Low-dimensional compartment models for biological systems can be fitted to time series data using Monte Carlo particle filter methods. As dimension increases, for example when analyzing a collection of spatially coupled populations, particle filter methods rapidly degenerate. We show that many independent Monte Carlo calculations, each of which does not attempt to solve the filtering problem, can be combined to give a global filtering solution with favorable theoretical scaling properties under a weak coupling condition. The independent Monte Carlo calculations are called islands, and the operation carried out on each island is called adapted simulation, so the complete algorithm is called an adapted simulation island filter. We demonstrate this methodology and some related algorithms on a model for measles transmission within and between cities.[-]

This course will give a gentle introduction to SMC (Sequential Monte Carlo algorithms):
• motivation: state-space (hidden Markov) models, sequential analysis of such models; non-sequential problems that may be tackled using SMC.
• Formalism: Markov kernels, Feynman-Kac distributions.
• Monte Carlo tricks: importance sampling and resampling
• standard particle filters: bootstrap, guided, auxiliary
• maximum likelihood estimation of state-stace models
• Bayesian estimation of these models: PMCMC, SMC$^2$.[-]

We discuss the problem of positive-semidefinite extension: extending a partially specified covariance kernel from a subdomain Ω of a rectangular domain I x I to a covariance kernel on the entire domain I x I. For a broad class of domains Ω called serrated domains, we present a complete theory. Namely, we demonstrate that a canonical completion always exists and can be explicitly constructed. We characterise all possible completions as suitable perturbations of the canonical completion, and determine necessary and sufficient conditions for a unique completion to exist. We interpret the canonical completion via the graphical model structure it induces on the associated Gaussian process. Furthermore, we show how the determination of the canonical completion reduces to the solution of a system of linear inverse problems in the space of Hilbert-Schmidt operators, and derive rates of convergence when the kernel is to be empirically estimated. We conclude by providing extensions of our theory to more general forms of domains, and by demonstrating how our results can be used in statistical inverse problems associated with stochastic processes.[-]