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 algorithm can be done to an arbitrary degree. This allows us to consider complex and high-dimensional models using SMC. We show results that motivate the efficacy of our approach on several filtering problems with dimensions in the order of 100 to 1 000.
There is an increasing interest in estimating expectations outside of the classical inference framework, such as for models expressed as probabilistic programs. Many of these contexts call for some form of nested inference to be applied. In this paper, we analyse the behaviour of nested Monte Carlo (NMC) schemes, for which classical convergence proofs are insufficient. We give conditions under which NMC will converge, establish a rate of convergence, and provide empirical data that suggests that this rate is observable in practice. Finally, we prove that general-purpose nested inference scheme…
Sequential Monte Carlo (SMC) methods comprise one of the most successful approaches to approximate Bayesian filtering. However, SMC without good proposal distributions struggle in high dimensions. We propose nested sequential Monte Carlo (NSMC), a methodology that generalises the SMC framework by requiring only approximate, properly weighted, samples from the SMC proposal distribution, while still resulting in a correct SMC algorithm. This way we can exactly approximate the locally optimal proposal, and extend the class of models for which we can perform efficient inference using SMC. We show …
Computing the variance of a conditional expectation has often been of importance in uncertainty quantification. Sun et al. has introduced an unbiased nested Monte Carlo estimator, which they call $1\frac{1}{2}$-level simulation since the optimal inner-level sample size is bounded as the computational budget increases. In this letter we construct unbiased non-nested Monte Carlo estimators based on the so-called pick-freeze scheme due to Sobol'. An extension of our approach to compute higher order moments of a conditional expectation is also discussed.
Bayesian phylogenetic inference is often conducted via local or sequential search over topologies and branch lengths using algorithms such as random-walk Markov chain Monte Carlo (MCMC) or Combinatorial Sequential Monte Carlo (CSMC). However, when MCMC is used for evolutionary parameter learning, convergence requires long runs with inefficient exploration of the state space. We introduce Variational Combinatorial Sequential Monte Carlo (VCSMC), a powerful framework that establishes variational sequential search to learn distributions over intricate combinatorial structures. We then develop nes…
Regularizing nested Monte Carlo Sobol' index estimators to balance the trade-off between explorations and repetitions in global sensitivity analysis of stochastic models
Many problems in machine learning and statistics involve nested expectations and thus do not permit conventional Monte Carlo (MC) estimation. For such problems, one must nest estimators, such that terms in an outer estimator themselves involve calculation of a separate, nested, estimation. We investigate the statistical implications of nesting MC estimators, including cases of multiple levels of nesting, and establish the conditions under which they converge. We derive corresponding rates of convergence and provide empirical evidence that these rates are observed in practice. We further establ…
Many recent advances in large scale probabilistic inference rely on variational methods. The success of variational approaches depends on (i) formulating a flexible parametric family of distributions, and (ii) optimizing the parameters to find the member of this family that most closely approximates the exact posterior. In this paper we present a new approximating family of distributions, the variational sequential Monte Carlo (VSMC) family, and show how to optimize it in variational inference. VSMC melds variational inference (VI) and sequential Monte Carlo (SMC), providing practitioners with…
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…
Nested sampling is a simulation method for approximating marginal likelihoods proposed by Skilling (2006). We establish that nested sampling has an approximation error that vanishes at the standard Monte Carlo rate and that this error is asymptotically Gaussian. We show that the asymptotic variance of the nested sampling approximation typically grows linearly with the dimension of the parameter. We discuss the applicability and efficiency of nested sampling in realistic problems, and we compare it with two current methods for computing marginal likelihood. We propose an extension that avoids r…
In this paper we will give a Monte Carlo algorithm by which the moments of a functions of Dirichlet probability distributions can be estimated. This algorithm is called Inner Nested Sampling and is an implementation of Skilling's general Nested Sampling framework.
