This paper introduces an open-ended sequential algorithm for computing the p-value of a test using Monte Carlo simulation. It guarantees that the resampling risk, the probability of a different decision than the one based on the theoretical p-value, is uniformly bounded by an arbitrarily small constant. Previously suggested sequential or non-sequential algorithms, using a bounded sample size, do not have this property. Although the algorithm is open-ended, the expected number of steps is finite, except when the p-value is on the threshold between rejecting and not rejecting. The algorithm is suitable as standard for implementing tests that require (re-)sampling. It can also be used in other situations: to check whether a test is conservative, iteratively to implement double bootstrap tests, and to determine the sample size required for a certain power.
Sequential Monte Carlo (SMC) methods are a class of techniques to sample approximately from any sequence of probability distributions using a combination of importance sampling and resampling steps. This paper is concerned with the convergence analysis of a class of SMC methods where the times at which resampling occurs are computed online using criteria such as the effective sample size. This is a popular approach amongst practitioners but there are very few convergence results available for these methods. By combining semigroup techniques with an original coupling argument, we obtain functio…
Sequential Monte Carlo (SMC) algorithms were originally designed for estimating intractable conditional expectations within state-space models, but are now routinely used to generate approximate samples in the context of general-purpose Bayesian inference. In particular, SMC algorithms are often used as subroutines within larger Monte Carlo schemes, and in this context, the demands placed on SMC are different: control of mean-squared error is insufficient---one needs to control the divergence from the target distribution directly. Towards this goal, we introduce the conditional adaptive resamp…
Sequential Monte Carlo (SMC), also known as particle filters, has been widely accepted as a powerful computational tool for making inference with dynamical systems. A key step in SMC is resampling, which plays the role of steering the algorithm towards the future dynamics. Several strategies have been proposed and used in practice, including multinomial resampling, residual resampling (Liu and Chen 1998), optimal resampling (Fearnhead and Clifford 2003), stratified resampling (Kitagawa 1996), and optimal transport resampling (Reich 2013). We show that, in the one dimensional case, optimal tran…
Sequential importance sampling algorithms have been defined to estimate likelihoods in models of ancestral population processes. However, these algorithms are based on features of the models with constant population size, and become inefficient when the population size varies in time, making likelihood-based inferences difficult in many demographic situations. In this work, we modify a previous sequential importance sampling algorithm to improve the efficiency of the likelihood estimation. Our procedure is still based on features of the model with constant size, but uses a resampling technique…
Sequential Monte Carlo (SMC) methods are a class of Monte Carlo methods that are used to obtain random samples of a high dimensional random variable in a sequential fashion. Many problems encountered in applications often involve different types of constraints. These constraints can make the problem much more challenging. In this paper, we formulate a general framework of using SMC for constrained sampling problems based on forward and backward pilot resampling strategies. We review some existing methods under the framework and develop several new algorithms. It is noted that all information o…
Sequential Monte Carlo algorithms, or Particle Filters, are Bayesian filtering algorithms which propagate in time a discrete and random approximation of the a posteriori distribution of interest. Such algorithms are based on Importance Sampling with a bootstrap resampling step which aims at struggling against weights degeneracy. However, in some situations (informative measurements, high dimensional model), the resampling step can prove inefficient. In this paper, we revisit the fundamental resampling mechanism which leads us back to Rubin's static resampling mechanism. We propose an alternati…
This paper brings explicit considerations of distributed computing architectures and data structures into the rigorous design of Sequential Monte Carlo (SMC) methods. A theoretical result established recently by the authors shows that adapting interaction between particles to suitably control the Effective Sample Size (ESS) is sufficient to guarantee stability of SMC algorithms. Our objective is to leverage this result and devise algorithms which are thus guaranteed to work well in a distributed setting. We make three main contributions to achieve this. Firstly, we study mathematical propertie…
Among Sequential Monte Carlo (SMC) methods,Sampling Importance Resampling (SIR) algorithms are based on Importance Sampling (IS) and on some resampling-based)rejuvenation algorithm which aims at fighting against weight degeneracy. However %whichever the resampling technique used this mechanism tends to be insufficient when applied to informative or high-dimensional models. In this paper we revisit the rejuvenation mechanism and propose a class of parameterized SIR-based solutions which enable to adjust the tradeoff between computational cost and statistical performances.
