Log-linear models for mutations in the HIV genome

We discuss a general application of categorical data analysis to mutations along the HIV genome. We consider a multidimensional table for several positions at the same time. Due to the complexity of the multidimensional table, we may collapse it by pooling some categories. However, the association between the remaining variables may not be the same as before collapsing. We discuss the collapsibility of tables and the change in the meaning of parameters after collapsing categories. We also address this problem with a log-linear model. We present a parameterization with the consensus output as the reference cell as is appropriate to explain genomic mutations in HIV. We also consider five null hypotheses and some classical methods to address them. We illustrate methods for six positions along the HIV genome, through consideration of all triples of positions.     

The Burr XII System of densities: properties,regression model and applications

We introduce a new class of distributions called the Burr XII system of densities with two extra positive parameters. We provide a comprehensive treatment of some of its mathematical properties. We estimate the model parameters by maximum likelihood. We assess the performance of the maximum likelihood estimators in terms of biases and mean squared errors by means of a simulation study. We also introduce a new family of regression models based on this system of densities. The usefulness of the proposed models is illustrated by means of three real data sets.     

Bayesian Semiparametric Cure Rate Model with an Unknown Threshold

Abstract.  We propose a Bayesian semiparametric model for survival data with a cure fraction. We explicitly consider a finite cure time in the model, which allows us to separate the cured and the uncured populations. We take a mixture prior of a Markov gamma process and a point mass at zero to model the baseline hazard rate function of the entire population. We focus on estimating the cure threshold after which subjects are considered cured. We can incorporate covariates through a structure similar to the proportional hazards model and allow the cure threshold also to depend on the covariates. For illustration, we undertake simulation studies and a full Bayesian analysis of a bone marrow transplant data set.     

A classifier under the strongly spiked eigenvalue model in high-dimension,low-sample-size context

Abstract

We consider the classification of high-dimensional data under the strongly spiked eigenvalue (SSE) model. We create a new classification procedure on the basis of the high-dimensional eigenstructure in high-dimension, low-sample-size context. We propose a distance-based classification procedure by using a data transformation. We also prove that our proposed classification procedure has consistency property for misclassification rates. We discuss performances of our classification procedure in simulations and real data analyses using microarray data sets.     

Non-parametric estimation of the long-range dependence exponent for Gaussian processes

We consider a class of long-range-dependent Gaussian processes defined in a semiparametric framework. We propose a new estimator of the long-range dependence parameter, based on the integration of the periodogram in two windows. We show that it is asymptotically Gaussian and calculate the rate of convergence. We optimise parameters defining the window function for the minimum mean-square-error criterion. In a Monte-Carlo study, we compare the proposed estimator with previously studied estimators.     

Covariance structure of wavelet coefficients: theory and models in a Bayesian perspective

We present theoretical results on the random wavelet coefficients covariance structure. We use simple properties of the coefficients to derive a recursive way to compute the within- and across-scale covariances. We point out a useful link between the algorithm proposed and the two-dimensional discrete wavelet transform. We then focus on Bayesian wavelet shrinkage for estimating a function from noisy data. A prior distribution is imposed on the coefficients of the unknown function. We show how our findings on the covariance structure make it possible to specify priors that take into account the full correlation between coefficients through a parsimonious number of hyperparameters. We use Markov chain Monte Carlo methods to estimate the parameters and illustrate our method on bench-mark simulated signals.     

Joint Estimation of Intersecting Context Tree Models

We study a problem of model selection for data produced by two different context tree sources. Motivated by linguistic questions, we consider the case where the probabilistic context trees corresponding to the two sources are finite and share many of their contexts. In order to understand the differences between the two sources, it is important to identify which contexts and which transition probabilities are specific to each source. We consider a class of probabilistic context tree models with three types of contexts: those which appear in one, the other, or both sources. We use a BIC penalized maximum likelihood procedure that jointly estimates the two sources. We propose a new algorithm which efficiently computes the estimated context trees. We prove that the procedure is strongly consistent. We also present a simulation study showing the practical advantage of our procedure over a procedure that works separately on each data set.     

Failure time regression with continuous covariates measured with error

We consider failure time regression analysis with an auxiliary variable in the presence of a validation sample. We extend the nonparametric inference procedure of Zhou and Pepe to handle a continuous auxiliary or proxy covariate. We estimate the induced relative risk function with a kernel smoother and allow the selection probability of the validation set to depend on the observed covariates. We present some asymptotic properties for the kernel estimator and provide some simulation results. The method proposed is illustrated with a data set from an on-going epidemiologic study.     

Fractions of permutations. An application to Sudoku

We study how to simplify fractional factorial design generation by exploiting the a priori knowledge that can be derived from the orthogonality constraints that the fractional factorial design itself must satisfy. We work on Sudoku puzzles that can be considered as a special case of Latin squares in the class of gerechte designs. We prove that the generation of a Sudoku is equivalent to that of a fraction of a proper set of permutations. We analyse both the 4×4 and the 9×9 Sudoku types.     

Oracle GMM estimation for misspecified models via thresholding

We propose a thresholding generalized method of moments (GMM) estimator for misspecified time series moment condition models. This estimator has the following oracle property: its asymptotic behavior is the same as of any efficient GMM estimator obtained under the a priori information that the true model were known. We propose data adaptive selection methods for thresholding parameter using multiple testing procedures. We determine the limiting null distributions of classical parameter tests and show the consistency of the corresponding block-bootstrap tests used in conjunction with thresholding GMM inference. We present the results of a simulation study for a misspecified instrumental variable regression model and for a vector autoregressive model with measurement error. We illustrate an application of the proposed methodology to data analysis of a real-world dataset.     

