On agnostic post hoc approaches to false positive control
This document is a book chapter which gives a partial survey on post hoc approaches to false positive control.
math.ST↗
arXiv subjects
Etienne Roquain
Publications and source records attributed to Etienne Roquain.
Graph inference with clustering and false discovery rate control
In this paper, a noisy version of the stochastic block model (NSBM) is introduced and we investigate the three following statistical inferences in this model: estimation of the model parameters, clustering of the nodes and identification of the underlying graph. While the two first inferences are done by using a variational expectation-maximization (VEM) algorithm, the graph inference is done by controlling the false discovery rate (FDR), that is, the average proportion of errors among the edges declared significant, and by maximizing the true discovery rate (TDR), that is, the average proportion of edges declared significant among the true edges. Provided that the VEM algorithm provides reliable parameter estimates and clustering, we theoretically show that our procedure does control the FDR while satisfying an optimal TDR property, up to remainder terms that become small when the size of the graph grows. Numerical experiments show that our method outperforms the classical FDR controlling methods that ignore the underlying SBM topology. In addition, these simulations demonstrate that the FDR/TDR properties of our method are robust to model mis-specification, that is, are essentially maintained outside our model.
math.ST↗
On spike and slab empirical Bayes multiple testing
This paper explores a connection between empirical Bayes posterior distributions and false discovery rate (FDR) control. In the Gaussian sequence model, this work shows that empirical Bayes-calibrated spike and slab posterior distributions allow a correct FDR control under sparsity. Doing so, it offers a frequentist theoretical validation of empirical Bayes methods in the context of multiple testing. Our theoretical results are illustrated with numerical experiments.
math.ST↗
DiscreteFDR: An R package for controlling the false discovery rate for discrete test statistics
The simultaneous analysis of many statistical tests is ubiquitous in applications. Perhaps the most popular error rate used for avoiding type one error inflation is the false discovery rate (FDR). However, most theoretical and software development for FDR control has focused on the case of continuous test statistics. For discrete data, methods that provide proven FDR control and good performance have been proposed only recently. The R package DiscreteFDR provides an implementation of these methods. For particular commonly used discrete tests such as Fisher's exact test, it can be applied as an off-the-shelf tool by taking only the raw data as input. It can also be used for any arbitrary discrete test statistics by using some additional information on the distribution of these statistics. The paper reviews the statistical methods in a non-technical way, provides a detailed description of the implementation in DiscreteFDR and presents some sample code and analyses.
stat.CO↗
Estimating minimum effect with outlier selection
We introduce one-sided versions of Huber's contamination model, in which corrupted samples tend to take larger values than uncorrupted ones. Two intertwined problems are addressed: estimation of the mean of uncorrupted samples (minimum effect) and selection of corrupted samples (outliers). Regarding the minimum effect estimation, we derive the minimax risks and introduce adaptive estimators to the unknown number of contaminations. Interestingly, the optimal convergence rate highly differs from that in classical Huber's contamination model. Also, our analysis uncovers the effect of particular structural assumptions on the distribution of the contaminated samples. As for the problem of selecting the outliers, we formulate the problem in a multiple testing framework for which the location/scaling of the null hypotheses are unknown. We rigorously prove how estimating the null hypothesis is possible while maintaining a theoretical guarantee on the amount of the falsely selected outliers, both through false discovery rate (FDR) or post hoc bounds. As a by-product, we address a long-standing open issue on FDR control under equi-correlation, which reinforces the interest of removing dependency when making multiple testing.
math.ST↗
Post hoc false positive control for spatially structured hypotheses
In a high dimensional multiple testing framework, we present new confidence bounds on the false positives contained in subsets S of selected null hypotheses. The coverage probability holds simultaneously over all subsets S, which means that the obtained confidence bounds are post hoc. Therefore, S can be chosen arbitrarily, possibly by using the data set several times. We focus in this paper specifically on the case where the null hypotheses are spatially structured. Our method is based on recent advances in post hoc inference and particularly on the general methodology of Blanchard et al. (2017); we build confidence bounds for some pre-specified forest-structured subsets {R k , k $\in$ K}, called the reference family, and then we deduce a bound for any subset S by interpolation. The proposed bounds are shown to improve substantially previous ones when the signal is locally structured. Our findings are supported both by theoretical results and numerical experiments. Moreover, we show that our bound can be obtained by a low-complexity algorithm, which makes our approach completely operational for a practical use. The proposed bounds are implemented in the open-source R package sansSouci.
math.ST↗
Post hoc inference via joint family-wise error rate control
We introduce a general methodology for post hoc inference in a large-scale multiple testing framework. The approach is called "user-agnostic" in the sense that the statistical guarantee on the number of correct rejections holds for any set of candidate items selected by the user (after having seen the data). This task is investigated by defining a suitable criterion, named the joint-family-wise-error rate (JER for short). We propose several procedures for controlling the JER, with a special focus on incorporating dependencies while adapting to the unknown quantity of signal (via a step-down approach). We show that our proposed setting incorporates as particular cases a version of the higher criticism as well as the closed testing based approach of Goeman and Solari (2011). Our theoretical statements are supported by numerical experiments.
