arXiv subjects

Alexandros Beskos

Publications and source records attributed to Alexandros Beskos.

At least 19 recordsLinked to original sources

arXiv2026

Similarity-Driven Proposals for MCMC Algorithms on Discrete Spaces

Recent research has led to the development of MCMC algorithms with likelihood-informed proposals when targeting posterior distributions supported on discrete state spaces. Our work is placed within this field and puts forward a new MCMC methodology based upon similarity-driven proposals. Such proposals sway transitions towards states favored by the posterior via use of a data-driven measure of discrepancy between observations and the proposed model. Our approach can naturally cover classes of hierarchical models that involve both discrete variables and additional latent ones, without a requirement of integrating our the latter, in contrast to previous works in this field. The new algorithms are illustrated in simulation settings and in a involved real data scenario with a Dirichlet-Multinomial regression model.

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arXiv2026

Particle Filtering for a Class of State-Space Models with Low and Degenerate Observational Noise

We consider the discrete-time filtering problem in scenarios where the observation noise is low or degenerate. We focus on the case where the observation equation is a linear function of the state and the data involve additive noise. However, we place minimal assumptions on the hidden state process. For such a class of models we derive new particle filters (PFs) with the key property that their performance is robust to the size of the observation noise. As a consequence, the developed PFs are well-defined in the limiting case of degenerate observation noise. Indicatively, we prove (under assumptions) that the PF applied in this low noise setting inherits the properties of the PF used in the degenerate case. We extend our framework to the case where the hidden states are drawn from a diffusion process. In this scenario we develop new PFs which are robust to both low noise and fine levels of time discretization. We illustrate our algorithms numerically on several examples.

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arXiv2025

On a Reinforcement Learning Methodology for Epidemic Control, with application to COVID-19

This paper presents a real time, data driven decision support framework for epidemic control. We combine a compartmental epidemic model with sequential Bayesian inference and reinforcement learning (RL) controllers that adaptively choose intervention levels to balance disease burden, such as intensive care unit (ICU) load, against socio economic costs. We construct a context specific cost function using empirical experiments and expert feedback. We study two RL policies: an ICU threshold rule computed via Monte Carlo grid search, and a policy based on a posterior averaged Q learning agent. We validate the framework by fitting the epidemic model to publicly available ICU occupancy data from the COVID 19 pandemic in England and then generating counterfactual roll out scenarios under each RL controller, which allows us to compare the RL policies to the historical government strategy. Over a 300 day period and for a range of cost parameters, both controllers substantially reduce ICU burden relative to the observed interventions, illustrating how Bayesian sequential learning combined with RL can support the design of epidemic control policies.

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arXiv2025

Sequential Markov Chain Monte Carlo for Filtering of State-Space Models with Low or Degenerate Observation Noise

We consider the discrete-time filtering problem in scenarios where the observation noise is degenerate or low. More precisely, one is given access to a discrete time observation sequence which at any time $k$ depends only on the state of an unobserved Markov chain. We specifically assume that the functional relationship between observations and hidden Markov chain has either degenerate or low noise. In this article, under suitable assumptions, we derive the filtering density and its recursions for this class of problems on a specific sequence of manifolds defined through the observation function. We then design sequential Markov chain Monte Carlo methods to approximate the filter serially in time. For a certain linear observation model, we show that using sequential Markov chain Monte Carlo for low noise will converge as the noise disappears to that of using sequential Markov chain Monte Carlo for degenerate noise. We illustrate the performance of our methodology on several challenging stochastic models arising in statistics and applied mathematics.

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arXiv2025

Parameter Estimation for Weakly Interacting Hypoelliptic Diffusions

We study parameter estimation for interacting particle systems (IPSs) consisting of $N$ weakly interacting multivariate hypoelliptic SDEs. We propose a locally Gaussian approximation of the transition dynamics, carefully designed to address the degenerate structure of the noise (diffusion matrix), thus leading to the formation of a well-defined full likelihood. Our approach permits carrying out statistical inference for a wide class of hypoelliptic IPSs that are not covered by recent works as the latter rely on the Euler-Maruyama scheme. We analyze a contrast estimator based on the developed likelihood with $n$ high-frequency particle observations over a fixed period $[0,T]$ and show its asymptotic normality as $n, N \to \infty$ with a requirement that the step-size $\Delta_n = T/n$ is such that $N\Delta_n\rightarrow 0$, assuming that all particle coordinates (e.g.~position and velocity) are observed. In practical situations where only partial observations (e.g. particle positions but not velocities) are available, the proposed locally Gaussian approximation offers greater flexibility for inference, when combined with established Bayesian techniques. In particular, unlike the Euler-Maruyama-based approaches, we do not have to impose restrictive structures on the hypoelliptic IPSs. We present numerical experiments that illustrate the effectiveness of our approach, both with complete and partial particle observations.

