Marginal likelihood estimation from the Metropolis output: tips and tricks for efficient implementation in generalized linear latent variable models

The marginal likelihood can be notoriously difficult to compute, and particularly so in high-dimensional problems. Chib and Jeliazkov employed the local reversibility of the Metropolis–Hastings algorithm to construct an estimator in models where full conditional densities are not available analytically. The estimator is free of distributional assumptions and is directly linked to the simulation algorithm. However, it generally requires a sequence of reduced Markov chain Monte Carlo runs which makes the method computationally demanding especially in cases when the parameter space is large. In this article, we study the implementation of this estimator on latent variable models which embed independence of the responses to the observables given the latent variables (conditional or local independence). This property is employed in the construction of a multi-block Metropolis-within-Gibbs algorithm that allows to compute the estimator in a single run, regardless of the dimensionality of the parameter space. The counterpart one-block algorithm is also considered here, by pointing out the difference between the two approaches. The paper closes with the illustration of the estimator in simulated and real-life data sets.     

Information geodesics for gamma models of communication clustering

Recently, Akyildiz called for further work on non-Poisson models for communication arrivals in distributed networks such as cellular phone systems. The basic ‘random’ model for stochastic events is the Poisson process; for events on a line this resuits in an exponential disiribuuon of intervals between events. Network designers and managers need too monotor and quantify call clustering in order to optimize resaurce usage; the natural reference state from which to measure departures is that arising from a Poisson, process of calls. Here we consider gamma distributions, which contain exponential distributions as a special case. The surface representing gamma models has a natural Riemannian information metric and we obtain some geodesic sprays for this metric. The exponential distributions form a 1-dimensional subspace of the 2-dimensional space of all gamma distributions, so we have an isometric embedding of the random model as a subspace of the gamma models. This geometry may provide an appropriate structure on which to represent clustering as quantifiable departures from randomness and on which to impose dynamic control algorithms to optimize traffic at receiving nodes in distributed communication networks. In practice, we may expect correlation between call arrival times and call duration, reflecting for example peaks of different users of internet services. This would give rise to a twisted product of two surfaces with the twisting controlled by the correlation. Though bivariate gamma models do exist, such as Kibble's, none has tractabie information geometry nor sufficiently general marginal gammas,but a simulation method of approach is suggested.     

Multilevel embeddedness: The case of the global fisheries governance complex

This paper explores how bilateral and multilateral clustering are embedded in a multilevel system of interdependent networks. We argue that in complex systems in which bilateral and multilateral relations are themselves interrelated, such as global fisheries governance, embeddedness cannot be reduced to unipartite or bipartite clustering but implicates multilevel closure. We elaborate expectations for ties’ multilevel embeddedness based on network theory and substantive considerations and explore them using a multilevel ERGM. We find states’ bilateral ties are embedded in their shared membership in multilateral fisheries agreements, which is itself clustered around foci represented by similar content and treaty secretariats.     

Diffusion Indexes With Sparse Loadings

The use of large-dimensional factor models in forecasting has received much attention in the literature with the consensus being that improvements on forecasts can be achieved when comparing with standard models. However, recent contributions in the literature have demonstrated that care needs to be taken when choosing which variables to include in the model. A number of different approaches to determining these variables have been put forward. These are, however, often based on ad hoc procedures or abandon the underlying theoretical factor model. In this article, we will take a different approach to the problem by using the least absolute shrinkage and selection operator (LASSO) as a variable selection method to choose between the possible variables and thus obtain sparse loadings from which factors or diffusion indexes can be formed. This allows us to build a more parsimonious factor model that is better suited for forecasting compared to the traditional principal components (PC) approach. We provide an asymptotic analysis of the estimator and illustrate its merits empirically in a forecasting experiment based on U.S. macroeconomic data. Overall we find that compared to PC we obtain improvements in forecasting accuracy and thus find it to be an important alternative to PC. Supplementary materials for this article are available online.     

Discovering hidden statistical issues through individual-level models in ecological studies

ABSTRACT

In ecological studies, individual inference is made based on results from ecological models. Interpretation of the results requires caution since ecological analysis on group level may not hold in the individual level within the groups, leading to ecological fallacy. Using an ecological regression example for analyzing voting behaviors, we highlight that the explicit use of individual-level models is crucial in understanding the results of ecological studies. In particular, we clarify three relevant statistical issues for each individual-level models: assessment of the uncertainty of parameter estimates obtained from a wrong model, the use of shrinkage estimation method for simultaneous estimation of many parameters, and the necessity of sensitivity analysis rather than adhering to one seemingly most compelling assumption.     

