Structural reliability analysis is concerned with estimation of the probability of a critical event taking place, described by $P(g(\textbf{X}) \leq 0)$ for some $n$-dimensional random variable $\textbf{X}$ and some real-valued function $g$. In many applications the function $g$ is practically unknown, as function evaluation involves time consuming numerical simulation or some other form of experiment that is expensive to perform. The problem we address in this paper is how to optimally design experiments, in a Bayesian decision theoretic fashion, when the goal is to estimate the probability $P(g(\textbf{X}) \leq 0)$ using a minimal amount of resources. As opposed to existing methods that have been proposed for this purpose, we consider a general structural reliability model given in hierarchical form. We therefore introduce a general formulation of the experimental design problem, where we distinguish between the uncertainty related to the random variable $\textbf{X}$ and any additional epistemic uncertainty that we want to reduce through experimentation. The effectiveness of a design strategy is evaluated through a measure of residual uncertainty, and efficient approximation of this quantity is crucial if we want to apply algorithms that search for an optimal strategy. The method we propose is based on importance sampling combined with the unscented transform for epistemic uncertainty propagation. We implement this for the myopic (one-step look ahead) alternative, and demonstrate the effectiveness through a series of numerical experiments.
Scientific researchers utilize randomized experiments to draw casual statements. Most early studies as well as current work on experiments with sequential intervention decisions has been focusing on estimating the causal effects among sequential treatments, ignoring the non-compliance issues that experimental units might not be compliant with the treatment assignments that they were originally allocated. A series of methodologies have been developed to address the non-compliance issues in randomized experiments with time-fixed treatment. However, to our best knowledge, there is little literatu…
Systems Innovation, Faculty of Engineering, The University of Tokyo（东京大学工学部系统创新）
Bayesian experimental design (BED) has been used as a method for conducting efficient experiments based on Bayesian inference. The existing methods, however, mostly focus on maximizing the expected information gain (EIG); the cost of experiments and sample efficiency are often not taken into account. In order to address this issue and enhance practical applicability of BED, we provide a new approach Sequential Experimental Design via Reinforcement Learning to construct BED in a sequential manner by applying reinforcement learning in this paper. Here, reinforcement learning is a branch of machi…
The design of multiple experiments is commonly undertaken via suboptimal strategies, such as batch (open-loop) design that omits feedback or greedy (myopic) design that does not account for future effects. This paper introduces new strategies for the optimal design of sequential experiments. First, we rigorously formulate the general sequential optimal experimental design (sOED) problem as a dynamic program. Batch and greedy designs are shown to result from special cases of this formulation. We then focus on sOED for parameter inference, adopting a Bayesian formulation with an information theo…
We introduce Deep Adaptive Design (DAD), a method for amortizing the cost of adaptive Bayesian experimental design that allows experiments to be run in real-time. Traditional sequential Bayesian optimal experimental design approaches require substantial computation at each stage of the experiment. This makes them unsuitable for most real-world applications, where decisions must typically be made quickly. DAD addresses this restriction by learning an amortized design network upfront and then using this to rapidly run (multiple) adaptive experiments at deployment time. This network represents a …
Recently, it has been shown how sampling actions from the predictive distribution over the optimal action-sometimes called Thompson sampling-can be applied to solve sequential adaptive control problems, when the optimal policy is known for each possible environment. The predictive distribution can then be constructed by a Bayesian superposition of the optimal policies weighted by their posterior probability that is updated by Bayesian inference and causal calculus. Here we discuss three important features of this approach. First, we discuss in how far such Thompson sampling can be regarded as …
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…
A method for sequential inference of the fixed parameters of a dynamic latent Gaussian models is proposed and evaluated that is based on the iterated Laplace approximation. The method provides a useful trade-off between computational performance and the accuracy of the approximation to the true posterior distribution. Approximation corrections are shown to improve the accuracy of the approximation in simulation studies. A population-based approach is also shown to provide a more robust inference method.