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arXiv2025

A Closed-Form Transition Density Expansion for Elliptic and Hypo-Elliptic SDEs

We introduce a closed-form expansion for the transition density of elliptic and hypo-elliptic multivariate Stochastic Differential Equations (SDEs), over a period $\Delta\in (0,1)$, in terms of powers of $\Delta^{j/2}$, $j\ge 0$. Our methodology provides approximations of the transition density, easily evaluated via any software that performs symbolic calculations. A major part of the paper is devoted to an analytical control of the remainder in our expansion for fixed $\Delta\in(0,1)$. The obtained error bounds validate theoretically the methodology, by characterising the size of the distance from the true value. It is the first time that such a closed-form expansion becomes available for the important class of hypo-elliptic SDEs, to the best of our knowledge. For elliptic SDEs, closed-form expansions are available, with some works identifying the size of the error for fixed $\Delta$, as per our contribution. Our methodology allows for a uniform treatment of elliptic and hypo-elliptic SDEs, when earlier works are intrinsically restricted to an elliptic setting. We show numerical applications highlighting the effectiveness of our method, by carrying out parameter inference for hypo-elliptic SDEs that do not satisfy stated conditions. The latter are sufficient for controlling the remainder terms, but the closed-form expansion itself is applicable in general settings.

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arXiv2024

Graph of Graphs: From Nodes to Supernodes in Graphical Models

High-dimensional data analysis typically focuses on low-dimensional structure, often to aid interpretation and computational efficiency. Graphical models provide a powerful methodology for learning the conditional independence structure in multivariate data by representing variables as nodes and dependencies as edges. Inference is often focused on individual edges in the latent graph. Nonetheless, there is increasing interest in determining more complex structures, such as communities of nodes, for multiple reasons, including more effective information retrieval and better interpretability. In this work, we propose a hierarchical graphical model where we first cluster nodes and then, at the higher level, investigate the relationships among groups of nodes. Specifically, nodes are partitioned into supernodes with a data-coherent size-biased tessellation prior which combines ideas from Bayesian nonparametrics and Voronoi tessellations. This construct also allows accounting for the dependence of nodes within supernodes. At the higher level, dependence structure among supernodes is modeled through a Gaussian graphical model, where the focus of inference is on superedges. We provide theoretical justification for our modeling choices. We design tailored Markov chain Monte Carlo schemes, which also enable parallel computations. We demonstrate the effectiveness of our approach for large-scale structure learning in simulations and a transcriptomics application.

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arXiv2024

Parameter Inference for Hypo-Elliptic Diffusions under a Weak Design Condition

We address the problem of parameter estimation for degenerate diffusion processes defined via the solution of Stochastic Differential Equations (SDEs) with diffusion matrix that is not full-rank. For this class of hypo-elliptic diffusions recent works have proposed contrast estimators that are asymptotically normal, provided that the step-size in-between observations $Δ=Δ_n$ and their total number $n$ satisfy $n \to \infty$, $n Δ_n \to \infty$, $Δ_n \to 0$, and additionally $Δ_n = o (n^{-1/2})$. This latter restriction places a requirement for a so-called `rapidly increasing experimental design'. In this paper, we overcome this limitation and develop a general contrast estimator satisfying asymptotic normality under the weaker design condition $Δ_n = o(n^{-1/p})$ for general $p \ge 2$. Such a result has been obtained for elliptic SDEs in the literature, but its derivation in a hypo-elliptic setting is highly non-trivial. We provide numerical results to illustrate the advantages of the developed theory.

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arXiv2024

Particle Based Inference for Continuous-Discrete State Space Models

This article develops a methodology allowing application of the complete machinery of particle-based inference methods upon the class of continuous-discrete State Space Models (CD-SSMs). Such models correspond to a latent continuous-time It\^o diffusion process which is observed with noise at discrete time instances. Due to the continuous-time nature of the hidden signal, standard Feynman-Kac formulations and their accompanying particle-based approximations have to overcome several challenges, arising mainly due to the following considerations: (i) finite-time transition densities of the signal are typically intractable; (ii) ancestors of sampled signals are determined w.p.~1, thus cannot be resampled; (iii) diffusivity parameters given a sampled signal yield Dirac distributions. We overcome all above issues by introducing a framework based on carefully designed path proposals and reparameterisations thereof. That is, we obtain new expressions for the Feynman-Kac model that accommodate the effects of a continuous-time signal and overcome induced degeneracies. The constructed formulations enable use of the full range of particle-based algorithms for CD-SSMs: for filtering/smoothing and parameter inference, whether online or offline. Our framework is compatible with guided proposals in the filtering steps that are essential for efficient algorithmic performance in the presence of informative observations or in higher dimensions, and is applicable for a very general class of CD-SSMs, including the case when the signal is modelled as a hypo-elliptic diffusion. We incorporate our methods into an established probabilistic programming package and present several numerical examples.

