Statistical Sources of Variable Selection Bias in Classification Tree Algorithms Based on the Gini Index

Evidence for variable selection bias in classification tree algorithms based on the Gini Index is reviewed from the literature and embedded into a broader explanatory scheme: Variable selection bias in classification tree algorithms based on the Gini Index can be caused not only by the statistical effect of multiple comparisons, but also by an increasing estimation bias and variance of the splitting criterion when plug-in estimates of entropy measures like the Gini Index are employed. The relevance of these sources of variable selection bias in the different simulation study designs is examined. Variable selection bias due to the explored sources applies to all classification tree algorithms based on empirical entropy measures like the Gini Index, Deviance and Information Gain, and to both binary and multiway splitting algorithms

Variable Selection Bias in Classification Trees Based on Imprecise Probabilities

Classification trees based on imprecise probabilities provide an advancement of classical classification trees. The Gini Index is the default splitting criterion in classical classification trees, while in classification trees based on imprecise probabilities, an extension of the Shannon entropy has been introduced as the splitting criterion. However, the use of these empirical entropy measures as split selection criteria can lead to a bias in variable selection, such that variables are preferred for features other than their information content. This bias is not eliminated by the imprecise probability approach. The source of variable selection bias for the estimated Shannon entropy, as well as possible corrections, are outlined. The variable selection performance of the biased and corrected estimators are evaluated in a simulation study. Additional results from research on variable selection bias in classical classification trees are incorporated, implying further investigation of alternative split selection criteria in classification trees based on imprecise probabilities

Danger: High Power! – Exploring the Statistical Properties of a Test for Random Forest Variable Importance

Random forests have become a widely-used predictive model in many scientific disciplines within the past few years. Additionally, they are increasingly popular for assessing variable importance, e.g., in genetics and bioinformatics. We highlight both advantages and limitations of different variable importance scores and associated testing procedures, especially in the context of correlated predictor variables. For the test of Breiman and Cutler (2008), we investigate the statistical properties and find that the power of the test depends both on the sample size and the number of trees, an arbitrarily chosen tuning parameter, leading to undesired results that nullify any significance judgments. Moreover, the specification of the null hypothesis of this test is discussed in the context of correlated predictor variables

Optimal classifier selection and negative bias in error rate estimation: An empirical study on high-dimensional prediction

In biometric practice, researchers often apply a large number of different methods in a "trial-and-error" strategy to get as much as possible out of their data and, due to publication pressure or pressure from the consulting customer, present only the most favorable results. This strategy may induce a substantial optimistic bias in prediction error estimation, which is quantitatively assessed in the present manuscript. The focus of our work is on class prediction based on high-dimensional data (e.g. microarray data), since such analyses are particularly exposed to this kind of bias. In our study we consider a total of 124 variants of classifiers (possibly including variable selection or tuning steps) within a cross-validation evaluation scheme. The classifiers are applied to original and modified real microarray data sets, some of which are obtained by randomly permuting the class labels to mimic non-informative predictors while preserving their correlation structure. We then assess the minimal misclassification rate over the different variants of classifiers in order to quantify the bias arising when the optimal classifier is selected a posteriori in a data-driven manner. The bias resulting from the parameter tuning (including gene selection parameters as a special case) and the bias resulting from the choice of the classification method are examined both separately and jointly. We conclude that the strategy to present only the optimal result is not acceptable, and suggest alternative approaches for properly reporting classification accuracy

Maximally selected chi-square statistics and umbrella orderings

Binary outcomes that depend on an ordinal predictor in a non-monotonic way are common in medical data analysis. Such patterns can be addressed in terms of cutpoints: for example, one looks for two cutpoints that define an interval in the range of the ordinal predictor for which the probability of a positive outcome is particularly high (or low). A chi-square test may then be performed to compare the proportions of positive outcomes in and outside this interval. However, if the two cutpoints are chosen to maximize the chi-square statistic, referring the obtained chi-square statistic to the standard chi-square distribution is an inappropriate approach. It is then necessary to correct the p-value for multiple comparisons by considering the distribution of the maximally selected chi-square statistic instead of the nominal chi-square distribution. Here, we derive the exact distribution of the chi-square statistic obtained by the optimal two cutpoints. We suggest a combinatorial computation method and illustrate our approach by a simulation study and an application to varicella data

Advances in Social Science Research Using R

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