Computational Methods in Science and Engineering

Using Approximate Bayesian Computation by Subset Simulation for Efficient Posterior Assessment of Dynamic State-Space Model Classes

Abstract

Approximate Bayesian Computation (ABC) methods have gained in popularity over the last decade because they expand the horizon of Bayesian parameter inference methods to the range of models for which an analytical formula for the likelihood function might be difficult, or even impossible, to establish. The majority of the ABC methods rely on the choice of a set of summary statistics to reduce the dimension of the data. However, as has been noted in the ABC literature, the lack of convergence guarantees induced by the absence of a vector of sufficient summary statistics that assures intermodel sufficiency over the set of competing models hinders the use of the usual ABC methods when applied to Bayesian model selection or assessment. In this paper, we present a novel ABC model selection procedure for dynamical systems based on a recently introduced multilevel Markov chain Monte Carlo method, self-regulating ABC-SubSim, and a hierarchical state-space formulation of dynamic models. We show that this formulation makes it possible to independently approximate the model evidence required for assessing the posterior probability of each of the competing models. We also show that ABC-SubSim not only provides an estimate of the model evidence as a simple by-product but also gives the posterior probability of each model as a function of the tolerance level, which allows the ABC model choices made in previous studies to be understood. We illustrate the performance of the proposed framework for ABC model updating and model class selection by applying it to two problems in Bayesian system identification: a single-degree-of-freedom bilinear hysteretic oscillator and a three-story shear building with Masing hysteresis, both of which are subject to a seismic excitation.

Keywords

  1. Approximate Bayesian Computation
  2. Subset Simulation
  3. Bayesian model selection
  4. system identification
  5. bilinear and Masing hysteretic models