We present simple conditions under which the limiting genealogical process associated with a class of interacting particle systems with non-neutral selection mechanisms, as the number of particles grows, is a time-rescaled Kingman coalescent. Sequential Monte Carlo algorithms are popular methods for approximating integrals in problems such as non-linear filtering and smoothing which employ this type of particle system. Their performance depends strongly on the properties of the induced genealogical process. We verify the conditions of our main result for standard sequential Monte Carlo algorit…
Resampling is a standard step in particle filters and more generally sequential Monte Carlo methods. We present an algorithm, called chopthin, for resampling weighted particles. In contrast to standard resampling methods the algorithm does not produce a set of equally weighted particles; instead it merely enforces an upper bound on the ratio between the weights. Simulation studies show that the chopthin algorithm consistently outperforms standard resampling methods. The algorithms chops up particles with large weight and thins out particles with low weight, hence its name. It implicitly guaran…
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…
This paper concerns the use of sequential Monte Carlo methods (SMC) for smoothing in general state space models. A well-known problem when applying the standard SMC technique in the smoothing mode is that the resampling mechanism introduces degeneracy of the approximation in the path space. However, when performing maximum likelihood estimation via the EM algorithm, all functionals involved are of additive form for a large subclass of models. To cope with the problem in this case, a modification of the standard method (based on a technique proposed by Kitagawa and Sato) is suggested. Our algor…
We introduce a new version of particle filter in which the number of "children" of a particle at a given time has a Poisson distribution. As a result, the number of particles is random and varies with time. An advantage of this scheme is that descendants of different particles can evolve independently. It makes easy to parallelize computations. Moreover, particle filter with Poisson resampling is readily adapted to the case when a hidden process is a continuous time, piecewise deterministic semi-Markov process. We show that the basic techniques of particle MCMC, namely particle independent Met…
We consider particle filters with weakly informative observations (or `potentials') relative to the latent state dynamics. The particular focus of this work is on particle filters to approximate time-discretisations of continuous-time Feynman--Kac path integral models -- a scenario that naturally arises when addressing filtering and smoothing problems in continuous time -- but our findings are indicative about weakly informative settings beyond this context too. We study the performance of different resampling schemes, such as systematic resampling, SSP (Srinivasan sampling process) and strati…
Based on the principles of importance sampling and resampling, sequential Monte Carlo (SMC) encompasses a large set of powerful techniques dealing with complex stochastic dynamic systems. Many of these systems possess strong memory, with which future information can help sharpen the inference about the current state. By providing theoretical justification of several existing algorithms and introducing several new ones, we study systematically how to construct efficient SMC algorithms to take advantage of the "future" information without creating a substantially high computational burden. The m…
We introduce a general form of sequential Monte Carlo algorithm defined in terms of a parameterized resampling mechanism. We find that a suitably generalized notion of the Effective Sample Size (ESS), widely used to monitor algorithm degeneracy, appears naturally in a study of its convergence properties. We are then able to phrase sufficient conditions for time-uniform convergence in terms of algorithmic control of the ESS, in turn achievable by adaptively modulating the interaction between particles. This leads us to suggest novel algorithms which are, in senses to be made precise, provably s…
Particle filtering is a numerical Bayesian technique that has great potential for solving sequential estimation problems involving non-linear and non-Gaussian models. Since the estimation accuracy achieved by particle filters improves as the number of particles increases, it is natural to consider as many particles as possible. MapReduce is a generic programming model that makes it possible to scale a wide variety of algorithms to Big data. However, despite the application of particle filters across many domains, little attention has been devoted to implementing particle filters using MapReduc…
Modern parallel computing devices, such as the graphics processing unit (GPU), have gained significant traction in scientific and statistical computing. They are particularly well-suited to data-parallel algorithms such as the particle filter, or more generally Sequential Monte Carlo (SMC), which are increasingly used in statistical inference. SMC methods carry a set of weighted particles through repeated propagation, weighting and resampling steps. The propagation and weighting steps are straightforward to parallelise, as they require only independent operations on each particle. The resampli…
