Efficient data augmentation techniques for some classes of state space models

Data augmentation improves the convergence of iterative algorithms, such as the EM algorithm and Gibbs sampler by introducing carefully designed latent variables. In this article, we first propose a data augmentation scheme for the first-order autoregression plus noise model, where optimal values of working parameters introduced for recentering and rescaling of the latent states, can be derived analytically by minimizing the fraction of missing information in the EM algorithm. The proposed data augmentation scheme is then utilized to design efficient Markov chain Monte Carlo (MCMC) algorithms for Bayesian inference of some non-Gaussian and nonlinear state space models, via a mixture of normals approximation coupled with a block-specific reparametrization strategy. Applications on simulated and benchmark real datasets indicate that the proposed MCMC sampler can yield improvements in simulation efficiency compared with centering, noncentering and even the ancillarity-sufficiency interweaving strategy.Comment: Keywords: Data augmentation, State space model, Stochastic volatility model, EM algorithm, Reparametrization, Markov chain Monte Carlo, Ancillarity-sufficiency interweaving strateg

Stochastic variational inference for large-scale discrete choice models using adaptive batch sizes

Discrete choice models describe the choices made by decision makers among alternatives and play an important role in transportation planning, marketing research and other applications. The mixed multinomial logit (MMNL) model is a popular discrete choice model that captures heterogeneity in the preferences of decision makers through random coefficients. While Markov chain Monte Carlo methods provide the Bayesian analogue to classical procedures for estimating MMNL models, computations can be prohibitively expensive for large datasets. Approximate inference can be obtained using variational methods at a lower computational cost with competitive accuracy. In this paper, we develop variational methods for estimating MMNL models that allow random coefficients to be correlated in the posterior and can be extended easily to large-scale datasets. We explore three alternatives: (1) Laplace variational inference, (2) nonconjugate variational message passing and (3) stochastic linear regression. Their performances are compared using real and simulated data. To accelerate convergence for large datasets, we develop stochastic variational inference for MMNL models using each of the above alternatives. Stochastic variational inference allows data to be processed in minibatches by optimizing global variational parameters using stochastic gradient approximation. A novel strategy for increasing minibatch sizes adaptively within stochastic variational inference is proposed

A stochastic variational framework for fitting and diagnosing generalized linear mixed models

In stochastic variational inference, the variational Bayes objective function is optimized using stochastic gradient approximation, where gradients computed on small random subsets of data are used to approximate the true gradient over the whole data set. This enables complex models to be fit to large data sets as data can be processed in mini-batches. In this article, we extend stochastic variational inference for conjugate-exponential models to nonconjugate models and present a stochastic nonconjugate variational message passing algorithm for fitting generalized linear mixed models that is scalable to large data sets. In addition, we show that diagnostics for prior-likelihood conflict, which are useful for Bayesian model criticism, can be obtained from nonconjugate variational message passing automatically, as an alternative to simulation-based Markov chain Monte Carlo methods. Finally, we demonstrate that for moderate-sized data sets, convergence can be accelerated by using the stochastic version of nonconjugate variational message passing in the initial stage of optimization before switching to the standard version.Comment: 42 pages, 13 figures, 9 table

Variational Inference for Generalized Linear Mixed Models Using Partially Noncentered Parametrizations

The effects of different parametrizations on the convergence of Bayesian computational algorithms for hierarchical models are well explored. Techniques such as centering, noncentering and partial noncentering can be used to accelerate convergence in MCMC and EM algorithms but are still not well studied for variational Bayes (VB) methods. As a fast deterministic approach to posterior approximation, VB is attracting increasing interest due to its suitability for large high-dimensional data. Use of different parametrizations for VB has not only computational but also statistical implications, as different parametrizations are associated with different factorized posterior approximations. We examine the use of partially noncentered parametrizations in VB for generalized linear mixed models (GLMMs). Our paper makes four contributions. First, we show how to implement an algorithm called nonconjugate variational message passing for GLMMs. Second, we show that the partially noncentered parametrization can adapt to the quantity of information in the data and determine a parametrization close to optimal. Third, we show that partial noncentering can accelerate convergence and produce more accurate posterior approximations than centering or noncentering. Finally, we demonstrate how the variational lower bound, produced as part of the computation, can be useful for model selection.Comment: Published in at http://dx.doi.org/10.1214/13-STS418 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org