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Reproducible parameter inference using bagged posteriors. (English) Zbl 07855836

Summary: Under model misspecification, it is known that Bayesian posteriors often do not properly quantify uncertainty about true or pseudo-true parameters. Even more fundamentally, misspecification leads to a lack of reproducibility in the sense that the same model will yield contradictory posteriors on independent data sets from the true distribution. To define a criterion for reproducible uncertainty quantification under misspecification, we consider the probability that two credible sets constructed from independent data sets have nonempty overlap, and we establish a lower bound on this overlap probability that holds whenever the credible sets are valid confidence sets. We prove that credible sets from the standard posterior can strongly violate this bound, indicating that it is not internally coherent under misspecification. To improve reproducibility in an easy-to-use and widely applicable way, we propose to apply bagging to the Bayesian posterior (“BayesBag”); that is, to use the average of posterior distributions conditioned on bootstrapped datasets. We motivate BayesBag from first principles based on Jeffrey conditionalization and show that the bagged posterior typically satisfies the overlap lower bound. Further, we prove a Bernstein-Von Mises theorem for the bagged posterior, establishing its asymptotic normal distribution. We demonstrate the benefits of BayesBag via simulation experiments and an application to crime rate prediction.

MSC:

62F15 Bayesian inference
62F40 Bootstrap, jackknife and other resampling methods
62A01 Foundations and philosophical topics in statistics
62F35 Robustness and adaptive procedures (parametric inference)

References:

