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In applications of Gaussian processes (GPs) where quantification of uncertainty is a strict requirement, it is necessary to accurately characterize the posterior distribution over Gaussian process covariance parameters. This is normally done by means of standard Markov chain Monte Carlo (MCMC) algorithms, which require repeated expensive calculations involving the marginal likelihood. Motivated by the desire to avoid the inefficiencies of MCMC algorithms rejecting a considerable amount of expensive proposals, this paper develops an alternative inference framework based on adaptive multiple importance sampling (AMIS). In particular, this paper studies the application of AMIS for GPs in the case of a Gaussian likelihood, and proposes a novel pseudo-marginal-based AMIS algorithm for non-Gaussian likelihoods, where the marginal likelihood is unbiasedly estimated. The results suggest that the proposed framework outperforms MCMC-based inference of covariance parameters in a wide range of scenarios. [ABSTRACT FROM AUTHOR]

In this paper, we introduce a novel Bayesian data augmentation approach for estimating the parameters of the generalized logistic regression model. We propose a Pólya–Gamma sampler algorithm that allows us to sample from the exact posterior distribution, rather than relying on approximations. A simulation study illustrates the flexibility and accuracy of the proposed approach to capture heavy and light tails in binary response data of different dimensions. The algorithm performance is tested on simulated data. Furthermore, the methodology is applied to two different real datasets, where we demonstrate that the Pólya–Gamma sampler provides more precise estimates than the empirical likelihood method, outperforming approximate approaches. [ABSTRACT FROM AUTHOR]

In this paper, we consider observations arising out from a hidden truncation Pareto (IV) distribution and to be used to make inferences about the inequality, precision, shape and truncation parameter(s). Two different types of dependent prior analyses are reviewed and compared with each other. We conjecture that mathematical tractability should be, perhaps, a minor consideration in choosing the appropriate choices of the hyper-parameters for the prior densities. Some illustrative examples are provided. A simulation study is conducted to illustrate the applicability of the proposed model. [ABSTRACT FROM AUTHOR]

This paper extends stochastic conditional duration (SCD) models for financial transaction data to allow for correlation between error processes and innovations of observed duration process and latent log duration process. Suitable algorithms of Markov Chain Monte Carlo (MCMC) are developed to fit the resulting SCD models under various distributional assumptions about the innovation of the measurement equation. Unlike the estimation methods commonly used to estimate the SCD models in the literature, we work with the original specification of the model, without subjecting the observation equation to a logarithmic transformation. Results of simulation studies suggest that our proposed models and corresponding estimation methodology perform quite well. We also apply an auxiliary particle filter technique to construct one-step-ahead in-sample and out-of-sample duration forecasts of the fitted models. Applications to the IBM transaction data allow comparison of our models and methods to those existing in the literature. [ABSTRACT FROM PUBLISHER]

Markov chain Monte Carlo (MCMC) methods provide an important means to simulate from almost any probability density. To approximate non-standard discrete distributions, the equation-solving MCMC estimator was developed as an alternative to the classical frequency estimator. The used simulation scheme is the Metropolis–Hastings (M–H) algorithm. Recently, this estimator has been extended to the specific context of 2-step Metropolis-Hastings with delayed rejection (MHDR) algorithm, which allowed a considerable reduction in asymptotic variance. In this paper, we propose an adaptation of equation-solving estimator to the case of general n-step MHDR sampler. The aim is to further improve the precision. An application to a Bayesian hypothesis test problem shows the high performance, in terms of accuracy, of the equation-solving estimator, based on a MHDR algorithm with more than two stages. [ABSTRACT FROM AUTHOR]

This paper proposes a two-sided monitoring algorithm of changes in the exponential family. We adopt a Bayesian approach which uses a loss function and takes into account the run length of the process. It also extends the monitoring scheme proposed in [Harrison, P.J., Veerapen, P.P., 1994, A Bayesian decision approach to model monitoring and Cusums. Journal of Forecasting, 13, 29-36.] The algorithm is illustrated with several examples, which analyze the power of the monitor. [ABSTRACT FROM AUTHOR]

