The use of non-differentiable priors in Bayesian statistics has become increasingly popular, in particular in Bayesian imaging analysis. Current state of the art methods are approximate in the sense that they replace the posterior with a smooth approximation via Moreau-Yosida envelopes, and apply gradient-based discretized diffusions to sample from the resulting distribution. We characterize the error of the Moreau-Yosida approximation and propose a novel implementation using underdamped Langevin dynamics. In misson-critical cases, however, replacing the posterior with an approximation may not be a viable option. Instead, we show that Piecewise-Deterministic Markov Processes (PDMP) can be utilized for exact posterior inference from distributions satisfying almost everywhere differentiability. Furthermore, in contrast with diffusion-based methods, the suggested PDMP-based samplers place no assumptions on the prior shape, nor require access to a computationally cheap proximal operator, and consequently have a much broader scope of application. Through detailed numerical examples, including a non-differentiable circular distribution and a non-convex genomics model, we elucidate the relative strengths of these sampling methods on problems of moderate to high dimensions, underlining the benefits of PDMP-based methods when accurate sampling is decisive.
Bayesian inference for Markov jump processes (MJPs) where available observations relate to either system states or jumps typically relies on data-augmentation Markov Chain Monte Carlo. State-of-the-art developments involve representing MJP paths with auxiliary candidate jump times that are later thinned. However, these algorithms are i) unfeasible in situations involving large or infinite capacity systems and ii) not amenable for all observation types. In this paper we establish and present a general data-augmentation framework for population MJPs based on uniformized representations of the un…
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 consider the modeling of data generated by a latent continuous-time Markov jump process with a state space of finite but unknown dimensions. Typically in such models, the number of states has to be pre-specified, and Bayesian inference for a fixed number of states has not been studied until recently. In addition, although approaches to address the problem for discrete-time models have been developed, no method has been successfully implemented for the continuous-time case. We focus on reversible jump Markov chain Monte Carlo which allows the trans-dimensional move among different numbers of…
We present new methodologies for Bayesian inference on the rate parameters of a discretely observed continuous-time Markov jump processes with a countably infinite state space. The usual method of choice for inference, particle Markov chain Monte Carlo (particle MCMC), struggles when the observation noise is small. We consider the most challenging regime of exact observations and provide two new methodologies for inference in this case: the minimal extended state space algorithm (MESA) and the nearly minimal extended state space algorithm (nMESA). By extending the Markov chain Monte Carlo stat…
Learning the structure of Bayesian networks is a difficult combinatorial optimization problem. In this paper, we consider learning of tree-augmented naive Bayes (TAN) structures for Bayesian network classifiers with discrete input features. Instead of performing a combinatorial optimization over the space of possible graph structures, the proposed method learns a distribution over graph structures. After training, we select the most probable structure of this distribution. This allows for a joint training of the Bayesian network parameters along with its TAN structure using gradient-based opti…
ETH Zurich（苏黎世联邦理工学院）；MPI for Intelligent Systems（马克斯·普朗克智能系统研究所）
Bayesian structure learning allows inferring Bayesian network structure from data while reasoning about the epistemic uncertainty -- a key element towards enabling active causal discovery and designing interventions in real world systems. In this work, we propose a general, fully differentiable framework for Bayesian structure learning (DiBS) that operates in the continuous space of a latent probabilistic graph representation. Contrary to existing work, DiBS is agnostic to the form of the local conditional distributions and allows for joint posterior inference of both the graph structure and t…
When statistical analyses consider multiple data sources, Markov melding provides a method for combining the source-specific Bayesian models. Markov melding joins together submodels that have a common quantity. One challenge is that the prior for this quantity can be implicit, and its prior density must be estimated. We show that error in this density estimate makes the two-stage Markov chain Monte Carlo sampler employed by Markov melding unstable and unreliable. We propose a robust two-stage algorithm that estimates the required prior marginal self-density ratios using weighted samples, drama…
The literature on Bayesian methods for the analysis of discrete-time semi-Markov processes is sparse. In this paper, we introduce the semi-Markov beta-Stacy process, a stochastic process useful for the Bayesian non-parametric analysis of semi-Markov processes. The semi-Markov beta-Stacy process is conjugate with respect to data generated by a semi-Markov process, a property which makes it easy to obtain probabilistic forecasts. Its predictive distributions are characterized by a reinforced random walk on a system of urns.
