Bayesian Monte Carlo estimation for profile hidden Markov models

Hidden Markov models are used as tools for pattern recognition in a number of areas, ranging from speech processing to biological sequence analysis. Profile hidden Markov models represent a class of so-called “left–right” models that have an architecture that is specifically relevant to classification of proteins into structural families based on their amino acid sequences. Standard learning methods for such models employ a variety of heuristics applied to the expectation-maximization implementation of the maximum likelihood estimation procedure in order to find the global maximum of the likelihood function. Here, we compare maximum likelihood estimation to fully Bayesian estimation of parameters for profile hidden Markov models with a small number of parameters. We find that, relative to maximum likelihood methods, Bayesian methods assign higher scores to data sequences that are distantly related to the pattern consensus, show better performance in classifying these sequences correctly, and continue to perform robustly with regard to misspecification of the number of model parameters. Though our study is limited in scope, we expect our results to remain relevant for models with a large number of parameters and other types of left–right hidden Markov models.     

基于EM算法隐Markov模型参数估计

描述最大似然参数估计问题,介绍如何用EM算法求解最大似然参数估计.首先给出EM算法的抽象形式,然后介绍EM算法的一个应用:求隐Markov模型中的参数估计.用EM算法推导出隐Markov模型中参数的迭代公式.     

Interactive hidden Markov models and their applications

^** Email: wching{at}hkusua.hku.hk In this paper, we propose an Interactive hidden Markov model(IHMM). In a traditional HMM, the observable states are affecteddirectly by the hidden states, but not vice versa. In the proposedIHMM, the transitions of hidden states depend on the observablestates. We also develop an efficient estimation method for themodel parameters. Numerical examples on the sales demand dataand economic data are given to demonstrate the applicabilityof the model.     

基于动态规划的高阶隐马氏模型推广的Viterbi算法

首先通过Hadar等价变换方法将高阶隐马氏模型转换为与之等价的一阶向量值隐马氏模型,然后利用动态规划原理建立了一阶向量值隐马氏模型的Viterbi算法,最后通过高阶隐马氏模型和一阶向量值隐马氏模型之间的等价关系建立了高阶隐马氏模型基于动态规划推广的Viterbi算法．研究结果在一定程度上推广了几乎所有隐马氏模型文献中所涉及到的解码问题的Viterbi算法,从而进一步丰富和发展了高阶隐马氏模型的算法理论．     

可列非齐次隐Markov模型的强大数定律

隐马尔科夫模型被广泛的应用于弱相依随机变量的建模,是研究神经生理学、发音过程和生物遗传等问题的有力工具。研究了可列非齐次隐 Markov 模型的若干性质,得到了这类模型的强大数定律,推广了有限非齐次马氏链的一类强大数定律。     

Maximum likelihood estimator for hidden Markov models in continuous time

The paper studies large sample asymptotic properties of the Maximum Likelihood Estimator (MLE) for the parameter of a continuous time Markov chain, observed in white noise. Using the method of weak convergence of likelihoods due to Ibragimov and Khasminskii (Statistical estimation, vol 16 of Applications of mathematics. Springer-Verlag, New York), consistency, asymptotic normality and convergence of moments are established for MLE under certain strong ergodicity assumptions on the chain. This article has been written during the author’s visit at Laboratoire de Statistique et Processus, Universite du Maine, France, supported by the Chateaubriand fellowship.     

Asymptotic behavior of Bayes estimators for hidden Markov models with application to ion channels

In this paper we study the asymptotic behavior of Bayes estimators for hidden Markov models as the number of observations goes to infinity. The theorem that we prove is similar to the Bernstein—von Mises theorem on the asymptotic behavior of the posterior distribution for the case of independent observations. We show that our theorem is applicable to a wide class of hidden Markov models. We also discuss the implication of the theorem’s assumptions for several models that are used in practical applications such as ion channel kinetics.      

隐马尔可夫因子分析模型的半参数贝叶斯分析

因子模型在刻画潜在因素(因子)与观测变量间的影响关系并进而解释多元观测指标(变量)间的相关性方面具有重要作用.在实际应用中,观测数据往往呈现出时序变异多峰,偏态等特性.将经典的因子分析延伸到带有时齐隐马尔可夫模型的动力因子模型,并建立了半参数贝叶斯分析程序.分块GIBBS抽样器用以后验抽样.经验结果展示所建立的统计程序是有效的.     

