Particle Markov Chain Monte Carlo (PMCMC) is a general computational approach to Bayesian inference for general state space models. Our article scales up PMCMC in terms of the number of observations and parameters by generating the parameters that are highly correlated with the states \lq integrated out\rq{} in a pseudo marginal step; the rest of the parameters are generated conditional on the states. The novel contribution of our article is to make the pseudo-marginal step much more efficient by positively correlating the numerator and denominator in the Metropolis-Hastings acceptance probability. This is done in a novel way by expressing the target density of the PMCMC in terms of the basic uniform or normal random numbers used in the sequential Monte Carlo algorithm instead of the standard way in terms of state particles. We also show that the new sampler combines and generalizes two separate particle MCMC approaches: particle Gibbs and the correlated pseudo marginal Metropolis-Hastings. We investigate the performance of the hybrid sampler empirically by applying it to univariate and multivariate stochastic volatility models having both a large number of parameters and a large number of latent states and show that it is much more efficient than competing PMCMC methods.

Particle Markov Chain Monte Carlo methods are used to carry out inference in nonlinear and non-Gaussian state space models, where the posterior density of the states is approximated using particles. Current approaches usually perform Bayesian inference using either a particle marginal Metropolis-Hastings (PMMH) algorithm or a particle Gibbs (PG) sampler. This paper shows how the two ways of generating variables mentioned above can be combined in a flexible manner to give sampling schemes that converge to a desired target distribution. The advantage of our approach is that the sampling scheme can be tailored to obtain good results for different applications. For example, when some parameters and the states are highly correlated, such parameters can be generated using PMMH, while all other parameters are generated using PG because it is easier to obtain good proposals for the parameters within the PG framework. We derive some convergence properties of our sampling scheme and also investigate its performance empirically by applying it to univariate and multivariate stochastic volatility models and comparing it to other PMCMC methods proposed in the literature.

Particle Markov Chain Monte Carlo methods are used to carry out inference in non-linear and non-Gaussian state space models, where the posterior density of the states is approximated using particles. Deligiannidis (2017) introduce the correlated pseudo marginal sampler and show that it can be much more efficient than the standard pseudo marginal approach. Mendes (2018) propose a particle MCMC sampler that generates parameters that are highly correlated with the states using a pseudo marginal method that integrates out the states, while all other parameters are generated using particle Gibbs. Our article shows how to combine these two approaches to particle MCMC to obtain a flexible sampler with a superior performance to each of these two approaches. We illustrate the new sampler using a multivariate factor stochastic volatility model with leverage.

The problem we consider considers estimating a multivariate longitudinal panel data model whose outcomes can be a combination of discrete and continuous variables. This problem is challenging because the likelihood is usually analytically intractable. Our article makes both a methodological contribution and also a substantive contribution to the application. The methodological contribution is to introduce into the panel data literature a particle Metropolis within Gibbs method to carry out Bayesian inference, using a Hamiltonian Monte Carlo (Neal 2011} proposal for sampling the vector of unknown parameters. We note that in panel data models the Our second contribution is to apply our method to carry out a serious analysis of the impact of serious life events on mental health and excessive alcohol consumption. The dependence between these two outcomes may be more pronounced when consumption of alcohol is excessive and mental health poor, which in turn has implications for how life events impact the joint distribution of the outcomes.

This paper discusses the efficient Bayesian estimation of a multivariate factor stochastic volatility (Factor MSV) model with leverage. We propose a novel approach to construct the sampling schemes that converges to the posterior distribution of the latent volatilities and the parameters of interest of the Factor MSV model based on recent advances in Particle Markov chain Monte Carlo (PMCMC). As opposed to the approach of Chib et al. (2006} and Omori et al. (2007}, our approach does not require approximating the joint distribution of outcome and volatility innovations by a mixture of bivariate normal distributions. To sample the free elements of the loading matrix we employ the interweaving method used in Kastner et al. (2017} in the Particle Metropolis within Gibbs (PMwG) step. The proposed method is illustrated empirically using a simulated dataset and a sample of daily US stock returns.

Particle Markov Chain Monte Carlo methods [Andrieu et al., 2010] are used to carry out inference in non-linear and non-Gaussian state space models, where the posterior density of the states is approximated using particles. Current approaches have usually carried out Bayesian inference using a particle Metropolis-Hastings algorithm or a particle Gibbs sampler. In this paper, we give a general approach to constructing sampling schemes that converge to the target distributions given in Andrieu et al. [2010] and Olsson and Ryden [2011]. We describe our methods as a particle Metropolis within Gibbs sampler (PMwG). The advantage of our general approach is that the sampling scheme can be tailored to obtain good results for different applications. We investigate the properties of the general sampling scheme, including conditions for uniform convergence to the posterior. We illustrate our methods with examples of state space models where one group of parameters can be generated in a straightforward manner in a particle Gibbs step by conditioning on the states, but where it is cumbersome and inefficient to generate such parameters when the states are integrated out. Conversely, it may be necessary to generate a second group of parameters without conditioning on the states because of the high dependence between such parameters and the states. Our examples include state space models with diffuse initial conditions, where we introduce two methods to deal with the initial conditions.