We propose a new Bayesian Markov switching regression model for multidimensional arrays (tensors) of binary time series. We assume a zero-inflated logit regression with time-varying parameters and apply it to multilayer temporal networks. The original contribution is threefold. First, to avoid over-fitting we propose a parsimonious parametrization based on a low-rank decomposition of the tensor of regression coefficients. Second, we assume the parameters are driven by a hidden Markov chain, thus allowing for structural changes in the network topology. We follow a Bayesian approach to inference…
We develop clustering procedures for longitudinal trajectories based on a continuous-time hidden Markov model (CTHMM) and a generalized linear observation model. Specifically in this paper, we carry out finite and infinite mixture model-based clustering for a CTHMM and achieve inference using Markov chain Monte Carlo (MCMC). For a finite mixture model with prior on the number of components, we implement reversible-jump MCMC to facilitate the trans-dimensional move between different number of clusters. For a Dirichlet process mixture model, we utilize restricted Gibbs sampling split-merge propo…
We consider the problem of flexible modeling of higher order hidden Markov models when the number of latent states and the nature of the serial dependence, including the true order, are unknown. We propose Bayesian nonparametric methodology based on tensor factorization techniques that can characterize any transition probability with a specified maximal order, allowing automated selection of the important lags and capturing higher order interactions among the lags. Theoretical results provide insights into identifiability of the emission distributions and asymptotic behavior of the posterior. …
We consider the problem of flexible modeling of higher order Markov chains when an upper bound on the order of the chain is known but the true order and nature of the serial dependence are unknown. We propose Bayesian nonparametric methodology based on conditional tensor factorizations, which can characterize any transition probability with a specified maximal order. The methodology selects the important lags and captures higher order interactions among the lags, while also facilitating calculation of Bayes factors for a variety of hypotheses of interest. We design efficient Markov chain Monte…
In this article a flexible Bayesian non-parametric model is proposed for non-homogeneous hidden Markov models. The model is developed through the amalgamation of the ideas of hidden Markov models and predictor dependent stick-breaking processes. Computation is carried out using auxiliary variable representation of the model which enable us to perform exact MCMC sampling from the posterior. Furthermore, the model is extended to the situation when the predictors can simultaneously in influence the transition dynamics of the hidden states as well as the emission distribution. Estimates of few ste…
There is much interest in the Hierarchical Dirichlet Process Hidden Markov Model (HDP-HMM) as a natural Bayesian nonparametric extension of the ubiquitous Hidden Markov Model for learning from sequential and time-series data. However, in many settings the HDP-HMM's strict Markovian constraints are undesirable, particularly if we wish to learn or encode non-geometric state durations. We can extend the HDP-HMM to capture such structure by drawing upon explicit-duration semi-Markovianity, which has been developed mainly in the parametric frequentist setting, to allow construction of highly interp…
We propose a Bayesian inference approach for a class of latent Markov models. These models are widely used for the analysis of longitudinal categorical data, when the interest is in studying the evolution of an individual unobservable characteristic. We consider, in particular, the basic latent Markov, which does not account for individual covariates, and its version that includes such covariates in the measurement model. The proposed inferential approach is based on a system of priors formulated on a transformation of the initial and transition probabilities of the latent Markov chain. This s…
We propose a Bayesian hidden Markov model for analyzing time series and sequential data where a special structure of the transition probability matrix is embedded to model explicit-duration semi-Markovian dynamics. Our formulation allows for the development of highly flexible and interpretable models that can integrate available prior information on state durations while keeping a moderate computational cost to perform efficient posterior inference. We show the benefits of choosing a Bayesian approach for HSMM estimation over its frequentist counterpart, in terms of model selection and out-of-…
Gatsby Computational Neuroscience Unit（盖比计算神经科学单元）；University College London（伦敦大学学院）
Markov jump processes and continuous time Bayesian networks are important classes of continuous time dynamical systems. In this paper, we tackle the problem of inferring unobserved paths in these models by introducing a fast auxiliary variable Gibbs sampler. Our approach is based on the idea of uniformization, and sets up a Markov chain over paths by sampling a finite set of virtual jump times and then running a standard hidden Markov model forward filtering-backward sampling algorithm over states at the set of extant and virtual jump times. We demonstrate significant computational benefits ov…
We develop two models for Bayesian estimation and selection in high-order, discrete-state Markov chains. Both are based on the mixture transition distribution, which constructs a transition probability tensor with additive mixing of probabilities from first-order transition matrices. We demonstrate two uses for the proposed models: parsimonious approximation of high-order dynamics by mixing lower-order transition models, and order/lag selection through over-specification and shrinkage via priors for sparse probability vectors. The priors further shrink all models to an identifiable and interpr…
Studying the neurological, genetic and evolutionary basis of human vocal communication mechanisms using animal vocalization models is an important field of neuroscience. The data sets typically comprise structured sequences of syllables or `songs' produced by animals from different genotypes under different social contexts. We develop a novel Bayesian semiparametric framework for inference in such data sets. Our approach is built on a novel class of mixed effects Markov transition models for the songs that accommodates exogenous influences of genotype and context as well as animal-specific het…
This paper presents a Bayesian method for identification of jump Markov linear system parameters. A primary motivation is to provide accurate quantification of parameter uncertainty without relying on asymptotic in data-length arguments. To achieve this, the paper details a particle-Gibbs sampling approach that provides samples from the desired posterior distribution. These samples are produced by utilising a modified discrete particle filter and carefully chosen conjugate priors.