This paper proposes new methodology for sequential state and parameter estimation within the ensemble Kalman filter. The method is fully Bayesian and propagates the joint posterior density of states and parameters over time. In order to implement the method we consider two representations of the marginal posterior distribution of the parameters: a grid-based approach and a Gaussian approximation. Contrary to existing algorithms, the new method explicitly accounts for parameter uncertainty and provides a formal way to combine information about the parameters from data at different time periods.…
We present the Sequential Ensemble Transform (SET) method, an approach for generating approximate samples from a Bayesian posterior distribution. The method explores the posterior distribution by solving a sequence of discrete optimal transport problems to produce a series of transport plans which map prior samples to posterior samples. We prove that the sequence of Dirac mixture distributions produced by the SET method converges weakly to the true posterior as the sample size approaches infinity. Furthermore, our numerical results indicate that, when compared to standard Sequential Monte Carl…
A current challenge for many Bayesian analyses is determining when to terminate high-dimensional Markov chain Monte Carlo simulations. To this end, we propose using an automated sequential stopping procedure that terminates the simulation when the computational uncertainty is small relative to the posterior uncertainty. Such a stopping rule has previously been shown to work well in settings with posteriors of moderate dimension. In this paper, we illustrate its utility in high-dimensional simulations while overcoming some current computational issues. Further, we investigate the relationship b…
Hidden Markov models can describe time series arising in various fields of science, by treating the data as noisy measurements of an arbitrarily complex Markov process. Sequential Monte Carlo (SMC) methods have become standard tools to estimate the hidden Markov process given the observations and a fixed parameter value. We review some of the recent developments allowing the inclusion of parameter uncertainty as well as model uncertainty. The shortcomings of the currently available methodology are emphasised from an algorithmic complexity perspective. The statistical objects of interest for ti…
We develop a new class of dynamic multivariate Poisson count models that allow for fast online updating and we refer to these models as multivariate Poisson-scaled beta (MPSB). The MPSB model allows for serial dependence in the counts as well as dependence across multiple series with a random common environment. Other notable features include analytic forms for state propagation and predictive likelihood densities. Sequential updating occurs through the updating of the sufficient statistics for static model parameters, leading to a fully adapted particle learning algorithm and a new class of p…
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 consider the problem of optimizing a real-valued continuous function $f$ using a Bayesian approach, where the evaluations of $f$ are chosen sequentially by combining prior information about $f$, which is described by a random process model, and past evaluation results. The main difficulty with this approach is to be able to compute the posterior distributions of quantities of interest which are used to choose evaluation points. In this article, we decide to use a Sequential Monte Carlo (SMC) approach.
The logistic specification has been used extensively in non-Bayesian statistics to model the dependence of discrete outcomes on the values of specified covariates. Because the likelihood function is globally weakly concave estimation by maximum likelihood is generally straightforward even in commonly arising applications with scores or hundreds of parameters. In contrast Bayesian inference has proven awkward, requiring normal approximations to the likelihood or specialized adaptations of existing Markov chain Monte Carlo and data augmentation methods. This paper approaches Bayesian inference i…
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…
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…
Bayesian filtering aims at tracking sequentially a hidden process from an observed one. In particular, sequential Monte Carlo (SMC) techniques propagate in time weighted trajectories which represent the posterior probability density function (pdf) of the hidden process given the available observations. On the other hand, Conditional Monte Carlo (CMC) is a variance reduction technique which replaces the estimator of a moment of interest by its conditional expectation given another variable. In this paper we show that up to some adaptations, one can make use of the time recursive nature of SMC a…
University of Edinburgh（爱丁堡大学）；Queensland University of Technology（昆士兰科技大学）
Bayesian experimental design (BED) is a framework that uses statistical models and decision making under uncertainty to optimise the cost and performance of a scientific experiment. Sequential BED, as opposed to static BED, considers the scenario where we can sequentially update our beliefs about the model parameters through data gathered in the experiment. A class of models of particular interest for the natural and medical sciences are implicit models, where the data generating distribution is intractable, but sampling from it is possible. Even though there has been a lot of work on static B…
University of Warwick（华威大学）；The Alan Turing Institute（艾伦·图灵研究所）
We introduce a framework for inference in general state-space hidden Markov models (HMMs) under likelihood misspecification. In particular, we leverage the loss-theoretic perspective of Generalized Bayesian Inference (GBI) to define generalised filtering recursions in HMMs, that can tackle the problem of inference under model misspecification. In doing so, we arrive at principled procedures for robust inference against observation contamination by utilising the $β$-divergence. Operationalising the proposed framework is made possible via sequential Monte Carlo methods (SMC), where most standard…
Objective priors for sequential experiments are considered. Common priors, such as the Jeffreys prior and the reference prior, will typically depend on the stopping rule used for the sequential experiment. New expressions for reference priors are obtained in various contexts, and computational issues involving such priors are considered.
