Bagging (i.e., bootstrap aggregating) involves combining an ensemble of bootstrap estimators. We consider bagging for inference from noisy or incomplete measurements on a collection of interacting stochastic dynamic systems. Each system is called a unit, and each unit is associated with a spatial location. A motivating example arises in epidemiology, where each unit is a city: the majority of transmission occurs within a city, with smaller yet epidemiologically important interactions arising from disease transmission between cities. Monte Carlo filtering methods used for inference on nonlinear non-Gaussian systems can suffer from a curse of dimensionality as the number of units increases. We introduce bagged filter (BF) methodology which combines an ensemble of Monte Carlo filters, using spatiotemporally localized weights to select successful filters at each unit and time. We obtain conditions under which likelihood evaluation using a BF algorithm can beat a curse of dimensionality, and we demonstrate applicability even when these conditions do not hold. BF can out-perform an ensemble Kalman filter on a coupled population dynamics model describing infectious disease transmission. A block particle filter also performs well on this task, though the bagged filter respects smoothness and conservation laws that a block particle filter can violate.
In this paper we introduce a novel particle filter scheme for a class of partially-observed multivariate diffusions. %continuous-time dynamic models where the %signal is given by a multivariate diffusion process. We consider a variety of observation schemes, including diffusion observed with error, observation of a subset of the components of the multivariate diffusion and arrival times of a Poisson process whose intensity is a known function of the diffusion (Cox process). Unlike currently available methods, our particle filters do not require approximations of the transition and/or the obser…
Partially-observed Boolean dynamical systems (POBDS) are a general class of nonlinear models with application in estimation and control of Boolean processes based on noisy and incomplete measurements. The optimal minimum mean square error (MMSE) algorithms for POBDS state estimation, namely, the Boolean Kalman filter (BKF) and Boolean Kalman smoother (BKS), are intractable in the case of large systems, due to computational and memory requirements. To address this, we propose approximate MMSE filtering and smoothing algorithms based on the auxiliary particle filter (APF) method from sequential …
In this article we consider a Monte Carlo-based method to filter partially observed diffusions observed at regular and discrete times. Given access only to Euler discretizations of the diffusion process, we present a new procedure which can return online estimates of the filtering distribution with no discretization bias and finite variance. Our approach is based upon a novel double application of the randomization methods of Rhee & Glynn (2015) along with the multilevel particle filter (MLPF) approach of Jasra et al (2017). A numerical comparison of our new approach with the MLPF, on a single…
We consider inference for a collection of partially observed, stochastic, interacting, nonlinear dynamic processes. Each process is identified with a label called its unit, and our primary motivation arises in biological metapopulation systems where a unit corresponds to a spatially distinct sub-population. Metapopulation systems are characterized by strong dependence through time within a single unit and relatively weak interactions between units, and these properties make block particle filters an effective tool for simulation-based likelihood evaluation. Iterated filtering algorithms can fa…
Parameter estimation in multidimensional diffusion models with only one coordinate observed is highly relevant in many biological applications, but a statistically difficult problem. In neuroscience, the membrane potential evolution in single neurons can be measured at high frequency, but biophysical realistic models have to include the unobserved dynamics of ion channels. One such model is the stochastic Morris-Lecar model, defined by a nonlinear two-dimensional stochastic differential equation. The coordinates are coupled, that is, the unobserved coordinate is nonautonomous, the model exhibi…
Partially observed Markov process (POMP) models, also known as hidden Markov models or state space models, are ubiquitous tools for time series analysis. The R package pomp provides a very flexible framework for Monte Carlo statistical investigations using nonlinear, non-Gaussian POMP models. A range of modern statistical methods for POMP models have been implemented in this framework including sequential Monte Carlo, iterated filtering, particle Markov chain Monte Carlo, approximate Bayesian computation, maximum synthetic likelihood estimation, nonlinear forecasting, and trajectory matching. …
Real-time transmission line outage detection is difficult because of partial phasor measurement unit (PMU) deployment and varying outage signal strength. Existing detection approaches focus on monitoring PMU-measured nodal algebraic states, i.e., voltage phase angle and magnitude. The success of such approaches, however, is largely predicated on strong outage signals and the presence of PMUs in the outage location's vicinity. To overcome these limitations, a unified framework is proposed in this work by utilizing both nodal voltage information and generator dynamic states, e.g., rotor angular …
We consider the problem of inference for nonlinear, multivariate diffusion processes, satisfying Itô stochastic differential equations (SDEs), using data at discrete times that may be incomplete and subject to measurement error. Our starting point is a state-of-the-art correlated pseudo-marginal Metropolis-Hastings algorithm, that uses correlated particle filters to induce strong and positive correlation between successive likelihood estimates. However, unless the measurement error or the dimension of the SDE is small, correlation can be eroded by the resampling steps in the particle filter. W…
We consider multiscale stochastic systems that are partially observed at discrete points of the slow time scale. We introduce a particle filter that takes advantage of the multiscale structure of the system to efficiently approximate the optimal filter.
