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Adaptive sampling for Bayesian variable selection


  • David J. Nott
  • Robert Kohn


Our paper proposes adaptive Monte Carlo sampling schemes for Bayesian variable selection in linear regression that improve on standard Markov chain methods. We do so by considering Metropolis--Hastings proposals that make use of accumulated information about the posterior distribution obtained during sampling. Adaptation needs to be done carefully to ensure that sampling is from the correct ergodic distribution. We give conditions for the validity of an adaptive sampling scheme in this problem, and for simulating from a distribution on a finite state space in general, and suggest a class of adaptive proposal densities which uses best linear prediction to approximate the Gibbs sampler. Our sampling scheme is computationally much faster per iteration than the Gibbs sampler, and when this is taken into account the efficiency gains when using our sampling scheme compared to alternative approaches are substantial in terms of precision of estimation of posterior quantities of interest for a given amount of computation time. We compare our method with other sampling schemes for examples involving both real and simulated data. The methodology developed in the paper can be extended to variable selection in more general problems. Copyright 2005, Oxford University Press.

Suggested Citation

  • David J. Nott & Robert Kohn, 2005. "Adaptive sampling for Bayesian variable selection," Biometrika, Biometrika Trust, vol. 92(4), pages 747-763, December.
  • Handle: RePEc:oup:biomet:v:92:y:2005:i:4:p:747-763

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    References listed on IDEAS

    1. Joel L. Horowitz, 1998. "Bootstrap Methods for Median Regression Models," Econometrica, Econometric Society, vol. 66(6), pages 1327-1352, November.
    2. Yingyao Hu & Susanne M. Schennach, 2008. "Instrumental Variable Treatment of Nonclassical Measurement Error Models," Econometrica, Econometric Society, vol. 76(1), pages 195-216, January.
    3. Wei, Ying & Carroll, Raymond J., 2009. "Quantile Regression With Measurement Error," Journal of the American Statistical Association, American Statistical Association, vol. 104(487), pages 1129-1143.
    4. Delaigle, Aurore & Hall, Peter, 2008. "Using SIMEX for Smoothing-Parameter Choice in Errors-in-Variables Problems," Journal of the American Statistical Association, American Statistical Association, vol. 103, pages 280-287, March.
    5. Hong, Han & Tamer, Elie, 2003. "A simple estimator for nonlinear error in variable models," Journal of Econometrics, Elsevier, vol. 117(1), pages 1-19, November.
    6. Schennach, Susanne M., 2008. "Quantile Regression With Mismeasured Covariates," Econometric Theory, Cambridge University Press, vol. 24(04), pages 1010-1043, August.
    7. Hua Liang & Suojin Wang & Raymond J. Carroll, 2007. "Partially linear models with missing response variables and error-prone covariates," Biometrika, Biometrika Trust, vol. 94(1), pages 185-198.
    8. Purdom Elizabeth & Holmes Susan P, 2005. "Error Distribution for Gene Expression Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 4(1), pages 1-35, July.
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    Cited by:

    1. Villani, Mattias & Kohn, Robert & Giordani, Paolo, 2009. "Regression density estimation using smooth adaptive Gaussian mixtures," Journal of Econometrics, Elsevier, vol. 153(2), pages 155-173, December.
    2. Ley, Eduardo & Steel, Mark F.J., 2012. "Mixtures of g-priors for Bayesian model averaging with economic applications," Journal of Econometrics, Elsevier, vol. 171(2), pages 251-266.
    3. Xibin Zhang & Maxwell L. King & Han Lin Shang, 2016. "Bayesian Bandwidth Selection for a Nonparametric Regression Model with Mixed Types of Regressors," Econometrics, MDPI, Open Access Journal, vol. 4(2), pages 1-27, April.
    4. Eduardo Ley & Mark F.J. Steel, 2009. "On the effect of prior assumptions in Bayesian model averaging with applications to growth regression This article was published online on 30 March 2009. An error was subsequently identified. This not," Journal of Applied Econometrics, John Wiley & Sons, Ltd., vol. 24(4), pages 651-674.
    5. Zhang, Xibin & King, Maxwell L. & Shang, Han Lin, 2014. "A sampling algorithm for bandwidth estimation in a nonparametric regression model with a flexible error density," Computational Statistics & Data Analysis, Elsevier, vol. 78(C), pages 218-234.
    6. Ley, Eduardo & Steel, Mark F. J., 2007. "On the effect of prior assumptions in Bayesian model averaging with applications to growth regression," Policy Research Working Paper Series 4238, The World Bank.
    7. Villani, Mattias & Kohn, Robert & Giordani, Paolo, 2007. "Nonparametric Regression Density Estimation Using Smoothly Varying Normal Mixtures," Working Paper Series 211, Sveriges Riksbank (Central Bank of Sweden).
    8. Fouskakis, D., 2012. "Bayesian variable selection in generalized linear models using a combination of stochastic optimization methods," European Journal of Operational Research, Elsevier, vol. 220(2), pages 414-422.
    9. Steel, Mark F. J., 2017. "Model Averaging and its Use in Economics," MPRA Paper 81568, University Library of Munich, Germany.
    10. Giordani, Paolo & Kohn, Robert, 2008. "Efficient Bayesian Inference for Multiple Change-Point and Mixture Innovation Models," Journal of Business & Economic Statistics, American Statistical Association, vol. 26, pages 66-77, January.
    11. Ouysse, Rachida & Kohn, Robert, 2010. "Bayesian variable selection and model averaging in the arbitrage pricing theory model," Computational Statistics & Data Analysis, Elsevier, vol. 54(12), pages 3249-3268, December.
    12. Pasanisi, Alberto & Fu, Shuai & Bousquet, Nicolas, 2012. "Estimating discrete Markov models from various incomplete data schemes," Computational Statistics & Data Analysis, Elsevier, vol. 56(9), pages 2609-2625.
    13. Paroli, Roberta & Spezia, Luigi, 2008. "Bayesian inference in non-homogeneous Markov mixtures of periodic autoregressions with state-dependent exogenous variables," Computational Statistics & Data Analysis, Elsevier, vol. 52(5), pages 2311-2330, January.
    14. Villani, Mattias & Kohn, Robert & Nott, David J., 2012. "Generalized smooth finite mixtures," Journal of Econometrics, Elsevier, vol. 171(2), pages 121-133.
    15. repec:gam:jecnmx:v:4:y:2016:i:2:p:24:d:68757 is not listed on IDEAS
    16. Panagiotelis, Anastasios & Smith, Michael, 2008. "Bayesian identification, selection and estimation of semiparametric functions in high-dimensional additive models," Journal of Econometrics, Elsevier, vol. 143(2), pages 291-316, April.

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