We present a general approach to constructing permutation tests that are both exact for the null hypothesis of equality of distributions and asymptotically correct for testing equality of parameters of distributions while allowing the distributions themselves to differ. These robust permutation tests transform a given test statistic by a consistent estimator of its limiting distribution function before enumerating its permutation distribution. This transformation, known as prepivoting, aligns the unconditional limiting distribution for the test statistic with the probability limit of its permutation distribution. Through prepivoting, the tests permute one minus an asymptotically valid $p$-value for testing the null of equality of parameters. We describe two approaches for prepivoting within permutation tests, one directly using asymptotic normality and the other using the bootstrap. We further illustrate that permutation tests using bootstrap prepivoting can provide improvements to the order of the error in rejection probability relative to competing transformations when testing equality of parameters, while maintaining exactness under equality of distributions. Simulation studies highlight the versatility of the proposal, illustrating the restoration of asymptotic validity to a wide range of permutation tests conducted when only the parameters of distributions are equal.
The role played by the composite analogue of the log likelihood ratio in hypothesis testing and in setting confidence regions is not as prominent as it is in the canonical likelihood setting, since its asymptotic distribution depends on the unknown parameter. Approximate pivots based on the composite log likelihood ratio can be derived by using asymptotic arguments. However, the actual distribution of such pivots may differ considerably from the asymptotic reference, leading to tests and confidence regions whose levels are distant from the nominal ones. The use of bootstrap rather than asympto…
In this paper, we investigate local permutation tests for testing conditional independence between two random vectors $X$ and $Y$ given $Z$. The local permutation test determines the significance of a test statistic by locally shuffling samples which share similar values of the conditioning variables $Z$, and it forms a natural extension of the usual permutation approach for unconditional independence testing. Despite its simplicity and empirical support, the theoretical underpinnings of the local permutation test remain unclear. Motivated by this gap, this paper aims to establish theoretical …
In order to adapt the Wasserstein distance to the large sample multivariate non-parametric two-sample problem, making its application computationally feasible, permutation tests based on the Sinkhorn divergence between probability vectors associated to data dependent partitions are considered. Different ways of implementing these tests are evaluated and the asymptotic distribution of the underlying statistic is established in some cases. The statistics proposed are compared, in simulated examples, with the test of Schilling's, one of the best non-parametric tests available in the literature.
When permutation methods are used in practice, often a limited number of random permutations are used to decrease the computational burden. However, most theoretical literature assumes that the whole permutation group is used, and methods based on random permutations tend to be seen as approximate. There exists a very limited amount of literature on exact testing with random permutations and only recently a thorough proof of exactness was given. In this paper we provide an alternative proof, viewing the test as a "conditional Monte Carlo test" as it has been called in the literature. We also p…
The traditional approaches to false discovery rate (FDR) control in multiple hypothesis testing are usually based on the null distribution of a test statistic. However, all types of null distributions, including the theoretical, permutation-based and empirical ones, have some inherent drawbacks. For example, the theoretical null might fail because of improper assumptions on the sample distribution. Here, we propose a null distribution-free approach to FDR control for multiple hypothesis testing. This approach, named target-decoy procedure, simply builds on the ordering of tests by some statist…
The Hilbert--Schmidt Independence Criterion (HSIC) is a popular measure of the dependency between two random variables. The statistic dHSIC is an extension of HSIC that can be used to test joint independence of $d$ random variables. Such hypothesis testing for (joint) independence is often done using a permutation test, which compares the observed data with randomly permuted datasets. The main contribution of this work is proving that the power of such independence tests converges to 1 as the sample size converges to infinity. This answers a question that was asked in (Pfister, 2018) Additiona…
Classical two-sample permutation tests for equality of distributions have exact size in finite samples, but they fail to control size for testing equality of parameters that summarize each distribution. This paper proposes permutation tests for equality of parameters that are estimated at root-$n$ or slower rates. Our general framework applies to both parametric and nonparametric models, with two samples or one sample split into two subsamples. Our tests have correct size asymptotically while preserving exact size in finite samples when distributions are equal. They have no loss in local asymp…
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.