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arXiv2024

Parameter Inference for Degenerate Diffusion Processes

We study parametric inference for ergodic diffusion processes with a degenerate diffusion matrix. Existing research focuses on a particular class of hypo-elliptic SDEs, with components split into `rough'/`smooth' and noise from rough components propagating directly onto smooth ones, but some critical model classes arising in applications have yet to be explored. We aim to cover this gap, thus analyse the highly degenerate class of SDEs, where components split into further sub-groups. Such models include e.g. the notable case of generalised Langevin equations. We propose a tailored time-discretisation scheme and provide asymptotic results supporting our scheme in the context of high-frequency, full observations. The proposed discretisation scheme is applicable in much more general data regimes and is shown to overcome biases via simulation studies also in the practical case when only a smooth component is observed. Joint consideration of our study for highly degenerate SDEs and existing research provides a general `recipe' for the development of time-discretisation schemes to be used within statistical methods for general classes of hypo-elliptic SDEs.

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arXiv2024

Antithetic Multilevel Methods for Elliptic and Hypo-Elliptic Diffusions with Applications

We present a new antithetic multilevel Monte Carlo (MLMC) method for the estimation of expectations with respect to laws of diffusion processes that can be elliptic or hypo-elliptic. In particular, we consider the case where one has to resort to time discretization of the diffusion and numerical simulation of such schemes. Inspired by recent works, we introduce a new MLMC estimator of expectations, which does not require any L\'evy area simulation and has a strong error of order 2 and a weak error of order 2. We then show how this approach can be used in the context of the filtering problem associated to partially observed diffusions with discrete time observations. We illustrate that in numerical simulations our new approaches provide efficiency gains for several problems, particularly when the diffusion process is hypo-elliptic, relative to some existing methods.

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arXiv2024

Sequential Markov Chain Monte Carlo for Lagrangian Data Assimilation with Applications to Unknown Data Locations

We consider a class of high-dimensional spatial filtering problems, where the spatial locations of observations are unknown and driven by the partially observed hidden signal. This problem is exceptionally challenging as not only is high-dimensional, but the model for the signal yields longer-range time dependencies through the observation locations. Motivated by this model we revisit a lesser-known and \emph{provably convergent} computational methodology from \cite{berzuini, cent, martin} that uses sequential Markov Chain Monte Carlo (MCMC) chains. We extend this methodology for data filtering problems with unknown observation locations. We benchmark our algorithms on Linear Gaussian state space models against competing ensemble methods and demonstrate a significant improvement in both execution speed and accuracy. Finally, we implement a realistic case study on a high-dimensional rotating shallow water model (of about $10^4-10^5$ dimensions) with real and synthetic data. The data is provided by the National Oceanic and Atmospheric Administration (NOAA) and contains observations from ocean drifters in a domain of the Atlantic Ocean restricted to the longitude and latitude intervals $[-51^{\circ}, -41^{\circ}]$, $[17^{\circ}, 27^{\circ}]$ respectively.

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arXiv2024

Parameter Estimation with Increased Precision for Elliptic and Hypo-elliptic Diffusions

This work aims at making a comprehensive contribution in the general area of parametric inference for discretely observed diffusion processes. Established approaches for likelihood-based estimation invoke a time-discretisation scheme for the approximation of the intractable transition dynamics of the Stochastic Differential Equation (SDE) model over finite time periods. The scheme is applied for a step-size that is either user-selected or determined by the data. Recent research has highlighted the critical ef-fect of the choice of numerical scheme on the behaviour of derived parameter estimates in the setting of hypo-elliptic SDEs. In brief, in our work, first, we develop two weak second order sampling schemes (to cover both hypo-elliptic and elliptic SDEs) and produce a small time expansion for the density of the schemes to form a proxy for the true intractable SDE transition density. Then, we establish a collection of analytic results for likelihood-based parameter estimates obtained via the formed proxies, thus providing a theoretical framework that showcases advantages from the use of the developed methodology for SDE calibration. We present numerical results from carrying out classical or Bayesian inference, for both elliptic and hypo-elliptic SDEs.