math.ST↗
Improving the Benjamini-Hochberg Procedure for Discrete Tests
To find interesting items in genome-wide association studies or next generation sequencing data, a crucial point is to design powerful false discovery rate (FDR) controlling procedures that suitably combine discrete tests (typically binomial or Fisher tests). In particular, recent research has been striving for appropriate modifications of the classical Benjamini-Hochberg (BH) step-up procedure that accommodate discreteness. However, despite an important number of attempts, these procedures did not come with theoretical guarantees. The present paper contributes to fill the gap: it presents new modifications of the BH procedure that incorporate the discrete structure of the data and provably control the FDR for any fixed number of null hypotheses (under independence). Markedly, our FDR controlling methodology allows to incorporate simultaneously the discreteness and the quantity of signal of the data (corresponding therefore to a so-called $π\_0$-adaptive procedure). The power advantage of the new methods is demonstrated in a numerical experiment and for some appropriate real data sets.
math.ST↗
Continuous testing for Poisson process intensities: A new perspective on scanning statistics
We propose a novel continuous testing framework to test the intensities of Poisson Processes. This framework allows a rigorous definition of the complete testing procedure, from an infinite number of hypothesis to joint error rates. Our work extends traditional procedures based on scanning windows, by controlling the family-wise error rate and the false discovery rate in a non-asymptotic manner and in a continuous way. The decision rule is based on a \pvalue process that can be estimated by a Monte-Carlo procedure. We also propose new test statistics based on kernels. Our method is applied in Neurosciences and Genomics through the standard test of homogeneity, and the two-sample test.
stat.ME↗
New procedures controlling the false discovery proportion via Romano-Wolf's heuristic
The false discovery proportion (FDP) is a convenient way to account for false positives when a large number $m$ of tests are performed simultaneously. Romano and Wolf [Ann. Statist. 35 (2007) 1378-1408] have proposed a general principle that builds FDP controlling procedures from $k$-family-wise error rate controlling procedures while incorporating dependencies in an appropriate manner; see Korn et al. [J. Statist. Plann. Inference 124 (2004) 379-398]; Romano and Wolf (2007). However, the theoretical validity of the latter is still largely unknown. This paper provides a careful study of this heuristic: first, we extend this approach by using a notion of "bounding device" that allows us to cover a wide range of critical values, including those that adapt to $m\_0$, the number of true null hypotheses. Second, the theoretical validity of the latter is investigated both nonasymptotically and asymptotically. Third, we introduce suitable modifications of this heuristic that provide new methods, overcoming the existing procedures with a proven FDP control.
math.ST↗
Testing over a continuum of null hypotheses with False Discovery Rate control
We consider statistical hypothesis testing simultaneously over a fairly general, possibly uncountably infinite, set of null hypotheses, under the assumption that a suitable single test (and corresponding $p$-value) is known for each individual hypothesis. We extend to this setting the notion of false discovery rate (FDR) as a measure of type I error. Our main result studies specific procedures based on the observation of the $p$-value process. Control of the FDR at a nominal level is ensured either under arbitrary dependence of $p$-values, or under the assumption that the finite dimensional distributions of the $p$-value process have positive correlations of a specific type (weak PRDS). Both cases generalize existing results established in the finite setting. Its interest is demonstrated in several non-parametric examples: testing the mean/signal in a Gaussian white noise model, testing the intensity of a Poisson process and testing the c.d.f. of i.i.d. random variables.
stat.ME↗
On empirical distribution function of high-dimensional Gaussian vector components with an application to multiple testing
This paper introduces a new framework to study the asymptotical behavior of the empirical distribution function (e.d.f.) of Gaussian vector components, whose correlation matrix $Γ^{(m)}$ is dimension-dependent. Hence, by contrast with the existing literature, the vector is not assumed to be stationary. Rather, we make a "vanishing second order" assumption ensuring that the covariance matrix $Γ^{(m)}$ is not too far from the identity matrix, while the behavior of the e.d.f. is affected by $Γ^{(m)}$ only through the sequence $γ_m=m^{-2} \sum_{i\neq j} Γ_{i,j}^{(m)}$, as $m$ grows to infinity. This result recovers some of the previous results for stationary long-range dependencies while it also applies to various, high-dimensional, non-stationary frameworks, for which the most correlated variables are not necessarily next to each other. Finally, we present an application of this work to the multiple testing problem, which was the initial statistical motivation for developing such a methodology.