In this paper we consider fully Bayesian inference in general state space models. Existing particle Markov chain Monte Carlo (MCMC) algorithms use an augmented model that takes into account all the variable sampled in a sequential Monte Carlo algorithm. This paper describes an approach that also uses sequential Monte Carlo to construct an approximation to the state space, but generates extra states using MCMC runs at each time point. We construct an augmented model for our extended space with the marginal distribution of the sampled states matching the posterior distribution of the state vector. We show how our method may be combined with particle independent Metropolis-Hastings or particle Gibbs steps to obtain a smoothing algorithm. All the Metropolis acceptance probabilities are identical to those obtained in existing approaches, so there is no extra cost in term of Metropolis-Hastings rejections when using our approach. The number of MCMC iterates at each time point is chosen by the used and our augmented model collapses back to the model in Olsson and Ryden (2011) when the number of MCMC iterations reduces. We show empirically that our approach works well on applied examples and can outperform existing methods.

Particle Markov Chain Monte Carlo methods are used to carry out inference in non-linear and non-Gaussian state space models, where the posterior density of the states is approximated using particles. Current approaches usually perform Bayesian inference using a particle Marginal Metropolis-Hastings algorithm, a particle Gibbs sampler, or a particle Metropolis within Gibbs sampler. This paper shows how the three ways of generating variables mentioned above can be combined in a flexible manner to give sampling schemes that converge to a desired target distribution. The advantage of our approach is that the sampling scheme can be tailored to obtain good results for different applications, for example when some parameters and the states are highly correlated. We investigate the properties of this flexible sampling scheme, including conditions for uniform convergence to the posterior. We illustrate our methods with a factor stochastic volatility state space model where one group of parameters can be generated in a straightforward manner in a particle Gibbs step by conditioning on the states, and a second group of parameters are generated without conditioning on the states because of the high dependence between such parameters and the states.

This paper describes experiments, on two domains, to investigate the effect of averaging over predictions of multiple decision trees, instead of using a single tree. Other authors have pointed out theoretical and commonsense reasons for preferring the multiple tree approach. Ideally, we would like to consider predictions from all trees, weighted by their probability. However, there is a vast number of different trees, and it is difficult to estimate the probability of each tree. We sidestep the estimation problem by using a modified version of the ID3 algorithm to build good trees, and average over only these trees. Our results are encouraging. For each domain, we managed to produce a small number of good trees. We find that it is best to average across sets of trees with different structure; this usually gives better performance than any of the constituent trees, including the ID3 tree.

Daily counts of computer records of hospital emergency department arrivals grouped according to diagnosis (called here syndrome groupings) can be monitored by epidemiologists for changes in frequency that could provide early warning of bioterrorism events or naturally occurring disease outbreaks and epidemics. This type of public health surveillance is sometimes called syndromic surveillance. We used transitional Poisson regression models to obtain one-day-ahead arrival forecasts. Regression parameter estimates and forecasts were updated for each day using the latest 365 days of data. The resulting time series of recursive estimates of parameters such as the amplitude and location of the seasonal peaks as well as the one-day-ahead forecasts and forecast errors can be monitored to understand changes in epidemiology of each syndrome grouping. The counts for each syndrome grouping were autocorrelated and non-homogeneous Poisson. As such, the main methodological contribution of the article is the adaptation of Cumulative Sum (CUSUM) and Exponentially Weighted Moving Average (EWMA) plans for monitoring non-homogeneous counts. These plans were valid for small counts where the assumption of normally distributed one-day-ahead forecasts errors, typically used in other papers, breaks down. In addition, these adaptive plans have the advantage that control limits do not have to be trained for different syndrome groupings or aggregations of emergency departments. Conventional methods for signaling increases in syndrome grouping counts, Shewhart, CUSUM, and EWMA control charts of the standardized forecast errors were also examined. Shewhart charts were, at times, insensitive to shifts of interest. CUSUM and EWMA charts were only reasonable for large counts. We illustrate our methods with respiratory, influenza, diarrhea, and abdominal pain syndrome groupings.

A method for constructing priors is proposed that allows the off-diagonal elements of the concentration matrix of Gaussian data to be zero. The priors have the property that the marginal prior distribution of the number of nonzero off-diagonal elements of the concentration matrix (referred to below as model size) can be specified flexibly. The priors have normalizing constants for each model size, rather than for each model, giving a tractable number of normalizing constants that need to be estimated. The article shows how to estimate the normalizing constants using Markov chain Monte Carlo simulation and supersedes the method of Wong et al. (2003) [24] because it is more accurate and more general. The method is applied to two examples. The first is a mixture of constrained Wisharts. The second is from Wong et al. (2003) [24] and decomposes the concentration matrix into a function of partial correlations and conditional variances using a mixture distribution on the matrix of partial correlations. The approach detects structural zeros in the concentration matrix and estimates the covariance matrix parsimoniously if the concentration matrix is sparse. (c) 2011 Elsevier Inc. All rights reserved.

