Estimating the order of a hidden markov model

While the estimation of the parameters of a hidden Markov model has been studied extensively, the consistent estimation of the number of hidden states is still an unsolved problem. The AIC and BIC methods are used most commonly, but their use in this context has not been justified theoretically. The author shows that for many common models, the penalized minimum‐distance method yields a consistent estimate of the number of hidden states in a stationary hidden Markov model. In addition to addressing the identifiability issues, she applies her method to a multiple sclerosis data set and assesses its performance via simulation.     

Semiparametric hidden Markov model with non-parametric regression

The hidden Markov model regression (HMMR) has been popularly used in many fields such as gene expression and activity recognition. However, the traditional HMMR requires the strong linearity assumption for the emission model. In this article, we propose a hidden Markov model with non-parametric regression (HMM-NR), where the mean and variance of emission model are unknown smooth functions. The new semiparametric model might greatly reduce the modeling bias and thus enhance the applicability of the traditional hidden Markov model regression. We propose an estimation procedure for the transition probability matrix and the non-parametric mean and variance functions by combining the ideas of the EM algorithm and the kernel regression. Simulation studies and a real data set application are used to demonstrate the effectiveness of the new estimation procedure.     

A Monte Carlo method for filtering a marked doubly stochastic Poisson process

The author provides an approximated solution for the filtering of a state-space model, where the hidden state process is a continuous-time pure jump Markov process and the observations come from marked point processes. Each state k corresponds to a different marked point process, defined by its conditional intensity function λ _k (t). When a state is visited by the hidden process, the corresponding marked point process is observed. The filtering equations are obtained by applying the innovation method and the integral representation theorem of a point process martingale. Since the filtering equations belong to the family of Kushner–Stratonovich equations, an iterative solution is calculated. The theoretical solution is approximated and a Monte Carlo integration technique employed to implement it. The sequential method has been tested on a simulated data set based on marked point processes widely used in the statistical analysis of seismic sequences: the Poisson model, the stress release model and the Etas model.     

High-order extensions of the Double Chain Markov Model

The Double Chain Markov Model is a fully Markovian model for the representation of time-series in random environments. In this article, we show that it can handle transitions of high-order between both a set of observations and a set of hidden states. In order to reduce the number of parameters, each transition matrix can be replaced by a Mixture Transition Distribution model. We provide a complete derivation of the algorithms needed to compute the model. Three applications, the analysis of a sequence of DNA, the song of the wood pewee, and the behavior of young monkeys show that this model is of great interest for the representation of data that can be decomposed into a finite set of patterns.     

MAP segmentation in Bayesian hidden Markov models: a case study

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 goal of the paper is to test the Bayesian setup against the frequentist one, where the parameters of HMM are estimated using the training data.     

VARIATIONAL BAYESIAN ANALYSIS FOR HIDDEN MARKOV MODELS

The variational approach to Bayesian inference enables simultaneous estimation of model parameters and model complexity. An interesting feature of this approach is that it also leads to an automatic choice of model complexity. Empirical results from the analysis of hidden Markov models with Gaussian observation densities illustrate this. If the variational algorithm is initialized with a large number of hidden states, redundant states are eliminated as the method converges to a solution, thereby leading to a selection of the number of hidden states. In addition, through the use of a variational approximation, the deviance information criterion for Bayesian model selection can be extended to the hidden Markov model framework. Calculation of the deviance information criterion provides a further tool for model selection, which can be used in conjunction with the variational approach.     

Forecasting with non-homogeneous hidden Markov models

We present a Bayesian forecasting methodology of discrete-time finite state-space hidden Markov models with non-constant transition matrix that depends on a set of exogenous covariates. We describe an MCMC reversible jump algorithm for predictive inference, allowing for model uncertainty regarding the set of covariates that affect the transition matrix. We apply our models to interest rates and we show that our general model formulation improves the predictive ability of standard homogeneous hidden Markov models.     

