Choice of Estimators Based on Different Observations: Modified AIC and LCV Criteria

Abstract. It is quite common in epidemiology that we wish to assess the quality of estimators on a particular set of information, whereas the estimators may use a larger set of information. Two examples are studied: the first occurs when we construct a model for an event which happens if a continuous variable is above a certain threshold. We can compare estimators based on the observation of only the event or on the whole continuous variable. The other example is that of predicting the survival based only on survival information or using in addition information on a disease. We develop modified Akaike information criterion (AIC) and Likelihood cross‐validation (LCV) criteria to compare estimators in this non‐standard situation. We show that a normalized difference of AIC has a bias equal to o ( n ^{? 1} ) if the estimators are based on well‐specified models; a normalized difference of LCV always has a bias equal to o ( n ^{? 1} ). A simulation study shows that both criteria work well, although the normalized difference of LCV tends to be better and is more robust. Moreover in the case of well‐specified models the difference of risks boils down to the difference of statistical risks which can be rather precisely estimated. For ‘compatible’ models the difference of risks is often the main term but there can also be a difference of mis‐specification risks.     

Radiocarbon peat chronologies and environmental change

Summary.  Raised bog peat deposits form important archives for reconstructing past changes in climate. Precise and reliable age models are of vital importance for interpreting such archives. We propose enhanced, Markov chain Monte Carlo based methods for obtaining age models from radiocarbon-dated peat cores, based on the assumption of piecewise linear accumulation. Included are automatic choice of sections, a measure of the goodness of fit and outlier downweighting. The approach is illustrated by using a peat core from the Netherlands.     

Simulated Likelihood Approximations for Stochastic Volatility Models

Abstract. This paper deals with parametric inference for continuous-time stochastic volatility models observed at discrete points in time. We consider approximate maximum likelihood estimation: for the k th-order approximation, we pretend that the observations form a k th-order Markov chain, find the corresponding approximate log-likelihood function, and maximize it with respect to θ . The approximate log-likelihood function is not known analytically, but can easily be calculated by simulation. For each k , the method yields consistent and asymptotically normal estimators. Simulations from a model based on the Cox–Ingersoll–Ross model are used for illustration.     

Sparse Markov Chains for Sequence Data

Finite memory sources and variable‐length Markov chains have recently gained popularity in data compression and mining, in particular, for applications in bioinformatics and language modelling. Here, we consider denser data compression and prediction with a family of sparse Bayesian predictive models for Markov chains in finite state spaces. Our approach lumps transition probabilities into classes composed of invariant probabilities, such that the resulting models need not have a hierarchical structure as in context tree‐based approaches. This can lead to a substantially higher rate of data compression, and such non‐hierarchical sparse models can be motivated for instance by data dependence structures existing in the bioinformatics context. We describe a Bayesian inference algorithm for learning sparse Markov models through clustering of transition probabilities. Experiments with DNA sequence and protein data show that our approach is competitive in both prediction and classification when compared with several alternative methods on the basis of variable memory length.     

Estimating models based on Markov jump processes given fragmented observation series

We consider the problem of estimating the rate matrix governing a finite-state Markov jump process given a number of fragmented time series. We propose to concatenate the observed series and to employ the emerging non-Markov process for estimation. We describe the bias arising if standard methods for Markov processes are used for the concatenated process, and provide a post-processing method to correct for this bias. This method applies to discrete-time Markov chains and to more general models based on Markov jump processes where the underlying state process is not observed directly. This is demonstrated in detail for a Markov switching model. We provide applications to simulated time series and to financial market data, where estimators resulting from maximum likelihood methods and Markov chain Monte Carlo sampling are improved using the presented correction.     

Multivariate Poisson hidden Markov models with a case study of modelling seismicity

While the literature on multivariate models for continuous data flourishes, there is a lack of models for multivariate counts. We aim to contribute to this framework by extending the well known class of univariate hidden Markov models to the multidimensional case, by introducing multivariate Poisson hidden Markov models. Each state of the extended model is associated with a different multivariate discrete distribution. We consider different distributions with Poisson marginals, starting from the multivariate Poisson distribution and then extending to copula based distributions to allow flexible dependence structures. An EM type algorithm is developed for maximum likelihood estimation. A real data application is presented to illustrate the usefulness of the proposed models. In particular, we apply the models to the occurrence of strong earthquakes (surface wave magnitude ≥5), in three seismogenic subregions in the broad region of the North Aegean Sea for the time period from 1 January 1981 to 31 December 2008. Earthquakes occurring in one subregion may trigger events in adjacent ones and hence the observed time series of events are cross‐correlated. It is evident from the results that the three subregions interact with each other at times differing by up to a few months. This migration of seismic activity is captured by the model as a transition to a state of higher seismicity.     