[1] ANTONIANO-VILLALOBOS, I. and WALKER, S. G. (2013). Bayesian Nonparametric Inference for the Power Likelihood. Journal of Computational and Graphical Statistics 22 801-813. MathSciNet: MR3173743
[2] BHATTACHARYA, A., PATI, D. and YANG, Y. (2019). Bayesian fractional posteriors. The Annals of Statistics 47 39-66. MathSciNet: MR3909926 · Zbl 1473.62116
[3] BISSIRI, P. G., HOLMES, C. C. and WALKER, S. G. (2016). A general framework for updating belief distributions. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 78 1103-1130. MathSciNet: MR3557191 · Zbl 1414.62039
[4] BOX, G. E. P. (1979). Robustness in the Strategy of Scientific Model Building. In Robustness in Statistics 201-236. Elsevier.
[5] BOX, G. E. P. (1980). Sampling and Bayes’ Inference in Scientific Modelling and Robustness. Journal of the Royal Statistical Society. Series A (General) 143 383-430. MathSciNet: MR0603745 · Zbl 0471.62036
[6] Breiman, L. (1996). Bagging Predictors. Machine Learning 24 123-140. · Zbl 0858.68080
[7] Bühlmann, P. (2014). Discussion of Big Bayes Stories and BayesBag. Statistical Science 29 91-94. Digital Object Identifier: 10.1214/13-STS460 Google Scholar: Lookup Link MathSciNet: MR3201850 · Zbl 1332.62086 · doi:10.1214/13-STS460
[8] CHAMBERLAIN, G. and IMBENS, G. (2003). Nonparametric applications of Bayesian inference. Journal of Business Economic Statistics 21 12-18. MathSciNet: MR1973803
[9] CLYDE, M. and LEE, H. (2001). Bagging and the Bayesian bootstrap. In International Workshop on Artificial Intelligence and Statistics 57-62. PMLR.
[10] COX, D. R. (1990). Role of Models in Statistical Analysis. Statistical Science 5 169-174. MathSciNet: MR1062575 · Zbl 0955.62518
[11] DE BLASI, P. and WALKER, S. G. (2013). Bayesian asymptotics with misspecified models. Statistica Sinica 1-19. MathSciNet: MR3076163
[12] DE HEIDE, R., KIRICHENKO, A., MEHTA, N. and GRÜNWALD, P. D. (2019). Safe-Bayesian Generalized Linear Regression. arXiv.org arXiv:1910.09227 [math.ST].
[13] DIACONIS, P. and ZABELL, S. L. (1982). Updating subjective probability. Journal of the American Statistical Association 77 822-830. MathSciNet: MR0686405 · Zbl 0504.62004
[14] DOMINGOS, P. M. (1997). Why Does Bagging Work? A Bayesian Account and its Implications. In KDD 155-158.
[15] Douady, C. J., Delsuc, F., Boucher, Y., Doolittle, W. F. and Douzery, E. J. P. (2003). Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability. Molecular Biology and Evolution 20 248-254.
[16] DURRETT, R. (2019). Probability: Theory and Examples. Cambridge Series in Statistical and Probabilistic Mathematics. Cambridge University Press. MathSciNet: MR3930614 · Zbl 1440.60001
[17] EFRON, B. (2015). Frequentist accuracy of Bayesian estimates. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 77 617-646. MathSciNet: MR3351448 · Zbl 1414.62089
[18] GRECO, L., RACUGNO, W. and VENTURA, L. (2008). Robust likelihood functions in Bayesian inference. Journal of Statistical Planning and Inference 138 1258 - 1270. Digital Object Identifier: 10.1016/j.jspi.2007.05.001 Google Scholar: Lookup Link MathSciNet: MR2388009 · Zbl 1133.62017 · doi:10.1016/j.jspi.2007.05.001
[19] GRÜNWALD, P. D. (2012). The Safe Bayesian: Learning the Learning Rate via the Mixability Gap. In Algorithmic Learning Theory 169-183. MathSciNet: MR3042889 · Zbl 1255.68086
[20] GRÜNWALD, P. D. and VAN OMMEN, T. (2017). Inconsistency of Bayesian Inference for Misspecified Linear Models, and a Proposal for Repairing It. Bayesian Analysis 12 1069-1103. MathSciNet: MR3724979 · Zbl 1384.62088
[21] HOFF, P. and WAKEFIELD, J. (2012). Bayesian sandwich posteriors for pseudo-true parameters. arXiv preprint arXiv:1211.0087.
[22] HOLMES, C. C. and WALKER, S. G. (2017). Assigning a value to a power likelihood in a general Bayesian model. Biometrika 104 497-503. MathSciNet: MR3698270 · Zbl 1506.62264
[23] HUGGINS, J. H. and MILLER, J. W. (2023). Reproducible Model Selection Using Bagged Posteriors. Bayesian Analysis 18 79-104. MathSciNet: MR4515726 · Zbl 07810174
[24] JEFFREY, R. C. (1968). Probable Knowledge. In The Problem of Inductive Logic (I. Lakatos, ed.) 166-180. North-Holland, Amsterdam. MathSciNet: MR0228305 · Zbl 0169.00504
[25] JEFFREY, R. C. (1990). The Logic of Decision, 2nd ed. University of Chicago Press. MathSciNet: MR0745132