Nonlinear differential equations (DEs) are used in a wide range of scientific problems to model complex dynamic systems. The differential equations often contain unknown parameters that are of scientific interest, which have to be estimated from noisy measurements of the dynamic system. Generally, there is no closed-form solution for nonlinear DEs, and the likelihood surface for the parameter of interest is multi-modal and very sensitive to different parameter values. We propose a Bayesian framework for nonlinear DE systems. A flexible nonparametric function is used to represent the dynamic pr…
A method for sequential Bayesian inference of the static parameters of a dynamic state space model is proposed. The method is based on the observation that many dynamic state space models have a relatively small number of static parameters (or hyper-parameters), so that in principle the posterior can be computed and stored on a discrete grid of practical size which can be tracked dynamically. Further to this, this approach is able to use any existing methodology which computes the filtering and prediction distributions of the state process. Kalman filter and its extensions to non-linear/non-Ga…
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…
An important feature of Bayesian statistics is the opportunity to do sequential inference: the posterior distribution obtained after seeing a dataset can be used as prior for a second inference. However, when Monte Carlo sampling methods are used for inference, we only have a set of samples from the posterior distribution. To do sequential inference, we then either have to evaluate the second posterior at only these locations and reweight the samples accordingly, or we can estimate a functional description of the posterior probability distribution from the samples and use that as prior for the…
In this article we consider a Bayesian inverse problem associated to elliptic partial differential equations (PDEs) in two and three dimensions. This class of inverse problems is important in applications such as hydrology, but the complexity of the link function between unknown field and measurements can make it difficult to draw inference from the associated posterior. We prove that for this inverse problem a basic SMC method has a Monte Carlo rate of convergence with constants which are independent of the dimension of the discretization of the problem; indeed convergence of the SMC method i…
Advances in digital sensors, digital data storage and communications have resulted in systems being capable of accumulating large collections of data. In the light of dealing with the challenges that massive data present, this work proposes solutions to inference and filtering problems within the Bayesian framework. Two novel Bayesian inference algorithms are developed for non-linear and non-Gaussian state space models, able to deal with large volumes of data (or observations). These are sequential Markov chain Monte Carlo (MCMC) approaches relying on two key ideas: 1) subsample the massive da…
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…
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…
We develop a spatio-temporal model to forecast sensor output at five locations in North East England. The signal is described using coupled dynamic linear models, with spatial effects specified by a Gaussian process. Data streams are analysed using a stochastic algorithm which sequentially approximates the parameter posterior through a series of reweighting and resampling steps. An iterated batch importance sampling scheme is used to circumvent particle degeneracy through a resample-move step. The algorithm is modified to make it more efficient and parallisable. The model is shown to give a go…
Nonlinear non-Gaussian state-space models arise in numerous applications in statistics and signal processing. In this context, one of the most successful and popular approximation techniques is the Sequential Monte Carlo (SMC) algorithm, also known as particle filtering. Nevertheless, this method tends to be inefficient when applied to high dimensional problems. In this paper, we focus on another class of sequential inference methods, namely the Sequential Markov Chain Monte Carlo (SMCMC) techniques, which represent a promising alternative to SMC methods. After providing a unifying framework f…
We study sequential Bayesian inference in stochastic kinetic models with latent factors. Assuming continuous observation of all the reactions, our focus is on joint inference of the unknown reaction rates and the dynamic latent states, modeled as a hidden Markov factor. Using insights from nonlinear filtering of continuous-time jump Markov processes we develop a novel sequential Monte Carlo algorithm for this purpose. Our approach applies the ideas of particle learning to minimize particle degeneracy and exploit the analytical jump Markov structure. A motivating application of our methods is m…
