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A second-order iterated smoothing algorithm. (English) Zbl 1384.62284

Summary: Simulation-based inference for partially observed stochastic dynamic models is currently receiving much attention due to the fact that direct computation of the likelihood is not possible in many practical situations. Iterated filtering methodologies enable maximization of the likelihood function using simulation-based sequential Monte Carlo filters. A. Doucet et al. [“Derivative-free estimation of the score vector and observed information matrix with application to state-space models”, Preprint, arXiv:1304.5768] developed an approximation for the first and second derivatives of the log likelihood via simulation-based sequential Monte Carlo smoothing and proved that the approximation has some attractive theoretical properties. We investigated an iterated smoothing algorithm carrying out likelihood maximization using these derivative approximations. Further, we developed a new iterated smoothing algorithm, using a modification of these derivative estimates, for which we establish both theoretical results and effective practical performance. On benchmark computational challenges, this method beat the first-order iterated filtering algorithm. The method’s performance was comparable to a recently developed iterated filtering algorithm based on an iterated Bayes map. Our iterated smoothing algorithm and its theoretical justification provide new directions for future developments in simulation-based inference for latent variable models such as partially observed Markov process models.

MSC:

62M05 Markov processes: estimation; hidden Markov models
65C05 Monte Carlo methods

Software:

pomp; is2

References:

[1] Andrieu, C., Doucet, A., Holenstein, R.: Particle Markov chain Monte Carlo methods. J. R. Stat. Soc. Ser. B 72(3), 269-342 (2010) · Zbl 1184.65001 · doi:10.1111/j.1467-9868.2009.00736.x
[2] Bhadra, A., Ionides, E.L., Laneri, K., Pascual, M., Bouma, M., Dhiman, R.C.: Malaria in Northwest India: data analysis via partially observed stochastic differential equation models driven by Lévy noise. J. Am. Stat. Assoc. 106, 440-451 (2011) · Zbl 1232.62143 · doi:10.1198/jasa.2011.ap10323
[3] Bjørnstad, O.N., Grenfell, B.T.: Noisy clockwork: time series analysis of population fluctuations in animals. Science 293, 638-643 (2001) · doi:10.1126/science.1062226
[4] Blackwood, J.C., Cummings, D.A.T., Broutin, H., Iamsirithaworn, S., Rohani, P.: Deciphering the impacts of vaccination and immunity on pertussis epidemiology in Thailand. Proc. Natl. Acad. Sci. USA 110, 9595-9600 (2013a) · doi:10.1073/pnas.1220908110
[5] Blackwood, J.C., Streicker, D.G., Altizer, S., Rohani, P.: Resolving the roles of immunity, pathogenesis, and immigration for rabies persistence in vampire bats. Proc. Natl. Acad. Sci. USA 110, 2083720842 (2013b)
[6] Blake, I.M., Martin, R., Goel, A., Khetsuriani, N., Everts, J., Wolff, C., Wassilak, S., Aylward, R.B., Grassly, N.C.: The role of older children and adults in wild poliovirus transmission. Proc. Natl. Acad. Sci. USA 111(29), 10604-10609 (2014) · doi:10.1073/pnas.1323688111
[7] Bretó, C., He, D., Ionides, E.L., King, A.A.: Time series analysis via mechanistic models. Ann. Appl. Stat. 3, 319-348 (2009) · Zbl 1160.62080 · doi:10.1214/08-AOAS201
[8] Camacho, A., Ballesteros, S., Graham, A.L., Carrat, F., Ratmann, O., Cazelles, B.: Explaining rapid reinfections in multiple-wave influenza outbreaks: Tristan da Cunha 1971 epidemic as a case study. Proc. R. Soc. Lond. Ser. B 278(1725), 3635-3643 (2011) · doi:10.1098/rspb.2011.0300
[9] Chopin, N., Jacob, P.E., Papaspiliopoulos, O.: SMC \[^22\]: an efficient algorithm for sequential analysis of state space models. J. R. Stat. Soc. Ser. B 75(3), 397-426 (2013) · Zbl 1411.62242 · doi:10.1111/j.1467-9868.2012.01046.x
[10] Dahlin, J., Lindsten, F., Schön, T.B.: Particle Metropolis-Hastings using gradient and Hessian information. Stat. Comput. 25(1), 81-92 (2015) · Zbl 1331.62134 · doi:10.1007/s11222-014-9510-0
[11] Douc, R., Cappé, O., Moulines, E.: Comparison of resampling schemes for particle filtering. In: Proceedings of the 4th International Symposium on Image and Signal Processing and Analysis, 2005, pp 64-69. IEEE, New York (2005)
[12] Doucet, A., Jacob, P. E., and Rubenthaler, S.: Derivative-free estimation of the score vector and observed information matrix with application to state-space models (version 2). arXiv:1304.5768v2 (2013) · Zbl 1359.62345
[13] Earn, D.J., He, D., Loeb, M.B., Fonseca, K., Lee, B.E., Dushoff, J.: Effects of school closure on incidence of pandemic influenza in Alberta. Ann. Int. Med. 156(3), 173-181 (2012) · doi:10.7326/0003-4819-156-3-201202070-00005
[14] Gordon, N.J., Salmond, D.J., Smith, A.F.: Novel approach to nonlinear/non-Gaussian Bayesian state estimation. IEE Proc. F. Radar Signal Process. 140, 107-113 (1993) · doi:10.1049/ip-f-2.1993.0015
[15] He, D., Dushoff, J., Day, T., Ma, J., Earn, D.J.D.: Inferring the causes of the three waves of the 1918 influenza pandemic in England and Wales. Proc. R. Soc. Lond. Ser. B 280(1766), 20131345 (2013) · doi:10.1098/rspb.2013.1345
[16] He, D., Ionides, E.L., King, A.A.: Plug-and-play inference for disease dynamics: measles in large and small populations as a case study. J. R. Soc. Interface 7(43), 271-283 (2010) · doi:10.1098/rsif.2009.0151
[17] Ionides, E.L., Bhadra, A., Atchadé, Y., King, A.: Iterated filtering. Ann. Stat. 39, 1776-1802 (2011) · Zbl 1220.62103 · doi:10.1214/11-AOS886
[18] Ionides, E.L., Bretó, C., King, A.A.: Inference for nonlinear dynamical systems. Proc. Natl. Acad. Sci. USA 103, 18438-18443 (2006) · doi:10.1073/pnas.0603181103
[19] Ionides, E.L., Nguyen, D., Atchadé, Y., Stoev, S., King, A.A.: Inference for dynamic and latent variable models via iterated, perturbed Bayes maps. P. Natl. Acad. Sci. USA 112(3), 719-724 (2015) · Zbl 1359.62345 · doi:10.1073/pnas.1410597112
[20] Kevrekidis, I.G., Gear, C.W., Hummer, G.: Equation-free: the computer-assisted analysis of complex, multiscale systems. Am. Inst. Chem. Eng. J. 50, 1346-1354 (2004) · doi:10.1002/aic.10106
[21] King, A.A., Domenech de Celle, M., Magpantay, F.M.G., Rohani, P.: Avoidable errors in the modelling of outbreaks of emerging pathogens, with special reference to Ebola. Proc. R. Soc. Lond. Ser. B 282, 20150347 (2015) · doi:10.1098/rspb.2015.0347