[26] JEWSON, J., SMITH, J. Q. and HOLMES, C. (2018). Principles of Bayesian Inference Using General Divergence Criteria. Entropy 20 442. MathSciNet: MR3879894
[27] KALLENBERG, O. (2002). Foundations of Modern Probability, 2nd ed. Springer, New York, NY. MathSciNet: MR1876169 · Zbl 0996.60001
[28] KLEIJN, B. J. K. and VAN DER VAART, A. W. (2012). The Bernstein-Von-Mises theorem under misspecification. Electronic Journal of Statistics 6 354-381. MathSciNet: MR2988412 · Zbl 1274.62203
[29] KOEHLER, E., BROWN, E. and HANEUSE, S. J. P. A. (2009). On the Assessment of Monte Carlo Error in Simulation-Based Statistical Analyses. The American Statistician 63 155-162. MathSciNet: MR2750076 · Zbl 1404.62150
[30] LAIRD, N. M. and LOUIS, T. A. (1987). Empirical Bayes Confidence Intervals Based on Bootstrap Samples. Journal of the American Statistical Association 82 739-750. MathSciNet: MR0909979 · Zbl 0643.62018
[31] LEE, H. K. and CLYDE, M. A. (2004). Lossless online Bayesian bagging. Journal of Machine Learning Research 5 143-151. MathSciNet: MR2247976
[32] LEHMANN, E. L. (1990). Model specification: the views of Fisher and Neyman, and later developments. Statistical Science 5 160-168. MathSciNet: MR1062574 · Zbl 0955.62516
[33] LYDDON, S. P., HOLMES, C. C. and WALKER, S. G. (2019). General Bayesian updating and the loss-likelihood bootstrap. Biometrika 106 465-478. MathSciNet: MR3949315 · Zbl 1454.62098
[34] LYDDON, S. P., WALKER, S. G. and HOLMES, C. C. (2018). Nonparametric learning from Bayesian models with randomized objective functions. In Advances in Neural Information Processing Systems.
[35] MILLER, J. W. and DUNSON, D. B. (2018). Robust Bayesian Inference via Coarsening. Journal of the American Statistical Association 114 1113-1125. MathSciNet: MR4011766 · Zbl 1428.62287
[36] MÜLLER, U. K. (2013). Risk of Bayesian Inference in Misspecified Models, and the Sandwich Covariance Matrix. Econometrica: Journal of the Econometric Society 81 1805-1849. MathSciNet: MR3117034 · Zbl 1291.62069
[37] NEWTON, M. A. and RAFTERY, A. E. (1994). Approximate Bayesian Inference with the Weighted Likelihood Bootstrap. Journal of the Royal Statistical Society. Series B (Methodological) 56 3-46. MathSciNet: MR1257793
[38] PIIRONEN, J. and VEHTARI, A. (2017). Sparsity information and regularization in the horseshoe and other shrinkage priors. Electronic Journal of Statistics 11 5018-5051. MathSciNet: MR3738204 · Zbl 1459.62141
[39] ROYALL, R. and TSOU, T.-S. (2003). Interpreting statistical evidence by using imperfect models: robust adjusted likelihood functions. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 65 391-404. MathSciNet: MR1983754 · Zbl 1065.62047
[40] Rubin, D. B. (1981). The Bayesian Bootstrap. The Annals of Statistics 9 130-134. MathSciNet: MR0600538
[41] SYRING, N. and MARTIN, R. (2019). Calibrating general posterior credible regions. Biometrika 106 479-486. MathSciNet: MR3949316 · Zbl 1454.62105
[42] VAN DER VAART, A. W. (1998). Asymptotic Statistics. University of Cambridge. MathSciNet: MR1652247 · Zbl 0910.62001
[43] VAN DER VAART, A. W. and WELLNER, J. A. (1996). Weak Convergence and Empirical Processes. With Applications to Statistics. Springer, New York. MathSciNet: MR1385671 · Zbl 0862.60002
[44] WADDELL, P. J., KISHINO, H. and OTA, R. (2002). Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data. Genome informatics. International Conference on Genome Informatics 13 82-92.
[45] WALKER, S. G. (2013). Bayesian inference with misspecified models. Journal of statistical planning and inference 143 1621-1633. MathSciNet: MR3082220 · Zbl 1279.62066
[46] WALKER, S. G. and HJORT, N. L. (2001). On Bayesian consistency. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 63 811-821. MathSciNet: MR1872068 · Zbl 0987.62021
[47] WHITE, H. (1982). Maximum Likelihood Estimation of Misspecified Models. Econometrica: Journal of the Econometric Society 50 1-25. MathSciNet: MR0640163 · Zbl 0478.62088
[48] Yang, Z. and Zhu, T. (2018). Bayesian Selection of Misspecified Models is Overconfident and May Cause Spurious Posterior Probabilities for Phylogenetic Trees. Proceedings of the National Academy of Sciences 115 1854-1859. Digital Object Identifier: 10.1073/pnas.1712673115 Google Scholar: Lookup Link MathSciNet: MR3779786 · Zbl 1416.62066 · doi:10.1073/pnas.1712673115
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