We study the problem of independence testing given independent and identically distributed pairs taking values in a $σ$-finite, separable measure space. Defining a natural measure of dependence $D(f)$ as the squared $L^2$-distance between a joint density $f$ and the product of its marginals, we first show that there is no valid test of independence that is uniformly consistent against alternatives of the form $\{f: D(f) \geq ρ^2 \}$. We therefore restrict attention to alternatives that impose additional Sobolev-type smoothness constraints, and define a permutation test based on a basis expansi…
We consider a permutation method for testing whether observations given in their natural pairing exhibit an unusual level of similarity in situations where any two observations may be similar at some unknown baseline level. Under a null hypotheses where there is no distinguished pairing of the observations, a normal approximation with explicit bounds and rates is presented for determining approximate critical test levels.
Permutation testing in linear models, where the number of nuisance coefficients is smaller than the sample size, is a well-studied topic. The common approach of such tests is to permute residuals after regressing on the nuisance covariates. Permutation-based tests are valuable in particular because they can be highly robust to violations of the standard linear model, such as non-normality and heteroscedasticity. Moreover, in some cases they can be combined with existing, powerful permutation-based multiple testing methods. Here, we propose permutation tests for models where the number of nuisa…
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…
The scan statistic is by far the most popular method for anomaly detection, being popular in syndromic surveillance, signal and image processing, and target detection based on sensor networks, among other applications. The use of the scan statistics in such settings yields a hypothesis testing procedure, where the null hypothesis corresponds to the absence of anomalous behavior. If the null distribution is known, then calibration of a scan-based test is relatively easy, as it can be done by Monte Carlo simulation. When the null distribution is unknown, it is less straightforward. We investigat…
Confidence intervals are central to statistical inference as a tool to evaluate the type I error risk at a given significance level. We devise a method to construct confidence intervals using a single run of a permutation test. This methodology is extended to a multivariate setting, where we are able to handle multiple testing under arbitrary dependence. We demonstrate the method on a weather data set and in a simulation example.
Measures of local and global spatial association are key tools for exploratory spatial data analysis. Many such measures exist including Moran's $I$, Geary's $C$, and the Getis-Ord $G$ and $G^*$ statistics. A parametric approach to testing for significance relies on strong assumptions, which are often not met by real world data. Alternatively, the most popular nonparametric approach, the permutation test, imposes a large computational burden especially for massive graphical networks. Hence, we propose a computation-free approach to nonparametric permutation testing for local and global measure…
In nonparametric independence testing, we observe i.i.d.\ data $\{(X_i,Y_i)\}_{i=1}^n$, where $X \in \mathcal{X}, Y \in \mathcal{Y}$ lie in any general spaces, and we wish to test the null that $X$ is independent of $Y$. Modern test statistics such as the kernel Hilbert-Schmidt Independence Criterion (HSIC) and Distance Covariance (dCov) have intractable null distributions due to the degeneracy of the underlying U-statistics. Thus, in practice, one often resorts to using permutation testing, which provides a nonasymptotic guarantee at the expense of recalculating the quadratic-time statistics …
We formulate and analyze a novel hypothesis testing problem for inferring the edge structure of an infection graph. In our model, a disease spreads over a network via contagion or random infection, where the random variables governing the rates of contracting the disease from neighbors or random infection are independent exponential random variables with unknown rate parameters. A subset of nodes is also censored uniformly at random. Given the statuses of nodes in the network, the goal is to determine the underlying graph. We present a procedure based on permutation testing, and we derive suff…
In this paper, our interest is in the problem of simultaneous hypothesis testing when the test statistics corresponding to the individual hypotheses are possibly correlated. Specifically, we consider the case when the test statistics together have a multivariate normal distribution (with equal correlation between each pair) with an unknown mean vector and our goal is to decide which components of the mean vector are zero and which are non-zero. This problem was taken up earlier in Bogdan et al. (2011) for the case when the test statistics are independent normals. Asymptotic optimality in a Bay…
