Smoothing for discrete-valued time series

We deal with smoothed estimators for conditional probability functions of discrete-valued time series { Y_t } under two different settings. When the conditional distribution of Y_t given its lagged values falls in a parametric family and depends on exogenous random variables, a smoothed maximum (partial) likelihood estimator for the unknown parameter is proposed. While there is no prior information on the distribution, various nonparametric estimation methods have been compared and the adjusted Nadaraya–Watson estimator stands out as it shares the advantages of both Nadaraya–Watson and local linear regression estimators. The asymptotic normality of the estimators proposed has been established in the manner of sparse asymptotics, which shows that the smoothed methods proposed outperform their conventional, unsmoothed, parametric counterparts under very mild conditions. Simulation results lend further support to this assertion. Finally, the new method is illustrated via a real data set concerning the relationship between the number of daily hospital admissions and the levels of pollutants in Hong Kong in 1994–1995. An ad hoc model selection procedure based on a local Akaike information criterion is proposed to select the significant pollutant indices.     

Error rates in classification consisting of discrete and continuous variables in the presence of covariates

We consider classifying an object based on mixed continuous and discrete variables between two populations. Mixed discrete and continuous covariates with identical means in both populations are amongst the variables. Under the location model with homogeneous location specific conditional dispersion matrices for both populations, the Bayes rule is given. Classification is implemented by a plug-in version of the Bayes rule with full covariate adjustment. An asymptotic expansion of the overall expected error of the procedure is derived. Our findings generalize several classical results.     

Approximating probability density functions in hybrid Bayesian networks with mixtures of truncated exponentials

Mixtures of truncated exponentials (MTE) potentials are an alternative to discretization and Monte Carlo methods for solving hybrid Bayesian networks. Any probability density function (PDF) can be approximated by an MTE potential, which can always be marginalized in closed form. This allows propagation to be done exactly using the Shenoy-Shafer architecture for computing marginals, with no restrictions on the construction of a join tree. This paper presents MTE potentials that approximate standard PDF’s and applications of these potentials for solving inference problems in hybrid Bayesian networks. These approximations will extend the types of inference problems that can be modelled with Bayesian networks, as demonstrated using three examples.     

Nonparametric empirical Bayes for the Dirichlet process mixture model

The Dirichlet process prior allows flexible nonparametric mixture modeling. The number of mixture components is not specified in advance and can grow as new data arrive. However, analyses based on the Dirichlet process prior are sensitive to the choice of the parameters, including an infinite-dimensional distributional parameter G ₀. Most previous applications have either fixed G ₀ as a member of a parametric family or treated G ₀ in a Bayesian fashion, using parametric prior specifications. In contrast, we have developed an adaptive nonparametric method for constructing smooth estimates of G ₀. We combine this method with a technique for estimating α, the other Dirichlet process parameter, that is inspired by an existing characterization of its maximum-likelihood estimator. Together, these estimation procedures yield a flexible empirical Bayes treatment of Dirichlet process mixtures. Such a treatment is useful in situations where smooth point estimates of G ₀ are of intrinsic interest, or where the structure of G ₀ cannot be conveniently modeled with the usual parametric prior families. Analysis of simulated and real-world datasets illustrates the robustness of this approach.     

Bootstrap confidence regions computed from autoregressions of arbitrary order

Given a linear time series, e.g. an autoregression of infinite order, we may construct a finite order approximation and use that as the basis for confidence regions. The sieve or autoregressive bootstrap, as this method is often called, is generally seen as a competitor with the better-understood block bootstrap approach. However, in the present paper we argue that, for linear time series, the sieve bootstrap has significantly better performance than blocking methods and offers a wider range of opportunities. In particular, since it does not corrupt second-order properties then it may be used in a double-bootstrap form, with the second bootstrap application being employed to calibrate a basic percentile method confidence interval. This approach confers second-order accuracy without the need to estimate variance. That offers substantial benefits, since variances of statistics based on time series can be difficult to estimate reliably, and—partly because of the relatively small amount of information contained in a dependent process—are notorious for causing problems when used to Studentize. Other advantages of the sieve bootstrap include considerably greater robustness against variations in the choice of the tuning parameter, here equal to the autoregressive order, and the fact that, in contradistinction to the case of the block bootstrap, the percentile t version of the sieve bootstrap may be based on the 'raw' estimator of standard error. In the process of establishing these properties we show that the sieve bootstrap is second order correct.     