We develop a novel parallel resampling algorithm for fully parallelized particle filters, which is designed with GPUs (graphics processing units) or similar parallel computing devices in mind. With our new algorithm, a full cycle of particle filtering (computing the value of the likelihood for each particle, constructing the cumulative distribution function (CDF) for resampling, resampling the particles with the CDF, and propagating new particles for the next cycle) can be executed in a massively and completely parallel manner. One of the advantages of our algorithm is that every single numeri…
We propose two new Bayesian smoothing methods for general state-space models with unknown parameters. The first approach is based on the particle learning and smoothing algorithm, but with an adjustment in the backward resampling weights. The second is a new method combining sequential parameter learning and smoothing algorithms for general state-space models. This method is straightforward but effective, and we find it is the best existing Sequential Monte Carlo algorithm to solve the joint Bayesian smoothing problem. We first illustrate the methods on three benchmark models using simulated d…
Particle filters are key algorithms for object tracking under non-linear, non-Gaussian dynamics. The high computational cost of particle filters, however, hampers their applicability in cases where the likelihood model is costly to evaluate, or where large numbers of particles are required to represent the posterior. We introduce the approximate sequential importance sampling/resampling (ASIR) algorithm, which aims at reducing the cost of traditional particle filters by approximating the likelihood with a mixture of uniform distributions over pre-defined cells or bins. The particles in each bi…
Sequential Monte Carlo methods are typically not straightforward to implement on parallel architectures. This is because standard resampling schemes involve communication between all particles. The $α$-sequential Monte Carlo method was proposed recently as a potential solution to this which limits communication between particles. This limited communication is controlled through a sequence of stochastic matrices known as $α$-matrices. We study the influence of the communication structure on the convergence and stability properties of the resulting algorithms. In particular, we quantitatively sh…
We investigate the properties of a sequential Monte Carlo method where the particle weight that appears in the algorithm is estimated by a positive, unbiased estimator. We present broadly-applicable convergence results, including a central limit theorem, and we discuss their relevance for applications in statistical physics. Using these results, we show that the resampling step reduces the impact of the randomness of the weights on the asymptotic variance of the estimator. In addition, we explore the limits of convergence of the sequential Monte Carlo method, with a focus on almost sure conver…
Sequential Monte Carlo (SMC) methods are widely used to draw samples from intractable target distributions. Particle degeneracy can hinder the use of SMC when the target distribution is highly constrained or multimodal. As a motivating application, we consider the problem of sampling protein structures from the Boltzmann distribution. This paper proposes a general SMC method that propagates multiple descendants for each particle, followed by resampling to maintain the desired number of particles. Simulation studies demonstrate the efficacy of the method for tackling the protein sampling proble…
University of Cambridge（剑桥大学）；Zuse Institute Berlin（柏林图灵研究所）；dida Datenschmiede GmbH（dida数据安全公司）；NVIDIA（NVIDIA公司）；Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院）；California Institute of Technology（加州理工学院）
We prove finite sample complexities for sequential Monte Carlo (SMC) algorithms which require only local mixing times of the associated Markov kernels. Our bounds are particularly useful when the target distribution is multimodal and global mixing of the Markov kernel is slow; in such cases our approach establishes the benefits of SMC over the corresponding Markov chain Monte Carlo (MCMC) estimator. The lack of global mixing is addressed by sequentially controlling the bias introduced by SMC resampling procedures. We apply these results to obtain complexity bounds for approximating expectation…
Multi-sample, importance-weighted variational autoencoders (IWAE) give tighter bounds and more accurate uncertainty estimates than variational autoencoders (VAE) trained with a standard single-sample objective. However, IWAEs scale poorly: as the latent dimensionality grows, they require exponentially many samples to retain the benefits of importance weighting. While sequential Monte-Carlo (SMC) can address this problem, it is prohibitively slow because the resampling step imposes sequential structure which cannot be parallelised, and moreover, resampling is non-differentiable which is problem…
We investigate the stability of a Sequential Monte Carlo (SMC) method applied to the problem of sampling from a target distribution on $\mathbb{R}^d$ for large $d$. It is well known that using a single importance sampling step one produces an approximation for the target that deteriorates as the dimension $d$ increases, unless the number of Monte Carlo samples $N$ increases at an exponential rate in $d$. We show that this degeneracy can be avoided by introducing a sequence of artificial targets, starting from a `simple' density and moving to the one of interest, using an SMC method to sample f…