We introduce a framework for efficient Markov Chain Monte Carlo (MCMC) algorithms targeting discrete-valued high-dimensional distributions, such as posterior distributions in Bayesian variable selection (BVS) problems. We show that many recently introduced algorithms, such as the locally informed sampler and the Adaptively Scaled Individual adaptation sampler (ASI), can be viewed as particular cases within the framework. We then describe a novel algorithm, the Adaptive Random Neighbourhood Informed sampler (ARNI), by combining ideas from both of these existing approaches. We show using several…
We formulate Bayesian updates in Markov processes by means of path integral techniques and derive the imaginary-time Schrödinger equation with likelihood to direct the inference incorporated as a potential for the posterior probability distribution
We consider the analysis of sets of categorical sequences consisting of piecewise homogeneous Markov segments. The sequences are assumed to be governed by a common underlying process with segments occurring in the same order for each sequence. Segments are defined by a set of unobserved changepoints where the positions and number of changepoints can vary from sequence to sequence. We propose a Bayesian framework for analyzing such data, placing priors on the locations of the changepoints and on the transition matrices and using Markov chain Monte Carlo (MCMC) techniques to obtain posterior sam…
This paper reviews recent advances in Bayesian nonparametric techniques for constructing and performing inference in infinite hidden Markov models. We focus on variants of Bayesian nonparametric hidden Markov models that enhance a posteriori state-persistence in particular. This paper also introduces a new Bayesian nonparametric framework for generating left-to-right and other structured, explicit-duration infinite hidden Markov models that we call the infinite structured hidden semi-Markov model.
This paper presents a complete methodology for Bayesian inference on a semi-Markov process, from the elicitation of the prior distribution, to the computation of posterior summaries, including a guidance for its JAGS implementation. The holding times (conditional on the transition between two given states) are assumed to be Weibull-distributed. We examine the elicitation of the joint prior density of the shape and scale parameters of the Weibull distributions, deriving a specific class of priors in a natural way, along with a method for the determination of hyperparameters based on ``learning …
The Markov Chain Monte Carlo method is the dominant paradigm for posterior computation in Bayesian analysis. It is common to control computation time by making approximations to the Markov transition kernel. Comparatively little attention has been paid to computational optimality in these approximating Markov Chains, or when such approximations are justified relative to obtaining shorter paths from the exact kernel. We give simple, sharp bounds for uniform approximations of uniformly mixing Markov chains. We then suggest a notion of optimality that incorporates computation time and approximati…
University of Tartu（塔尔图大学）；Royal Holloway, University of London（伦敦大学皇家霍洛威学院）
We consider the problem of estimating the maximum posterior probability (MAP) state sequence for a finite state and finite emission alphabet hidden Markov model (HMM) in the Bayesian setup, where both emission and transition matrices have Dirichlet priors. We study a training set consisting of thousands of protein alignment pairs. The training data is used to set the prior hyperparameters for Bayesian MAP segmentation. Since the Viterbi algorithm is not applicable any more, there is no simple procedure to find the MAP path, and several iterative algorithms are considered and compared. The main…
Battery impedance spectroscopy models are given by fractional order (FO) differential equations. In the discrete-time domain, they give rise to state-space models where the latent process is not Markovian. Parameter estimation for these models is therefore challenging, especially for non-commensurate FO models. In this paper, we propose a Bayesian approach to identify the parameters of generic FO systems. The computational challenge is tackled with particle Markov chain Monte Carlo methods, with an implementation specifically designed for the non-Markovian setting. The approach is then applied…
We generalise an existing construction of Bayesian Lenses to admit lenses between pairs of objects where the backwards object is dependent on states on the forwards object (interpreted as probability distributions). This gives a natural setting for studying stochastic maps with Bayesian inverses restricted to the points supported by a given prior. In order to state this formally we develop a proposed definition by Fritz of a support object in a Markov category and show that these give rise to a section into the category of dependent Bayesian lenses encoding a more canonical notion of Bayesian …
