Using unlabelled data to update classification rules with applications in food authenticity studies

Summary.  An authentic food is one that is what it purports to be. Food processors and consumers need to be assured that, when they pay for a specific product or ingredient, they are receiving exactly what they pay for. Classification methods are an important tool in food authenticity studies where they are used to assign food samples of unknown type to known types. A classification method is developed where the classification rule is estimated by using both the labelled and the unlabelled data, in contrast with many classical methods which use only the labelled data for estimation. This methodology models the data as arising from a Gaussian mixture model with parsimonious covariance structure, as is done in model-based clustering. A missing data formulation of the mixture model is used and the models are fitted by using the EM and classification EM algorithms. The methods are applied to the analysis of spectra of food-stuffs recorded over the visible and near infra-red wavelength range in food authenticity studies. A comparison of the performance of model-based discriminant analysis and the method of classification proposed is given. The classification method proposed is shown to yield very good misclassification rates. The correct classification rate was observed to be as much as 15% higher than the correct classification rate for model-based discriminant analysis.     

Modelling change in cognitive understanding with finite mixtures

Psychological theories often posit the existence of several different states. Individuals are viewed as belonging to one of the states at a given age, but with development pass to another state. A main problem in evaluating such theories is representing the transition from one state to another over age. A stochastic transition framework is proposed which should be useful in many different settings. The model is illustrated with data from a cognitive development task.     

Adaptive Estimation Using Weighted Least Squares

This paper proposes an adaptive estimator that is more precise than the ordinary least squares estimator if the distribution of random errors is skewed or has long tails. The adaptive estimates are computed using a weighted least squares approach with weights based on the lengths of the tails of the distribution of residuals. Smaller weights are assigned to those observations that have residuals in the tails of long-tailed distributions and larger weights are assigned to observations having residuals in the tails of short-tailed distributions. Monte Carlo methods are used to compare the performance of the proposed estimator and the performance of the ordinary least squares estimator. The estimates that were studied in this simulation include the difference between the means of two populations, the mean of a symmetric distribution, and the slope of a regression line. The adaptive estimators are shown to have lower mean squared errors than those for the ordinary least squares estimators for short-tailed, long-tailed, and skewed distributions, provided the sample size is at least 20. The ordinary least squares estimator has slightly lower mean squared error for normally distributed errors. The adaptive estimator is recommended for general use for studies having sample sizes of at least 20 observations unless the random errors are known to be normally distributed.     

Using adaptive weighted least squares to reduce the lengths of confidence intervals

The author proposes an adaptive method which produces confidence intervals that are often narrower than those obtained by the traditional procedures. The proposed methods use both a weighted least squares approach to reduce the length of the confidence interval and a permutation technique to insure that its coverage probability is near the nominal level. The author reports simulations comparing the adaptive intervals to the traditional ones for the difference between two population means, for the slope in a simple linear regression, and for the slope in a multiple linear regression having two correlated exogenous variables. He is led to recommend adaptive intervals for sample sizes superior to 40 when the error distribution is not known to be Gaussian.     

A flexible semiparametric transformation model for survival data

I suggest an extension of the semiparametric transformation model that specifies a time-varying regression structure for the transformation, and thus allows time-varying structure in the data. Special cases include a stratified version of the usual semiparametric transformation model. The model can be thought of as specifying a first order Taylor expansion of a completely flexible baseline. Large sample properties are derived and estimators of the asymptotic variances of the regression coefficients are given. The method is illustrated by a worked example and a small simulation study. A goodness of fit procedure for testing if the regression effects lead to a satisfactory fit is also suggested.     

Measuring people's trust

Summary. We measure trust and trustworthiness in British society with a newly designed experiment using real monetary rewards and a sample of the British population. The study also asks the typical survey question that aims to measure trust, showing that it does not predict 'trust' as measured in the experiment. Overall, about 40% of people were willing to trust a stranger in our experiment, and their trust was rewarded half of the time. Analysis of variation in the trust behaviour in our survey suggests that trusting is more likely if people are older, their financial situation is either 'comfortable' or 'difficult' compared with 'doing alright' or 'just getting by', they are a homeowner or they are divorced, separated or never married compared with those who are married or cohabiting. Trustworthiness also is more likely among subjects who are divorced or separated relative to those who are married or cohabiting, and less likely among subjects who perceive their financial situation as 'just getting by' or 'difficult'. We also analyse the effect of attitudes towards risks on trust.     

Parametric non-mixture cure models for schedule finding of therapeutic agents

We propose a phase I clinical trial design that seeks to determine the cumulative safety of a series of administrations of a fixed dose of an investigational agent. In contrast with traditional phase I trials that are designed solely to find the maximum tolerated dose of the agent, our design instead identifies a maximum tolerated schedule that includes a maximum tolerated dose as well as a vector of recommended administration times. Our model is based on a non-mixture cure model that constrains the probability of dose limiting toxicity for all patients to increase monotonically with both dose and the number of administrations received. We assume a specific parametric hazard function for each administration and compute the total hazard of dose limiting toxicity for a schedule as a sum of individual administration hazards. Throughout a variety of settings motivated by an actual study in allogeneic bone marrow transplant recipients, we demonstrate that our approach has excellent operating characteristics and performs as well as the only other currently published design for schedule finding studies. We also present arguments for the preference of our non-mixture cure model over the existing model.     

On pseudo-values for regression analysis in competing risks models

For regression on state and transition probabilities in multi-state models Andersen et al. (Biometrika 90:15–27, 2003) propose a technique based on jackknife pseudo-values. In this article we analyze the pseudo-values suggested for competing risks models and prove some conjectures regarding their asymptotics (Klein and Andersen, Biometrics 61:223–229, 2005). The key is a second order von Mises expansion of the Aalen-Johansen estimator which yields an appropriate representation of the pseudo-values. The method is illustrated with data from a clinical study on total joint replacement. In the application we consider for comparison the estimates obtained with the Fine and Gray approach (J Am Stat Assoc 94:496–509, 1999) and also time-dependent solutions of pseudo-value regression equations.     

A Bayesian approach to non-parametric monotone function estimation

Summary.  The paper proposes two Bayesian approaches to non-parametric monotone function estimation. The first approach uses a hierarchical Bayes framework and a characterization of smooth monotone functions given by Ramsay that allows unconstrained estimation. The second approach uses a Bayesian regression spline model of Smith and Kohn with a mixture distribution of constrained normal distributions as the prior for the regression coefficients to ensure the monotonicity of the resulting function estimate. The small sample properties of the two function estimators across a range of functions are provided via simulation and compared with existing methods. Asymptotic results are also given that show that Bayesian methods provide consistent function estimators for a large class of smooth functions. An example is provided involving economic demand functions that illustrates the application of the constrained regression spline estimator in the context of a multiple-regression model where two functions are constrained to be monotone.