The expected value of partial perfect information (EVPPI) denotes the value of eliminating uncertainty on a subset of unknown parameters involved in a decision model. The EVPPI can be regarded as a decision-theoretic sensitivity index, and has been widely used for identifying relatively important unknown parameters. It follows from Jensen's inequality, however, that the standard nested Monte Carlo computation of the EVPPI results in biased estimates. In this paper we introduce two unbiased Monte Carlo estimators for the EVPPI based on multilevel Monte Carlo method, introduced by Heinrich (1998…
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…
We propose a new framework for how to use sequential Monte Carlo (SMC) algorithms for inference in probabilistic graphical models (PGM). Via a sequential decomposition of the PGM we find a sequence of auxiliary distributions defined on a monotonically increasing sequence of probability spaces. By targeting these auxiliary distributions using SMC we are able to approximate the full joint distribution defined by the PGM. One of the key merits of the SMC sampler is that it provides an unbiased estimate of the partition function of the model. We also show how it can be used within a particle Marko…
Objective: The Expected Value of Sample Information (EVSI) quantifies the economic benefit of reducing uncertainty in a health economic model by collecting additional information. This has the potential to improve the allocation of research budgets. Despite this, practical EVSI evaluations are limited, partly due to the computational cost of estimating this value using the "gold-standard" nested simulation methods. Recently, however, Heath et al developed an estimation procedure that reduces the number of simulations required for this "gold-standard" calculation. Up to this point, this new met…
The Integrated Nested Laplace Approximation (INLA) is a convenient way to obtain approximations to the posterior marginals for parameters in Bayesian hierarchical models when the latent effects can be expressed as a Gaussian Markov Random Field (GMRF). In addition, its implementation in the R-INLA package for the R statistical software provides an easy way to fit models using INLA in practice. R-INLA implements a number of widely used latent models, including several spatial models. In addition, R-INLA can fit models in a fraction of the time than other computer intensive methods (e.g. Markov …
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 sequential Monte Carlo based algorithms for maximum likelihood estimation of the static parameters in hidden Markov models with an intractable likelihood using ideas from approximate Bayesian computation. The static parameter estimation algorithms are gradient based and cover both offline and online estimation. We demonstrate their performance by estimating the parameters of three intractable models, namely the alpha-stable distribution, g-and-k distribution, and the stochastic volatility model with alpha-stable returns, using both real and synthetic data.
We introduce a new sequential Monte Carlo algorithm we call the particle cascade. The particle cascade is an asynchronous, anytime alternative to traditional particle filtering algorithms. It uses no barrier synchronizations which leads to improved particle throughput and memory efficiency. It is an anytime algorithm in the sense that it can be run forever to emit an unbounded number of particles while keeping within a fixed memory budget. We prove that the particle cascade is an unbiased marginal likelihood estimator which means that it can be straightforwardly plugged into existing pseudomar…
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…
We propose kernel sequential Monte Carlo (KSMC), a framework for sampling from static target densities. KSMC is a family of sequential Monte Carlo algorithms that are based on building emulator models of the current particle system in a reproducing kernel Hilbert space. We here focus on modelling nonlinear covariance structure and gradients of the target. The emulator's geometry is adaptively updated and subsequently used to inform local proposals. Unlike in adaptive Markov chain Monte Carlo, continuous adaptation does not compromise convergence of the sampler. KSMC combines the strengths of s…
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…
The paper proposes a new Monte-Carlo simulator combining the advantages of Sequential Monte Carlo simulators and Hamiltonian Monte Carlo simulators. The result is a method that is robust to multimodality and complex shapes to use for inference in presence of difficult likelihoods or target functions. Several examples are provided.
In this paper we propose a flexible and efficient framework for handling multi-armed bandits, combining sequential Monte Carlo algorithms with hierarchical Bayesian modeling techniques. The framework naturally encompasses restless bandits, contextual bandits, and other bandit variants under a single inferential model. Despite the model's generality, we propose efficient Monte Carlo algorithms to make inference scalable, based on recent developments in sequential Monte Carlo methods. Through two simulation studies, the framework is shown to outperform other empirical methods, while also natural…
A discussion on the possibility of reducing the variance of quasi-Monte Carlo estimators in applications. Further details are provided in the accompanying paper "Variance Reduction for Quasi-Monte Carlo".
