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 Carlo (SMC) methods, the SET approach is more robust to the choice of Markov mutation kernels and requires less computational efforts to reach a similar accuracy when used to explore complex posterior distributions. Finally, we describe adaptive schemes that allow to completely automate the use of the SET method.
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.…
Clinical trials usually involve sequential patient entry. When designing a clinical trial, it is often desirable to include a provision for interim analyses of accumulating data with the potential for stopping the trial early. We review Bayesian sequential clinical trial designs based on posterior probabilities, posterior predictive probabilities, and decision-theoretic frameworks. A pertinent question is whether Bayesian sequential designs need to be adjusted for the planning of interim analyses. We answer this question from three perspectives: a frequentist-oriented perspective, a calibrated…
Ensembles of networks arise in various fields where multiple independent networks are observed on the same set of nodes, for example, a collection of brain networks constructed on the same brain regions for different individuals. However, there are few models that describe both the variations and characteristics of networks in an ensemble at the same time. In this paper, we propose to model the ensemble of networks using a Dirichlet Process Mixture of Exponential Random Graph Models (DPM-ERGMs), which divides the ensemble into different clusters and models each cluster of networks using a sepa…
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…
Accelerated life testing (ALT) is typically used to assess the reliability of material's lifetime under desired stress levels. Recent advances in material engineering have made a variety of material alternatives readily available. To identify the most reliable material setting with efficient experimental design, a sequential test planning strategy is preferred. To guarantee a tractable statistical mechanism for information collection and update, we develop explicit model parameter update formulas via approximate Bayesian inference. Theories show that our explicit update formulas give consisten…
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 …
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.
We develop an efficient Bayesian sequential inference framework for factor analysis models observed via various data types, such as continuous, binary and ordinal data. In the continuous data case, where it is possible to marginalise over the latent factors, the proposed methodology tailors the Iterated Batch Importance Sampling (IBIS) of Chopin (2002) to handle such models and we incorporate Hamiltonian Markov Chain Monte Carlo. For binary and ordinal data, we develop an efficient IBIS scheme to handle the parameter and latent factors, combining with Laplace or Variational Bayes approximation…
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…
Methods based on Bayesian decision tree ensembles have proven valuable in constructing high-quality predictions, and are particularly attractive in certain settings because they encourage low-order interaction effects. Despite adapting to the presence of low-order interactions for prediction purpose, we show that Bayesian decision tree ensembles are generally anti-conservative for the purpose of conducting interaction detection. We address this problem by introducing Dirichlet process forests (DP-Forests), which leverage the presence of low-order interactions by clustering the trees so that tr…
We propose a general formalism of iterated random functions with semigroup property, under which exact and approximate Bayesian posterior updates can be viewed as specific instances. A convergence theory for iterated random functions is presented. As an application of the general theory we analyze convergence behaviors of exact and approximate message-passing algorithms that arise in a sequential change point detection problem formulated via a latent variable directed graphical model. The sequential inference algorithm and its supporting theory are illustrated by simulated examples.
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.