A non-homogeneous hidden Markov model for predicting the distribution of sea surface elevation

The prediction problem of sea state based on the field measurements of wave and meteorological factors is a topic of interest from the standpoints of navigation safety and fisheries. Various statistical methods have been considered for the prediction of the distribution of sea surface elevation. However, prediction of sea state in the transitional situation when waves are developing by blowing wind has been a difficult problem until now, because the statistical expression of the dynamic mechanism during this situation is very complicated. In this article, we consider this problem through the development of a statistical model. More precisely, we develop a model for the prediction of the time-varying distribution of sea surface elevation, taking into account a non-homogeneous hidden Markov model in which the time-varying structures are influenced by wind speed and wind direction. Our prediction experiments suggest the possibility that the proposed model contributes to an improvement of the prediction accuracy by using a homogenous hidden Markov model. Furthermore, we found that the prediction accuracy is influenced by the circular distribution of the circular hidden Markov model for the directional time series wind direction data.     

Logistic regression analysis of non‐randomized response data collected by the parallel model in sensitive surveys

To study the relationship between a sensitive binary response variable and a set of non‐sensitive covariates, this paper develops a hidden logistic regression to analyse non‐randomized response data collected via the parallel model originally proposed by Tian (2014). This is the first paper to employ the logistic regression analysis in the field of non‐randomized response techniques. Both the Newton–Raphson algorithm and a monotone quadratic lower bound algorithm are developed to derive the maximum likelihood estimates of the parameters of interest. In particular, the proposed logistic parallel model can be used to study the association between a sensitive binary variable and another non‐sensitive binary variable via the measure of odds ratio. Simulations are performed and a study on people's sexual practice data in the United States is used to illustrate the proposed methods.     

Analysis of nonlinear state space model with dependent measurement noises

This paper presents a nonlinear state space model with considering a first-order autoregressive model for measurement noises. A recursive method using Taylor series based approximations for filtering, prediction and smoothing problem of hidden states from the noisy observations is designed. Also, an expectation-maximization algorithm for calculating the maximum likelihood estimators of parameters is presented. The closed form solutions are obtained for estimating of the hidden states and the unknown parameters. Finally, the performance of the designed methods are verified in a simulation study.     

REVERSIBLE JUMP MARKOV CHAIN MONTE CARLO METHODS AND SEGMENTATION ALGORITHMS IN HIDDEN MARKOV MODELS

We consider hidden Markov models with an unknown number of regimes for the segmentation of the pixel intensities of digital images that consist of a small set of colours. New reversible jump Markov chain Monte Carlo algorithms to estimate both the dimension and the unknown parameters of the model are introduced. Parameters are updated by random walk Metropolis–Hastings moves, without updating the sequence of the hidden Markov chain. The segmentation (i.e. the estimation of the hidden regimes) is a further aim and is performed by means of a number of competing algorithms. We apply our Bayesian inference and segmentation tools to digital images, which are linearized through the Peano–Hilbert scan, and perform experiments and comparisons on both synthetic images and a real brain magnetic resonance image.     

A non-homogeneous hidden Markov model for precipitation occurrence

A non-homogeneous hidden Markov model is proposed for relating precipitation occurrences at multiple rain-gauge stations to broad scale atmospheric circulation patterns (the so-called 'downscaling problem'). We model a 15-year sequence of winter data from 30 rain stations in south-western Australia. The first 10 years of data are used for model development and the remaining 5 years are used for model evaluation. The fitted model accurately reproduces the observed rainfall statistics in the reserved data despite a shift in atmospheric circulation (and, consequently, rainfall) between the two periods. The fitted model also provides some useful insights into the processes driving rainfall in this region.     

Bayesian neural networks for nonlinear time series forecasting

In this article, we apply Bayesian neural networks (BNNs) to time series analysis, and propose a Monte Carlo algorithm for BNN training. In addition, we go a step further in BNN model selection by putting a prior on network connections instead of hidden units as done by other authors. This allows us to treat the selection of hidden units and the selection of input variables uniformly. The BNN model is compared to a number of competitors, such as the Box-Jenkins model, bilinear model, threshold autoregressive model, and traditional neural network model, on a number of popular and challenging data sets. Numerical results show that the BNN model has achieved a consistent improvement over the competitors in forecasting future values. Insights on how to improve the generalization ability of BNNs are revealed in many respects of our implementation, such as the selection of input variables, the specification of prior distributions, and the treatment of outliers.     

Hierarchical Bayesian Approach to a Multi-Site Hidden Markov Model

Multivariate data with a sequential or temporal structure occur in various fields of study. The hidden Markov model (HMM) provides an attractive framework for modeling long-term persistence in areas of pattern recognition through the extension of independent and identically distributed mixture models. Unlike in typical mixture models, the heterogeneity of data is represented by hidden Markov states. This article extends the HMM to a multi-site or multivariate case by taking a hierarchical Bayesian approach. This extension has many advantages over a single-site HMM. For example, it can provide more information for identifying the structure of the HMM than a single-site analysis. We evaluate the proposed approach by exploiting a spatial correlation that depends on the distance between sites.     