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arXiv2023

Unbiased approximation of posteriors via coupled particle Markov chain Monte Carlo

Markov chain Monte Carlo (MCMC) is a powerful methodology for the approximation of posterior distributions. However, the iterative nature of MCMC does not naturally facilitate its use with modern highly parallel computation on HPC and cloud environments. Another concern is the identification of the bias and Monte Carlo error of produced averages. The above have prompted the recent development of fully ('embarrassingly') parallel unbiased Monte Carlo methodology based on coupling of MCMC algorithms. A caveat is that formulation of effective coupling is typically not trivial and requires model-specific technical effort. We propose coupling of MCMC chains deriving from sequential Monte Carlo (SMC) by considering adaptive SMC methods in combination with recent advances in unbiased estimation for state-space models. Coupling is then achieved at the SMC level and is, in principle, not problem-specific. The resulting methodology enjoys desirable theoretical properties. A central motivation is to extend unbiased MCMC to more challenging targets compared to the ones typically considered in the relevant literature. We illustrate the effectiveness of the algorithm via application to two complex statistical models: (i) horseshoe regression; (ii) Gaussian graphical models.

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arXiv2023

The G-Wishart Weighted Proposal Algorithm: Efficient Posterior Computation for Gaussian Graphical Models

Gaussian graphical models can capture complex dependency structures among variables. For such models, Bayesian inference is attractive as it provides principled ways to incorporate prior information and to quantify uncertainty through the posterior distribution. However, posterior computation under the conjugate G-Wishart prior distribution on the precision matrix is expensive for general non-decomposable graphs. We therefore propose a new Markov chain Monte Carlo (MCMC) method named the G-Wishart weighted proposal algorithm (WWA). WWA's distinctive features include delayed acceptance MCMC, Gibbs updates for the precision matrix and an informed proposal distribution on the graph space that enables embarrassingly parallel computations. Compared to existing approaches, WWA reduces the frequency of the relatively expensive sampling from the G-Wishart distribution. This results in faster MCMC convergence, improved MCMC mixing and reduced computing time. Numerical studies on simulated and real data show that WWA provides a more efficient tool for posterior inference than competing state-of-the-art MCMC algorithms.

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arXiv2022

A Bayesian framework for genome-wide inference of DNA methylation levels

DNA methylation is an important epigenetic mark that has been studied extensively for its regulatory role in biological processes and diseases. WGBS allows for genome-wide measurements of DNA methylation up to single-base resolutions, yet poses challenges in identifying significantly different methylation patterns across distinct biological conditions. We propose a novel methylome change-point model which describes the joint dynamics of methylation regimes of a case and a control group and benefits from taking into account the information of neighbouring methylation sites among all available samples. We also devise particle filtering and smoothing algorithms to perform efficient inference of the latent methylation patterns. We illustrate that our approach can detect and test for very flexible differential methylation signatures with high power while controlling Type-I error measures.

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arXiv2022

Bayesian Learning of Graph Substructures

Graphical models provide a powerful methodology for learning the conditional independence structure in multivariate data. Inference is often focused on estimating individual edges in the latent graph. Nonetheless, there is increasing interest in inferring more complex structures, such as communities, for multiple reasons, including more effective information retrieval and better interpretability. Stochastic blockmodels offer a powerful tool to detect such structure in a network. We thus propose to exploit advances in random graph theory and embed them within the graphical models framework. A consequence of this approach is the propagation of the uncertainty in graph estimation to large-scale structure learning. We consider Bayesian nonparametric stochastic blockmodels as priors on the graph. We extend such models to consider clique-based blocks and to multiple graph settings introducing a novel prior process based on a Dependent Dirichlet process. Moreover, we devise a tailored computation strategy of Bayes factors for block structure based on the Savage-Dickey ratio to test for presence of larger structure in a graph. We demonstrate our approach in simulations as well as on real data applications in finance and transcriptomics.

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arXiv2022

Unbiased Estimation using a Class of Diffusion Processes

We study the problem of unbiased estimation of expectations with respect to (w.r.t.) $π$ 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 Schrödinger-Föllmer 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 $X_1\sim π$. 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.~$π$. We show that for this methodology to achieve a mean square error of $\mathcal{O}(ε^2)$, for arbitrary $ε>0$, the associated cost is $\mathcal{O}(ε^{-5})$. We then introduce an alternative approach that provides unbiased estimates of expectations w.r.t.~$π$, 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 $\mathcal{O}(ε^2)$, the associated cost is, with high probability, $\mathcal{O}(ε^{-2}|\log(ε)|^{2+δ})$, for any $δ>0$. We implement our method on several examples including Bayesian inverse problems.

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