arXiv subjects

Tristan Mary-Huard

Publications and source records attributed to Tristan Mary-Huard.

6 recordsLinked to original sources

arXiv2021

Querying multiple sets of $p$-values through composed hypothesis testing

Motivation: Combining the results of different experiments to exhibit complex patterns or to improve statistical power is a typical aim of data integration. The starting point of the statistical analysis often comes as sets of p-values resulting from previous analyses, that need to be combined in a flexible way to explore complex hypotheses, while guaranteeing a low proportion of false discoveries. Results: We introduce the generic concept of composed hypothesis, which corresponds to an arbitrary complex combination of simple hypotheses. We rephrase the problem of testing a composed hypothesis as a classification task, and show that finding items for which the composed null hypothesis is rejected boils down to fitting a mixture model and classify the items according to their posterior probabilities. We show that inference can be efficiently performed and provide a thorough classification rule to control for type I error. The performance and the usefulness of the approach are illustrated on simulations and on two different applications. The method is scalable, does not require any parameter tuning, and provided valuable biological insight on the considered application cases. Availability: The QCH methodology is implemented in the qch R package hosted on CRAN.

stat.ME↗

arXiv2021

Error rate control for classification rules in multiclass mixture models

In the context of finite mixture models one considers the problem of classifying as many observations as possible in the classes of interest while controlling the classification error rate in these same classes. Similar to what is done in the framework of statistical test theory, different type I and type II-like classification error rates can be defined, along with their associated optimal rules, where optimality is defined as minimizing type II error rate while controlling type I error rate at some nominal level. It is first shown that finding an optimal classification rule boils down to searching an optimal region in the observation space where to apply the classical Maximum A Posteriori (MAP) rule. Depending on the misclassification rate to be controlled, the shape of the optimal region is provided, along with a heuristic to compute the optimal classification rule in practice. In particular, a multiclass FDR-like optimal rule is defined and compared to the thresholded MAP rules that is used in most applications. It is shown on both simulated and real datasets that the FDR-like optimal rule may be significantly less conservative than the thresholded MAP rule.

cs.LG↗

arXiv2017

Theoretical analysis of cross-validation for estimating the risk of the k-Nearest Neighbor classifier

The present work aims at deriving theoretical guaranties on the behavior of some cross-validation procedures applied to the $k$-nearest neighbors ($k$NN) rule in the context of binary classification. Here we focus on the leave-$p$-out cross-validation (L$p$O) used to assess the performance of the $k$NN classifier. Remarkably this L$p$O estimator can be efficiently computed in this context using closed-form formulas derived by \cite{CelisseMaryHuard11}. We describe a general strategy to derive moment and exponential concentration inequalities for the L$p$O estimator applied to the $k$NN classifier. Such results are obtained first by exploiting the connection between the L$p$O estimator and U-statistics, and second by making an intensive use of the generalized Efron-Stein inequality applied to the L$1$O estimator. One other important contribution is made by deriving new quantifications of the discrepancy between the L$p$O estimator and the classification error/risk of the $k$NN classifier. The optimality of these bounds is discussed by means of several lower bounds as well as simulation experiments.

math.ST↗

arXiv2015

SegCorr: a statistical procedure for the detection of genomic regions of correlated expression

Motivation: Detecting local correlations in expression between neighbor genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been successfully used to illustrate the role of mechanisms such as copy number variation (CNV) or epigenetic alterations as factors that may significantly alter expression in large chromosomic regions (gene silencing or gene activation). Results: The identification of correlated regions requires segmenting the gene expression correlation matrix into regions of homogeneously correlated genes and assessing whether the observed local correlation is significantly higher than the background chromosomal correlation. A unified statistical framework is proposed to achieve these two tasks, where optimal segmentation is efficiently performed using dynamic programming algorithm, and detection of highly correlated regions is then achieved using an exact test procedure. We also propose a simple and efficient procedure to correct the expression signal for mechanisms already known to impact expression correlation. The performance and robustness of the proposed procedure, called SegCorr, are evaluated on simulated data. The procedure is illustrated on cancer data, where the signal is corrected for correlations possibly caused by copy number variation. The correction permitted the detection of regions with high correlations linked to DNA methylation. Availability and implementation: R package SegCorr is available on the CRAN.

stat.ME↗

arXiv2014

Structured Regularization for conditional Gaussian Graphical Models

Conditional Gaussian graphical models (cGGM) are a recent reparametrization of the multivariate linear regression model which explicitly exhibits $i)$ the partial covariances between the predictors and the responses, and $ii)$ the partial covariances between the responses themselves. Such models are particularly suitable for interpretability since partial covariances describe strong relationships between variables. In this framework, we propose a regularization scheme to enhance the learning strategy of the model by driving the selection of the relevant input features by prior structural information. It comes with an efficient alternating optimization procedure which is guaranteed to converge to the global minimum. On top of showing competitive performance on artificial and real datasets, our method demonstrates capabilities for fine interpretation of its parameters, as illustrated on three high-dimensional datasets from spectroscopy, genetics, and genomics.

stat.ME↗

arXiv2012

Risk Bounds for Embedded Variable Selection in Classification Trees

The problems of model and variable selections for classification trees are jointly considered. A penalized criterion is proposed which explicitly takes into account the number of variables, and a risk bound inequality is provided for the tree classifier minimizing this criterion. This penalized criterion is compared to the one used during the pruning step of the CART algorithm. It is shown that the two criteria are similar under some specific margin assumptions. In practice, the tuning parameter of the CART penalty has to be calibrated by hold-out. Simulation studies are performed which confirm that the hold-out procedure mimics the form of the proposed penalized criterion.

math.ST↗