math.ST↗
On false discovery rate thresholding for classification under sparsity
We study the properties of false discovery rate (FDR) thresholding, viewed as a classification procedure. The "0"-class (null) is assumed to have a known density while the "1"-class (alternative) is obtained from the "0"-class either by translation or by scaling. Furthermore, the "1"-class is assumed to have a small number of elements w.r.t. the "0"-class (sparsity). We focus on densities of the Subbotin family, including Gaussian and Laplace models. Nonasymptotic oracle inequalities are derived for the excess risk of FDR thresholding. These inequalities lead to explicit rates of convergence of the excess risk to zero, as the number m of items to be classified tends to infinity and in a regime where the power of the Bayes rule is away from 0 and 1. Moreover, these theoretical investigations suggest an explicit choice for the target level $α_m$ of FDR thresholding, as a function of m. Our oracle inequalities show theoretically that the resulting FDR thresholding adapts to the unknown sparsity regime contained in the data. This property is illustrated with numerical experiments.
stat.ME↗
On least favorable configurations for step-up-down tests
This paper investigates an open issue related to false discovery rate (FDR) control of step-up-down (SUD) multiple testing procedures. It has been established in earlier literature that for this type of procedure, under some broad conditions, and in an asymptotical sense, the FDR is maximum when the signal strength under the alternative is maximum. In other words, so-called "Dirac uniform configurations" are asymptotically {\em least favorable} in this setting. It is known that this property also holds in a non-asymptotical sense (for any finite number of hypotheses), for the two extreme versions of SUD procedures, namely step-up and step-down (with extra conditions for the step-down case). It is therefore very natural to conjecture that this non-asymptotical {\em least favorable configuration} property could more generally be true for all "intermediate" forms of SUD procedures. We prove that this is, somewhat surprisingly, not the case. The argument is based on the exact calculations proposed earlier by Roquain and Villers (2011), that we extend here by generalizing Steck's recursion to the case of two populations. Secondly, we quantify the magnitude of this phenomenon by providing a nonasymptotic upper-bound and explicit vanishing rates as a function of the total number of hypotheses.
stat.ME↗
Type I error rate control for testing many hypotheses: a survey with proofs
This paper presents a survey on some recent advances for the type I error rate control in multiple testing methodology. We consider the problem of controlling the $k$-family-wise error rate (kFWER, probability to make $k$ false discoveries or more) and the false discovery proportion (FDP, proportion of false discoveries among the discoveries). The FDP is controlled either via its expectation, which is the so-called false discovery rate (FDR), or via its upper-tail distribution function. We aim at deriving general and unified results together with concise and simple mathematical proofs. Furthermore, while this paper is mainly meant to be a survey paper, some new contributions for controlling the kFWER and the upper-tail distribution function of the FDP are provided. In particular, we derive a new procedure based on the quantiles of the binomial distribution that controls the FDP under independence.
stat.ME↗
Spatial clustering of array CGH features in combination with hierarchical multiple testing
We propose a new approach for clustering DNA features using array CGH data from multiple tumor samples. We distinguish data-collapsing: joining contiguous DNA clones or probes with extremely similar data into regions, from clustering: joining contiguous, correlated regions based on a maximum likelihood principle. The model-based clustering algorithm accounts for the apparent spatial patterns in the data. We evaluate the randomness of the clustering result by a cluster stability score in combination with cross-validation. Moreover, we argue that the clustering really captures spatial genomic dependency by showing that coincidental clustering of independent regions is very unlikely. Using the region and cluster information, we combine testing of these for association with a clinical variable in an hierarchical multiple testing approach. This allows for interpreting the significance of both regions and clusters while controlling the Family-Wise Error Rate simultaneously. We prove that in the context of permutation tests and permutation-invariant clusters it is allowed to perform clustering and testing on the same data set. Our procedures are illustrated on two cancer data sets.
stat.AP↗
On the false discovery proportion convergence under Gaussian equi-correlation
We study the convergence of the false discovery proportion (FDP) of the Benjamini-Hochberg procedure in the Gaussian equi-correlated model, when the correlation $ρ_m$ converges to zero as the hypothesis number $m$ grows to infinity. By contrast with the standard convergence rate $m^{1/2}$ holding under independence, this study shows that the FDP converges to the false discovery rate (FDR) at rate $\{\min(m,1/ρ_m)\}^{1/2}$ in this equi-correlated model.
math.ST↗
Exact calculations for false discovery proportion with application to least favorable configurations
In a context of multiple hypothesis testing, we provide several new exact calculations related to the false discovery proportion (FDP) of step-up and step-down procedures. For step-up procedures, we show that the number of erroneous rejections conditionally on the rejection number is simply a binomial variable, which leads to explicit computations of the c.d.f., the {$s$-th} moment and the mean of the FDP, the latter corresponding to the false discovery rate (FDR). For step-down procedures, we derive what is to our knowledge the first explicit formula for the FDR valid for any alternative c.d.f. of the $p$-values. We also derive explicit computations of the power for both step-up and step-down procedures. These formulas are "explicit" in the sense that they only involve the parameters of the model and the c.d.f. of the order statistics of i.i.d. uniform variables. The $p$-values are assumed either independent or coming from an equicorrelated multivariate normal model and an additional mixture model for the true/false hypotheses is used. This new approach is used to investigate new results which are of interest in their own right, related to least/most favorable configurations for the FDR and the variance of the FDP.
math.ST↗