Sequential Monte Carlo (SMC) methods are a widely used set of computational tools for inference in non-linear non-Gaussian state-space models. We propose a new SMC algorithm to compute the expectation of additive functionals recursively. Essentially, it is an online or forward-only implementation of a forward filtering backward smoothing SMC algorithm proposed in Doucet .et .al (2000). Compared to the standard path space SMC estimator whose asymptotic variance increases quadratically with time even under favourable mixing assumptions, the asymptotic variance of the proposed SMC estimator only …
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.
In performing a Bayesian analysis, two difficult problems often emerge. First, in estimating the parameters of some model for the data, the resulting posterior distribution may be multi-modal or exhibit pronounced (curving) degeneracies. Secondly, in selecting between a set of competing models, calculation of the Bayesian evidence for each model is computationally expensive using existing methods such as thermodynamic integration. Nested Sampling is a Monte Carlo method targeted at the efficient calculation of the evidence, but also produces posterior inferences as a by-product and therefore p…
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…
We introduce a general Monte Carlo method based on Nested Sampling (NS), for sampling complex probability distributions and estimating the normalising constant. The method uses one or more particles, which explore a mixture of nested probability distributions, each successive distribution occupying ~e^-1 times the enclosed prior mass of the previous distribution. While NS technically requires independent generation of particles, Markov Chain Monte Carlo (MCMC) exploration fits naturally into this technique. We illustrate the new method on a test problem and find that it can achieve four times …
SMC (Sequential Monte Carlo) is a class of Monte Carlo algorithms for filtering and related sequential problems. Gerber and Chopin (2015) introduced SQMC (Sequential quasi-Monte Carlo), a QMC version of SMC. This paper has two objectives: (a) to introduce Sequential Monte Carlo to the QMC community, whose members are usually less familiar with state-space models and particle filtering; (b) to extend SQMC to the filtering of continuous-time state-space models, where the latent process is a diffusion. A recurring point in the paper will be the notion of dimension reduction, that is how to implem…
An algorithm is proposed that enables the imposition of shape constraints on regression curves, without requiring the constraints to be written as closed-form expressions, nor assuming the functional form of the loss function. This algorithm is based on Sequential Monte Carlo-Simulated Annealing and only relies on an indicator function that assesses whether or not the constraints are fulfilled, thus allowing the enforcement of various complex constraints by specifying an appropriate indicator function without altering other parts of the algorithm. The algorithm is illustrated by fitting ration…
The expected information gain is an important quality criterion of Bayesian experimental designs, which measures how much the information entropy about uncertain quantity of interest $θ$ is reduced on average by collecting relevant data $Y$. However, estimating the expected information gain has been considered computationally challenging since it is defined as a nested expectation with an outer expectation with respect to $Y$ and an inner expectation with respect to $θ$. In fact, the standard, nested Monte Carlo method requires a total computational cost of $O(\varepsilon^{-3})$ to achieve a r…
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…
Sequential Monte Carlo algorithms (also known as particle filters) are popular methods to approximate filtering (and related) distributions of state-space models. However, they converge at the slow $1/\sqrt{N}$ rate, which may be an issue in real-time data-intensive scenarios. We give a brief outline of SQMC (Sequential Quasi-Monte Carlo), a variant of SMC based on low-discrepancy point sets proposed by Gerber and Chopin (2015), which converges at a faster rate, and we illustrate the greater performance of SQMC on autonomous positioning problems.
We describe an "embarrassingly parallel" method for Bayesian phylogenetic inference, annealed Sequential Monte Carlo, based on recent advances in the Sequential Monte Carlo literature such as adaptive determination of annealing parameters. The algorithm provides an approximate posterior distribution over trees and evolutionary parameters as well as an unbiased estimator for the marginal likelihood. This unbiasedness property can be used for the purpose of testing the correctness of posterior simulation software. We evaluate the performance of phylogenetic annealed Sequential Monte Carlo by rev…
This is a collection of three written discussions of the paper "sequential quasi-Monte Carlo sampling" by M. Gerber and N. Chopin, following the presentation given before the Royal Statistical Society in London on December 10th, 2014.