Permutation methods are commonly used to test significance of regressors of interest in general linear models (GLMs) for functional (image) data sets, in particular for neuroimaging applications as they rely on mild assumptions. Permutation inference for GLMs typically consists of three parts: choosing a relevant test statistic, computing pointwise permutation tests and applying a multiple testing correction. We propose new multiple testing methods as an alternative to the commonly used maximum value of test statistics across the image. The new methods improve power and robustness against inho…
Motivated by the prevalence of high dimensional low sample size datasets in modern statistical applications, we propose a general nonparametric framework, Direction-Projection-Permutation (DiProPerm), for testing high dimensional hypotheses. The method is aimed at rigorous testing of whether lower dimensional visual differences are statistically significant. Theoretical analysis under the non-classical asymptotic regime of dimension going to infinity for fixed sample size reveals that certain natural variations of DiProPerm can have very different behaviors. An empirical power study both confi…
Neural networks are powerful predictive models, but they provide little insight into the nature of relationships between predictors and outcomes. Although numerous methods have been proposed to quantify the relative contributions of input features, statistical inference and hypothesis testing of feature associations remain largely unexplored. We propose a permutation-based approach to testing that uses the partial derivatives of the network output with respect to specific inputs to assess both the significance of input features and whether significant features are linearly associated with the …
Re-sampling based statistical tests are known to be computationally heavy, but reliable when small sample sizes are available. Despite their nice theoretical properties not much effort has been put to make them efficient. In this paper we treat the case of Pearson correlation coefficient and two independent samples t-test. We propose a highly computationally efficient method for calculating permutation based p-values in these two cases. The method is general and can be applied or be adopted to other similar two sample mean or two mean vectors cases.
Presented is an inductive formula for computing the sample moments of the distribution of Pearson's sample correlation over permutation of data. These exact formulas for the sample moments suggest the possibility of more precise and computationally efficient methods of evaluating the p-value for a hypothesis test of Pearson's correlation.
In genome-wide association (GWA) studies the goal is to detect associations between genetic markers and a given phenotype. The number of genetic markers can be large and effective methods for control of the overall error rate is a central topic when analyzing GWA data. The Bonferroni method is known to be conservative when the tests are dependent. Permutation methods give exact control of the overall error rate when the assumption of exchangeability is satisfied, but are computationally intensive for large datasets. For regression models the exchangeability assumption is in general not satisfi…
In this article, we derive and compare methods to derive \textit{p}-values and sets of confidence intervals with strong control of the family-wise error rates and coverage for estimates of treatment effects in cluster randomised trials with multiple outcomes. There are few methods for \textit{p}-value corrections and deriving confidence intervals, limiting their application in this setting. We discuss the methods of Bonferroni, Holm, and Romano \& Wolf (2005) and adapt them to cluster randomised trial inference using permutation-based methods with different test statistics. We develop a novel …
A Scalable Nystrom-Based Kernel Two-Sample Test with Permutations
CNRS, Univ. Grenoble-Alpes, GIPSA-lab, France e1；MaLGa Center - DIBRIS, Università di Genova, Genoa, Italy e2,e4；CNRS, Laboratoire d'Informatique Gaspard Monge, Champs-sur-Marne, France e3；CBMM - Massachusets Institute of Technology, Cambridge, MA, USA
In this paper, we generalize the metric-based permutation test for the equality of covariance operators proposed by Pigoli et al. (2014) to the case of multiple samples of functional data. To this end, the non-parametric combination methodology of Pesarin and Salmaso (2010) is used to combine all the pairwise comparisons between samples into a global test. Different combining functions and permutation strategies are reviewed and analyzed in detail. The resulting test allows to make inference on the equality of the covariance operators of multiple groups and, if there is evidence to reject the …
