In this article, an overview of Bayesian methods for sequential simulation from posterior distributions of nonlinear and non-Gaussian dynamic systems is presented. The focus is mainly laid on sequential Monte Carlo methods, which are based on particle representations of probability densities and can be seamlessly generalized to any state-space representation. Within this context, a unified framework of the various Particle Filter (PF) alternatives is presented for the solution of state, state-parameter and input-state-parameter estimation problems on the basis of sparse measurements. The algorithmic steps of each filter are thoroughly presented and a simple illustrative example is utilized for the inference of i) unobserved states, ii) unknown system parameters and iii) unmeasured driving inputs.
Reinforcement Learning (RL) is a computational approach to reward-driven learning in sequential decision problems. It implements the discovery of optimal actions by learning from an agent interacting with an environment rather than from supervised data. We contrast and compare RL with traditional sequential design, focusing on simulation-based Bayesian sequential design (BSD). Recently, there has been an increasing interest in RL techniques for healthcare applications. We introduce two related applications as motivating examples. In both applications, the sequential nature of the decisions is …
In the Bayesian paradigm for presenting forensic evidence to court, it is recommended that the weight of the evidence be summarized as a likelihood ratio (LR) between two opposing hypotheses of how the evidence could have been produced. Such LRs are necessarily based on probabilistic models, the parameters of which may be uncertain. It has been suggested by some authors that the value of the LR, being a function of the model parameters should therefore also be considered uncertain and that this uncertainty should be communicated to the court. In this tutorial, we consider a simple example of a…
University of Western Australia（西澳大学）；Murdoch University（莫道克大学）；Monash University（莫纳什大学）
Modern deep learning methods constitute incredibly powerful tools to tackle a myriad of challenging problems. However, since deep learning methods operate as black boxes, the uncertainty associated with their predictions is often challenging to quantify. Bayesian statistics offer a formalism to understand and quantify the uncertainty associated with deep neural network predictions. This tutorial provides an overview of the relevant literature and a complete toolset to design, implement, train, use and evaluate Bayesian Neural Networks, i.e. Stochastic Artificial Neural Networks trained using B…
On-line estimation plays an important role in process control and monitoring. Obtaining a theoretical solution to the simultaneous state-parameter estimation problem for non-linear stochastic systems involves solving complex multi-dimensional integrals that are not amenable to analytical solution. While basic sequential Monte-Carlo (SMC) or particle filtering (PF) algorithms for simultaneous estimation exist, it is well recognized that there is a need for making these on-line algorithms non-degenerate, fast and applicable to processes with missing measurements. To overcome the deficiencies in …
Bayesian optimization is an approach to optimizing objective functions that take a long time (minutes or hours) to evaluate. It is best-suited for optimization over continuous domains of less than 20 dimensions, and tolerates stochastic noise in function evaluations. It builds a surrogate for the objective and quantifies the uncertainty in that surrogate using a Bayesian machine learning technique, Gaussian process regression, and then uses an acquisition function defined from this surrogate to decide where to sample. In this tutorial, we describe how Bayesian optimization works, including Gau…
Simulation models of epidemiological, biological, ecological, and environmental processes are increasingly being calibrated using Bayesian statistics. The Bayesian approach provides simple rules to synthesise multiple data sources and to calculate uncertainty in model output due to uncertainty in the calibration data. As the number of tutorials and studies published grow, the solutions to common difficulties in Bayesian calibration across these fields have become more apparent, and a step-by-step process for successful calibration across all these fields is emerging. We provide a statement of …
Duke University（杜克大学）；University at Buffalo（布法罗大学）
Learning probability distributions on the weights of neural networks (NNs) has recently proven beneficial in many applications. Bayesian methods, such as Stein variational gradient descent (SVGD), offer an elegant framework to reason about NN model uncertainty. However, by assuming independent Gaussian priors for the individual NN weights (as often applied), SVGD does not impose prior knowledge that there is often structural information (dependence) among weights. We propose efficient posterior learning of structural weight uncertainty, within an SVGD framework, by employing matrix variate Gau…
Sequential model-based optimization sequentially selects a candidate point by constructing a surrogate model with the history of evaluations, to solve a black-box optimization problem. Gaussian process (GP) regression is a popular choice as a surrogate model, because of its capability of calculating prediction uncertainty analytically. On the other hand, an ensemble of randomized trees is another option and has practical merits over GPs due to its scalability and easiness of handling continuous/discrete mixed variables. In this paper we revisit various ensembles of randomized trees to investig…
Sequential Inference for Gaussian Processes: A Signal Processing Perspective
