Holsclaw, Tracy, Greene, Arthur M., Robertson, Andrew W., Smyth, Padhraic

Discrete-time hidden Markov models are a broadly useful class of latent-variable models with applications in areas such as speech recognition, bioinformatics, and climate data analysis. It is common in practice to introduce temporal non-homogeneity into such models by making the transition probabilities dependent on time-varying exogenous input variables via a multinomial logistic parametrization. We extend such models to introduce additional non-homogeneity into the emission distribution using a generalized linear model (GLM), with data augmentation for sampling-based inference. However, the presence of the logistic function in the state transition model significantly complicates parameter inference for the overall model, particularly in a Bayesian context. To address this we extend the recently-proposed Polya-Gamma data augmentation approach to handle non-homogeneous hidden Markov models (NHMMs), allowing the development of an efficient Markov chain Monte Carlo (MCMC) sampling scheme. We apply our model and inference scheme to 30 years of daily rainfall in India, leading to a number of insights into rainfall-related phenomena in the region. Our proposed approach allows for fully Bayesian analysis of relatively complex NHMMs on a scale that was not possible with previous methods. Software implementing the methods described in the paper is available via the R package NHMM.

Everitt, Richard G., Rowińska, Paulina A.

Approximate Bayesian computation (ABC) is now an established technique for statistical inference used in cases where the likelihood function is computationally expensive or not available. It relies on the use of a model that is specified in the form of a simulator, and approximates the likelihood at a parameter $\theta$ by simulating auxiliary data sets $x$ and evaluating the distance of $x$ from the true data $y$. However, ABC is not computationally feasible in cases where using the simulator for each $\theta$ is very expensive. This paper investigates this situation in cases where a cheap, but approximate, simulator is available. The approach is to employ delayed acceptance Markov chain Monte Carlo (MCMC) within an ABC sequential Monte Carlo (SMC) sampler in order to, in a first stage of the kernel, use the cheap simulator to rule out parts of the parameter space that are not worth exploring, so that the "true" simulator is only run (in the second stage of the kernel) where there is a reasonable chance of accepting proposed values of $\theta$. We show that this approach can be used quite automatically, with the only tuning parameter choice additional to ABC-SMC being the number of particles we wish to carry through to the second stage of the kernel. Applications to stochastic differential equation models and latent doubly intractable distributions are presented.

Fox, Emily B., Sudderth, Erik B., Jordan, Michael I., Willsky, Alan S.

We propose a Bayesian nonparametric approach to the problem of jointly modeling multiple related time series. Our approach is based on the discovery of a set of latent, shared dynamical behaviors. Using a beta process prior, the size of the set and the sharing pattern are both inferred from data. We develop efficient Markov chain Monte Carlo methods based on the Indian buffet process representation of the predictive distribution of the beta process, without relying on a truncated model. In particular, our approach uses the sum-product algorithm to efficiently compute Metropolis-Hastings acceptance probabilities, and explores new dynamical behaviors via birth and death proposals. We examine the benefits of our proposed feature-based model on several synthetic datasets, and also demonstrate promising results on unsupervised segmentation of visual motion capture data.

Volant, Stevenn, Magniette, Marie-Laure Martin, Robin, Stéphane

We consider a binary unsupervised classification problem where each observation is associated with an unobserved label that we want to retrieve. More precisely, we assume that there are two groups of observation: normal and abnormal. The `normal' observations are coming from a known distribution whereas the distribution of the `abnormal' observations is unknown. Several models have been developed to fit this unknown distribution. In this paper, we propose an alternative based on a mixture of Gaussian distributions. The inference is done within a variational Bayesian framework and our aim is to infer the posterior probability of belonging to the class of interest. To this end, it makes no sense to estimate the mixture component number since each mixture model provides more or less relevant information to the posterior probability estimation. By computing a weighted average (named aggregated estimator) over the model collection, Bayesian Model Averaging (BMA) is one way of combining models in order to account for information provided by each model. The aim is then the estimation of the weights and the posterior probability for one specific model. In this work, we derive optimal approximations of these quantities from the variational theory and propose other approximations of the weights. To perform our method, we consider that the data are dependent (Markovian dependency) and hence we consider a Hidden Markov Model. A simulation study is carried out to evaluate the accuracy of the estimates in terms of classification. We also present an application to the analysis of public health surveillance systems.

The question of how to determine the number of independent latent factors (topics) in mixture models such as Latent Dirichlet Allocation (LDA) is of great practical importance. In most applications, the exact number of topics is unknown, and depends on the application and the size of the data set. Bayesian nonparametric methods can avoid the problem of topic number selection, but they can be impracticably slow for large sample sizes and are subject to local optima. We develop a guaranteed procedure for topic number recovery that does not necessitate learning the model's latent parameters beforehand. Our procedure relies on adapting results from random matrix theory. Performance of our topic number recovery procedure is superior to hLDA, a nonparametric method. We also discuss some implications of our results on the sample complexity and accuracy of popular spectral learning algorithms for LDA. Our results and procedure can be extended to spectral learning algorithms for other exchangeable mixture models as well as Hidden Markov Models.