This paper presents new theory and methodology for the Bayesian estimation of overfitted hidden Markov models, with finite state space. The goal is then to achieve posterior emptying of extra states. A prior configuration is constructed which favours configurations where the hidden Markov chain remains ergodic although it empties out some of the states. Asymptotic posterior convergence rates are proven theoretically, and demonstrated with a large sample simulation. The problem of overfitted HMMs is then considered in the context of smaller sample sizes, and due to computational and mixing issues two alternative prior structures are studied, one commonly used in practice, and a mixture of the two priors. The Prior Parallel Tempering approach of van Havre (2015) is also extended to HMMs to allow MCMC estimation of the complex posterior space. A replicate simulation study and an in-depth exploration is performed to compare the three priors with hyperparameters chosen according to the asymptotic constraints alongside less informative alternatives.
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.
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.
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…
The use of non parametric hidden Markov models with finite state space is flourishing in practice while few theoretical guarantees are known in this framework. Here, we study asymptotic guarantees for these models in the Bayesian framework. We obtain posterior concentration rates with respect to the $L_1$-norm on joint marginal densities of consecutive observations in a general theorem. We apply this theorem to two cases and obtain minimax concentration rates. We consider discrete observations with emission distributions distributed from a Dirichlet process and continuous observations with emi…
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.
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…
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…
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…
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…
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）
University Lumiere of Lyon 2（里昂第二吕米埃大学）；Chengdu University（成都大学）
As one of Bayesian analysis tools, Hidden Markov Model (HMM) has been used to in extensive applications. Most HMMs are solved by Baum-Welch algorithm (BWHMM) to predict the model parameters, which is difficult to find global optimal solutions. This paper proposes an optimized Hidden Markov Model with Particle Swarm Optimization (PSO) algorithm and so is called PSOHMM. In order to overcome the statistical constraints in HMM, the paper develops re-normalization and re-mapping mechanisms to ensure the constraints in HMM. The experiments have shown that PSOHMM can search better solution than BWHMM…
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.
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 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 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.
In this work, we deal with a bivariate time series of wind speed and direction. Our observed data have peculiar features, such as informative missing values, non-reliable measures under a specific condition and interval-censored data, that we take into account in the model specification. We analyze the time series with a non-parametric Bayesian hidden Markov model, introducing a new emission distribution based on the invariant wrapped Poisson, the Poisson and the hurdle density, suitable to model our data. The model is estimated on simulated datasets and on the real data example that motivated…
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.
We propose to model time-varying periodic and oscillatory processes by means of a hidden Markov model where the states are defined through the spectral properties of a periodic regime. The number of states is unknown along with the relevant periodicities, the role and number of which may vary across states. We address this inference problem by a Bayesian nonparametric hidden Markov model assuming a sticky hierarchical Dirichlet process for the switching dynamics between different states while the periodicities characterizing each state are explored by means of a trans-dimensional Markov chain …
Financial markets exhibit alternating periods of rising and falling prices. Stock traders seeking to make profitable investment decisions have to account for those trends, where the goal is to accurately predict switches from bullish towards bearish markets and vice versa. Popular tools for modeling financial time series are hidden Markov models, where a latent state process is used to explicitly model switches among different market regimes. In their basic form, however, hidden Markov models are not capable of capturing both short- and long-term trends, which can lead to a misinterpretation o…
Paris Nord University（巴黎第十三大学）；IFSTTAR（法国交通与安全科学技术研究所）；Heudiasyc Lab（Heudiasyc实验室）
This paper introduces a novel model-based clustering approach for clustering time series which present changes in regime. It consists of a mixture of polynomial regressions governed by hidden Markov chains. The underlying hidden process for each cluster activates successively several polynomial regimes during time. The parameter estimation is performed by the maximum likelihood method through a dedicated Expectation-Maximization (EM) algorithm. The proposed approach is evaluated using simulated time series and real-world time series issued from a railway diagnosis application. Comparisons with…