Sparse Approximations of Fractional Matérn Fields

We consider fast lattice approximation methods for a solution of a certain stochastic non‐local pseudodifferential operator equation. This equation defines a Matérn class random field. We approximate the pseudodifferential operator with truncated Taylor expansion, spectral domain error functional minimization and rounding approximations. This allows us to construct Gaussian Markov random field approximations. We construct lattice approximations with finite‐difference methods. We show that the solutions can be constructed with overdetermined systems of stochastic matrix equations with sparse matrices, and we solve the system of equations with a sparse Cholesky decomposition. We consider convergence of the truncated Taylor approximation by studying band‐limited Matérn fields. We consider the convergence of the discrete approximations to the continuous limits. Finally, we study numerically the accuracy of different approximation methods with an interpolation problem.     

Bias-calibrated estimation from sample surveys containing outliers

We discuss the problem of estimating finite population parameters on the basis of a sample containing representative outliers. We clarify the motivation for Chambers's bias-calibrated estimator of the population total and show that bias calibration is a key idea in constructing estimators of finite population parameters. We then link the problem of estimating the population total to distribution function or quantile estimation and explore a methodology based on the use of Chambers's estimator. We also propose methodology based on the use of robust estimates and a bias-calibrated form of the Chambers and Dunstan estimator of the population distribution function. This proposal leads to a bias-calibrated estimator of the population total which is an alternative to that of Chambers. We present a small simulation study to illustrate the utility of these estimators.     

Alternative diff-in-diffs estimators with several pretreatment periods

This paper deals with the identification of treatment effects using difference-in-differences estimators when several pretreatment periods are available. We define a family of identifying nonnested assumptions that lead to alternative difference-in-differences estimators. We show that the most usual difference-in-differences estimators imply equivalence conditions for the identifying nonnested assumptions. We further propose a model that can be used to test multiple equivalence conditions without imposing any of them. We conduct a Monte Carlo analysis and apply our approach to several recent papers to show its practical relevance.     

Kolmogorov–Smirnov,Fluctuation, and Z g Tests for Convergence of Markov Chain Monte Carlo Draws

We examine the sizes and powers of three tests of convergence of Markov Chain Monte Carlo draws: the Kolmogorov–Smirnov test, fluctuation test, and Geweke's test. We show that the sizes and powers are sensitive to the existence of autocorrelation in the draws. We propose a filtered test that is corrected for autocorrelation. We present a numerical illustration using the Federal funds rate.     

Some partially sequential nonparametric tests for detecting linear trend

In the present study, we develop two nonparametric partially sequential tests for detecting possible presence of linear trend among the incoming series of observations. We assume that a sample of fixed size is available a priori from some unknown univariate continuous population and there is no sign of trend among these historical observations. Our proposed tests can be viewed as the sequential type tests for monitoring structural changes. We use partial sequential sampling schemes based on usual ranks as well as on sequential ranks. We provide detailed discussion on asymptotic studies related to the proposed tests. We compare the two tests under various situations. We also present some numerical results based on simulation studies. Proposed tests are extremely important in profit making in volatile market through Margin Trading. We illustrate the mechanism with a detailed analysis of a stock price data.     

Testing the equality of several multivariate normal mean vectors under heteroscedasticity: A fiducial approach and an approximate test

We consider the problem of testing the equality of several multivariate normal mean vectors under heteroscedasticity. We first construct a fiducial confidence region (FCR) for the differences between normal mean vectors and we then propose a fiducial test for comparing mean vectors by inverting the FCR. We also propose a simple approximate test that is based on a modification of the χ² approximation. This simple test avoids the complications of simulation-based inference methods. We show that the proposed fiducial test has correct type one error rate asymptotically. We compare the proposed fiducial and approximate tests with the parametric bootstrap test in terms of controlling the type one error rate via an extensive simulation study. Our simulation results show that the proposed fiducial and approximate tests control the type one error rate, while there are cases that the parametric bootstrap test is out of control. We also discuss the power performance of the tests. Finally, we illustrate with a real example how our proposed methods are applicable in analyzing repeated measure designs including a single grouping variable.     

Bayesian mismeasurement t-models for censored responses

This paper aims at introducing a Bayesian robust error-in-variable regression model in which the dependent variable is censored. We extend previous works by assuming a multivariate t distribution for jointly modelling the behaviour of the errors and the latent explanatory variable. Inference is done under the Bayesian paradigm. We use a data augmentation approach and develop a Markov chain Monte Carlo algorithm to sample from the posterior distributions. We run a Monte Carlo study to evaluate the efficiency of the posterior estimators in different settings. We compare the proposed model to three other models previously discussed in the literature. As a by-product we also provide a Bayesian analysis of the t-tobit model. We fit all four models to analyse the 2001 Medical Expenditure Panel Survey data.     

An optimization interpretation of integration and back-fitting estimators for separable nonparametric models

We provide an optimization interpretation of both back-fitting and integration estimators for additive nonparametric regression. We find that the integration estimator is a projection with respect to a product measure. We also provide further understanding of the back-fitting method.     

Non linear parametric mode regression

In this article, we propose a semi-parametric mode regression for a non linear model. We use an expectation-maximization algorithm in order to estimate the regression coefficients of modal non linear regression. We also establish asymptotic properties for the proposed estimator under assumptions of the error density. We investigate the performance through a simulation study.