Many real-world problems require one to estimate parameters of interest, in a Bayesian framework, from data that are collected sequentially in time. Conventional methods for sampling from posterior distributions, such as {Markov Chain Monte Carlo} can not efficiently address such problems as they do not take advantage of the data's sequential structure. To this end, sequential methods which seek to update the posterior distribution whenever a new collection of data become available are often used to solve these types of problems. Two popular choices of sequential method are the Ensemble Kalman filter (EnKF) and the sequential Monte Carlo sampler (SMCS). While EnKF only computes a Gaussian approximation of the posterior distribution, SMCS can draw samples directly from the posterior. Its performance, however, depends critically upon the kernels that are used. In this work, we present a method that constructs the kernels of SMCS using an EnKF formulation, and we demonstrate the performance of the method with numerical examples.
Statisticians often use Monte Carlo methods to approximate probability distributions, primarily with Markov chain Monte Carlo and importance sampling. Sequential Monte Carlo samplers are a class of algorithms that combine both techniques to approximate distributions of interest and their normalizing constants. These samplers originate from particle filtering for state space models and have become general and scalable sampling techniques. This article describes sequential Monte Carlo samplers and their possible implementations, arguing that they remain under-used in statistics, despite their ab…
In this paper, we provide bounds on the asymptotic variance for a class of sequential Monte Carlo (SMC) samplers designed for approximating multimodal distributions. Such methods combine standard SMC methods and Markov chain Monte Carlo (MCMC) kernels. Our bounds improve upon previous results, and unlike some earlier work, they also apply in the case when the MCMC kernels can move between the modes. We apply our results to the Potts model from statistical physics. In this case, the problem of sharp peaks is encountered. Earlier methods, such as parallel tempering, are only able to sample from …
We present a sequential Monte Carlo sampler variant of the partial rejection control algorithm, and show that this variant can be considered as a sequential Monte Carlo sampler with a modified mutation kernel. We prove that the new sampler can reduce the variance of the incremental importance weights when compared with standard sequential Monte Carlo samplers. We provide a study of theoretical properties of the new algorithm, and make connections with some existing algorithms. Finally, the sampler is adapted for application under the challenging "likelihood free," approximate Bayesian computat…
This paper addresses finite sample stability properties of sequential Monte Carlo methods for approximating sequences of probability distributions. The results presented herein are applicable in the scenario where the start and end distributions in the sequence are fixed and the number of intermediate steps is a parameter of the algorithm. Under assumptions which hold on non-compact spaces, it is shown that the effect of the initial distribution decays exponentially fast in the number of intermediate steps and the corresponding stochastic error is stable in \mathbb{L}_{p} norm.
This Chapter, "ABC Samplers", is to appear in the forthcoming Handbook of Approximate Bayesian Computation (2018). It details the main ideas and algorithms used to sample from the ABC approximation to the posterior distribution, including methods based on rejection/importance sampling, MCMC and sequential Monte Carlo.
In this paper we assume a multivariate risk model has been developed for a portfolio and its capital derived as a homogeneous risk measure. The Euler (or gradient) principle, then, states that the capital to be allocated to each component of the portfolio has to be calculated as an expectation conditional to a rare event, which can be challenging to evaluate in practice. We exploit the copula-dependence within the portfolio risks to design a Sequential Monte Carlo Samplers based estimate to the marginal conditional expectations involved in the problem, showing its efficiency through a series o…
By facilitating the generation of samples from arbitrary probability distributions, Markov Chain Monte Carlo (MCMC) is, arguably, \emph{the} tool for the evaluation of Bayesian inference problems that yield non-standard posterior distributions. In recent years, however, it has become apparent that Sequential Monte Carlo (SMC) samplers have the potential to outperform MCMC in a number of ways. SMC samplers are better suited to highly parallel computing architectures and also feature various tuning parameters that are not available to MCMC. One such parameter - the `L-kernel' - is a user-defined…
Sequential Monte Carlo (SMC) methods are not only a popular tool in the analysis of state space models, but offer an alternative to MCMC in situations where Bayesian inference must proceed via simulation. This paper introduces a new SMC method that uses adaptive MCMC kernels for particle dynamics. The proposed algorithm features an online stochastic optimization procedure to select the best MCMC kernel and simultaneously learn optimal tuning parameters. Theoretical results are presented that justify the approach and give guidance on how it should be implemented. Empirical results, based on ana…
