Anne-Laure Boulesteix

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BACKGROUND Random forests are becoming increasingly popular in many scientific fields because they can cope with "small n large p" problems, complex interactions and even highly correlated predictor variables. Their variable importance measures have recently been suggested as screening tools for, e.g., gene expression studies. However, these variable(More)
BACKGROUND Variable importance measures for random forests have been receiving increased attention as a means of variable selection in many classification tasks in bioinformatics and related scientific fields, for instance to select a subset of genetic markers relevant for the prediction of a certain disease. We show that random forest variable importance(More)
Partial least squares (PLS) is an efficient statistical regression technique that is highly suited for the analysis of genomic and proteomic data. In this article, we review both the theory underlying PLS as well as a host of bioinformatics applications of PLS. In particular, we provide a systematic comparison of the PLS approaches currently employed, and(More)
BACKGROUND The study of the network between transcription factors and their targets is important for understanding the complex regulatory mechanisms in a cell. Unfortunately, with standard microarray experiments it is not possible to measure the transcription factor activities (TFAs) directly, as their own transcription levels are subject to(More)
Partial Least Squares (PLS) dimension reduction is known to give good prediction accuracy in the context of classification with high-dimensional microarray data. In this paper, the classification procedure consisting of PLS dimension reduction and linear discriminant analysis on the new components is compared with some of the best state-of-the-art(More)
The association between a binary variable Y and a variable X having an at least ordinal measurement scale might be examined by selecting a cutpoint in the range of X and then performing an association test for the obtained 2 x 2 contingency table using the chi-square statistic. The distribution of the maximally selected chi-square statistic (i.e. the(More)
MOTIVATION In the context of clinical bioinformatics methods are needed for assessing the additional predictive value of microarray data compared to simple clinical parameters alone. Such methods should also provide an optimal prediction rule making use of all potentialities of both types of data: they should ideally be able to catch subtypes which are not(More)
MOTIVATION Cancer diagnosis using gene expression profiles requires supervised learning and gene selection methods. Of the many suggested approaches, the method of emerging patterns (EPs) has the particular advantage of explicitly modeling interactions among genes, which improves classification accuracy. However, finding useful (i.e. short and statistically(More)
BACKGROUND 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(More)
BACKGROUND While high-dimensional molecular data such as microarray gene expression data have been used for disease outcome prediction or diagnosis purposes for about ten years in biomedical research, the question of the additional predictive value of such data given that classical predictors are already available has long been under-considered in the(More)