[22] King, A.A., Ionides, E.L., Pascual, M., Bouma, M.J.: Inapparent infections and cholera dynamics. Nature 454, 877-880 (2008) · doi:10.1038/nature07084
[23] King, A.A., Nguyen, D., Ionides, E.L.: Statistical inference for partially observed Markov processes via the R package pomp. J. Stat. Softw 69, 1-43 (2016) · doi:10.18637/jss.v069.i12
[24] Kloeden, P.E., Platen, E.: Numerical Soluion of Stochastic Differential Equations, 3rd edn. Springer, New York (1999)
[25] Kushner, H.J., Clark, D.S.: Stochastic Approximation Methods for Constrained and Unconstrained Systems. Springer, New York (1978) · Zbl 0381.60004 · doi:10.1007/978-1-4684-9352-8
[26] Laneri, K., Bhadra, A., Ionides, E.L., Bouma, M., Dhiman, R.C., Yadav, R.S., Pascual, M.: Forcing versus feedback: epidemic malaria and monsoon rains in Northwest India. PLoS Comput. Biol. 6(9), e1000898 (2010) · doi:10.1371/journal.pcbi.1000898
[27] Laneri, K., Paul, R.E., Tall, A., Faye, J., Diene-Sarr, F., Sokhna, C., Trape, J.-F., Rodó, X.: Dynamical malaria models reveal how immunity buffers effect of climate variability. Proc. Natl. Acad. Sci. USA 112(28), 8786-8791 (2015) · doi:10.1073/pnas.1419047112
[28] Lavine, J.S., King, A.A., Andreasen, V., Bjrnstad, O.N.: Immune boosting explains regime-shifts in prevaccine-era pertussis dynamics. PLoS ONE 8(8), e72086 (2013) · doi:10.1371/journal.pone.0072086
[29] Lavine, J.S., Rohani, P.: Resolving pertussis immunity and vaccine effectiveness using incidence time series. Expert Rev. Vaccines 11, 1319-1329 (2012) · doi:10.1586/erv.12.109
[30] Macdonald, G.: The Epidemiology and Control of Malaria. Oxford University Press, Oxford (1957)
[31] Martinez-Bakker, M., King, A.A., Rohani, P.: Unraveling the transmission ecology of polio. PLoS Biol. 13(6), e1002172 (2015) · doi:10.1371/journal.pbio.1002172
[32] Nemeth, C., Fearnhead, P., Mihaylova, L.: Particle approximations of the score and observed information matrix for parameter estimation in state space models with linear computational cost. arXiv:1306.0735 (2013)
[33] Nguyen, D. (2015). Iterated smoothing r package, is2. https://r-forge.r-project.org/projects/is2
[34] Olsson, J., Cappé, O., Douc, R., Moulines, E.: Sequential Monte Carlo smoothing with application to parameter estimation in nonlinear state space models. Bernoulli 14(1), 155-179 (2008) · Zbl 1155.62055 · doi:10.3150/07-BEJ6150
[35] Poyiadjis, G., Doucet, A., Singh, S.S.: Particle approximations of the score and observed information matrix in state space models with application to parameter estimation. Biometrika 98(1), 65-80 (2011) · Zbl 1214.62093 · doi:10.1093/biomet/asq062
[36] Romero-Severson, E., Volz, E., Koopman, J., Leitner, T., Ionides, E.: Dynamic variation in sexual contact rates in a cohort of HIV-negative gay men. Am. J. Epidemiol. 182, 255-262 (2015) · doi:10.1093/aje/kwv044
[37] Ross, R.: The Prevention of Malaria. Dutton, Boston (1910)
[38] Roy, M., Bouma, M.J., Ionides, E.L., Dhiman, R.C., Pascual, M.: The potential elimination of plasmodium vivax malaria by relapse treatment: Insights from a transmission model and surveillance data from NW India. PLoS Negl. Trop. Dis. 7, e1979 (2013) · doi:10.1371/journal.pntd.0001979
[39] Shrestha, S., Foxman, B., Weinberger, D.M., Steiner, C., Viboud, C., Rohani, P.: Identifying the interaction between influenza and pneumococcal pneumonia using incidence data. Sci. Transl. Med. 5(191), 191ra84 (2013) · doi:10.1126/scitranslmed.3005982
[40] Shrestha, S., King, A.A., Rohani, P.: Statistical inference for multi-pathogen systems. PLoS Comput. Biol. 7(8), e1002135 (2011)
[41] Sisson, S.A., Fan, Y., Tanaka, M.M.: Sequential Monte Carlo without likelihoods. Proc. Natl. Acad. Sci. USA 104(6), 1760-1765 (2007) · Zbl 1160.65005 · doi:10.1073/pnas.0607208104
[42] Spall, J.C.: Introduction to Stochastic Search and Optimization. Wiley, Hoboken (2003) · Zbl 1088.90002 · doi:10.1002/0471722138
[43] Toni, T., Welch, D., Strelkowa, N., Ipsen, A., Stumpf, M.P.: Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. J. R. Soc. Interface 6, 187-202 (2009)
[44] Wood, S.N.: Statistical inference for noisy nonlinear ecological dynamic systems. Nature 466(7310), 1102-1104 (2010) · doi:10.1038/nature09319
[45] Yıldırım, S., Singh, S.S., Dean, T., Jasra, A.: Parameter estimation in hidden Markov models with intractable likelihoods using sequential Monte Carlo. J. Comput. Graph. Stat. 24, 846-865 (2015) · doi:10.1080/10618600.2014.938811
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