MSC codes

  1. 62F15
  2. 65C40
  3. 65C60
  4. 93B30
  5. 37N15

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References

1.
P. Angelikopoulos, C. Papadimitriou, and P. Koumoutsakos, X-TMCMC: Adaptive kriging for Bayesian inverse modeling, Comput. Methods Appl. Mech. Engrg., 289 (2015), pp. 409--428.
2.
S. A. Ashrafi and A. W. Smyth, Generalized Masing approach to modeling hysteretic deteriorating behavior, J. Eng. Mech., 133 (2007), pp. 495--505.
3.
S.-K. Au and J. L. Beck, Estimation of small failure probabilities in high dimensions by subset simulation, Prob. Eng. Mech., 16 (2001), pp. 263--277.
4.
S.-K. Au and F.-L. Zhang, Fundamental two-stage formulation for Bayesian system identification, Part I: General theory, Mech. Syst. Signal Process., 66 (2016), pp. 31--42.
5.
S. Barthelmé and N. Chopin, Expectation propagation for likelihood-free inference, J. Amer. Statist. Assoc., 109 (2014), pp. 315--333.
6.
M. A. Beaumont, J.-M. Cornuet, J.-M. Marin, and C. P. Robert, Adaptive approximate Bayesian computation, Biometrika, 96 (2009), pp. 983--990.
7.
J. L. Beck, Bayesian system identification based on probability logic, Struct. Control Health Monitoring, 17 (2010), pp. 825--847.
8.
J. L. Beck and S.-K. Au, Bayesian updating of structural models and reliability using Markov chain Monte Carlo simulation, J. Eng. Mech., 128 (2002), pp. 380--391.
9.
J. L. Beck and L. S. Katafygiotis, Updating models and their uncertainties. I: Bayesian statistical framework, J. Eng. Mech., 124 (1998), pp. 455--461.
10.
J. L. Beck and K.-V. Yuen, Model selection using response measurements: Bayesian probabilistic approach, J. Eng. Mech., 130 (2004), pp. 192--203.
11.
J. O. Berger, B. Liseo, and R. L. Wolpert, Integrated likelihood methods for eliminating nuisance parameters, Statist. Sci., 14 (1999), pp. 1--28.
12.
P. Bortot, S. G. Coles, and S. A. Sisson, Inference for stereological extremes, J. Amer. Statist. Assoc., 102 (2007), pp. 84--92.
13.
G. E. P. Box and N. R. Draper, Empirical Model-Building and Response Surfaces, Wiley, New York, 1987.
14.
Y. Chen, A. Linderholt, and T. Abrahamsson, An efficient simulation method for large-scale systems with local nonlinearities, in Special Topics in Structural Dynamics, Vol. 6, Springer, Cham, 2016, pp. 259--267.
15.
S. H. Cheung and J. L. Beck, Bayesian model updating using hybrid Monte Carlo simulation with application to structural dynamic models with many uncertain parameters, J. Eng. Mech., 135 (2009), pp. 243--255.
16.
S. H. Cheung and J. L. Beck, Calculation of posterior probabilities for Bayesian model class assessment and averaging from posterior samples based on dynamic system data, Comput. Aided Civil Infrastruct. Eng., 25 (2010), pp. 304--321.
17.
M. Chiachio, J. L. Beck, J. Chiachio, and G. Rus, Approximate Bayesian computation by subset simulation, SIAM J. Sci. Comput., 36 (2014), pp. A1339--A1358, https://doi.org/10.1137/130932831.
18.
J. Ching, J. L. Beck, and K. A. Porter, Bayesian state and parameter estimation of uncertain dynamical systems, Prob. Eng. Mech., 21 (2006), pp. 81--96.
19.
J. Ching, J. L. Beck, K. A. Porter, and R. Shaikhutdinov, Bayesian state estimation method for nonlinear systems and its application to recorded seismic response, J. Eng. Mech., 132 (2006), pp. 396--410.
20.
J. Ching and Y.-C. Chen, Transitional Markov chain Monte Carlo method for Bayesian model updating, model class selection, and model averaging, J. Eng. Mech., 133 (2007), pp. 816--832.
21.
J. Ching, M. Muto, and J. L. Beck, Structural model updating and health monitoring with incomplete modal data using Gibbs sampler, Comput. Aided Civil Infrastruct. Eng., 21 (2006), pp. 242--257.
22.
D. R. Cox and N. Reid, Parameter orthogonality and approximate conditional inference, J. Roy. Statist. Soc. Ser. B, 49 (1987), pp. 1--39.
23.
P. Del Moral, A. Doucet, and A. Jasra, An adaptive sequential Monte Carlo method for approximate Bayesian computation, Stat. Comput., 22 (2012), pp. 1009--1020.
24.
X. Didelot, R. G. Everitt, A. M. Johansen, and D. J. Lawson, Likelihood-free estimation of model evidence, Bayesian Anal., 6 (2011), pp. 49--76.
25.
C. C. Drovandi and A. N. Pettitt, Estimation of parameters for macroparasite population evolution using approximate Bayesian computation, Biometrics, 67 (2011), pp. 225--233.
26.
B. Goller, H. Pradlwarter, and G. Schueller, Robust model updating with insufficient data, Comput. Methods Appl. Mech. Engrg., 198 (2009), pp. 3096--3104.
27.
P. Green and K. Worden, Bayesian and Markov chain Monte Carlo methods for identifying nonlinear systems in the presence of uncertainty, Philos. Trans. R. Soc. A, 373 (2015), 20140405.
28.
A. Grelaud, C. P. Robert, J.-M. Marin, F. Rodolphe, and J.-F. Taly, ABC likelihood-free methods for model choice in Gibbs random fields, Bayesian Anal., 4 (2009), pp. 317--335.
29.
P. Jayakumar, Modeling and Identification in Structural Dynamics, Technical Report EERL-87-01, California Institute of Technology, Pasadena, CA, 1987.
30.
P. Jayakumar and J. L. Beck, System identification using nonlinear structural models, in Structural Safety Evaluation Based on System Identification Approaches, Vieweg$+$Teubner Verlag, Wiesbaden, Germany, 1988, pp. 82--102.
31.
E. T. Jaynes, Information theory and statistical mechanics, Phys. Rev., 106 (1957), pp. 620--630.
32.