Item response theory (IRT) comprises a set of statistical models which are useful in many fields, especially when there is an interest in studying latent variables (or latent traits). Usually such latent traits are assumed to be random variables and a convenient distribution is assigned to them. A very common choice for such a distribution has been the standard normal. Recently, Azevedo et al. [Bayesian inference for a skew-normal IRT model under the centred parameterization, Comput. Stat. Data Anal. 55 (2011), pp. 353–365] proposed a skew-normal distribution under the centred parameterization (SNCP) as had been studied in [R.B. Arellano-Valle and A. Azzalini, The centred parametrization for the multivariate skew-normal distribution, J. Multivariate Anal. 99(7) (2008), pp. 1362–1382], to model the latent trait distribution. This approach allows one to represent any asymmetric behaviour concerning the latent trait distribution. Also, they developed a Metropolis–Hastings within the Gibbs sampling (MHWGS) algorithm based on the density of the SNCP. They showed that the algorithm recovers all parameters properly. Their results indicated that, in the presence of asymmetry, the proposed model and the estimation algorithm perform better than the usual model and estimation methods. Our main goal in this paper is to propose another type of MHWGS algorithm based on a stochastic representation (hierarchical structure) of the SNCP studied in [N. Henze, A probabilistic representation of the skew-normal distribution, Scand. J. Statist. 13 (1986), pp. 271–275]. Our algorithm has only one Metropolis–Hastings step, in opposition to the algorithm developed by Azevedo et al., which has two such steps. This not only makes the implementation easier but also reduces the number of proposal densities to be used, which can be a problem in the implementation of MHWGS algorithms, as can be seen in [R.J. Patz and B.W. Junker, A straightforward approach to Markov Chain Monte Carlo methods for item response models, J. Educ. Behav. Stat. 24(2) (1999), pp. 146–178; R.J. Patz and B.W. Junker, The applications and extensions of MCMC in IRT: Multiple item types, missing data, and rated responses, J. Educ. Behav. Stat. 24(4) (1999), pp. 342–366; A. Gelman, G.O. Roberts, and W.R. Gilks, Efficient Metropolis jumping rules, Bayesian Stat. 5 (1996), pp. 599–607]. Moreover, we consider a modified beta prior (which generalizes the one considered in [3]) and a Jeffreys prior for the asymmetry parameter. Furthermore, we study the sensitivity of such priors as well as the use of different kernel densities for this parameter. Finally, we assess the impact of the number of examinees, number of items and the asymmetry level on the parameter recovery. Results of the simulation study indicated that our approach performed equally as well as that in [3], in terms of parameter recovery, mainly using the Jeffreys prior. Also, they indicated that the asymmetry level has the highest impact on parameter recovery, even though it is relatively small. A real data analysis is considered jointly with the development of model fitting assessment tools. The results are compared with the ones obtained by Azevedo et al. The results indicate that using the hierarchical approach allows us to implement MCMC algorithms more easily, it facilitates diagnosis of the convergence and also it can be very useful to fit more complex skew IRT models. [ABSTRACT FROM PUBLISHER]

Assume that K independent copies are made from a common prototype DNA sequence whose length is a random variable. In this paper, the problem of aligning those copies and therefore the problem of estimating the prototype sequence that produced the copies is addressed. A hidden Markov chain is used to model the copying procedure, and a reversible jump Markov chain Monte Carlo algorithm is used to sample the parameters of the model from their posterior distribution. Using the sample obtained, the Bayesian model and the prototype sequence may be selected using the maximum a posteriori estimate. A prior distribution for the prototype DNA sequence that incorporates a correlation among neighbouring bases is also considered. In addition, an analysis of the performance of the algorithm is presented when different scenarios are taken into account. [ABSTRACT FROM AUTHOR]

In this article, mixed-effects state space models (MESSM, [Liu D, Lu T, Niu X-F, et al. Mixed-effects state-space models for analysis of longitudinal dynamic systems. Biometrics. 2011;67(2):476–485.]) are revisited. MESSM can be considered as an alternative to study the HIV dynamic in a longitudinal data environment, defining the mixed-effects component into state-space models setup. As in Liu et al.[Liu D, Lu T, Niu X-F, et al. Mixed-effects state-space models for analysis of longitudinal dynamic systems. Biometrics. 2011;67(2):476–485.], we consider a hierarchical structure to capture possible differences between the immune systems for different patients. We extend MESSM, allowing observational errors to follow a more flexible distribution to take account for heavy tails. Using the Bayesian paradigm, an efficient Markov Chain Monte Carlo (MCMC) algorithm based on McCausland et al. [McCausland WJ, Miller S, Pelletier D. Simulation smoothing for state.space models: A computational efficiency analysis. Comput Stat Data Anal. 2011;55(1):199–212.] is introduced for parameter and latent variables estimation. Moreover, the mixing variables obtained as a by-product of the scale mixture representation can be used to identify outliers. The methodology is illustrated using artificial and real datasets in order to investigate the properties and performance of the proposed model. [ABSTRACT FROM AUTHOR]