MAP segmentation in Bayesian hidden Markov models: a case study

We consider the problem of estimating the maximum posterior probability (MAP) state sequence for a finite state and finite emission alphabet hidden Markov model (HMM) in the Bayesian setup, where both emission and transition matrices have Dirichlet priors. We study a training set consisting of thousands of protein alignment pairs. The training data is used to set the prior hyperparameters for Bayesian MAP segmentation. Since the Viterbi algorithm is not applicable any more, there is no simple procedure to find the MAP path, and several iterative algorithms are considered and compared. The main goal of the paper is to test the Bayesian setup against the frequentist one, where the parameters of HMM are estimated using the training data.     

Objective Bayesian analysis of counting experiments with correlated sources of background

Searches for faint signals in counting experiments are often encountered in particle physics and astrophysics, as well as in other fields. Many problems can be reduced to the case of a model with independent and Poisson-distributed signal and background. Often several background contributions are present at the same time, possibly correlated. We provide the analytic solution of the statistical inference problem of estimating the signal in the presence of multiple backgrounds, in the framework of objective Bayes statistics. The model can be written in the form of a product of a single Poisson distribution with a multinomial distribution. The first is related to the total number of events, whereas the latter describes the fraction of events coming from each individual source. Correlations among different backgrounds can be included in the inference problem by a suitable choice of the priors.     

Geometric Anisotropic Spatial Point Pattern Analysis and Cox Processes

We consider spatial point processes with a pair correlation function, which depends only on the lag vector between a pair of points. Our interest is in statistical models with a special kind of ‘structured’ anisotropy: the pair correlation function is geometric anisotropic if it is elliptical but not spherical. In particular, we study Cox process models with an elliptical pair correlation function, including shot noise Cox processes and log Gaussian Cox processes, and we develop estimation procedures using summary statistics and Bayesian methods. Our methodology is illustrated on real and synthetic datasets of spatial point patterns.     

A test for the equality of k medians against the simple tree alternative under right censorship

We consider a test for the equality of k population medians, θ_i i=1,2,….,k, when it is believed a priori, that θ _i: The observations are subject to right censorhip. The distributions of the censoring variables for each population are assumed to be equal. This test is compared with the general k-sample test proposed by Breslow     

Gibbs sampling for marginal posterior expectations

In earlier work (Gelfand and Smith, 1990 and Gelfand et al, 1990) a sampling based approach using the Gibbs sampler was offered as a means for developing marginal posterior densities for a wide range of Bayesian problems several of which were previously inaccessible. Our purpose here is two-fold. First we flesh out the implementation of this approach for calculation of arbitrary expectations of interest. Secondly we offer comparison with perhaps the most prominent approach for calculating posterior expectations, analytic approximation involving application of the LaPlace method. Several illustrative examples are discussed as well. Clear advantages for the sampling based approach emerge.     

Bayesian inference of asymmetric stochastic conditional duration models

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.     

Approximate Bayesian Computation for Exponential Random Graph Models for Large Social Networks

We consider the issue of sampling from the posterior distribution of exponential random graph (ERG) models and other statistical models with intractable normalizing constants. Existing methods based on exact sampling are either infeasible or require very long computing time. We study a class of approximate Markov chain Monte Carlo (MCMC) sampling schemes that deal with this issue. We also develop a new Metropolis–Hastings kernel to sample sparse large networks from ERG models. We illustrate the proposed methods on several examples.     

Testing non-oblique hypotheses

This paper considers a likelihood ratio test for testing hypotheses defined by non-oblique closed convex cones, satisfying the so called iteration projection property, in a set of k normal means. We obtain the critical values of the test using the Chi-Bar-Squared distribution. The obtuse cones are introduced as a particular class of cones which are non-oblique with every one of their faces. Examples with the simple tree order cone and the total order cone are given to illustrate the results.     

Distribution theory and inference for polynomial-normal densities

This paper considers a class of densities formed by taking the product of nonnegative polynomials and normal densities. These densities provide a rich class of distributions that can be used in modelling when faced with non-normal characteristics such as skewness and multimodality. In this paper we address inferential and computational issues arising in the practical implementation of this parametric family in the context of the linear model. Exact results are recorded for the conditional analysis of location-scale models and an importance sampling algorithm is developed for the implementation of a conditional analysis for the general linear model when using polynomial-normal distributions for the error.     

Bayesian Estimation of the Regression Model with Autocorrelated Errors Under Contamination

In this article, the Bayesian analysis of the regression model with errors terms generated by a first-order autoregressive model is considered. Our aim is to study the effect of two kinds of contamination of this model via the posterior distribution of the regression parameter.