Bayesian Static Parameter Estimation for Partially Observed Diffusions via Multilevel Monte Carlo

In this article we consider static Bayesian parameter estimation for partially observed diffusions that are discretely observed. We work under the assumption that one must resort to discretizing the underlying diffusion process, for instance using the Euler-Maruyama method. Given this assumption, we show how one can use Markov chain Monte Carlo (MCMC) and particularly particle MCMC [Andrieu, C., Doucet, A. and Holenstein, R. (2010). Particle Markov chain Monte Carlo methods (with discussion). J. R. Statist. Soc. Ser. B, 72, 269--342] to implement a new approximation of the multilevel (ML) Monte Carlo (MC) collapsing sum identity. Our approach comprises constructing an approximate coupling of the posterior density of the joint distribution over parameter and hidden variables at two different discretization levels and then correcting by an importance sampling method. The variance of the weights are independent of the length of the observed data set. The utility of such a method is that, for a prescribed level of mean square error, the cost of this MLMC method is provably less than i.i.d. sampling from the posterior associated to the most precise discretization. However the method here comprises using only known and efficient simulation methodologies. The theoretical results are illustrated by inference of the parameters of two prototypical processes given noisy partial observations of the process: the first is an Ornstein Uhlenbeck process and the second is a more general Langevin equation

Bayesian Parameter Inference for Partially Observed Diffusions using Multilevel Stochastic Runge-Kutta Methods

We consider the problem of Bayesian estimation of static parameters associated to a partially and discretely observed diffusion process. We assume that the exact transition dynamics of the diffusion process are unavailable, even up-to an unbiased estimator and that one must time-discretize the diffusion process. In such scenarios it has been shown how one can introduce the multilevel Monte Carlo method to reduce the cost to compute posterior expected values of the parameters for a pre-specified mean square error (MSE). These afore-mentioned methods rely on upon the Euler-Maruyama discretization scheme which is well-known in numerical analysis to have slow convergence properties. We adapt stochastic Runge-Kutta (SRK) methods for Bayesian parameter estimation of static parameters for diffusions. This can be implemented in high-dimensions of the diffusion and seemingly under-appreciated in the uncertainty quantification and statistics fields. For a class of diffusions and SRK methods, we consider the estimation of the posterior expectation of the parameters. We prove that to achieve a MSE of $\mathcal{O}(\epsilon^2)$, for $\epsilon>0$ given, the associated work is $\mathcal{O}(\epsilon^{-2})$. Whilst the latter is achievable for the Milstein scheme, this method is often not applicable for diffusions in dimension larger than two. We also illustrate our methodology in several numerical examples

Multilevel Monte Carlo for a class of Partially Observed Processes in Neuroscience

In this paper we consider Bayesian parameter inference associated to a class of partially observed stochastic differential equations (SDE) driven by jump processes. Such type of models can be routinely found in applications, of which we focus upon the case of neuroscience. The data are assumed to be observed regularly in time and driven by the SDE model with unknown parameters. In practice the SDE may not have an analytically tractable solution and this leads naturally to a time-discretization. We adapt the multilevel Markov chain Monte Carlo method of [11], which works with a hierarchy of time discretizations and show empirically and theoretically that this is preferable to using one single time discretization. The improvement is in terms of the computational cost needed to obtain a pre-specified numerical error. Our approach is illustrated on models that are found in neuroscience

A Multilevel Approach for Stochastic Nonlinear Optimal Control

We consider a class of finite time horizon nonlinear stochastic optimal control problem, where the control acts additively on the dynamics and the control cost is quadratic. This framework is flexible and has found applications in many domains. Although the optimal control admits a path integral representation for this class of control problems, efficient computation of the associated path integrals remains a challenging Monte Carlo task. The focus of this article is to propose a new Monte Carlo approach that significantly improves upon existing methodology. Our proposed methodology first tackles the issue of exponential growth in variance with the time horizon by casting optimal control estimation as a smoothing problem for a state space model associated with the control problem, and applying smoothing algorithms based on particle Markov chain Monte Carlo. To further reduce computational cost, we then develop a multilevel Monte Carlo method which allows us to obtain an estimator of the optimal control with $\mathcal{O}(\epsilon^2)$ mean squared error with a computational cost of $\mathcal{O}(\epsilon^{-2}\log(\epsilon)^2)$. In contrast, a computational cost of $\mathcal{O}(\epsilon^{-3})$ is required for existing methodology to achieve the same mean squared error. Our approach is illustrated on two numerical examples, which validate our theory

Unbiased Parameter Estimation for Partially Observed Diffusions

In this article we consider the estimation of static parameters for partially observed diffusion process with discrete-time observations over a fixed time interval. In particular, we assume that one must time-discretize the partially observed diffusion process and work with the model with bias and consider maximizing the resulting log-likelihood. Using a novel double randomization scheme, based upon Markovian stochastic approximation we develop a new method to unbiasedly estimate the static parameters, that is, to obtain the maximum likelihood estimator with no time discretization bias. Under assumptions we prove that our estimator is unbiased and investigate the method in several numerical examples, showing that it can empirically out-perform existing unbiased methodology.Comment: 27 pages, 8 figure

Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living things. Mathematical idealisations of biochemically reacting systems must be able to capture stochastic phenomena. While robust theory exists to describe such stochastic models, the computational challenges in exploring these models can be a significant burden in practice since realistic models are analytically intractable. Determining the expected behaviour and variability of a stochastic biochemical reaction network requires many probabilistic simulations of its evolution. Using a biochemical reaction network model to assist in the interpretation of time course data from a biological experiment is an even greater challenge due to the intractability of the likelihood function for determining observation probabilities. These computational challenges have been subjects of active research for over four decades. In this review, we present an accessible discussion of the major historical developments and state-of-the-art computational techniques relevant to simulation and inference problems for stochastic biochemical reaction network models. Detailed algorithms for particularly important methods are described and complemented with MATLAB implementations. As a result, this review provides a practical and accessible introduction to computational methods for stochastic models within the life sciences community

An Online Method for the Data Driven Stochastic Optimal Control Problem with Unknown Model Parameters

In this work, an efficient sample-wise data driven control solver will be developed to solve the stochastic optimal control problem with unknown model parameters. A direct filter method will be applied as an online parameter estimation method that dynamically estimates the target model parameters upon receiving the data, and a sample-wise optimal control solver will be provided to efficiently search for the optimal control. Then, an effective overarching algorithm will be introduced to combine the parameter estimator and the optimal control solver. Numerical experiments will be carried out to demonstrate the effectiveness and the efficiency of the sample-wise data driven control method