In many real-world engineering systems, the performance or reliability of the system is characterised by a scalar parameter. The distribution of this performance parameter is important in many uncertainty quantification problems, ranging from risk management to utility optimisation. In practice, this distribution usually cannot be derived analytically and has to be obtained numerically by simulations. To this end, standard Monte Carlo simulations are often used, however, they cannot efficiently reconstruct the tail of the distribution which is essential in many applications. One possible remed…
A key limitation of sampling algorithms for approximate inference is that it is difficult to quantify their approximation error. Widely used sampling schemes, such as sequential importance sampling with resampling and Metropolis-Hastings, produce output samples drawn from a distribution that may be far from the target posterior distribution. This paper shows how to upper-bound the symmetric KL divergence between the output distribution of a broad class of sequential Monte Carlo (SMC) samplers and their target posterior distributions, subject to assumptions about the accuracy of a separate gold…
Particle filtering methods are widely applied in sequential state estimation within nonlinear non-Gaussian state space model. However, the traditional particle filtering methods suffer the weight degeneracy in the high-dimensional state space model. Currently, there are many methods to improve the performance of particle filtering in high-dimensional state space model. Among these, the more advanced method is to construct the Sequential Makov chian Monte Carlo (SMCMC) framework by implementing the Composite Metropolis-Hasting (MH) Kernel. In this paper, we proposed to discrete the Zig-Zag Samp…
Sequential Monte Carlo (SMC) samplers form an attractive alternative to MCMC for Bayesian computation. However, their performance depends strongly on the Markov kernels used to rejuvenate particles. We discuss how to calibrate automatically (using the current particles) Hamiltonian Monte Carlo kernels within SMC. To do so, we build upon the adaptive SMC approach of Fearnhead and Taylor (2013), and we also suggest alternative methods. We illustrate the advantages of using HMC kernels within an SMC sampler via an extensive numerical study.
Sequential Monte Carlo samplers represent a compelling approach to posterior inference in Bayesian models, due to being parallelisable and providing an unbiased estimate of the posterior normalising constant. In this work, we significantly accelerate sequential Monte Carlo samplers by adopting the L-BFGS Hessian approximation which represents the state-of-the-art in full-batch optimisation techniques. The L-BFGS Hessian approximation has only linear complexity in the parameter dimension and requires no additional posterior or gradient evaluations. The resulting sequential Monte Carlo algorithm…
Multilevel Sequential Monte Carlo Samplers for Normalizing Constants
Center INRIA Bordeaux Sud-Ouest & Institut de Mathematiques de Bordeaux, Universite de Bordeaux I（波尔多南西INRIA中心与波尔多数学研究所，波尔多第一大学）；Department of Statistics & Applied Probability, National University of Singapore（新加坡国立大学统计与应用概率系）；Computer Science and Mathematics Division, Oak Ridge National Laboratory（橡树岭国家实验室计算机科学与数学部）
The likelihood-free sequential Approximate Bayesian Computation (ABC) algorithms, are increasingly popular inference tools for complex biological models. Such algorithms proceed by constructing a succession of probability distributions over the parameter space conditional upon the simulated data lying in an $ε$--ball around the observed data, for decreasing values of the threshold $ε$. While in theory, the distributions (starting from a suitably defined prior) will converge towards the unknown posterior as $ε$ tends to zero, the exact sequence of thresholds can impact upon the computational ef…
We investigate nonlinear state-space models without a closed-form transition density, and propose reformulating such models over their latent noise variables rather than their latent state variables. In doing so the tractable noise density emerges in place of the intractable transition density. For importance sampling methods such as the auxiliary particle filter, this enables importance weights to be computed where they could not be otherwise. As case studies we take two multivariate marine biogeochemical models and perform state and parameter estimation using the particle marginal Metropolis…
In this article we consider the approximation of expectations w.r.t. probability distributions associated to the solution of partial differential equations (PDEs); this scenario appears routinely in Bayesian inverse problems. In practice, one often has to solve the associated PDE numerically, using, for instance finite element methods and leading to a discretisation bias, with the step-size level $h_L$. In addition, the expectation cannot be computed analytically and one often resorts to Monte Carlo methods. In the context of this problem, it is known that the introduction of the multilevel Mo…
Multivariate probit models (MPM) have the appealing feature of capturing some of the dependence structure between the components of multidimensional binary responses. The key for the dependence modelling is the covariance matrix of an underlying latent multivariate Gaussian. Most approaches to MLE in multivariate probit regression rely on MCEM algorithms to avoid computationally intensive evaluations of multivariate normal orthant probabilities. As an alternative to the much used Gibbs sampler a new SMC sampler for truncated multivariate normals is proposed. The algorithm proceeds in two stage…
Incorporating the ChEES Criterion into Sequential Monte Carlo Samplers
Dept. of EEE, University of Liverpool, United Kingdom（电子工程系，利物浦大学，英国）；Intelligent Sensor-Actuator-Systems Laboratory (ISAS), Karlsruhe Institute of Technology, Germany（智能传感器-执行器系统实验室（ISAS），卡尔斯鲁厄理工学院，德国）