H. Jensen, C. Vergara, C. Papadimitriou, and E. Millas, The use of updated robust reliability measures in stochastic dynamical systems, Comput. Methods Appl. Mech. Engrg., 267 (2013), pp. 293--317.
33.
J.-M. Marin, P. Pudlo, C. P. Robert, and R. J. Ryder, Approximate Bayesian computational methods, Stat. Comput., 22 (2012), pp. 1167--1180.
34.
P. Marjoram, J. Molitor, V. Plagnol, and S. Tavaré, Markov chain Monte Carlo without likelihoods, Proc. Natl. Acad. Sci. USA, 100 (2003), pp. 15324--15328.
35.
M. Muto and J. L. Beck, Bayesian updating and model class selection for hysteretic structural models using stochastic simulation, J. Vib. Control, 14 (2008), pp. 7--34.
36.
C. Papadimitriou, J. L. Beck, and L. S. Katafygiotis, Updating robust reliability using structural test data, Prob. Eng. Mech., 16 (2001), pp. 103--113.
37.
J. K. Pritchard, M. T. Seielstad, A. Perez-Lezaun, and M. W. Feldman, Population growth of human Y chromosomes: A study of Y chromosome microsatellites, Mol. Biol. Evol., 16 (1999), pp. 1791--1798.
38.
O. Ratmann, C. Andrieu, C. Wiuf, and S. Richardson, Model criticism based on likelihood-free inference, with an application to protein network evolution, Proc. Natl. Acad. Sci. USA, 106 (2009), pp. 10576--10581.
39.
C. Robert and G. Casella, Monte Carlo Statistical Methods, Springer Science & Business Media, 2013.
40.
C. P. Robert, J.-M. Cornuet, J.-M. Marin, and N. S. Pillai, Lack of confidence in approximate Bayesian computation model choice, Proc. Natl. Acad. Sci. USA, 108 (2011), pp. 15112--15117.
41.
G. O. Roberts and J. S. Rosenthal, Examples of adaptive MCMC, J. Comput. Graph. Statist., 18 (2009), pp. 349--367.
42.
S. Sisson, Y. Fan, and M. Tanaka, A Note on Backward Kernel Choice for Sequential Monte Carlo without Likelihoods, technical report, University of New South Wales, Sydney, Australia, 2008.
43.
S. A. Sisson and Y. Fan, Likelihood-free MCMC, in Handbook of Markov Chain Monte Carlo, CRC Press, Boca Raton, FL, 2011, pp. 313--335.
44.
S. A. Sisson, Y. Fan, and M. M. Tanaka, Sequential Monte Carlo without likelihoods, Proc. Natl. Acad. Sci. USA, 104 (2007), pp. 1760--1765.
45.
D. Straub and I. Papaioannou, Bayesian updating with structural reliability methods, J. Eng. Mech., 141 (2014), 04014134.
46.
T. Sweeting, Discussion of “Parameter orthogonality and approximate conditional inference” (by D. R. Cox and N. Reid), J. Roy. Statist. Soc. Ser. B, 49 (1987), pp. 20--21.
47.
S. Tavaré, D. J. Balding, R. C. Griffiths, and P. Donnelly, Inferring coalescence times from DNA sequence data, Genetics, 145 (1997), pp. 505--518.
48.
R. S. Thyagarajan, Modeling and Analysis of Hysteretic Structural Behavior, Technical Report EERL-89-03, California Institute of Technology, Pasadena, CA, 1989.
49.
L. Tierney and J. B. Kadane, Accurate approximations for posterior moments and marginal densities, J. Amer. Statist. Assoc., 81 (1986), pp. 82--86.
50.
T. Toni and M. P. Stumpf, Simulation-based model selection for dynamical systems in systems and population biology, Bioinformatics, 26 (2010), pp. 104--110.
51.
T. Toni, D. Welch, N. Strelkowa, A. Ipsen, and M. P. Stumpf, Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems, J. Roy. Soc. Interface, 6 (2009), pp. 187--202.
52.
M. K. Vakilzadeh, J. L. Beck, and T. Abrahamsson, Approximate Bayesian Computation by Subset Simulation for model selection in dynamical systems, Procedia Engineering (10th International Conference on Structural Dynamics, EURODYN 2017), 199 (2017), pp. 1056--1061.
53.
M. K. Vakilzadeh, Y. Huang, J. L. Beck, and T. Abrahamsson, Approximate Bayesian Computation by Subset Simulation using hierarchical state-space models, Mech. Syst. Signal Process., 84 (2017), pp. 2--20.
54.
R. D. Wilkinson, Bayesian Inference of Primate Divergence Times, Ph.D. thesis, University of Cambridge, Cambridge, UK, 2008.
55.
R. D. Wilkinson, Approximate Bayesian computation (ABC) gives exact results under the assumption of model error, Statist. Appl. Genetics Mol. Biol., 12 (2013), pp. 129--141.
56.
K. Worden and J. Hensman, Parameter estimation and model selection for a class of hysteretic systems using Bayesian inference, Mech. Syst. Signal Process., 32 (2012), pp. 153--169.
57.
K.-V. Yuen, Recent developments of Bayesian model class selection and applications in civil engineering, Struct. Safety, 32 (2010), pp. 338--346.
58.
K.-V. Yuen and J. L. Beck, Updating properties of nonlinear dynamical systems with uncertain input, J. Eng. Mech., 129 (2003), pp. 9--20.
59.
K. M. Zuev, J. L. Beck, S.-K. Au, and L. S. Katafygiotis, Bayesian post-processor and other enhancements of Subset Simulation for estimating failure probabilities in high dimensions, Comput. & Structures, 92 (2012), pp. 283--296.

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Information

Published In

cover image SIAM Journal on Scientific Computing
SIAM Journal on Scientific Computing
Pages: B168 - B195
ISSN (online): 1095-7197

History

Submitted: 22 August 2016
Accepted: 18 October 2017
Published online: 30 January 2018

Keywords

  1. Approximate Bayesian Computation
  2. Subset Simulation
  3. Bayesian model selection
  4. system identification
  5. bilinear and Masing hysteretic models

MSC codes

  1. 62F15
  2. 65C40
  3. 65C60
  4. 93B30
  5. 37N15

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