Wavelet Thresholding Estimation in a Poissonian Interactions Model with Application to Genomic Data

This paper deals with the study of dependencies between two given events modelled by point processes. In particular, we focus on the context of DNA to detect favoured or avoided distances between two given motifs along a genome suggesting possible interactions at a molecular level. For this, we naturally introduce a so‐called reproduction function h that allows to quantify the favoured positions of the motifs and that is considered as the intensity of a Poisson process. Our first interest is the estimation of this function h assumed to be well localized. The estimator based on random thresholds achieves an oracle inequality. Then, minimax properties of on Besov balls are established. Some simulations are provided, proving the good practical behaviour of our procedure. Finally, our method is applied to the analysis of the dependence between promoter sites and genes along the genome of the Escherichia coli bacterium.     

Maximum likelihood estimation of ARFIMA models with a Box-Cox transformation

In this paper we study the interaction between the estimation of the fractional differencing parameter d of ARFIMA models and the common practice of instantaneous transformation of the observed time series. At this aim, we first discuss the effect of a nonlinear transformation of the data on the identification of the process and on the estimate of d. Thus, we propose a joint estimation of the Box-Cox parameter and d by means of a modified normalized version of the Whittle likelihood. Then, the variance and covariance matrix of the parameters estimates is obtained. Finally, a Monte Carlo study is performed in order to check the behaviour of the proposed estimators in finite samples.The paper is the result of a joint research of the two authors. As far as it concerns this version of the work, A. DElia wrote Sects. 2, 3, 4, while D. Piccolo wrote Sects. 1, 5, 6.     

Reverse Foldovers for Blocked 2 m−k Fractional Factorial Designs

Two-level regular fractional factorial designs are often used in industry as screening designs to help identify early on in an experimental process those experimental or system variables which have significant effects on the process being studied. When the experimental material to be used in the experiment is heterogenous or the experiment must be performed over several well-defined time periods, blocking is often used as a means to improve experimental efficiency by removing the possible effects of heterogenous experimental material or possible time period effects. In a recent article, Li and Jacroux (2007 Li , F. , Jacroux , M. (2007). Optimal foldover plans for blocked 2 ^m?k fractional factorial designs. J. Statsist. Plann. Infer 137:2434–2452. [Google Scholar]) suggested a strategy for constructing optimal follow-up designs for blocked fractional factorial designs using the well-known foldover technique in conjunction with several optimality criteria. In this article, we consider the reverse foldover problem for blocked fractional factorial designs. In particular, given a 2^(m+p)?(p+k) blocked fractional factorial design D, we derive simple sufficient conditions which can be used to determine if there exists a 2^{(m+p?1)?(p?1+k+1)} initial fractional factorial design d which yields D as a foldover combined design as well how to generate all such d. Such information is useful in developing an overall experimental strategy in situations where an experimenter wants an overall blocked fractional factorial design with “desirable” properties but also wants the option of analyzing the observed data at the halfway mark to determine if the significant experimental variables are obvious (and the experiment can be terminated) or if a different path of experimentation should be taken from that initially planned.     

The univariate distribution function for a particular bilinear model

The aim of the paper is to find the univariate stationary distribution of a particular bilinear process. In this context, we propose a novel approach to derive the distribution function. It is based on a recursive formula and allows to relax the conditions on the moments of the process. We also show that the derived approximation converges to the true distribution function. The accuracy of the recursive formula is evaluated for finite sample dimensions by a small simulation study.Received: February 2003, Revised: May 2004,     

A comparison of mean squared error approximations for a small estimated state space model*

Summary: This paper investigates mean squared errors for unobserved states in state space models when estimation uncertainty of hyperparameters is taken into account. Three alternative approximations to mean squared errors with estimation uncertainty are compared in a Monte Carlo experiment, where the random walk with noise model serves as DGP: A naive method which neglects estimation uncertainty completely, an approximation based on an expansion around the true state with respect to the estimated parameters, and a bootstrap approach. Overall, the bootstrap method performs best in the simulations. However, the gains are not systematic, and the computationally burden of this method is relatively high.*This paper represents the authors personal opinions and does not necessarily reflect the views of the Deutsche Bundesbank. I am grateful to Malte Knüppel, Jeong-Ryeol Kurz-Kim, Karl-Heinz Tödter and a referee for helpful comments. The computer programs for this paper were written in Ox and SsfPack, see Doornik (1998) and Koopman et al. (1999). The used SsfPack version is 2.2.     

