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In unsupervised classification, Hidden Markov Models (HMM) are used to account for a neighborhood structure between observations. The emission distributions are often supposed to belong to some parametric family. In this paper, a semiparametric modeling where the emission distributions are a mixture of parametric distributions is proposed to get a higher flexibility. We show that the classical EM algorithm can be adapted to infer the model parameters. For the initialisation step, starting from a large number of components, a hierarchical method to combine them into the hidden states is proposed. Three likelihood-based criteria to select the components to be combined are discussed. To estimate the number of hidden states, BIC-like criteria are derived. A simulation study is carried out both to determine the best combination between the merging criteria and the model selection criteria and to evaluate the accuracy of classification. The proposed method is also illustrated using a biological dataset from the model plant Arabidopsis thaliana. A R package HMMmix is freely available on the CRAN.
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This paper gives a method for computing distributions associated with patterns in the state sequence of a hidden Markov model, conditional on observing all or part of the observation sequence. Probabilities are computed for very general classes of patterns (competing patterns and generalized later patterns), and thus, the theory includes as special cases results for a large class of problems that have wide application. The unobserved state sequence is assumed to be Markovian with a general order of dependence. An auxiliary Markov chain is associated with the state sequence and is used to simplify the computations. Two examples are given to illustrate the use of the methodology. Whereas the first application is more to illustrate the basic steps in applying the theory, the second is a more detailed application to DNA sequences, and shows that the methods can be adapted to include restrictions related to biological knowledge.
Mixtures-of-Experts models and their maximum likelihood estimation (MLE) via the EM algorithm have been thoroughly studied in the statistics and machine learning literature. They are subject of a growing investigation in the context of modeling with high-dimensional predictors with regularized MLE. We examine MoE with Gaussian gating network, for clustering and regression, and propose an $ell_1$-regularized MLE to encourage sparse models and deal with the high-dimensional setting. We develop an EM-Lasso algorithm to perform parameter estimation and utilize a BIC-like criterion to select the model parameters, including the sparsity tuning hyperparameters. Experiments conducted on simulated data show the good performance of the proposed regularized MLE compared to the standard MLE with the EM algorithm.
Mixture of Experts (MoE) are successful models for modeling heterogeneous data in many statistical learning problems including regression, clustering and classification. Generally fitted by maximum likelihood estimation via the well-known EM algorithm, their application to high-dimensional problems is still therefore challenging. We consider the problem of fitting and feature selection in MoE models, and propose a regularized maximum likelihood estimation approach that encourages sparse solutions for heterogeneous regression data models with potentially high-dimensional predictors. Unlike state-of-the art regularized MLE for MoE, the proposed modelings do not require an approximate of the penalty function. We develop two hybrid EM algorithms: an Expectation-Majorization-Maximization (EM/MM) algorithm, and an EM algorithm with coordinate ascent algorithm. The proposed algorithms allow to automatically obtaining sparse solutions without thresholding, and avoid matrix inversion by allowing univariate parameter updates. An experimental study shows the good performance of the algorithms in terms of recovering the actual sparse solutions, parameter estimation, and clustering of heterogeneous regression data.
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 proposals to expedite the MCMC algorithm. We employ proposed algorithms to the simulated data as well as a real data example, and the results demonstrate the desired performance of the new sampler.
Stochastic variational inference for collapsed models has recently been successfully applied to large scale topic modelling. In this paper, we propose a stochastic collapsed variational inference algorithm for hidden Markov models, in a sequential data setting. Given a collapsed hidden Markov Model, we break its long Markov chain into a set of short subchains. We propose a novel sum-product algorithm to update the posteriors of the subchains, taking into account their boundary transitions due to the sequential dependencies. Our experiments on two discrete datasets show that our collapsed algorithm is scalable to very large datasets, memory efficient and significantly more accurate than the existing uncollapsed algorithm.
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