Quantifying the Establishment Likelihood of Invasive Alien Species Introductions Through Ports with Application to Honeybees in Australia

The cost of an uncontrolled incursion of invasive alien species (IAS) arising from undetected entry through ports can be substantial, and knowledge of port‐specific risks is needed to help allocate limited surveillance resources. Quantifying the establishment likelihood of such an incursion requires quantifying the ability of a species to enter, establish, and spread. Estimation of the approach rate of IAS into ports provides a measure of likelihood of entry. Data on the approach rate of IAS are typically sparse, and the combinations of risk factors relating to country of origin and port of arrival diverse. This presents challenges to making formal statistical inference on establishment likelihood. Here we demonstrate how these challenges can be overcome with judicious use of mixed‐effects models when estimating the incursion likelihood into Australia of the European (Apis mellifera) and Asian (A. cerana) honeybees, along with the invasive parasites of biosecurity concern they host (e.g., Varroa destructor). Our results demonstrate how skewed the establishment likelihood is, with one‐tenth of the ports accounting for 80% or more of the likelihood for both species. These results have been utilized by biosecurity agencies in the allocation of resources to the surveillance of maritime ports.     

The precision of regression-type estimator for incremental cost–effectiveness ratio

The estimation of incremental cost–effectiveness ratio (ICER) has received increasing attention recently. It is expressed in terms of the ratio of the change in costs of a therapeutic intervention to the change in the effects of the intervention. Despite the intuitive interpretation of ICER as an additional cost per additional benefit unit, it is a challenge to estimate the distribution of a ratio of two stochastically dependent distributions. A vast literature regarding the statistical methods of ICER has developed in the past two decades, but none of these methods provide an unbiased estimator. Here, to obtain the unbiased estimator of the cost–effectiveness ratio (CER), the zero intercept of the bivariate normal regression is assumed. In equal sample sizes, the Iman–Conover algorithm is applied to construct the desired variance–covariance matrix of two random bivariate samples, and the estimation then follows the same approach as CER to obtain the unbiased estimator of ICER. The bootstrapping method with the Iman–Conover algorithm is employed for unequal sample sizes. Simulation experiments are conducted to evaluate the proposed method. The regression-type estimator performs overwhelmingly better than the sample mean estimator in terms of mean squared error in all cases.     

Results concerning the generalized partially linear single-index model

The central topic of this article is the estimation of parameters of the generalized partially linear single-index model (GPLSIM). Two numerical optimization procedures are presented and an S-plus program based on these procedures is compared to a program by Wand in a simulation setting. The results from these simulations indicate that the estimates for the new procedures are as good, if not better, than Wand's. Also, this program is much more flexible than Wand's since it can handle more general models. Other simulations are also conducted. The first compares the effects of using linear interpolation versus spline interpolation in an optimization procedure. The results indicate that by using spline interpolation one gets more stable estimates at a cost of increased computational time. A second simulation was conducted to assess the performance of a method for estimating the variance of alpha. A third set of simulations is carried out to determine the best criterion for testing that one of the elements of alpha is equal to zero. The GPLSIM is applied to a water quality data set and the results indicate an interesting relationship between gastrointestinal illness and turbidity (cloudiness) of drinking water.     

Books on probability ideas are reviewed

In this paper, semiparametric methods are applied to estimate multivariate volatility functions, using a residual approach as in [J. Fan and Q. Yao, Efficient estimation of conditional variance functions in stochastic regression, Biometrika 85 (1998), pp. 645–660; F.A. Ziegelmann, Nonparametric estimation of volatility functions: The local exponential estimator, Econometric Theory 18 (2002), pp. 985–991; F.A. Ziegelmann, A local linear least-absolute-deviations estimator of volatility, Comm. Statist. Simulation Comput. 37 (2008), pp. 1543–1564], among others. Our main goal here is two-fold: (1) describe and implement a number of semiparametric models, such as additive, single-index and (adaptive) functional-coefficient, in volatility estimation, all motivated as alternatives to deal with the curse of dimensionality present in fully nonparametric models; and (2) propose the use of a variation of the traditional cross-validation method to deal with model choice in the class of adaptive functional-coefficient models, choosing simultaneously the bandwidth, the number of covariates in the model and also the single-index smoothing variable. The modified cross-validation algorithm is able to tackle the computational burden caused by the model complexity, providing an important tool in semiparametric volatility estimation. We briefly discuss model identifiability when estimating volatility as well as nonnegativity of the resulting estimators. Furthermore, Monte Carlo simulations for several underlying generating models are implemented and applications to real data are provided.     

On partial linear additive isotonic regression

In this paper we discuss semiparametric additive isotonic regression models. We discuss the efficiency bound of the model and the least squares estimator under this model. We show that the ordinary least square estimator studied by Huang (2002) and Cheng (2009) for the semiparametric isotonic regression achieves the efficiency bound for the regular estimator when the true parameter belongs to the interior of the parameter space. We also show that the result by Cheng (2009) can be generalized to the case that the covariates are dependent on each other.