Robust empirical Bayes tests for continuous distributions

In this paper, we study the empirical Bayes two-action problem under linear loss function. Upper bounds on the regret of empirical Bayes testing rules are investigated. Previous results on this problem construct empirical Bayes tests using kernel type estimators of nonparametric functionals. Further, they have assumed specific forms, such as the continuous one-parameter exponential family for {F_θ:θΩ}, for the family of distributions of the observations. In this paper, we present a new general approach of establishing upper bounds (in terms of rate of convergence) of empirical Bayes tests for this problem. Our results are given for any family of continuous distributions and apply to empirical Bayes tests based on any type of nonparametric method of functional estimation. We show that our bounds are very sharp in the sense that they reduce to existing optimal or nearly optimal rates of convergence when applied to specific families of distributions.     

Posterior Bayes factor analysis for an exponential regression model

In the exponential regression model, Bayesian inference concerning the non-linear regression parameter has proved extremely difficult. In particular, standard improper diffuse priors for the usual parameters lead to an improper posterior for the non-linear regression parameter. In a recent paper Ye and Berger (1991) applied the reference prior approach of Bernardo (1979) and Berger and Bernardo (1989) yielding a proper informative prior for . This prior depends on the values of the explanatory variable, goes to 0 as goes to 1, and depends on the specification of a hierarchical ordering of importance of the parameters.This paper explains the failure of the uniform prior to give a proper posterior: the reason is the appearance of the determinant of the information matrix in the posterior density for . We apply the posterior Bayes factor approach of Aitkin (1991) to this problem; in this approach we integrate out nuisance parameters with respect to their conditional posterior density given the parameter of interest. The resulting integrated likelihood for requires only the standard diffuse prior for all the parameters, and is unaffected by orderings of importance of the parameters. Computation of the likelihood for is extremely simple. The approach is applied to the three examples discussed by Berger and Ye and the likelihoods compared with their posterior densities.     

Evaluation of Laplace distribution-based ANOVA models applied to microarray data

In a microarray experiment, intensity measurements tend to vary due to various systematic and random effects, which enter at the different stages of the measurement process. Common test statistics do not take these effects into account. An alternative is to use, for example, ANOVA models. In many cases, we can, however, not make the assumption of normally distributed error terms. Purdom and Holmes [6 Purdom, E. and Holmes, S. P. 2005. Error distribution for gene expression data. Stat. Appl. Genet. Mol. Biol., 4(1) article 16 [Google Scholar]] have concluded that the distribution of microarray intensity measurements can often be better approximated by a Laplace distribution. In this paper, we consider the analysis of microarray data by using ANOVA models under the assumption of Laplace-distributed error terms. We explain the methodology and discuss problems related to fitting of this type of models. In addition to evaluating the models using several real-life microarray experiments, we conduct a simulation study to investigate different aspects of the models in detail. We find that, while the normal model is less sensitive to model misspecifications, the Laplace model has more power when the data are truly Laplace distributed. However, in the latter situation, neither of the models is able to control the false discovery rate at the pre-specified significance level. This problem is most likely related to sample size issues.     

A generalized Fleming and Harrington's class of tests for interval‐censored data

The class $G^{\rho,\lambda }$ of weighted log‐rank tests proposed by Fleming & Harrington [Fleming & Harrington (1991) Counting Processes and Survival Analysis, Wiley, New York] has been widely used in survival analysis and is nowadays, unquestionably, the established method to compare, nonparametrically, k different survival functions based on right‐censored survival data. This paper extends the $G^{\rho,\lambda }$ class to interval‐censored data. First we introduce a new general class of rank based tests, then we show the analogy to the above proposal of Fleming & Harrington. The asymptotic behaviour of the proposed tests is derived using an observed Fisher information approach and a permutation approach. Aiming to make this family of tests interpretable and useful for practitioners, we explain how to interpret different choices of weights and we apply it to data from a cohort of intravenous drug users at risk for HIV infection. The Canadian Journal of Statistics 40: 501–516; 2012 © 2012 Statistical Society of Canada     

Response Time Distribution in a D-MAP/PH/1 Queue with General Customer Impatience

