, M. H., Lindley, D. V., and Smith, A. F. M. (eds.), Bayesian Statistics: Proceedings of the First International Meeting Held in Valencia, 585–603. Valencia: University of Valencia Press.
- Zhang, Z., Jordan, M. I., and Yeung, D. Y. (2009). "Posterior consistency of the Silverman $g$-prior in Bayesian model choice." In Koller, D., Bengio, Y., Schuurmans, D., and Bottou, L. (eds.), Advances in Neural Information Processing Systems (NIPS), volume 21.

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