The Pólya tree (PT) process is a general-purpose Bayesian nonparametric model that has found wide application in a range of inference problems. It has a simple analytic form and the posterior computation boils down to beta-binomial conjugate updates along a partition tree over the sample space. Recent development in PT models shows that performance of these models can be substantially improved by (i) allowing the partition tree to adapt to the structure of the underlying distributions and (ii) incorporating latent state variables that characterize local features of the underlying distributions. However, important limitations of the PT remain, including (i) the sensitivity in the posterior inference with respect to the choice of the partition tree, and (ii) the lack of scalability with respect to dimensionality of the sample space. We consider a modeling strategy for PT models that incorporates a flexible prior on the partition tree along with latent states with Markov dependency. We introduce a hybrid algorithm combining sequential Monte Carlo (SMC) and recursive message passing for posterior sampling that can scale up to 100 dimensions. While our description of the algorithm assumes a single computer environment, it has the potential to be implemented on distributed systems to further enhance the scalability. Moreover, we investigate the large sample properties of the tree structures and latent states under the posterior model. We carry out extensive numerical experiments in density estimation and two-group comparison, which show that flexible partitioning can substantially improve the performance of PT models in both inference tasks. We demonstrate an application to a mass cytometry data set with 19 dimensions and over 200,000 observations.
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.
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…
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…
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…
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…
Chopin (2007) introduced a sequentially ordered hidden Markov model, for which states are ordered according to their order of appearance, and claimed that such a model is a re-parametrisation of a standard Markov model. This note gives a formal proof that this equivalence holds in Bayesian terms, as both formulations generate equivalent posterior distributions, but does not hold in Frequentist terms, as both formulations generate incompatible likelihood functions. Perhaps surprisingly, this shows that Bayesian re-parametrisation and Frequentist re-parametrisation are not identical concepts.
Hidden Quantum Markov Models (HQMMs) can be thought of as quantum probabilistic graphical models that can model sequential data. We extend previous work on HQMMs with three contributions: (1) we show how classical hidden Markov models (HMMs) can be simulated on a quantum circuit, (2) we reformulate HQMMs by relaxing the constraints for modeling HMMs on quantum circuits, and (3) we present a learning algorithm to estimate the parameters of an HQMM from data. While our algorithm requires further optimization to handle larger datasets, we are able to evaluate our algorithm using several synthetic…
Hidden semi-Markov models (HSMMs) are latent variable models which allow latent state persistence and can be viewed as a generalization of the popular hidden Markov models (HMMs). In this paper, we introduce a novel spectral algorithm to perform inference in HSMMs. Unlike expectation maximization (EM), our approach correctly estimates the probability of given observation sequence based on a set of training sequences. Our approach is based on estimating moments from the sample, whose number of dimensions depends only logarithmically on the maximum length of the hidden state persistence. Moreove…
In this paper we study posterior consistency for different topologies on the parameters for hidden Markov models with finite state space. We first obtain weak and strong posterior consistency for the marginal density function of finitely many consecutive observations. We deduce posterior consistency for the different components of the parameter. We also obtain posterior consistency for marginal smoothing distributions in the discrete case. We finally apply our results to independent emission probabilities, translated emission probabilities and discrete HMMs, under various types of priors.