Inference for partially observed Markov process models has been a longstanding methodological challenge with many scientific and engineering applications. Iterated filtering algorithms maximize the likelihood function for partially observed Markov process models by solving a recursive sequence of filtering problems. We present new theoretical results pertaining to the convergence of iterated filtering algorithms implemented via sequential Monte Carlo filters. This theory complements the growing body of empirical evidence that iterated filtering algorithms provide an effective inference strateg…
This article discusses a partially adapted particle filter for estimating the likelihood of a nonlinear structural econometric state space models whose state transition density cannot be expressed in closed form. The filter generates the disturbances in the state transition equation and allows for multiple modes in the conditional disturbance distribution. The particle filter produces an unbiased estimate of the likelihood and so can be used to carry out Bayesian inference in a particle Markov chain Monte Carlo framework. We show empirically that when the signal to noise ratio is high, the new…
This paper uses stochastic dominance principles to construct upper and lower sample path bounds for Hidden Markov Model (HMM) filters. Given a HMM, by using convex optimization methods for nuclear norm minimization with copositive constraints, we construct low rank stochastic marices so that the optimal filters using these matrices provably lower and upper bound (with respect to a partially ordered set) the true filtered distribution at each time instant. Since these matrices are low rank (say R), the computational cost of evaluating the filtering bounds is O(XR) instead of O(X2). A Monte-Carl…
This article deals with the problem of functional classification for L2-valued random covariates when some of the covariates may have missing or unobservable fragments. Here, it is allowed for both the training sample as well as the new unclassified observation to have missing fragments in their functional covariates. Furthermore, unlike most previous results in the literature, where covariate fragments are typically assumed to be missing completely at random, we do not impose any such assumptions here. Given the observed segments of the curves, we construct a kernel-type classifier which is q…
We present a simulation methodology for Bayesian estimation of rate parameters in Markov jump processes arising for example in stochastic kinetic models. To handle the problem of missing components and measurement errors in observed data, we embed the Markov jump process into the framework of a general state space model. We do not use diffusion approximations. Markov chain Monte Carlo and particle filter type algorithms are introduced, which allow sampling from the posterior distribution of the rate parameters and the Markov jump process also in data-poor scenarios. The algorithms are illustra…
In this article we introduce two new estimates of the normalizing constant (or marginal likelihood) for partially observed diffusion (POD) processes, with discrete observations. One estimate is biased but non-negative and the other is unbiased but not almost surely non-negative. Our method uses the multilevel particle filter of Jasra et al (2015). We show that, under assumptions, for Euler discretized PODs and a given $\varepsilon>0$. in order to obtain a mean square error (MSE) of $\mathcal{O}(\varepsilon^2)$ one requires a work of $\mathcal{O}(\varepsilon^{-2.5})$ for our new estimates versu…
In this paper we consider the filtering of partially observed multi-dimensional diffusion processes that are observed regularly at discrete times. We assume that, for numerical reasons, one has to time-discretize the diffusion process which typically leads to filtering that is subject to discretization bias. The approach in [16] establishes that when only having access to the time-discretized diffusion it is possible to remove the discretization bias with an estimator of finite variance. We improve on the method in [16] by introducing a modified estimator based on the recent work of [17]. We s…