Basis Research Institute（基础研究机构）；Department of Electrical and Computer Engineering, Stony Brook University（石溪大学电气与计算机工程系）；Data Sciences Directorate, Brookhaven National Laboratory（布鲁赫斯国家实验室数据科学总局）
Gaussian processes (GPs) provide a framework for Bayesian inference that can offer principled uncertainty estimates for a large range of problems. For example, if we consider regression problems with Gaussian likelihoods, a GP model enjoys a posterior in closed form. However, identifying the posterior GP scales cubically with the number of training examples and requires to store all examples in memory. In order to overcome these obstacles, sparse GPs have been proposed that approximate the true posterior GP with pseudo-training examples. Importantly, the number of pseudo-training examples is u…
We consider an input-to-response (ItR) system characterized by (1) parameterized input with a known probability distribution and (2) stochastic ItR function with heteroscedastic randomness. Our purpose is to efficiently quantify the extreme response probability when the ItR function is expensive to evaluate. The problem setup arises often in physics and engineering problems, with randomness in ItR coming from either intrinsic uncertainties (say, as a solution to a stochastic equation) or additional (critical) uncertainties that are not incorporated in a low-dimensional input parameter space (a…
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…
University of Bern（伯尔尼大学）；University of Lausanne（洛桑大学）
We consider the use of Gaussian process (GP) priors for solving inverse problems in a Bayesian framework. As is well known, the computational complexity of GPs scales cubically in the number of datapoints. We here show that in the context of inverse problems involving integral operators, one faces additional difficulties that hinder inversion on large grids. Furthermore, in that context, covariance matrices can become too large to be stored. By leveraging results about sequential disintegrations of Gaussian measures, we are able to introduce an implicit representation of posterior covariance m…
Estimating percentiles of black-box deterministic functions with random inputs is a challenging task when the number of function evaluations is severely restricted, which is typical for computer experiments. This article proposes two new sequential Bayesian methods for percentile estimation based on the Gaussian Process metamodel. Both rely on the Stepwise Uncertainty Reduction paradigm, hence aim at providing a sequence of function evaluations that reduces an uncertainty measure associated with the percentile estimator. The proposed strategies are tested on several numerical examples, showing…
Technical University of Denmark（丹麦技术大学）；University of Copenhagen（哥本哈根大学）；Google DeepMind（谷歌DeepMind）
How can we efficiently propagate uncertainty in a latent state representation with recurrent neural networks? This paper introduces stochastic recurrent neural networks which glue a deterministic recurrent neural network and a state space model together to form a stochastic and sequential neural generative model. The clear separation of deterministic and stochastic layers allows a structured variational inference network to track the factorization of the model's posterior distribution. By retaining both the nonlinear recursive structure of a recurrent neural network and averaging over the unce…
Generative models for decision-making under distributional shift
Department of Mathematics, Duke University（杜克大学数学系）；H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology（佐治亚理工学院H. Milton Stewart工业与系统工程学院）
Gaussian process (GP) models have become a well-established frameworkfor the adaptive design of costly experiments, and notably of computerexperiments. GP-based sequential designs have been found practicallyefficient for various objectives, such as global optimization(estimating the global maximum or maximizer(s) of a function),reliability analysis (estimating a probability of failure) or theestimation of level sets and excursion sets. In this paper, we studythe consistency of an important class of sequential designs, known asstepwise uncertainty reduction (SUR) strategies. Our approach relies…
The method of maximum likelihood estimation (MLE) is a widely used statistical approach for estimating the values of one or more unknown parameters of a probabilistic model based on observed data. In this tutorial, I briefly review the mathematical foundations of MLE, then reformulate the problem for the measurement of a spatially-varying optical intensity distribution. In this context, the detection of each individual photon is treated as a random event, the outcome being the photon's location. A typical measurement consists of many detected photons, which accumulate to form a spatial intensi…
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…
An exploration of sequential Bayesian variable selection -- A comment on García-Donato et al. (2025). "Model uncertainty and missing data: An objective Bayesian perspective"
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…
We discuss Bayesian model uncertainty analysis and forecasting in sequential dynamic modeling of multivariate time series. The perspective is that of a decision-maker with a specific forecasting objective that guides thinking about relevant models. Based on formal Bayesian decision-theoretic reasoning, we develop a time-adaptive approach to exploring, weighting, combining and selecting models that differ in terms of predictive variables included. The adaptivity allows for changes in the sets of favored models over time, and is guided by the specific forecasting goals. A synthetic example illus…
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 $…