Flood extent mapping plays a crucial role in disaster management and national water forecasting. Unfortunately, traditional classification methods are often hampered by the existence of noise, obstacles and heterogeneity in spectral features as well as implicit anisotropic spatial dependency across class labels. In this paper, we propose geographical hidden Markov tree, a probabilistic graphical model that generalizes the common hidden Markov model from a one dimensional sequence to a two dimensional map. Anisotropic spatial dependency is incorporated in the hidden class layer with a reverse t…
In the 1960s, Shiryaev developed a Bayesian theory of change-point detection in the i.i.d. case, which was generalized in the beginning of the 2000s by Tartakovsky and Veeravalli for general stochastic models assuming a certain stability of the log-likelihood ratio process. Hidden Markov models represent a wide class of stochastic processes that are very useful in a variety of applications. In this paper, we investigate the performance of the Bayesian Shiryaev change-point detection rule for hidden Markov models. We propose a set of regularity conditions under which the Shiryaev procedure is f…
Advanced posterior analyses of hidden Markov models: finite Markov chain imbedding and hybrid decoding
National Centre for Register-based Research, Department of Public Health, Aarhus University（丹麦奥胡斯大学公共卫生系注册基于研究国家中心）；Bioinformatics Research Centre, Aarhus University（丹麦奥胡斯大学生物信息学研究中心）；Section for Evolutionary Genomics, Globe Institute, University of Copenhagen（丹麦哥本哈根大学全球研究所进化基因组学部门）；Department of Mathematics, Aarhus University（丹麦奥胡斯大学数学系）
We consider missing data in the context of hidden Markov models with a focus on situations where data is missing not at random (MNAR) and missingness depends on the identity of the hidden states. In simulations, we show that including a submodel for state-dependent missingness reduces bias when data is MNAR and state-dependent, whilst not reducing accuracy when data is missing at random (MAR). When missingness depends on time but not the hidden states, a model which only allows for state-dependent missingness is biased, whilst a model that allows for both state- and time-dependent missingness …
We propose sequential Monte Carlo based algorithms for maximum likelihood estimation of the static parameters in hidden Markov models with an intractable likelihood using ideas from approximate Bayesian computation. The static parameter estimation algorithms are gradient based and cover both offline and online estimation. We demonstrate their performance by estimating the parameters of three intractable models, namely the alpha-stable distribution, g-and-k distribution, and the stochastic volatility model with alpha-stable returns, using both real and synthetic data.
Hidden Markov models provide a natural statistical framework for the detection of the copy number variations (CNV) in genomics. In this paper, we consider a Hidden Markov Model involving several correlated hidden processes at the same time. When dealing with a large number of series, maximum likelihood inference (performed classically using the EM algorithm) becomes intractable. We thus propose an approximate inference algorithm based on a variational approach (VEM). A simulation study is performed to assess the performance of the proposed method and an application to the detection of structur…
In this paper, we prove that finite state space non parametric hidden Markov models are identifiable as soon as the transition matrix of the latent Markov chain has full rank and the emission probability distributions are linearly independent. We then propose several non parametric likelihood based estimation methods, which we apply to models used in applications. We finally show on examples that the use of non parametric modeling and estimation may improve the classification performances.
A simple linear algebraic explanation of the algorithm in "A Spectral Algorithm for Learning Hidden Markov Models" (COLT 2009). Most of the content is in Figure 2; the text just makes everything precise in four nearly-trivial claims.
We propose a unified framework that extends the inference methods for classical hidden Markov models to continuous settings, where both the hidden states and observations occur in continuous time. Two different settings are analyzed: hidden jump process with a finite state space, and hidden diffusion process with a continuous state space. For each setting, we first estimate the hidden states given the observations and model parameters, showing that the posterior distribution of the hidden states can be described by differential equations in continuous time. We then consider the estimation of u…
We introduce multiple hidden Markov models (MHMMs) where an observed multivariate categorical time series depends on an unobservable multivariate Mar- kov chain. MHMMs provide an elegant framework for specifying various independence relationships between multiple discrete time processes. These independencies are interpreted as Markov properties of a mixed graph and a chain graph associated to the latent and observable components of the MHMM, respectively. These Markov properties are also translated into zero restrictions on the parameters of marginal models for the transition probabilities and…
We consider the problem of filtering an unseen Markov chain from noisy observations, in the presence of uncertainty regarding the parameters of the processes involved. Using the theory of nonlinear expectations, we describe the uncertainty in terms of a penalty function, which can be propagated forward in time in the place of the filter.
We consider parameter estimation in finite hidden state space Markov models with time-dependent inhomogeneous noise, where the inhomogeneity vanishes sufficiently fast. Based on the concept of asymptotic mean stationary processes we prove that the maximum likelihood and a quasi-maximum likelihood estimator (QMLE) are strongly consistent. The computation of the QMLE ignores the inhomogeneity, hence, is much simpler and robust. The theory is motivated by an example from biophysics and applied to a Poisson- and linear Gaussian model.