A Bayesian approach is used to estimate the covariance matrix of Gaussian data. Ideas from Gaussian graphical models and model selection are used to construct a prior for the covariance matrix that is a mixture over all decomposable graphs. For this prior the probability of each graph size is specified by the user and graphs of equal size are assigned equal probability. Most previous approaches assume that all graphs are equally probable. We show empirically that the prior that assigns equal probability over graph sizes outperforms the prior that assigns equal probability over all graphs, both in identifying the correct decomposable graph and in more efficiently estimating the covariance matrix.

We discuss the implementation, development and performance of methods of stochastic computation in Gaussian graphical models. We view these methods from the perspective of high-dimensional model search, with a particular interest in the scalability with dimension of Markov chain Monte Carlo (MCMC) and other stochastic search methods. After reviewing the structure and context of undirected Gaussian graphical models and model uncertainty (covariance selection), we discuss prior specifications, including new priors over models, and then explore a number of examples using various methods of stochastic computation. Traditional MCMC methods are the point of departure for this experimentation; we then develop alternative stochastic search ideas and contrast this new approach with MCMC. Our examples range from low (12–20) to moderate (150) dimension, and combine simple synthetic examples with data analysis from gene expression studies. We conclude with comments about the need and potential for new computational methods in far higher dimensions, including constructive approaches to Gaussian graphical modeling and computation.

This article provides a general framework for Bayesian variable selection and covariance selection in a multivariate regression model with Gaussian errors. By variable selection we mean allowing certain regression coefficients to be zero. By covariance selection we mean allowing certain elements of the inverse covariance matrix to be zero. We estimate all the model parameters by model averaging using a Markov chain Monte Carlo simulation method. The methodology is illustrated by applying it to four real data sets. The effectiveness of variable selection and covariance selection in estimating the multivariate regression model is assessed by using four loss functions and four simulated data sets. Each of the simulated data sets is based on parameter estimates obtained from a corresponding real data set.

A Bayesian method is proposed for estimating an inverse covariance matrix from Gaussian data. The method is based on a prior that allows the off-diagonal elements of the inverse covariance matrix to be zero, and in many applications results in a parsimonious parameterisation of the covariance matrix. No assumption is made about the structure of the corresponding graphical model, so the method applies to both nondecomposable and decomposable graphs. All the parameters are estimated by model averaging using an efficient Metropolis-Hastings sampling scheme. A simulation study demonstrates that the method produces statistically efficient estimators of the covariance matrix, when the inverse covariance matrix is sparse. The methodology is illustrated by applying it to three examples that are high-dimensional relative to the sample size.

A Bayesian approach is presented for estimating a mixture of linear Gaussian state-space models. Such models are used to model interventions in time series and nonparametric regression. Markov chain Monte Carlo sampling is usually necessary to obtain the posterior distributions of such mixture models, because it is difficult to obtain them analytically. The methodological contribution of the article is to derive a set of recursions for dynamic mixture models that efficiently implement a Markov chain Monte Carlo sampling scheme that converges rapidly to the posterior distribution. The methodology is illustrated by fitting an autoregressive model subject to interventions to zinc concentration in sludge.

Test statistics are proposed to determine the goodness of fit of a time series model. The test statistics are based on a sequence of random variables that are independent and standard normal if the model is correct. The paper shows how to compute this sequence of random variables efficiently using a combination of Markov chain Monte Carlo and importance sampling. The power of the statistics to detect outliers and level shifts is studied for an autoregressive model. The methodology is illustrated using both simulated and real data.

A Bayesian analysis is presented of a time series which is the sum of a stationary component with a smooth spectral density and a deterministic component consisting of a linear combination of a trend and periodic terms. The periodic terms may have known or unknown frequencies. The advantage of our approach is that different features of the data - such as the regression parameters, the spectral density, unknown frequencies and missing observations - are combined in a hierarchical Bayesian framework and estimated simultaneously. A Bayesian test to detect deterministic components in the data is also constructed. By using an asymptotic approximation to the likelihood, the computation is carried out efficiently using the Markov chain Monte Carlo method in O(Mn) operations, where n is the sample size and M is the number of iterations. We show empirically that our approach works well on real and simulated samples.

A Bayesian analysis is given for a state space model with errors that are finite mixtures of normals and with coefficients that can assume a finite number of different values. A sequence of indicator variables determines which components the errors belong to and the values of the coefficients. The computation is carried out using Markov chain Monte Carlo, with the indicator variables generated without conditioning on the states. Previous approaches use the Gibbs sampler to generate the indicator variables conditional on the states. In many problems, however, there is a strong dependence between the indicator variables and the states causing the Gibbs sampler to converge unacceptably slowly, or even not to converge at all. The new sampler is implemented in O(n) operations, where n is the sample size, permitting an exact Bayesian analysis of problems that previously had no computationally tractable solution. We show empirically that the new sampler can be much more efficient than previous approaches, and illustrate its applicability to robust nonparametric regression with discontinuities and to a time series change point problem.