Particle smoothers are SMC (Sequential Monte Carlo) algorithms designed to approximate the joint distribution of the states given observations from a state-space model. We propose dSMC (de-Sequentialized Monte Carlo), a new particle smoother that is able to process $T$ observations in $\mathcal{O}(\log T)$ time on parallel architecture. This compares favourably with standard particle smoothers, the complexity of which is linear in $T$. We derive $\mathcal{L}_p$ convergence results for dSMC, with an explicit upper bound, polynomial in $T$. We then discuss how to reduce the variance of the smoot…
We consider a statistical test whose p-value can only be approximated using Monte Carlo simulations. We are interested in deciding whether the p-value for an observed data set lies above or below a given threshold such as 5%. We want to ensure that the resampling risk, the probability of the (Monte Carlo) decision being different from the true decision, is uniformly bounded. This article introduces a simple open-ended method with this property, the confidence sequence method (CSM). We compare our approach to another algorithm, SIMCTEST, which also guarantees an (asymptotic) uniform bound on th…
Constraints can be interpreted in a broad sense as any kind of explicit restriction over the parameters. While some constraints are defined directly on the parameter space, when they are instead defined by known behaviour on the model, transformation of constraints into features on the parameter space may not be possible. Difficulties in sampling from the posterior distribution as a result of incorporation of constraints into the model is a common challenge leading to truncations in the parameter space and inefficient sampling algorithms. We propose a variant of sequential Monte Carlo algorith…
Two key ingredients to carry out inference on the copula of multivariate observations are the empirical copula process and an appropriate resampling scheme for the latter. Among the existing techniques used for i.i.d. observations, the multiplier bootstrap of Rémillard and Scaillet (J. Multivariate Anal. 100 (2009) 377-386) frequently appears to lead to inference procedures with the best finite-sample properties. Bücher and Ruppert (J. Multivariate Anal. 116 (2013) 208-229) recently proposed an extension of this technique to strictly stationary strongly mixing observations by adapting the depe…
We consider online prediction of a latent dynamic spatiotemporal process and estimation of the associated model parameters based on noisy data. The problem is motivated by the analysis of spatial data arriving in real-time and the current parameter estimates and predictions are updated using the new data at a fixed computational cost. Estimation and prediction is performed within an empirical Bayes framework with the aid of Markov chain Monte Carlo samples. Samples for the latent spatial field are generated using a sampling importance resampling algorithm with a skewed-normal proposal and for …
Annealed Importance Sampling (AIS) and its Sequential Monte Carlo (SMC) extensions are state-of-the-art methods for estimating normalizing constants of probability distributions. We propose here a novel Monte Carlo algorithm, Annealed Flow Transport (AFT), that builds upon AIS and SMC and combines them with normalizing flows (NFs) for improved performance. This method transports a set of particles using not only importance sampling (IS), Markov chain Monte Carlo (MCMC) and resampling steps - as in SMC, but also relies on NFs which are learned sequentially to push particles towards the successi…
KTH Royal Institute of Technology（瑞典皇家理工学院）；Science for Life Laboratory（生命科学实验室）
Over the years, sequential Monte Carlo (SMC) and, equivalently, particle filter (PF) theory has gained substantial attention from researchers. However, the performance of the resampling methodology, also known as offspring selection, has not advanced recently. We propose two deterministic offspring selection methods, which strive to minimize the Kullback-Leibler (KL) divergence and the total variation (TV) distance, respectively, between the particle distribution prior and subsequent to the offspring selection. By reducing the statistical distance between the selected offspring and the joint d…
Consider an irreducible, Harris recurrent Markov chain of transition kernel Π and invariant probability measure π. If Π satisfies a minorization condition, then the split chain allows the identification of regeneration times which may be exploited to obtain perfect samples from π. Unfortunately, many transition kernels associated with complex Markov chain Monte Carlo algorithms are analytically intractable, so establishing a minorization condition and simulating the split chain is challenging, if not impossible. For uniformly ergodic Markov chains with intractable transition kernels, we propos…
Computation of the probability that a random graph is connected is a challenging problem, so it is natural to turn to approximations such as Monte Carlo methods. We describe sequential importance resampling and splitting algorithms for the estimation of these probabilities. The importance sampling steps of these algorithms involve identifying vertices that must be present in order for the random graph to be connected, and conditioning on the corresponding events. We provide numerical results demonstrating the effectiveness of the proposed algorithm.