We aim at modelling the appearance of distinct tags in a sequence of labelled objects. Common examples of this type of data include words in a corpus or distinct species in a sample. These sequential discoveries are often summarised via accumulation curves, which count the number of distinct entities observed in an increasingly large set of objects. We propose a novel Bayesian nonparametric method for species sampling modelling by directly specifying the probability of a new discovery, therefore allowing for flexible specifications. The asymptotic behavior and finite sample properties of such …
High throughput technologies have become the practice of choice for comparative studies in biomedical applications. Limited number of sample points due to sequencing cost or access to organisms of interest necessitates the development of efficient sample collections to maximize the power of downstream statistical analyses. We propose a method for sequentially choosing training samples under the Optimal Bayesian Classification framework. Specifically designed for RNA sequencing count data, the proposed method takes advantage of efficient Gibbs sampling procedure with closed-form updates. Our re…
We study the problem of sequential experimental design to estimate the parametric component of a partially linear model with a Gaussian process prior. We consider an active learning setting where an experimenter adaptively decides which data to collect to achieve their goal efficiently. The experimenter's goals may vary, such as reducing the classification error probability or improving the accuracy of estimating the parameters of the data generating process. This study aims to improve the accuracy of estimating the parametric component of a partially linear model. Under some assumptions, the …
We propose a novel "tree-averaging" model that utilizes the ensemble of classification and regression trees (CART). Each constituent tree is estimated with a subset of similar data. We treat this grouping of subsets as Bayesian ensemble trees (BET) and model them as an infinite mixture Dirichlet process. We show that BET adapts to data heterogeneity and accurately estimates each component. Compared with the bootstrap-aggregating approach, BET shows improved prediction performance with fewer trees. We develop an efficient estimating procedure with improved sampling strategies in both CART and m…
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…
We propose a generalised framework for the updating of a prior ensemble to a posterior ensemble, an essential yet challenging part in ensemble-based filtering methods. The proposed framework is based on a generalised and fully Bayesian view on the traditional ensemble Kalman filter (EnKF). In the EnKF, the updating of the ensemble is based on Gaussian assumptions, whereas in our general setup the updating may be based on another parametric family. In addition, we propose to formulate an optimality criterion and to find the optimal update with respect to this criterion. The framework is fully B…
We focus on causal inference for longitudinal treatments, where units are assigned to treatments at multiple time points, aiming to assess the effect of different treatment sequences on an outcome observed at a final point. A common assumption in similar studies is Sequential Ignorability (SI): treatment assignment at each time point is assumed independent of future potential outcomes given past observed outcomes and covariates. SI is questionable when treatment participation depends on individual choices, and treatment assignment may depend on unobservable quantities associated with future ou…
University of South Carolina（南卡罗来纳大学）；University of North Carolina at Charlotte（北卡罗来纳大学夏洛特分校）
Real-time nonlinear Bayesian filtering algorithms are overwhelmed by data volume, velocity and increasing complexity of computational models. In this paper, we propose a novel ensemble based nonlinear Bayesian filtering approach which only requires a small number of simulations and can be applied to high-dimensional systems in the presence of intractable likelihood functions. The proposed approach uses linear latent projections to estimate the joint probability distribution between states, parameters, and observables using a mixture of Gaussian components generated by the reconstruction error …
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…
Ensembles of decision trees are a useful tool for obtaining for obtaining flexible estimates of regression functions. Examples of these methods include gradient boosted decision trees, random forests, and Bayesian CART. Two potential shortcomings of tree ensembles are their lack of smoothness and vulnerability to the curse of dimensionality. We show that these issues can be overcome by instead considering sparsity inducing soft decision trees in which the decisions are treated as probabilistic. We implement this in the context of the Bayesian additive regression trees framework, and illustrate…
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…
We explore the use of the optimal statistical interpolation (OSI) data assimilation method for the statistical tracking of emerging epidemics and to study the spatial dynamics of a disease. The epidemic models that we used for this study are spatial variants of the common susceptible-infectious-removed (S-I-R) compartmental model of epidemiology. The spatial S-I-R epidemic model is illustrated by application to simulated spatial dynamic epidemic data from the historic "Black Death" plague of 14th century Europe. Bayesian statistical tracking of emerging epidemic diseases using the OSI as it un…
The ordinal endpoint is prevalent in clinical studies. For example, for the COVID-19, the most common endpoint used was 7-point ordinal scales. Another example is in phase II cancer studies, efficacy is often assessed as an ordinal variable based on a level of response of solid tumors with four categories: complete response, partial response, stable disease, and progression, though often a dichotomized approach is used in practices. However, there lack of designs for the ordinal endpoint despite Whitehead et al. (1993, 2017), Jaki et al. (2003) to list a few. In this paper, we propose a generi…
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…
Deep ensembles can be considered as the current state-of-the-art for uncertainty quantification in deep learning. While the approach was originally proposed as a non-Bayesian technique, arguments supporting its Bayesian footing have been put forward as well. We show that deep ensembles can be viewed as an approximate Bayesian method by specifying the corresponding assumptions. Our findings lead to an improved approximation which results in an enlarged epistemic part of the uncertainty. Numerical examples suggest that the improved approximation can lead to more reliable uncertainties. Analytica…
Cooperation is often implicitly assumed when learning from other agents. Cooperation implies that the agent selecting the data, and the agent learning from the data, have the same goal, that the learner infer the intended hypothesis. Recent models in human and machine learning have demonstrated the possibility of cooperation. We seek foundational theoretical results for cooperative inference by Bayesian agents through sequential data. We develop novel approaches analyzing consistency, rate of convergence and stability of Sequential Cooperative Bayesian Inference (SCBI). Our analysis of the eff…
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 work we perform outlier detection using ensembles of neural networks obtained by variational approximation of the posterior in a Bayesian neural network setting. The variational parameters are obtained by sampling from the true posterior by gradient descent. We show our outlier detection results are comparable to those obtained using other efficient ensembling methods.
