A lagged particle filter for stable filtering of certain high-dimensional state-space models

We consider the problem of high-dimensional filtering of state-space models (SSMs) at discrete times. This problem is particularly challenging as analytical solutions are typically not available and many numerical approximation methods can have a cost that scales exponentially with the dimension of the hidden state. Inspired by lag-approximation methods for the smoothing problem, we introduce a lagged approximation of the smoothing distribution that is necessarily biased. For certain classes of SSMs, particularly those that forget the initial condition exponentially fast in time, the bias of our approximation is shown to be uniformly controlled in the dimension and exponentially small in time. We develop a sequential Monte Carlo (SMC) method to recursively estimate expectations with respect to our biased filtering distributions. Moreover, we prove for a class of class of SSMs that can contain dependencies amongst coordinates that as the dimension $d\rightarrow\infty$ the cost to achieve a stable mean square error in estimation, for classes of expectations, is of $\mathcal{O}(Nd^2)$ per-unit time, where $N$ is the number of simulated samples in the SMC algorithm. Our methodology is implemented on several challenging high-dimensional examples including the conservative shallow-water model

Genomic epidemiology of the first epidemic wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Palestine.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the COVID-19 pandemic, continues to cause a significant public-health burden and disruption globally. Genomic epidemiology approaches point to most countries in the world having experienced many independent introductions of SARS-CoV-2 during the early stages of the pandemic. However, this situation may change with local lockdown policies and restrictions on travel, leading to the emergence of more geographically structured viral populations and lineages transmitting locally. Here, we report the first SARS-CoV-2 genomes from Palestine sampled from early March 2020, when the first cases were observed, through to August of 2020. SARS-CoV-2 genomes from Palestine fall across the diversity of the global phylogeny, consistent with at least nine independent introductions into the region. We identify one locally predominant lineage in circulation represented by 50 Palestinian SARS-CoV-2, grouping with genomes generated from Israel and the UK. We estimate the age of introduction of this lineage to 05/02/2020 (16/01/2020-19/02/2020), suggesting SARS-CoV-2 was already in circulation in Palestine predating its first detection in Bethlehem in early March. Our work highlights the value of ongoing genomic surveillance and monitoring to reconstruct the epidemiology of COVID-19 at both local and global scales

Score-based parameter estimation for a class of continuous-time state space models

We consider the problem of parameter estimation for a class of continuous-time state space models. In particular, we explore the case of a partially observed diffusion, with data also arriving according to a diffusion process. Based upon a standard identity of the score function, we consider two particle filter based methodologies to estimate the score function. Both methods rely on an online estimation algorithm for the score function of $\mathcal{O}(N^2)$ cost, with $N\in\mathbb{N}$ the number of particles. The first approach employs a simple Euler discretization and standard particle smoothers and is of cost $\mathcal{O}(N^2 + N\Delta_l^{-1})$ per unit time, where $\Delta_l=2^{-l}$, $l\in\mathbb{N}_0$, is the time-discretization step. The second approach is new and based upon a novel diffusion bridge construction. It yields a new backward type Feynman-Kac formula in continuous-time for the score function and is presented along with a particle method for its approximation. Considering a time-discretization, the cost is $\mathcal{O}(N^2\Delta_l^{-1})$ per unit time. To improve computational costs, we then consider multilevel methodologies for the score function. We illustrate our parameter estimation method via stochastic gradient approaches in several numerical examples

Unbiased estimation using a class of diffusion processes

We study the problem of unbiased estimation of expectations with respect to (w.r.t.) $\pi$ a given, general probability measure on $(\mathbb{R}^d,\mathcal{B}(\mathbb{R}^d))$ that is absolutely continuous with respect to a standard Gaussian measure. We focus on simulation associated to a particular class of diffusion processes, sometimes termed the Schr\"odinger-F\"ollmer Sampler, which is a simulation technique that approximates the law of a particular diffusion bridge process $\{X_t\}_{t\in [0,1]}$ on $\mathbb{R}^d$, $d\in \mathbb{N}_0$. This latter process is constructed such that, starting at $X_0=0$, one has $X_1\sim \pi$. Typically, the drift of the diffusion is intractable and, even if it were not, exact sampling of the associated diffusion is not possible. As a result, \cite{sf_orig,jiao} consider a stochastic Euler-Maruyama scheme that allows the development of biased estimators for expectations w.r.t.~$\pi$. We show that for this methodology to achieve a mean square error of $\mathcal{O}(\epsilon^2)$, for arbitrary $\epsilon>0$, the associated cost is $\mathcal{O}(\epsilon^{-5})$. We then introduce an alternative approach that provides unbiased estimates of expectations w.r.t.~$\pi$, that is, it does not suffer from the time discretization bias or the bias related with the approximation of the drift function. We prove that to achieve a mean square error of $\mathcal{O}(\epsilon^2)$, the associated cost is, with high probability, $\mathcal{O}(\epsilon^{-2}|\log(\epsilon)|^{2+\delta})$, for any $\delta>0$. We implement our method on several examples including Bayesian inverse problems