On predictive distributions and Bayesian networks

In this paper we are interested in discrete prediction problems for a decision-theoretic setting, where the task is to compute the predictive distribution for a finite set of possible alternatives. This question is first addressed in a general Bayesian framework, where we consider a set of probability distributions defined by some parametric model class. Given a prior distribution on the model parameters and a set of sample data, one possible approach for determining a predictive distribution is to fix the parameters to the instantiation with the maximum a posteriori probability. A more accurate predictive distribution can be obtained by computing the evidence (marginal likelihood), i.e., the integral over all the individual parameter instantiations. As an alternative to these two approaches, we demonstrate how to use Rissanen's new definition of stochastic complexity for determining predictive distributions, and show how the evidence predictive distribution with Jeffrey's prior approaches the new stochastic complexity predictive distribution in the limit with increasing amount of sample data. To compare the alternative approaches in practice, each of the predictive distributions discussed is instantiated in the Bayesian network model family case. In particular, to determine Jeffrey's prior for this model family, we show how to compute the (expected) Fisher information matrix for a fixed but arbitrary Bayesian network structure. In the empirical part of the paper the predictive distributions are compared by using the simple tree-structured Naive Bayes model, which is used in the experiments for computational reasons. The experimentation with several public domain classification datasets suggest that the evidence approach produces the most accurate predictions in the log-score sense. The evidence-based methods are also quite robust in the sense that they predict surprisingly well even when only a small fraction of the full training set is used.     

Diagnostic checks for discrete data regression models using posterior predictive simulations

Model checking with discrete data regressions can be difficult because the usual methods such as residual plots have complicated reference distributions that depend on the parameters in the model. Posterior predictive checks have been proposed as a Bayesian way to average the results of goodness-of-fit tests in the presence of uncertainty in estimation of the parameters. We try this approach using a variety of discrepancy variables for generalized linear models fitted to a historical data set on behavioural learning. We then discuss the general applicability of our findings in the context of a recent applied example on which we have worked. We find that the following discrepancy variables work well, in the sense of being easy to interpret and sensitive to important model failures: structured displays of the entire data set, general discrepancy variables based on plots of binned or smoothed residuals versus predictors and specific discrepancy variables created on the basis of the particular concerns arising in an application. Plots of binned residuals are especially easy to use because their predictive distributions under the model are sufficiently simple that model checks can often be made implicitly. The following discrepancy variables did not work well: scatterplots of latent residuals defined from an underlying continuous model and quantile–quantile plots of these residuals.     

Detecting homogeneous segments in DNA sequences by using hidden Markov models

In recent years there has been a rapid growth in the amount of DNA being sequenced and in its availability through genetic databases. Statistical techniques which identify structure within these sequences can be of considerable assistance to molecular biologists particularly when they incorporate the discrete nature of changes caused by evolutionary processes. This paper focuses on the detection of homogeneous segments within heterogeneous DNA sequences. In particular, we study an intron from the chimpanzee α-fetoprotein gene; this protein plays an important role in the embryonic development of mammals. We present a Bayesian solution to this segmentation problem using a hidden Markov model implemented by Markov chain Monte Carlo methods. We consider the important practical problem of specifying informative prior knowledge about sequences of this type. Two Gibbs sampling algorithms are contrasted and the sensitivity of the analysis to the prior specification is investigated. Model selection and possible ways to overcome the label switching problem are also addressed. Our analysis of intron 7 identifies three distinct homogeneous segment types, two of which occur in more than one region, and one of which is reversible.     

Estimating the propagation rate of a viral infection of potato plants via mixtures of regressions

A problem arising from the study of the spread of a viral infection among potato plants by aphids appears to involve a mixture of two linear regressions on a single predictor variable. The plant scientists studying the problem were particularly interested in obtaining a 95% confidence upper bound for the infection rate. We discuss briefly the procedure for fitting mixtures of regression models by means of maximum likelihood, effected via the EM algorithm. We give general expressions for the implementation of the M-step and then address the issue of conducting statistical inference in this context. A technique due to T. A. Louis may be used to estimate the covariance matrix of the parameter estimates by calculating the observed Fisher information matrix. We develop general expressions for the entries of this information matrix. Having the complete covariance matrix permits the calculation of confidence and prediction bands for the fitted model. We also investigate the testing of hypotheses concerning the number of components in the mixture via parametric and 'semiparametric' bootstrapping. Finally, we develop a method of producing diagnostic plots of the residuals from a mixture of linear regressions.     

Binary probability maps using a hidden conditional autoregressive Gaussian process with an application to Finnish common toad data

The Finnish common toad data of Heikkinen and Hogmander are reanalysed using an alternative fully Bayesian model that does not require a pseudolikelihood approximation and an alternative prior distribution for the true presence or absence status of toads in each 10 km×10 km square. Markov chain Monte Carlo methods are used to obtain posterior probability estimates of the square-specific presences of the common toad and these are presented as a map. The results are different from those of Heikkinen and Hogmander and we offer an explanation in terms of the prior used for square-specific presence of the toads. We suggest that our approach is more faithful to the data and avoids unnecessary confounding of effects. We demonstrate how to extend our model efficiently with square-specific covariates and illustrate this by introducing deterministic spatial changes.