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…
We deal with the efficient parallelization of Bayesian global optimization algorithms, and more specifically of those based on the expected improvement criterion and its variants. A closed form formula relying on multivariate Gaussian cumulative distribution functions is established for a generalized version of the multipoint expected improvement criterion. In turn, the latter relies on intermediate results that could be of independent interest concerning moments of truncated Gaussian vectors. The obtained expansion of the criterion enables studying its differentiability with respect to point …
Tree ensembles, such as random forests and boosted trees, are renowned for their high prediction performance. However, their interpretability is critically limited due to the enormous complexity. In this study, we present a method to make a complex tree ensemble interpretable by simplifying the model. Specifically, we formalize the simplification of tree ensembles as a model selection problem. Given a complex tree ensemble, we aim at obtaining the simplest representation that is essentially equivalent to the original one. To this end, we derive a Bayesian model selection algorithm that optimiz…
Feature selection represents a measure to reduce the complexity of high-dimensional datasets and gain insights into the systematic variation in the data. This aspect is of specific importance in domains that rely on model interpretability, such as life sciences. We propose UBayFS, an ensemble feature selection technique embedded in a Bayesian statistical framework. Our approach considers two sources of information: data and domain knowledge. We build a meta-model from an ensemble of elementary feature selectors and aggregate this information in a multinomial likelihood. The user guides UBayFS …
We explore the link between deep ensembles and Gaussian processes (GPs) through the lens of the Neural Tangent Kernel (NTK): a recent development in understanding the training dynamics of wide neural networks (NNs). Previous work has shown that even in the infinite width limit, when NNs become GPs, there is no GP posterior interpretation to a deep ensemble trained with squared error loss. We introduce a simple modification to standard deep ensembles training, through addition of a computationally-tractable, randomised and untrainable function to each ensemble member, that enables a posterior i…
Parameter ensembles or sets of point estimates constitute one of the cornerstones of modern statistical practice. This is especially the case in Bayesian hierarchical models, where different decision-theoretic frameworks can be deployed to summarize such parameter ensembles. The estimation of these parameter ensembles may thus substantially vary depending on which inferential goals are prioritised by the modeller. In this note, we consider the problem of classifying the elements of a parameter ensemble above or below a given threshold. Two threshold classification losses (TCLs) --weighted and …
In this paper, we employ variational arguments to establish a connection between ensemble methods for Neural Networks and Bayesian inference. We consider an ensemble-based scheme where each model/particle corresponds to a perturbation of the data by means of parametric bootstrap and a perturbation of the prior. We derive conditions under which any optimization steps of the particles makes the associated distribution reduce its divergence to the posterior over model parameters. Such conditions do not require any particular form for the approximation and they are purely geometrical, giving insig…
We study the sequential testing problem of two alternative hypotheses regarding an unknown parameter in an exponential family when observations are costly. In a Bayesian setting, the problem can be embedded in a Markovian framework. Using the conditional probability of one of the hypotheses as the underlying spatial variable, we show that the cost function is concave and that the posterior distribution becomes more concentrated as time goes on. Moreover, we study time monotonicity of the value function. For a large class of model specifications, the cost function is non-decreasing in time, and…
It has long been posited that there is a connection between the dynamical equations describing evolutionary processes in biology and sequential Bayesian learning methods. This manuscript describes new research in which this precise connection is rigorously established in the continuous time setting. Here we focus on a partial differential equation known as the Kushner-Stratonovich equation describing the evolution of the posterior density in time. Of particular importance is a piecewise smooth approximation of the observation path from which the discrete time filtering equations, which are sho…
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-…