The article studies different methods for estimating the Viterbi path in the Bayesian framework. The Viterbi path is an estimate of the underlying state path in hidden Markov models (HMMs), which has a maximum posterior probability (MAP). For an HMM with given parameters, the Viterbi path can be easily found with the Viterbi algorithm. In the Bayesian framework the Viterbi algorithm is not applicable and several iterative methods can be used instead. We introduce a new EM-type algorithm for finding the MAP path and compare it with various other methods for finding the MAP path, including the v…
We discuss and extend methods for estimating Markovian-Regime-Switching (MRS) and trend models for wholesale electricity prices. We argue the existing methods of trend estimation used in the electricity price modelling literature either require an ambiguous definition of an extreme price, or lead to issues when implementing model selection [23]. The first main contribution of this paper is to design and infer a model which has a model-based definition of extreme prices and permits the use of model selection criteria. Due to the complexity of the MRS models inference is not straightforward. In …
The Markov chain random field (MCRF) model/theory provides a non-linear spatial Bayesian updating solution at the neighborhood nearest data level for simulating categorical spatial variables. In the MCRF solution, the spatial dependencies among nearest data and the central random variable is a probabilistic directed acyclic graph that conforms to a neighborhood-based Bayesian network on spatial data. By selecting different neighborhood sizes and structures, applying the spatial conditional independence assumption to nearest neighbors, or incorporating ancillary information, one may construct s…
Optimal designs minimize the number of experimental runs (samples) needed to accurately estimate model parameters, resulting in algorithms that, for instance, efficiently minimize parameter estimate variance. Governed by knowledge of past observations, adaptive approaches adjust sampling constraints online as model parameter estimates are refined, continually maximizing expected information gained or variance reduced. We apply adaptive Bayesian inference to estimate transition rates of Markov chains, a common class of models for stochastic processes in nature. Unlike most previous studies, our…
This paper introduces a new model for panel data with Markov-switching GARCH effects. The model incorporates a series-specific hidden Markov chain process that drives the GARCH parameters. To cope with the high-dimensionality of the parameter space, the paper exploits the cross-sectional clustering of the series by first assuming a soft parameter pooling through a hierarchical prior distribution with two-step procedure, and then introducing clustering effects in the parameter space through a nonparametric prior distribution. The model and the proposed inference are evaluated through a simulati…
Graphical models express conditional independence relationships among variables. Although methods for vector-valued data are well established, functional data graphical models remain underdeveloped. We introduce a notion of conditional independence between random functions, and construct a framework for Bayesian inference of undirected, decomposable graphs in the multivariate functional data context. This framework is based on extending Markov distributions and hyper Markov laws from random variables to random processes, providing a principled alternative to naive application of multivariate m…
Due to the escalating growth of big data sets in recent years, new Bayesian Markov chain Monte Carlo (MCMC) parallel computing methods have been developed. These methods partition large data sets by observations into subsets. However, for Bayesian nested hierarchical models, typically only a few parameters are common for the full data set, with most parameters being group-specific. Thus, parallel Bayesian MCMC methods that take into account the structure of the model and split the full data set by groups rather than by observations are a more natural approach for analysis. Here, we adapt and e…
Stationary time series models built from parametric distributions are, in general, limited in scope due to the assumptions imposed on the residual distribution and autoregression relationship. We present a modeling approach for univariate time series data, which makes no assumptions of stationarity, and can accommodate complex dynamics and capture nonstandard distributions. The model for the transition density arises from the conditional distribution implied by a Bayesian nonparametric mixture of bivariate normals. This implies a flexible autoregressive form for the conditional transition dens…
When performing Bayesian computations in practice, one is often faced with the challenge that the constituent model components and/or the data are only available in a distributed fashion, e.g. due to privacy concerns or sheer volume. While various methods have been proposed for performing posterior inference in such federated settings, these either make very strong assumptions on the data and/or model or otherwise introduce significant bias when the local posteriors are combined to form an approximation of the target posterior. By leveraging recently developed methods for Markov Chain Monte Ca…