A Monte Carlo algorithm is said to be adaptive if it automatically calibrates its current proposal distribution using past simulations. The choice of the parametric family that defines the set of proposal distributions is critical for good performance. In this paper, we present such a parametric family for adaptive sampling on high-dimensional binary spaces. A practical motivation for this problem is variable selection in a linear regression context. We want to sample from a Bayesian posterior distribution on the model space using an appropriate version of Sequential Monte Carlo. Raw versions …
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…
One of the key challenges in identifying nonlinear and possibly non-Gaussian state space models (SSMs) is the intractability of estimating the system state. Sequential Monte Carlo (SMC) methods, such as the particle filter (introduced more than two decades ago), provide numerical solutions to the nonlinear state estimation problems arising in SSMs. When combined with additional identification techniques, these algorithms provide solid solutions to the nonlinear system identification problem. We describe two general strategies for creating such combinations and discuss why SMC is a natural tool…
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…
The Integrated Nested Laplace Approximation (INLA) has established itself as a widely used method for approximate inference on Bayesian hierarchical models which can be represented as a latent Gaussian model (LGM). INLA is based on producing an accurate approximation to the posterior marginal distributions of the parameters in the model and some other quantities of interest by using repeated approximations to intermediate distributions and integrals that appear in the computation of the posterior marginals. INLA focuses on models whose latent effects are a Gaussian Markov random field (GMRF). …
We build on auto-encoding sequential Monte Carlo (AESMC): a method for model and proposal learning based on maximizing the lower bound to the log marginal likelihood in a broad family of structured probabilistic models. Our approach relies on the efficiency of sequential Monte Carlo (SMC) for performing inference in structured probabilistic models and the flexibility of deep neural networks to model complex conditional probability distributions. We develop additional theoretical insights and introduce a new training procedure which improves both model and proposal learning. We demonstrate that…
This paper addresses the issue of estimating the expectation of a real-valued random variable of the form $X = g(\mathbf{U})$ where $g$ is a deterministic function and $\mathbf{U}$ can be a random finite- or infinite-dimensional vector. Using recent results on rare event simulation, we propose a unified framework for dealing with both probability and mean estimation for such random variables, \emph{i.e.} linking algorithms such as Tootsie Pop Algorithm (TPA) or Last Particle Algorithm with nested sampling. Especially, it extends nested sampling as follows: first the random variable $X$ does no…
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…
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…
In this comment we consider whether QMC methods can be further embedded within SMC schemes in settings in which the transition density of the latent process is intractable and pseudo-marginal methods are deployed.
Sequential Monte Carlo is a family of algorithms for sampling from a sequence of distributions. Some of these algorithms, such as particle filters, are widely used in the physics and signal processing researches. More recent developments have established their application in more general inference problems such as Bayesian modeling. These algorithms have attracted considerable attentions in recent years as they admit natural and scalable parallelizations. However, these algorithms are perceived to be difficult to implement. In addition, parallel programming is often unfamiliar to many research…
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…
Multifidelity approximate Bayesian computation (MF-ABC) is a likelihood-free technique for parameter inference that exploits model approximations to significantly increase the speed of ABC algorithms (Prescott and Baker, 2020). Previous work has considered MF-ABC only in the context of rejection sampling, which does not explore parameter space particularly efficiently. In this work, we integrate the multifidelity approach with the ABC sequential Monte Carlo (ABC-SMC) algorithm into a new MF-ABC-SMC algorithm. We show that the improvements generated by each of ABC-SMC and MF-ABC to the efficien…
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…
In this paper we consider a fractional stochastic volatility model, that is a model in which the volatility may exhibit a long-range dependent or a rough/antipersistent behavior. We propose a dynamic sequential Monte Carlo methodology that is applicable to both long memory and antipersistent processes in order to estimate the volatility as well as the unknown parameters of the model. We establish a central limit theorem for the state and parameter filters and we study asymptotic properties (consistency and asymptotic normality) for the filter. We illustrate our results with a simulation study …