Stochastic reaction network models are often used to explain and predict the dynamics of gene regulation in single cells. These models usually involve several parameters, such as the kinetic rates of chemical reactions, that are not directly measurable and must be inferred from experimental data. Bayesian inference provides a rigorous probabilistic framework for identifying these parameters by finding a posterior parameter distribution that captures their uncertainty. Traditional computational methods for solving inference problems such as Markov Chain Monte Carlo methods based on classical Me…
We introduce a dynamic generative model, Bayesian allocation model (BAM), which establishes explicit connections between nonnegative tensor factorization (NTF), graphical models of discrete probability distributions and their Bayesian extensions, and the topic models such as the latent Dirichlet allocation. BAM is based on a Poisson process, whose events are marked by using a Bayesian network, where the conditional probability tables of this network are then integrated out analytically. We show that the resulting marginal process turns out to be a Polya urn, an integer valued self-reinforcing …
Detection of induced polarisation (IP) effects in airborne electromagnetic (AEM) measurements does not yet have an established methodology. This contribution develops a Bayesian approach to the IP-detectability problem using decoupled transdimensional layered models, and applies an approach novel to geophysics whereby transdimensional proposals are used within the embarrassingly parallelisable and robust static Sequential Monte Carlo (SMC) class of algorithms for the simultaneous inference of parameters and models. Henceforth referring to this algorithm as Reversible Jump Sequential Monte Carl…
The advantages of sequential Monte Carlo (SMC) are exploited to develop parameter estimation and model selection methods for GARCH (Generalized AutoRegressive Conditional Heteroskedasticity) style models. It provides an alternative method for quantifying estimation uncertainty relative to classical inference. Even with long time series, it is demonstrated that the posterior distribution of model parameters are non-normal, highlighting the need for a Bayesian approach and an efficient posterior sampling method. Efficient approaches for both constructing the sequence of distributions in SMC, and…
In this paper, we explore the class of the Hidden Semi-Markov Model (HSMM), a flexible extension of the popular Hidden Markov Model (HMM) that allows the underlying stochastic process to be a semi-Markov chain. HSMMs are typically used less frequently than their basic HMM counterpart due to the increased computational challenges when evaluating the likelihood function. Moreover, while both models are sequential in nature, parameter estimation is mainly conducted via batch estimation methods. Thus, a major motivation of this paper is to provide methods to estimate HSMMs (1) in a computationally…
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…
Methods of approximate Bayesian computation (ABC) are increasingly used for analysis of complex models. A major challenge for ABC is over-coming the often inherent problem of high rejection rates in the accept/reject methods based on prior:predictive sampling. A number of recent developments aim to address this with extensions based on sequential Monte Carlo (SMC) strategies. We build on this here, introducing an ABC SMC method that uses data-based adaptive weights. This easily implemented and computationally trivial extension of ABC SMC can very substantially improve acceptance rates, as is d…
We consider the problem of estimating expectations with respect to a target distribution with an unknown normalizing constant, and where even the unnormalized target needs to be approximated at finite resolution. This setting is ubiquitous across science and engineering applications, for example in the context of Bayesian inference where a physics-based model governed by an intractable partial differential equation (PDE) appears in the likelihood. A multi-index Sequential Monte Carlo (MISMC) method is used to construct ratio estimators which provably enjoy the complexity improvements of multi-…
This article describes blavaan, an R package for estimating Bayesian structural equation models (SEMs) via JAGS and for summarizing the results. It also describes a novel parameter expansion approach for estimating specific types of models with residual covariances, which facilitates estimation of these models in JAGS. The methodology and software are intended to provide users with a general means of estimating Bayesian SEMs, both classical and novel, in a straightforward fashion. Users can estimate Bayesian versions of classical SEMs with lavaan syntax, they can obtain state-of-the-art Bayesi…
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…
