Epidemics are often modeled using non-linear dynamical systems observed through partial and noisy data. In this paper, we consider stochastic extensions in order to capture unknown influences (changing behaviors, public interventions, seasonal effects, etc.). These models assign diffusion processes to the time-varying parameters, and our inferential procedure is based on a suitably adjusted adaptive particle Markov chain Monte Carlo algorithm. The performance of the proposed computational methods is validated on simulated data and the adopted model is applied to the 2009 H1N1 pandemic in England. In addition to estimating the effective contact rate trajectories, the methodology is applied in real time to provide evidence in related public health decisions. Diffusion-driven susceptible exposed infected retired-type models with age structure are also introduced.

This document is the author's final manuscript accepted version of the journal article, incorporating any revisions agreed during the peer review process. Some differences between this version and the published version may remain. You are advised to consult the publisher's version if you wish to cite from it. Likelihood-based Inference for a Class of Multivariate Diffusions with Unobserved Paths Konstantinos Kalogeropoulos May 18, 2007Abstract This paper presents a Markov chain Monte Carlo algorithm for a class of multivariate diffusion models with unobserved paths. This class is of high practical interest as it includes most diffusion driven stochastic volatility models. The algorithm is based on a data augmentation scheme where the paths are treated as missing data. However, unless these paths are transformed so that the dominating measure is independent of any parameters, the algorithm becomes reducible. The methodology developed in Roberts and Stramer (2001 Biometrika 88(3):603-621) circumvents the problem for scalar diffusions. We extend this framework to the class of models of this paper by introducing an appropriate reparametrisation of the likelihood that can be used to construct an irreducible data augmentation scheme. Practical implementation issues are considered and the methodology is applied to simulated data from the Heston model.

The need to calibrate increasingly complex statistical models requires a persistent effort for further advances on available, computationally intensive Monte-Carlo methods. We study here an advanced version of familiar Markov-chain Monte-Carlo (MCMC) algorithms that sample from target distributions defined as change of measures from Gaussian laws on general Hilbert spaces. Such a model structure arises in several contexts: we focus here at the important class of statistical models driven by diffusion paths whence the Wiener process constitutes the reference Gaussian law. Particular emphasis is given on advanced Hybrid Monte-Carlo (HMC) which makes large, derivative-driven steps in the state space (in contrast with local-move Random-walk-type algorithms) with analytical and experimental results. We illustrate its computational advantages in various diffusion processes and observation regimes; examples include stochastic volatility and latent survival models. In contrast with their standard MCMC counterparts, the advanced versions have mesh-free mixing times, as these will not deteriorate upon refinement of the approximation of the inherently infinitedimensional diffusion paths by finite-dimensional ones used in practice when applying the algorithms on a computer.

We address the problem of parameter estimation for diffusion driven stochastic volatility models through Markov chain Monte Carlo (MCMC). To avoid degeneracy issues we introduce an innovative reparametrisation defined through transformations that operate on the time scale of the diffusion. A novel MCMC scheme which overcomes the inherent difficulties of time change transformations is also presented. The algorithm is fast to implement and applies to models with stochastic volatility. The methodology is tested through simulation based experiments and illustrated on data consisting of US treasury bill rates.

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