Exponential bounds for convergence of entropy rate approximations in hidden Markov models satisfying a path-mergeability condition

A hidden Markov model (HMM) is said to have path-mergeable states   if for any two states i,j$i,j$ there exist a word w$w$ and state k$k$ such that it is possible to transition from both i$i$ and j$j$ to k$k$ while emitting w$w$. We show that for a finite HMM with path-mergeable states the block estimates of the entropy rate converge exponentially fast. We also show that the path-mergeability property is asymptotically typical in the space of HMM topologies and easily testable.     

Parameter estimation for partially observable systems subject to random failure

In this paper, we present a parameter estimation procedure for a condition‐based maintenance model under partial observations. Systems can be in a healthy or unhealthy operational state, or in a failure state. System deterioration is driven by a continuous time homogeneous Markov chain and the system state is unobservable, except the failure state. Vector information that is stochastically related to the system state is obtained through condition monitoring at equidistant sampling times. Two types of data histories are available — data histories that end with observable failure, and censored data histories that end when the system has been suspended from operation but has not failed. The state and observation processes are modeled in the hidden Markov framework and the model parameters are estimated using the expectation–maximization algorithm. We show that both the pseudolikelihood function and the parameter updates in each iteration of the expectation–maximization algorithm have explicit formulas. A numerical example is developed using real multivariate spectrometric oil data coming from the failing transmission units of 240‐ton heavy hauler trucks used in the Athabasca oil sands of Alberta, Canada. Copyright © 2012 John Wiley & Sons, Ltd.     

A new approach for parameter estimation of finite Weibull mixture distributions for reliability modeling

The aim of this paper is to model lifetime data for systems that have failure modes by using the finite mixture of Weibull distributions. It involves estimating of the unknown parameters which is an important task in statistics, especially in life testing and reliability analysis. The proposed approach depends on different methods that will be used to develop the estimates such as MLE through the EM algorithm. In addition, Bayesian estimations will be investigated and some other extensions such as Graphic, Non-Linear Median Rank Regression and Monte Carlo simulation methods can be used to model the system under consideration. A numerical application will be used through the proposed approach. This paper also presents a comparison of the fitted probability density functions, reliability functions and hazard functions of the 3-parameter Weibull and Weibull mixture distributions using the proposed approach and other conventional methods which characterize the distribution of failure times for the system components. GOF is used to determine the best distribution for modeling lifetime data, the priority will be for the proposed approach which has more accurate parameter estimates.     

Optimal policy for minimizing risk models in Markov decision processes

We consider the minimizing risk problems in discounted Markov decisions processes with countable state space and bounded general rewards. We characterize optimal values for finite and infinite horizon cases and give two sufficient conditions for the existence of an optimal policy in an infinite horizon case. These conditions are closely connected with Lemma 3 in White (1993), which is not correct as Wu and Lin (1999) point out. We obtain a condition for the lemma to be true, under which we show that there is an optimal policy. Under another condition we show that an optimal value is a unique solution to some optimality equation and there is an optimal policy on a transient set.     

Bayesian Inference in Hidden Markov Random Fields for Binary Data Defined on Large Lattices

Hidden Markov random fields represent a complex hierarchical model, where the hidden latent process is an undirected graphical structure. Performing inference for such models is difficult primarily because the likelihood of the hidden states is often unavailable. The main contribution of this article is to present approximate methods to calculate the likelihood for large lattices based on exact methods for smaller lattices. We introduce approximate likelihood methods by relaxing some of the dependencies in the latent model, and also by extending tractable approximations to the likelihood, the so-called pseudolikelihood approximations, for a large lattice partitioned into smaller sublattices. Results are presented based on simulated data as well as inference for the temporal-spatial structure of the interaction between up- and down-regulated states within the mitochondrial chromosome of the Plasmodium falciparum organism. Supplemental material for this article is available online.     

Computational scheme for invariantly unbiased estimation of linear operators in a given class

The values of linear operators of a given class are estimated in the case of measurements including piecewise continuous noise of deterministic structure with unknown parameters. A computational scheme producing unbiased linear estimates that are invariant under the noise is developed. An illustrative example is presented.