We explore a general framework in Markov chain Monte Carlo (MCMC) sampling where sequential proposals are tried as a candidate for the next state of the Markov chain. This sequential-proposal framework can be applied to various existing MCMC methods, including Metropolis-Hastings algorithms using random proposals and methods that use deterministic proposals such as Hamiltonian Monte Carlo (HMC) or the bouncy particle sampler. Sequential-proposal MCMC methods construct the same Markov chains as those constructed by the delayed rejection method under certain circumstances. In the context of HMC,…
We propose nested sequential Monte Carlo (NSMC), a methodology to sample from sequences of probability distributions, even where the random variables are high-dimensional. NSMC generalises the SMC framework by requiring only approximate, properly weighted, samples from the SMC proposal distribution, while still resulting in a correct SMC algorithm. Furthermore, NSMC can in itself be used to produce such properly weighted samples. Consequently, one NSMC sampler can be used to construct an efficient high-dimensional proposal distribution for another NSMC sampler, and this nesting of the algorith…
State space models (SSM) have been widely applied for the analysis and visualization of large sequential datasets. Sequential Monte Carlo (SMC) is a very popular particle-based method to sample latent states from intractable posteriors. However, SSM is significantly influenced by the choice of the proposal. Recently Hamiltonian Monte Carlo (HMC) sampling has shown success in many practical problems. In this paper, we propose an SMC augmented by HMC (HSMC) for inference and model learning of nonlinear SSM, which can exempt us from learning proposals and reduce the model complexity significantly…
We present a sequential Monte Carlo sampler algorithm for the Bayesian analysis of generalised linear mixed models (GLMMs). These models support a variety of interesting regression-type analyses, but performing inference is often extremely difficult, even when using the Bayesian approach combined with Markov chain Monte Carlo (MCMC). The Sequential Monte Carlo sampler (SMC) is a new and general method for producing samples from posterior distributions. In this article we demonstrate use of the SMC method for performing inference for GLMMs. We demonstrate the effectiveness of the method on both…
Given the complexity of modern cosmological parameter inference where we are faced with non-Gaussian data and noise, correlated systematics and multi-probe correlated data sets, the Approximate Bayesian Computation (ABC) method is a promising alternative to traditional Markov Chain Monte Carlo approaches in the case where the Likelihood is intractable or unknown. The ABC method is called "Likelihood free" as it avoids explicit evaluation of the Likelihood by using a forward model simulation of the data which can include systematics. We introduce astroABC, an open source ABC Sequential Monte Ca…
We consider Particle Gibbs (PG) as a tool for Bayesian analysis of non-linear non-Gaussian state-space models. PG is a Monte Carlo (MC) approximation of the standard Gibbs procedure which uses sequential MC (SMC) importance sampling inside the Gibbs procedure to update the latent and potentially high-dimensional state trajectories. We propose to combine PG with a generic and easily implementable SMC approach known as Particle Efficient Importance Sampling (PEIS). By using SMC importance sampling densities which are approximately fully globally adapted to the targeted density of the states, PEI…
Approximate Bayesian computation (ABC) is computationally intensive for complex model simulators. To exploit expensive simulations, data-resampling via bootstrapping can be employed to obtain many artificial datasets at little cost. However, when using this approach within ABC, the posterior variance is inflated, thus resulting in biased posterior inference. Here we use stratified Monte Carlo to considerably reduce the bias induced by data resampling. We also show empirically that it is possible to obtain reliable inference using a larger than usual ABC threshold. Finally, we show that with st…
Variational inference (VI) combined with Bayesian nonlinear filtering produces state-of-the-art results for latent time-series modeling. A body of recent work has focused on sequential Monte Carlo (SMC) and its variants, e.g., forward filtering backward simulation (FFBSi). Although these studies have succeeded, serious problems remain in particle degeneracy and biased gradient estimators. In this paper, we propose Ensemble Kalman Variational Objective (EnKO), a hybrid method of VI and the ensemble Kalman filter (EnKF), to infer state space models (SSMs). Our proposed method can efficiently ide…
This paper focuses on Sequential Monte Carlo approximations of smoothing distributions in conditionally linear and Gaussian state spaces. To reduce Monte Carlo variance of smoothers, it is typical in these models to use Rao-Blackwellization: particle approximation is used to sample sequences of hidden regimes while the Gaussian states are explicitly integrated conditional on the sequence of regimes and observations, using variants of the Kalman filter / smoother. The first successful attempt to use Rao-Blackwellization for smoothing extends the Bryson-Frazier smoother for Gaussian linear state…