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…
University of Cambridge（剑桥大学）；CREST—ENSAE（法国国家统计与经济研究所-国立统计与经济管理学院）；HEC Paris（巴黎高等商学院）；University of Bristol（布里斯托大学）
We consider the inverse reinforcement learning problem, that is, the problem of learning from, and then predicting or mimicking a controller based on state/action data. We propose a statistical model for such data, derived from the structure of a Markov decision process. Adopting a Bayesian approach to inference, we show how latent variables of the model can be estimated, and how predictions about actions can be made, in a unified framework. A new Markov chain Monte Carlo (MCMC) sampler is devised for simulation from the posterior distribution. This step includes a parameter expansion step, wh…
Max-linear Bayesian networks have emerged as highly applicable models for causal inference via extreme value data. However, conditional independence (CI) for max-linear Bayesian networks behaves differently than for classical Gaussian Bayesian networks. We establish the parallel between the two theories via tropicalization, and establish the surprising result that the Markov equivalence classes for max-linear Bayesian networks coincide with the ones obtained by regular CI. Our paper opens up many problems at the intersection of extreme value statistics, causal inference and tropical geometry.
Background. Health economic evaluations of interventions against infectious diseases are commonly based on the predictions of ordinary differential equation (ODE) systems or Markov models (MMs). Standard MMs are static, whereas ODE systems are usually dynamic and account for herd immunity which is crucial to prevent overestimation of infection prevalence. Complex ODE systems including probabilistic model parameters are computationally intensive. Thus, mainly ODE-based models including deterministic parameters are presented in the literature. These do not account for parameter uncertainty. As a…
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…
Measure-valued Markov chains have raised interest in Bayesian nonparametrics since the seminal paper by (Math. Proc. Cambridge Philos. Soc. 105 (1989) 579--585) where a Markov chain having the law of the Dirichlet process as unique invariant measure has been introduced. In the present paper, we propose and investigate a new class of measure-valued Markov chains defined via exchangeable sequences of random variables. Asymptotic properties for this new class are derived and applications related to Bayesian nonparametric mixture modeling, and to a generalization of the Markov chain proposed by (M…
People are living longer than ever before, and with this arises new complications and challenges for humanity. Among the most pressing of these challenges is of understanding the role of aging in the development of dementia. This paper is motivated by the Mayo Clinic Study of Aging data for 4742 subjects since 2004, and how it can be used to draw inference on the role of aging in the development of dementia. We construct a hidden Markov model (HMM) to represent progression of dementia from states associated with the buildup of amyloid plaque in the brain, and the loss of cortical thickness. A …
The use of the Bayesian tools in system identification and model updating paradigms has been increased in the last ten years. Usually, the Bayesian techniques can be implemented to incorporate the uncertainties associated with measurements as well as the prediction made by the finite element model (FEM) into the FEM updating procedure. In this case, the posterior distribution function describes the uncertainty in the FE model prediction and the experimental data. Due to the complexity of the modeled systems, the analytical solution for the posterior distribution function may not exist. This le…
This paper considers a Bayesian view for estimating a sub-network in a Markov random field. The sub-network corresponds to the Markov blanket of a set of query variables, where the set of potential neighbours here is big. We factorize the posterior such that the Markov blanket is conditionally independent of the network of the potential neighbours. By exploiting this blockwise decoupling, we derive analytic expressions for posterior conditionals. Subsequently, we develop an inference scheme which makes use of the factorization. As a result, estimation of a sub-network is possible without infer…
In this paper, we consider Bayesian image denoising based on a Gaussian Markov random field (GMRF) model, for which we propose an new algorithm. Our method can solve Bayesian image denoising problems, including hyperparameter estimation, in $O(n)$-time, where $n$ is the number of pixels in a given image. From the perspective of the order of the computational time, this is a state-of-the-art algorithm for the present problem setting. Moreover, the results of our numerical experiments we show our method is in fact effective in practice.