Spatial hidden Markov models and species distributions

A spatial hidden Markov model (SHMM) is introduced to analyse the distribution of a species on an atlas, taking into account that false observations and false non-detections of the species can occur during the survey, blurring the true map of presence and absence of the species. The reconstruction of the true map is tackled as the restoration of a degraded pixel image, where the true map is an autologistic model, hidden behind the observed map, whose normalizing constant is efficiently computed by simulating an auxiliary map. The distribution of the species is explained under the Bayesian paradigm and Markov chain Monte Carlo (MCMC) algorithms are developed. We are interested in the spatial distribution of the bird species Greywing Francolin in the south of Africa. Many climatic and land-use explanatory variables are also available: they are included in the SHMM and a subset of them is selected by the mutation operators within the MCMC algorithm.     

The double chain markov model

In the class of discrete time Markovian processes, two models are widely used, the Markov chain and the hidden Markov model. A major difference between these two models lies in the relation between successive outputs of the observed variable. In a visible Markov chain, these are directly correlated while in hidden models they are not. However, in some situations it is possible to observe both a hidden Markov chain and a direct relation between successive observed outputs. Unfortunately, the use of either a visible or a hidden model implies the suppression of one of these hypothesis. This paper prsents a Markovian model under random environment called the Double Chain Markov Model which takes into account the maijn features of both visible and hidden models. Its main purpose is the modeling of non-homogeneous time-series. It is very flexible and can be estimated with traditional methods. The model is applied on a sequence of wind speeds and it appears to model data more successfully than both the usual Markov chains and hidden Markov models.     

Spatial modelling for binary data using␣a␣hidden conditional autoregressive Gaussian process: a multivariate extension of the probit model

A Bayesian approach to modelling binary data on a regular lattice is introduced. The method uses a hierarchical model where the observed data is the sign of a hidden conditional autoregressive Gaussian process. This approach essentially extends the familiar probit model to dependent data. Markov chain Monte Carlo simulations are used on real and simulated data to estimate the posterior distribution of the spatial dependency parameters and the method is shown to work well. The method can be straightforwardly extended to regression models.     

On-Line Learning for the Infinite Hidden Markov Model

We develop a sequential Monte Carlo algorithm for the infinite hidden Markov model (iHMM) that allows us to perform on-line inferences on both system states and structural (static) parameters. The algorithm described here provides a natural alternative to Markov chain Monte Carlo samplers previously developed for the iHMM, and is particularly helpful in applications where data is collected sequentially and model parameters need to be continuously updated. We illustrate our approach in the context of both a simulation study and a financial application.     

ESTIMATING COMPONENTS IN FINITE MIXTURES AND HIDDEN MARKOV MODELS

When the unobservable Markov chain in a hidden Markov model is stationary the marginal distribution of the observations is a finite mixture with the number of terms equal to the number of the states of the Markov chain. This suggests the number of states of the unobservable Markov chain can be estimated by determining the number of mixture components in the marginal distribution. This paper presents new methods for estimating the number of states in a hidden Markov model, and coincidentally the unknown number of components in a finite mixture, based on penalized quasi‐likelihood and generalized quasi‐likelihood ratio methods constructed from the marginal distribution. The procedures advocated are simple to calculate, and results obtained in empirical applications indicate that they are as effective as current available methods based on the full likelihood. Under fairly general regularity conditions, the methods proposed generate strongly consistent estimates of the unknown number of states or components.     

Inference for a Hidden Truncated (Both-Sided) Bivariate Pareto (II) Distribution

The Pareto distribution is a simple model for non negative data with a power law probability tail. Income and wealth data are typically modeled using some variant of the classical Pareto distribution. In practice, it is frequently likely that the observed data have been truncated with respect to some unobserved covariable. In this paper, a hidden truncation formulation of this scenario is proposed and analyzed. A bivariate Pareto (II) distribution is assumed for the variable of interest and the unobserved covariable. Distributional properties of the resulting model are investigated. A variety of parameter estimation strategies (under the classical set up) are investigated.