Markov Chain Monte Carlo (MCMC) is a well-established family of algorithms which are primarily used in Bayesian statistics to sample from a target distribution when direct sampling is challenging. Single instances of MCMC methods are widely considered hard to parallelise in a problem-agnostic fashion and hence, unsuitable to meet both constraints of high accuracy and high throughput. Sequential Monte Carlo (SMC) Samplers can address the same problem, but are parallelisable: they share with Particle Filters the same key tasks and bottleneck. Although a rich literature already exists on MCMC met…
We propose approaches for testing implementations of Markov Chain Monte Carlo methods as well as of general Monte Carlo methods. Based on statistical hypothesis tests, these approaches can be used in a unit testing framework to, for example, check if individual steps in a Gibbs sampler or a reversible jump MCMC have the desired invariant distribution. Two exact tests for assessing whether a given Markov chain has a specified invariant distribution are discussed. These and other tests of Monte Carlo methods can be embedded into a sequential method that allows low expected effort if the simulati…
A standard way to move particles in a SMC sampler is to apply several steps of a MCMC (Markov chain Monte Carlo) kernel. Unfortunately, it is not clear how many steps need to be performed for optimal performance. In addition, the output of the intermediate steps are discarded and thus wasted somehow. We propose a new, waste-free SMC algorithm which uses the outputs of all these intermediate MCMC steps as particles. We establish that its output is consistent and asymptotically normal. We use the expression of the asymptotic variance to develop various insights on how to implement the algorithm …
In a recent paper Beskos et al (2011), the Sequential Monte Carlo (SMC) sampler introduced in Del Moral et al (2006), Neal (2001) has been shown to be asymptotically stable in the dimension of the state space d at a cost that is only polynomial in d, when N the number of Monte Carlo samples, is fixed. More precisely, it has been established that the effective sample size (ESS) of the ensuing (approximate) sample and the Monte Carlo error of fixed dimensional marginals will converge as $d$ grows, with a computational cost of $\mathcal{O}(Nd^2)$. In the present work, further results on SMC metho…
We present bounds for the finite sample error of sequential Monte Carlo samplers on static spaces. Our approach explicitly relates the performance of the algorithm to properties of the chosen sequence of distributions and mixing properties of the associated Markov kernels. This allows us to give the first finite sample comparison to other Monte Carlo schemes. We obtain bounds for the complexity of sequential Monte Carlo approximations for a variety of target distributions including finite spaces, product measures, and log-concave distributions including Bayesian logistic regression. The bounds…
This paper explores the application of methods from information geometry to the sequential Monte Carlo (SMC) sampler. In particular the Riemannian manifold Metropolis-adjusted Langevin algorithm (mMALA) is adapted for the transition kernels in SMC. Similar to its function in Markov chain Monte Carlo methods, the mMALA is a fully adaptable kernel which allows for efficient sampling of high-dimensional and highly correlated parameter spaces. We set up the theoretical framework for its use in SMC with a focus on the application to the problem of sequential Bayesian inference for dynamical systems…
We introduce interacting particle Markov chain Monte Carlo (iPMCMC), a PMCMC method based on an interacting pool of standard and conditional sequential Monte Carlo samplers. Like related methods, iPMCMC is a Markov chain Monte Carlo sampler on an extended space. We present empirical results that show significant improvements in mixing rates relative to both non-interacting PMCMC samplers, and a single PMCMC sampler with an equivalent memory and computational budget. An additional advantage of the iPMCMC method is that it is suitable for distributed and multi-core architectures.
Data assimilation is concerned with sequentially estimating a temporally-evolving state. This task, which arises in a wide range of scientific and engineering applications, is particularly challenging when the state is high-dimensional and the state-space dynamics are unknown. This paper introduces a machine learning framework for learning dynamical systems in data assimilation. Our auto-differentiable ensemble Kalman filters (AD-EnKFs) blend ensemble Kalman filters for state recovery with machine learning tools for learning the dynamics. In doing so, AD-EnKFs leverage the ability of ensemble …
In the case of a linear state space model, we implement an MCMC sampler with two phases. In the learning phase, a self-tuning sampler is used to learn the parameter mean and covariance structure. In the estimation phase, the parameter mean and covariance structure informs the proposed mechanism and is also used in a delayed-acceptance algorithm. Information on the resulting state of the system is given by a Gaussian mixture. In on-line mode, the algorithm is adaptive and uses a sliding window approach to accelerate sampling speed and to maintain appropriate acceptance rates. We apply the algor…
This paper introduces methodology for performing Bayesian inference sequentially on a sequence of posteriors on spaces of different dimensions. We show how this may be achieved through the use of sequential Monte Carlo (SMC) samplers (Del Moral et al., 2006, 2007), making use of the full flexibility of this framework in order that the method is computationally efficient. In particular, we introduce the innovation of using deterministic transformations to move particles effectively between target distributions with different dimensions. This approach, combined with adaptive methods, yields an e…