University of Reading（雷丁大学）；Universidad Nacional del Nordeste（东北国立大学）；CONICET（阿根廷国家科学技术研究委员会）；National Centre for Earth Observation（国家地球观测中心）
In this work, a novel sequential Monte Carlo filter is introduced which aims at efficient sampling of high-dimensional state spaces with a limited number of particles. Particles are pushed forward from the prior to the posterior density using a sequence of mappings that minimizes the Kullback-Leibler divergence between the posterior and the sequence of intermediate densities. The sequence of mappings represents a gradient flow. A key ingredient of the mappings is that they are embedded in a reproducing kernel Hilbert space, which allows for a practical and efficient algorithm. The embedding pr…
We show how to speed up Sequential Monte Carlo (SMC) for Bayesian inference in large data problems by data subsampling. SMC sequentially updates a cloud of particles through a sequence of distributions, beginning with a distribution that is easy to sample from such as the prior and ending with the posterior distribution. Each update of the particle cloud consists of three steps: reweighting, resampling, and moving. In the move step, each particle is moved using a Markov kernel; this is typically the most computationally expensive part, particularly when the dataset is large. It is crucial to h…
Bayesian methods are critical for quantifying the behaviors of systems. They capture our uncertainty about a system's behavior using probability distributions and update this understanding as new information becomes available. Probabilistic predictions that incorporate this uncertainty can then be made to evaluate system performance and make decisions. While Bayesian methods are very useful, they are often computationally intensive. This necessitates the development of more efficient algorithms. Here, we discuss a group of population Markov Chain Monte Carlo (MCMC) methods for Bayesian updatin…
We propose sequential Monte Carlo (SMC) methods for sampling the posterior distribution of state-space models under highly informative observation regimes, a situation in which standard SMC methods can perform poorly. A special case is simulating bridges between given initial and final values. The basic idea is to introduce a schedule of intermediate weighting and resampling times between observation times, which guide particles towards the final state. This can always be done for continuous-time models, and may be done for discrete-time models under sparse observation regimes; our main focus …
We consider the generic problem of performing sequential Bayesian inference in a state-space model with observation process y, state process x and fixed parameter theta. An idealized approach would be to apply the iterated batch importance sampling (IBIS) algorithm of Chopin (2002). This is a sequential Monte Carlo algorithm in the theta-dimension, that samples values of theta, reweights iteratively these values using the likelihood increments p(y_t|y_1:t-1, theta), and rejuvenates the theta-particles through a resampling step and a MCMC update step. In state-space models these likelihood incr…
The "backward simulation" of a stochastic process is defined as the stochastic dynamics that trace a time-reversed path from the target region to the initial configuration. If the probabilities calculated by the original simulation are easily restored from those obtained by backward dynamics, we can use it as a computational tool. It is shown that the naive approach to backward simulation does not work as expected. As a remedy, the Time Reverse Monte Carlo method (TRMC) based on the ideas of Sequential Importance Sampling (SIS) and Sequential Monte Carlo (SMC) is proposed and successfully test…
Sequential Monte Carlo techniques are useful for state estimation in non-linear, non-Gaussian dynamic models. These methods allow us to approximate the joint posterior distribution using sequential importance sampling. In this framework, the dimension of the target distribution grows with each time step, thus it is necessary to introduce some resampling steps to ensure that the estimates provided by the algorithm have a reasonable variance. In many applications, we are only interested in the marginal filtering distribution which is defined on a space of fixed dimension. We present a Sequential…
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…
The aim of the history matching method is to locate non-implausible regions of the parameter space of complex deterministic or stochastic models by matching model outputs with data. It does this via a series of waves where at each wave an emulator is fitted to a small number of training samples. An implausibility measure is defined which takes into account the closeness of simulated and observed outputs as well as emulator uncertainty. As the waves progress, the emulator becomes more accurate so that training samples are more concentrated on promising regions of the space and poorer parts of t…
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…