ABSTRACT

This paper presents two methods to calculate the response time distribution of impatient customers in a discrete-time queue with Markovian arrivals and phase-type services, in which the customers’ patience is generally distributed (i.e., the D-MAP/PH/1 queue). The first approach uses a GI/M/1 type Markov chain and may be regarded as a generalization of the procedure presented in Van Houdt ^[14] Van Houdt , B. ; Lenin , R. B. ; Blondia , C. Delay distribution of (im)patient customers in a discrete time D-MAP/PH/1 queue with age dependent service times Queueing Systems and Applications 2003 , 45 1 , 59 – 73 . [CROSSREF]  [Google Scholar] for the D-MAP/PH/1 queue, where every customer has the same amount of patience. The key construction in order to obtain the response time distribution is to set up a Markov chain based on the age of the customer being served, together with the state of the D-MAP process immediately after the arrival of this customer. As a by-product, we can also easily obtain the queue length distribution from the steady state of this Markov chain.

We consider three different situations: (i) customers leave the system due to impatience regardless of whether they are being served or not, possibly wasting some service capacity, (ii) a customer is only allowed to enter the server if he is able to complete his service before reaching his critical age and (iii) customers become patient as soon as they are allowed to enter the server. In the second part of the paper, we reduce the GI/M/1 type Markov chain to a Quasi-Birth-Death (QBD) process. As a result, the time needed, in general, to calculate the response time distribution is reduced significantly, while only a relatively small amount of additional memory is needed in comparison with the GI/M/1 approach. We also include some numerical examples in which we apply the procedures being discussed.     

Estimation of a Copula when a Covariate Affects only Marginal Distributions

This paper is concerned with studying the dependence structure between two random variables Y₁ and Y₂ in the presence of a covariate X, which affects both marginal distributions but not the dependence structure. This is reflected in the property that the conditional copula of Y₁ and Y₂ given X, does not depend on the value of X. This latter independence often appears as a simplifying assumption in pair‐copula constructions. We introduce a general estimator for the copula in this specific setting and establish its consistency. Moreover, we consider some special cases, such as parametric or nonparametric location‐scale models for the effect of the covariate X on the marginals of Y₁ and Y₂ and show that in these cases, weak convergence of the estimator, at ‐rate, holds. The theoretical results are illustrated by simulations and a real data example.     

Testing sphericity and intraclass covariance structures under a growth curve model in high dimension

In this article, we consider the problem of testing (a) sphericity and (b) intraclass covariance structure under a growth curve model. The maximum likelihood estimator (MLE) for the mean in a growth curve model is a weighted estimator with the inverse of the sample covariance matrix which is unstable for large p close to N and singular for p larger than N. The MLE for the covariance matrix is based on the MLE for the mean, which can be very poor for p close to N. For both structures (a) and (b), we modify the MLE for the mean to an unweighted estimator and based on this estimator we propose a new estimator for the covariance matrix. This new estimator leads to new tests for (a) and (b). We also propose two other tests for each structure, which are just based on the sample covariance matrix.

To compare the performance of all four tests we compute for each structure (a) and (b) the attained significance level and the empirical power. We show that one of the tests based on the sample covariance matrix is better than the likelihood ratio test based on the MLE.     

Stochastic comparison of processes generated by random interruptions of monotone functions and related results

Many stochastic processes considered in applied probability models, and, in particular, in reliability theory, are processes of the following form: Shocks occur according to some point process, and each shock causes the process to have a random jump. Between shocks the process increases or decreases in some deterministic fashion. In this paper we study processes for which the rate of increase or decrease between shocks depends only on the height of the process. For such processes we find conditions under which the processes can be stochastically compared. We also study hybrid processes in which periods of increase and periods of decrease alternate. A further result yields a stochastic comparison of processes that start with a random jump, rather than processes in which there is at the beginning some random delay time before the first jump.Supported by NSF Grant DMS 9303891.     

Missing at random (MAR) in nonparametric regression - A simulation experiment

The additive model is considered when some observations on x are missing at random but corresponding observations on y are available. Especially for this model, missing at random is an interesting case because the complete case analysis is expected to be no more suitable. A simulation experiment is reported and the different methods are compared based on their superiority with respect to the sample mean squared error. Some focus is also given on the sample variance and the estimated bias. In detail, the complete case analysis, a kind of stochastic mean imputation, a single imputation and the nearest neighbor imputation are discussed.