This paper presents a simulation-based framework for sequential inference from partially and discretely observed point process (PP's) models with static parameters. Taking on a Bayesian perspective for the static parameters, we build upon sequential Monte Carlo (SMC) methods, investigating the problems of performing sequential filtering and smoothing in complex examples, where current methods often fail. We consider various approaches for approximating posterior distributions using SMC. Our approaches, with some theoretical discussion are illustrated on a doubly stochastic point process applie…
Ordinary Differential Equations are a simple but powerful framework for modeling complex systems. Parameter estimation from times series can be done by Nonlinear Least Squares (or other classical approaches), but this can give unsatisfactory results because the inverse problem can be ill-posed, even when the differential equation is linear. Following recent approaches that use approximate solutions of the ODE model, we propose a new method that converts parameter estimation into an optimal control problem: our objective is to determine a control and a parameter that are as close as possible to…
We deal with the problem of parameter estimation in stochastic differential equations (SDEs) in a partially observed framework. We aim to design a method working for both elliptic and hypoelliptic SDEs, the latters being characterized by degenerate diffusion coefficients. This feature often causes the failure of contrast estimators based on Euler Maruyama discretization scheme and dramatically impairs classic stochastic filtering methods used to reconstruct the unobserved states. All of theses issues make the estimation problem in hypoelliptic SDEs difficult to solve. To overcome this, we cons…
We consider partially observed multiscale diffusion models that are specified up to an unknown vector parameter. We establish for a very general class of test functions that the filter of the original model converges to a filter of reduced dimension. Then, this result is used to justify statistical estimation for the unknown parameters of interest based on the model of reduced dimension but using the original available data. This allows to learn the unknown parameters of interest while working in lower dimensions, as opposed to working with the original high dimensional system. Simulation stud…
We consider the problem of statistical inference for a class of partially-observed diffusion processes, with discretely-observed data and finite-dimensional parameters. We construct unbiased estimators of the score function, i.e. the gradient of the log-likelihood function with respect to parameters, with no time-discretization bias. These estimators can be straightforwardly employed within stochastic gradient methods to perform maximum likelihood estimation or Bayesian inference. As our proposed methodology only requires access to a time-discretization scheme such as the Euler-Maruyama method…
In this paper we consider filtering and smoothing of partially observed chaotic dynamical systems that are discretely observed, with an additive Gaussian noise in the observation. These models are found in a wide variety of real applications and include the Lorenz 96' model. In the context of a fixed observation interval $T$, observation time step $h$ and Gaussian observation variance $σ_Z^2$, we show under assumptions that the filter and smoother are well approximated by a Gaussian with high probability when $h$ and $σ^2_Z h$ are sufficiently small. Based on this result we show that the Maxim…
Dynamic epidemic models have proven valuable for public health decision makers as they provide useful insights into the understanding and prevention of infectious diseases. However, inference for these types of models can be difficult because the disease spread is typically only partially observed e.g. in form of reported incidences in given time periods. This chapter discusses how to perform likelihood-based inference for partially observed Markov epidemic models when it is relatively easy to generate samples from the Markov transmission model while the likelihood function is intractable. The…
In this article we consider the development of unbiased estimators of the Hessian, of the log-likelihood function with respect to parameters, for partially observed diffusion processes. These processes arise in numerous applications, where such diffusions require derivative information, either through the Jacobian or Hessian matrix. As time-discretizations of diffusions induce a bias, we provide an unbiased estimator of the Hessian. This is based on using Girsanov's Theorem and randomization schemes developed through Mcleish [2011] and Rhee & Glynn [2015]. We demonstrate our developed estimato…