Reference priors for linear models with general covariance structures

We develop a new class of reference priors for linear models with general covariance structures. A general Markov chain Monte Carlo algorithm is also proposed for implementing the computation. We present several examples to demonstrate the results: Bayesian penalized spline smoothing, a Bayesian approach to bivariate smoothing for a spatial model, and prior specification for structural equation models.     

Adaptive Bayesian Procedures Using Random Series Priors

We consider a general class of prior distributions for nonparametric Bayesian estimation which uses finite random series with a random number of terms. A prior is constructed through distributions on the number of basis functions and the associated coefficients. We derive a general result on adaptive posterior contraction rates for all smoothness levels of the target function in the true model by constructing an appropriate ‘sieve’ and applying the general theory of posterior contraction rates. We apply this general result on several statistical problems such as density estimation, various nonparametric regressions, classification, spectral density estimation and functional regression. The prior can be viewed as an alternative to the commonly used Gaussian process prior, but properties of the posterior distribution can be analysed by relatively simpler techniques. An interesting approximation property of B‐spline basis expansion established in this paper allows a canonical choice of prior on coefficients in a random series and allows a simple computational approach without using Markov chain Monte Carlo methods. A simulation study is conducted to show that the accuracy of the Bayesian estimators based on the random series prior and the Gaussian process prior are comparable. We apply the method on Tecator data using functional regression models.     

Structure Learning of Contextual Markov Networks using Marginal Pseudo‐likelihood

Markov networks are popular models for discrete multivariate systems where the dependence structure of the variables is specified by an undirected graph. To allow for more expressive dependence structures, several generalizations of Markov networks have been proposed. Here, we consider the class of contextual Markov networks which takes into account possible context‐specific independences among pairs of variables. Structure learning of contextual Markov networks is very challenging due to the extremely large number of possible structures. One of the main challenges has been to design a score, by which a structure can be assessed in terms of model fit related to complexity, without assuming chordality. Here, we introduce the marginal pseudo‐likelihood as an analytically tractable criterion for general contextual Markov networks. Our criterion is shown to yield a consistent structure estimator. Experiments demonstrate the favourable properties of our method in terms of predictive accuracy of the inferred models.     

Efficient construction of reversible jump Markov chain Monte Carlo proposal distributions

Summary. The major implementational problem for reversible jump Markov chain Monte Carlo methods is that there is commonly no natural way to choose jump proposals since there is no Euclidean structure in the parameter space to guide our choice. We consider mechanisms for guiding the choice of proposal. The first group of methods is based on an analysis of acceptance probabilities for jumps. Essentially, these methods involve a Taylor series expansion of the acceptance probability around certain canonical jumps and turn out to have close connections to Langevin algorithms. The second group of methods generalizes the reversible jump algorithm by using the so-called saturated space approach. These allow the chain to retain some degree of memory so that, when proposing to move from a smaller to a larger model, information is borrowed from the last time that the reverse move was performed. The main motivation for this paper is that, in complex problems, the probability that the Markov chain moves between such spaces may be prohibitively small, as the probability mass can be very thinly spread across the space. Therefore, finding reasonable jump proposals becomes extremely important. We illustrate the procedure by using several examples of reversible jump Markov chain Monte Carlo applications including the analysis of autoregressive time series, graphical Gaussian modelling and mixture modelling.     

Conditional Likelihood Estimators for Hidden Markov Models and Stochastic Volatility Models

ABSTRACT.  This paper develops a new contrast process for parametric inference of general hidden Markov models, when the hidden chain has a non-compact state space. This contrast is based on the conditional likelihood approach, often used for ARCH-type models. We prove the strong consistency of the conditional likelihood estimators under appropriate conditions. The method is applied to the Kalman filter (for which this contrast and the exact likelihood lead to asymptotically equivalent estimators) and to the discretely observed stochastic volatility models.     

Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations

Summary.  Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalized) linear models, (generalized) additive models, smoothing spline models, state space models, semiparametric regression, spatial and spatiotemporal models, log-Gaussian Cox processes and geostatistical and geoadditive models. We consider approximate Bayesian inference in a popular subset of structured additive regression models, latent Gaussian models , where the latent field is Gaussian, controlled by a few hyperparameters and with non-Gaussian response variables. The posterior marginals are not available in closed form owing to the non-Gaussian response variables. For such models, Markov chain Monte Carlo methods can be implemented, but they are not without problems, in terms of both convergence and computational time. In some practical applications, the extent of these problems is such that Markov chain Monte Carlo sampling is simply not an appropriate tool for routine analysis. We show that, by using an integrated nested Laplace approximation and its simplified version, we can directly compute very accurate approximations to the posterior marginals. The main benefit of these approximations is computational: where Markov chain Monte Carlo algorithms need hours or days to run, our approximations provide more precise estimates in seconds or minutes. Another advantage with our approach is its generality, which makes it possible to perform Bayesian analysis in an automatic, streamlined way, and to compute model comparison criteria and various predictive measures so that models can be compared and the model under study can be challenged.     

ML, PL, QL in Markov Chain Models

Abstract.  In many spatial and spatial-temporal models, and more generally in models with complex dependencies, it may be too difficult to carry out full maximum-likelihood (ML) analysis. Remedies include the use of pseudo-likelihood (PL) and quasi-likelihood (QL) (also called the composite likelihood). The present paper studies the ML, PL and QL methods for general Markov chain models, partly motivated by the desire to understand the precise behaviour of the PL and QL methods in settings where this can be analysed. We present limiting normality results and compare performances in different settings. For Markov chain models, the PL and QL methods can be seen as maximum penalized likelihood methods. We find that QL is typically preferable to PL, and that it loses very little to ML, while sometimes earning in model robustness. It has also appeal and potential as a modelling tool. Our methods are illustrated for consonant-vowel transitions in poetry and for analysis of DNA sequence evolution-type models.     

A flexible model for survival data with a cure rate: a Bayesian approach

In this paper we deal with a Bayesian analysis for right-censored survival data suitable for populations with a cure rate. We consider a cure rate model based on the negative binomial distribution, encompassing as a special case the promotion time cure model. Bayesian analysis is based on Markov chain Monte Carlo (MCMC) methods. We also present some discussion on model selection and an illustration with a real data set.     

Fitting Gaussian Markov Random Fields to Gaussian Fields

This paper discusses the following task often encountered in building Bayesian spatial models: construct a homogeneous Gaussian Markov random field (GMRF) on a lattice with correlation properties either as present in some observed data, or consistent with prior knowledge. The Markov property is essential in designing computationally efficient Markov chain Monte Carlo algorithms to analyse such models. We argue that we can restate both tasks as that of fitting a GMRF to a prescribed stationary Gaussian field on a lattice when both local and global properties are important. We demonstrate that using the KullbackLeibler discrepancy often fails for this task, giving severely undesirable behaviour of the correlation function for lags outside the neighbourhood. We propose a new criterion that resolves this difficulty, and demonstrate that GMRFs with small neighbourhoods can approximate Gaussian fields surprisingly well even with long correlation lengths. Finally, we discuss implications of our findings for likelihood based inference for general Markov random fields when global properties are also important.     

Multi-state Models: A Review

Multi-state models are models for a process, for example describing a life history of an individual, which at any time occupies one of a few possible states. This can describe several possible events for a single individual, or the dependence between several individuals. The events are the transitions between the states. This class of models allows for an extremely flexible approach that can model almost any kind of longitudinal failure time data. This is particularly relevant for modeling different events, which have an event-related dependence, like occurrence of disease changing the risk of death. It can also model paired data. It is useful for recurrent events, but has limitations. The Markov models stand out as much simpler than other models from a probability point of view, and this simplifies the likelihood evaluation. However, in many cases, the Markov models do not fit satisfactorily, and happily, it is reasonably simple to study non-Markov models, in particular the Markov extension models. This also makes it possible to consider, whether the dependence is of short-term or long-term nature. Applications include the effect of heart transplantation on the mortality and the mortality among Danish twins.     

Minimal Markov Basis for Tests of Main Effect Models for 2p-1 Fractional Factorial Designs of Resolution p

We consider conditional exact tests of factor effects in design of experiments for discrete response variables. Similarly to the analysis of contingency tables, Markov chain Monte Carlo methods can be used to perform exact tests, especially when large-sample approximations of the null distributions are poor and the enumeration of the conditional sample space is infeasible. In order to construct a connected Markov chain over the appropriate sample space, one approach is to compute a Markov basis. Theoretically, a Markov basis can be characterized as a generator of a well-specified toric ideal in a polynomial ring and is computed by computational algebraic software. However, the computation of a Markov basis sometimes becomes infeasible, even for problems of moderate sizes. In the present article, we obtain the closed-form expression of minimal Markov bases for the main effect models of 2^{p ? 1} fractional factorial designs of resolution p.