We propose a permutation-based method for testing a large collection of hypotheses simultaneously. Our method provides lower bounds for the number of true discoveries in any selected subset of hypotheses. These bounds are simultaneously valid with high confidence. The methodology is particularly useful in functional Magnetic Resonance Imaging cluster analysis, where it provides a confidence statement on the percentage of truly activated voxels within clusters of voxels, avoiding the well-known spatial specificity paradox. We offer a user-friendly tool to estimate the percentage of true discoveries for each cluster while controlling the family-wise error rate for multiple testing and taking into account that the cluster was chosen in a data-driven way. The method adapts to the spatial correlation structure that characterizes functional Magnetic Resonance Imaging data, gaining power over parametric approaches.
We consider the problem of estimating the proportion $θ$ of true null hypotheses in a multiple testing context. The setup is classically modeled through a semiparametric mixture with two components: a uniform distribution on interval $[0,1]$ with prior probability $θ$ and a nonparametric density $f$. We discuss asymptotic efficiency results and establish that two different cases occur whether $f$ vanishes on a set with non null Lebesgue measure or not. In the first case, we exhibit estimators converging at parametric rate, compute the optimal asymptotic variance and conjecture that no estimato…
When multiple hypotheses are tested, interest is often in ensuring that the proportion of false discoveries (FDP) is small with high confidence. In this paper, confidence upper bounds for the FDP are constructed, which are simultaneous over all rejection cut-offs. In particular this allows the user to select a set of hypotheses post hoc such that the FDP lies below some constant with high confidence. Our method uses permutations to account for the dependence structure in the data. So far only Meinshausen provided an exact, permutation-based and computationally feasible method for simultaneous …
Permutation tests are amongst the most commonly used statistical tools in modern genomic research, a process by which p-values are attached to a test statistic by randomly permuting the sample or gene labels. Yet permutation p-values published in the genomic literature are often computed incorrectly, understated by about 1/m, where m is the number of permutations. The same is often true in the more general situation when Monte Carlo simulation is used to assign p-values. Although the p-value understatement is usually small in absolute terms, the implications can be serious in a multiple testin…
The assumption that response and predictor belong to the same statistical unit may be violated in practice. Unbiased estimation and recovery of true label ordering based on unlabeled data are challenging tasks and have attracted increasing attentions in the recent literature. In this paper, we present a relatively complete analysis of label permutation problem for the generalized linear model with multivariate responses. The theory is established under different scenarios, with knowledge of true parameters, with partial knowledge of underlying label permutation matrix and without any knowledge…
Two recently introduced model based bias corrected estimators for proportion of true null hypotheses ($π_0$) under multiple hypotheses testing scenario have been restructured for exponentially distributed random observations available for each of the common hypotheses. Based on stochastic ordering, a new motivation behind formulation of some related estimators for $π_0$ is given. The reduction of bias for the model based estimators are theoretically justified and algorithms for computing the estimators are also presented. The estimators are also used to formulate a popular adaptive multiple te…
We study a class of permutation tests of the randomness of a collection of Bernoulli sequences and their application to analyses of the human tendency to perceive streaks of consecutive successes as overly representative of positive dependence - the hot hand fallacy. In particular, we study permutation tests of the null hypothesis of randomness (i.e., that trials are i.i.d.) based on test statistics that compare the proportion of successes that directly follow k consecutive successes with either the overall proportion of successes or the proportion of successes that directly follow k consecuti…
We consider multiple testing with false discovery rate (FDR) control when p-values have discrete and heterogeneous null distributions. We propose a new estimator of the proportion of true null hypotheses and demonstrate that it is less upwardly biased than Storey's estimator and two other estimators. The new estimator induces two adaptive procedures, i.e., an adaptive Benjamini-Hochberg (BH) procedure and an adaptive Benjamini-Hochberg-Heyse (BHH) procedure. We prove that the the adaptive BH procedure is conservative non-asymptotically. Through simulation studies, we show that these procedures…
Test statistics are often strongly dependent in large-scale multiple testing applications. Most corrections for multiplicity are unduly conservative for correlated test statistics, resulting in a loss of power to detect true positives. We show that the Westfall--Young permutation method has asymptotically optimal power for a broad class of testing problems with a block-dependence and sparsity structure among the tests, when the number of tests tends to infinity.
