Abstract
Markov chain Monte Carlo (MCMC) methods allow exploration of intractable probability distributions by constructing a Markov chain whose stationary distribution equals the desired distribution. The output from the Markov chain is typically used to estimate several features of the stationary distribution such as mean and variance parameters along with quantiles and so on. Unfortunately, most reported MCMC estimates do not include a clear notion of the associated uncertainty. For expectations one can assess the uncertainty by estimating the variance in an asymptotic normal distribution of the Monte Carlo error. For general functionals there is no such clear path. This article studies the applicability of subsampling bootstrap methods to assess the uncertainty in estimating general functionals from MCMC simulations.
Keywords
- Markov Chain
- Markov Chain Monte Carlo
- Coverage Probability
- Markov Chain Monte Carlo Method
- Quantile Function
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Patrice Bertail and Stéphan Clémençon. Regenerative block-bootstrap for Markov chains. Bernoulli, 12:689–712, 2006.
Peter Bühlmann. Bootstraps for time series. Statistical Science, 17:52–72, 2002.
Edward Carlstein. The use of subseries values for estimating the variance of a general statistic from a stationary sequence. The Annals of Statistics, 14:1171–1179, 1986.
Ming-Hui Chen, Qi-Man Shao, and Joseph George Ibrahim. Monte Carlo Methods in Bayesian Computation. Springer-Verlag Inc, 2000.
Mary Kathryn Cowles and Bradley P. Carlin. Markov chain Monte Carlo convergence diagnostics: A comparative review. Journal of the American Statistical Association, 91:883–904, 1996.
Mary Kathryn Cowles, Gareth O. Roberts, and Jeffrey S. Rosenthal. Possible biases induced by MCMC convergence diagnostics. Journal of Statistical Computing and Simulation, 64:87–104, 1999.
Somnath Datta and William P. McCormick. Regeneration-based bootstrap for Markov chains. The Canadian Journal of Statistics, 21:181–193, 1993.
James M. Flegal. Monte Carlo standard errors for Markov chain Monte Carlo. PhD thesis, University of Minnesota, School of Statistics, 2008.
James M. Flegal, Murali Haran, and Galin L. Jones. Markov chain Monte Carlo: Can we trust the third significant figure? Statistical Science, 23:250–260, 2008.
James M. Flegal and Galin L. Jones. Batch means and spectral variance estimators in Markov chain Monte Carlo. The Annals of Statistics, 38:1034–1070, 2010.
James M. Flegal and Galin L. Jones. Implementing Markov chain Monte Carlo: Estimating with confidence. In S.P. Brooks, A.E. Gelman, G.L. Jones, and X.L. Meng, editors, Handbook of Markov Chain Monte Carlo. Chapman & Hall/CRC Press, 2010.
James M. Flegal and Galin L. Jones. Quantile estimation via Markov chain Monte Carlo. Work in progress, 2011.
Charles J. Geyer. Practical Markov chain Monte Carlo (with discussion). Statistical Science, 7:473–511, 1992.
S. G. Giakoumatos, I. D. Vrontos, P. Dellaportas, and D. N. Politis. A Markov chain Monte Carlo convergence diagnostic using subsampling. Journal of Computational and Graphical Statistics, 8:431–451, 1999.
James S. Hodges. Some algebra and geometry for hierarchical models, applied to diagnostics (Disc: P521–536). Journal of the Royal Statistical Society, Series B: Statistical Methodology, 60:497–521, 1998.
Rob J. Hyndman and Yanan Fan. Sample quantiles in statistical packages. The American Statistician, 50:361–365, 1996.
Alicia A. Johnson and Galin L. Jones. Gibbs sampling for a Bayesian hierarchical general linear model. Electronic Journal of Statistics, 4:313–333, 2010.
Galin L. Jones. On the Markov chain central limit theorem. Probability Surveys, 1:299–320, 2004.
Galin L. Jones and James P. Hobert. Honest exploration of intractable probability distributions via Markov chain Monte Carlo. Statistical Science, 16:312–334, 2001.
Jun S. Liu. Monte Carlo Strategies in Scientific Computing. Springer, New York, 2001.
Dimitris N. Politis. The impact of bootstrap methods on time series analysis. Statistical Science, 18:219–230, 2003.
Dimitris N. Politis, Joseph P. Romano, and Michael Wolf. Subsampling. Springer-Verlag Inc, 1999.
Christian P. Robert and George Casella. Monte Carlo Statistical Methods. Springer, New York, 1999.
Gareth O. Roberts. A note on acceptance rate criteria for CLTs for Metropolis-Hastings algorithms. Journal of Applied Probability, 36:1210–1217, 1999.
Gareth O. Roberts and Jeffrey S. Rosenthal. Markov chain Monte Carlo: Some practical implications of theoretical results (with discussion). Canadian Journal of Statistics, 26:5–31, 1998.
Gareth O. Roberts and Jeffrey S. Rosenthal. General state space Markov chains and MCMC algorithms. Probability Surveys, 1:20–71, 2004.
Gareth O. Roberts and Jeffrey S. Rosenthal. Quantitative non-geometric convergence bounds for independence samplers. Methodology and Computing in Applied Probability, 13:391–403, 2011.
A. W. van der Vaart. Asymptotic Statistics. Cambridge University Press, New York, 1998.
Acknowledgements
I am grateful to Galin L. Jones and two anonymous referees for their constructive comments in preparing this article.
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Flegal, J.M. (2012). Applicability of Subsampling Bootstrap Methods in Markov Chain Monte Carlo. In: Plaskota, L., Woźniakowski, H. (eds) Monte Carlo and Quasi-Monte Carlo Methods 2010. Springer Proceedings in Mathematics & Statistics, vol 23. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-27440-4_18
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DOI: https://doi.org/10.1007/978-3-642-27440-4_18
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