We propose a new class of models for random permutations, which we call log-linear models, by the analogy with log-linear models used in the analysis of contingency tables. As a special case, we study the family of all Luce-decomposable distributions, and the family of those random permutations, for which the distribution of both the permutation and its inverse is Luce-decomposable. We show that these latter models can be described by conditional independence relations. We calculate the number of free parameters in these models, and describe an iterative algorithm for maximum likelihood estima…
In many psychometric applications, the relationship between the mean of an outcome and a quantitative covariate is too complex to be described by simple parametric functions; instead, flexible nonlinear relationships can be incorporated using penalized splines. Penalized splines can be conveniently represented as a linear mixed effects model (LMM), where the coefficients of the spline basis functions are random effects. The LMM representation of penalized splines makes the extension to multivariate outcomes relatively straightforward. In the LMM, no effect of the quantitative covariate on the …
Hypothesis tests based on linear models are widely accepted by organizations that regulate clinical trials. These tests are derived using strong assumptions about the data-generating process so that the resulting inference can be based on parametric distributions. Because these methods are well understood and robust, they are sometimes applied to data that depart from assumptions, such as ordinal integer scores. Permutation tests are a nonparametric alternative that require minimal assumptions which are often guaranteed by the randomization that was conducted. We compare analysis of covariance…
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…
One of the most popular class of tests for independence between two random variables is the general class of rank statistics which are invariant under permutations. This class contains Spearman's coefficient of rank correlation statistic, Fisher-Yates statistic, weighted Mann statistic and others. Under the null hypothesis of independence these test statistics have a permutation distribution that usually the normal asymptotic theory used to approximate the p-values for these tests. In this note we suggest using a saddlepoint approach that almost exact and need no extensive simulation calculati…
Stratified Permutational Berry--Esseen Bounds and Their Applications to Statistics
Qiuzhen College, Tsinghua University（清华大学邱成桐书院）；Yau Mathematical Sciences Center, Tsinghua University（清华大学丘成桐数学科学中心）；Department of Statistics, University of California, Berkeley（加州大学伯克利分校统计学系）
University of Washington（华盛顿大学）；Google Inc（谷歌公司）；University of Wisconsin-Madison（威斯康星大学麦迪逊分校）；Fred Hutchinson Cancer Research Center（弗雷德·哈钦森癌症研究中心）
This paper investigates the theoretical and empirical performance of Fisher-Pitman-type permutation tests for assessing the equality of unknown Poisson mixture distributions. Building on nonparametric maximum likelihood estimators (NPMLEs) of the mixing distribution, these tests are theoretically shown to be able to adapt to complicated unspecified structures of count data and also consistent against their corresponding ANOVA-type alternatives; the latter is a result in parallel to classic claims made by Robinson (Robinson, 1973). The studied methods are then applied to a single-cell RNA-seq d…
We present a novel algorithm, Westfall-Young light, for detecting patterns, such as itemsets and subgraphs, which are statistically significantly enriched in one of two classes. Our method corrects rigorously for multiple hypothesis testing and correlations between patterns through the Westfall-Young permutation procedure, which empirically estimates the null distribution of pattern frequencies in each class via permutations. In our experiments, Westfall-Young light dramatically outperforms the current state-of-the-art approach in terms of both runtime and memory efficiency on popular real-wor…
In nonlinear dynamics, and to a lesser extent in other fields, a widely used measure of complexity is the Permutation Entropy. But there is still no known method to determine the accuracy of this measure. There has been little research on the statistical properties of this quantity that characterize time series. The literature describes some resampling methods of quantities used in nonlinear dynamics - as the largest Lyapunov exponent - but all of these seems to fail. In this contribution we propose a parametric bootstrap methodology using a symbolic representation of the time series in order …