Permutation tests are a distribution free way of performing hypothesis tests. These tests rely on the condition that the observed data are exchangeable among the groups being tested under the null hypothesis. This assumption is easily satisfied for data obtained from a simple random sample or a controlled study after simple adjustments to the data, but there is no general method for adjusting survey data collected using a complex sample design to allow for permutation tests. In this article, we propose a general method for performing a pseudo- permutation test that accounts for the complex sam…
In this paper, we propose considering an exact likelihood score (ELS) test for non-inferiority comparison and we derive its test-based confidence interval for the difference between two independent binomial proportions. The p-value for this test is obtained by using exact binomial probabilities with the nuisance parameter being replaced by its restricted maximum likelihood estimate. Calculated type I errors revealed that the proposed ELS method has important advantages for non-inferiority comparisons over popular asymptotic methods for adequately powered confirmatory clinical trials, at 80% or…
Identification of features is a critical task in microbiome studies that is complicated by the fact that microbial data are high dimensional and heterogeneous. Masked by the complexity of the data, the problem of separating signals from noise becomes challenging and troublesome. For instance, when performing differential abundance tests, multiple testing adjustments tend to be overconservative, as the probability of a type I error (false positive) increases dramatically with the large numbers of hypotheses. Moreover, the grouping effect of interest can be obscured by heterogeneity. These facto…
Pearson's correlation is among the mostly widely reported measures of association. The strength of the statistical evidence for linear association is determined by the p-value of a hypothesis test. If the true distribution of a dataset is bivariate normal, then under specific data transformations a t-statistic returns the exact p-value, otherwise it is an approximation. Alternatively, the p-value can be estimated by analyzing the distribution of the sample correlation under permutations of the data. Moment approximations of this distribution are not as widely used since estimation of the momen…
Statistics Netherlands（荷兰统计局）；Radboud University（拉德堡德大学）；Eindhoven Univ. of Technology（埃因霍温理工大学）
Binary classifiers trained on a certain proportion of positive items introduce a bias when applied to data sets with different proportions of positive items. Most solutions for dealing with this issue assume that some information on the latter distribution is known. However, this is not always the case, certainly when this proportion is the target variable. In this paper a maximum likelihood estimator for the true proportion of positives in data sets is suggested and tested on synthetic and real world data.
University of Wisconsin（威斯康星大学）；Massachusetts Institute of Technology（麻省理工学院）
We consider the problem of learning a Bayesian network or directed acyclic graph (DAG) model from observational data. A number of constraint-based, score-based and hybrid algorithms have been developed for this purpose. For constraint-based methods, statistical consistency guarantees typically rely on the faithfulness assumption, which has been show to be restrictive especially for graphs with cycles in the skeleton. However, there is only limited work on consistency guarantees for score-based and hybrid algorithms and it has been unclear whether consistency guarantees can be proven under weak…
The Benjamini-Hochberg (BH) procedure is a celebrated method for multiple testing with false discovery rate (FDR) control. In this paper, we consider large-scale distributed networks where each node possesses a large number of p-values and the goal is to achieve the global BH performance in a communication-efficient manner. We propose that every node performs a local test with an adjusted test size according to the (estimated) global proportion of true null hypotheses. With suitable assumptions, our method is asymptotically equivalent to the global BH procedure. Motivated by this, we develop a…
There are over 55 different ways to construct a confidence respectively credible interval (CI) for the binomial proportion. Methods to compare them are necessary to decide which should be used in practice. The interval score has been suggested to compare prediction intervals. This score is a proper scoring rule that combines the coverage as a measure of calibration and the width as a measure of sharpness. We evaluate eleven CIs for the binomial proportion based on the expected interval score and propose a summary measure which can take into account different weighting of the underlying true pr…
Voxel-based lesion-symptom mapping (VLSM) is a major method for studying brain-behavior relationships that leverages modern neuroimaging analysis techniques to build on the classic approach of examining the relationship between location of brain damage and cognitive deficits. Testing an association between deficit severity and lesion status in each voxel involves very many individual tests and requires statistical correction for multiple comparisons. Several strategies have been adapted from analysis of functional neuroimaging data, though VLSM faces a more difficult trade-off between avoiding…
Cluster-level inference procedures are widely used for brain mapping. These methods compare the size of clusters obtained by thresholding brain maps to an upper bound under the global null hypothesis, computed using Random Field Theory or permutations. However, the guarantees obtained by this type of inference - i.e. at least one voxel is truly activated in the cluster - are not informative with regards to the strength of the signal therein. There is thus a need for methods to assess the amount of signal within clusters; yet such methods have to take into account that clusters are defined base…
