This research deals with massive multiple hypothesis testing. First regarding multiple tests as an estimation problem under a proper population model, an error measurement called Erroneous Rejection Ratio (ERR) is introduced and related to the False Discovery Rate (FDR). ERR is an error measurement similar in spirit to FDR, and it greatly simplifies the analytical study of error properties of multiple test procedures. Next an improved estimator of the proportion of true null hypotheses and a data adaptive significance threshold criterion are developed. Some asymptotic error properties of the significant threshold criterion is established in terms of ERR under distributional assumptions widely satisfied in recent applications. A simulation study provides clear evidence that the proposed estimator of the proportion of true null hypotheses outperforms the existing estimators of this important parameter in massive multiple tests. Both analytical and simulation studies indicate that the proposed significance threshold criterion can provide a reasonable balance between the amounts of false positive and false negative errors, thereby complementing and extending the various FDR control procedures. S-plus/R code is available from the author upon request.
In many large multiple testing problems the hypotheses are divided into families. Given the data, families with evidence for true discoveries are selected, and hypotheses within them are tested. Neither controlling the error-rate in each family separately nor controlling the error-rate over all hypotheses together can assure that an error-rate is controlled in the selected families. We formulate this concern about selective inference in its generality, for a very wide class of error-rates and for any selection criterion, and present an adjustment of the testing level inside the selected famili…
We propose a method for constructing p-values for general hypotheses in a high-dimensional linear model. The hypotheses can be local for testing a single regression parameter or they may be more global involving several up to all parameters. Furthermore, when considering many hypotheses, we show how to adjust for multiple testing taking dependence among the p-values into account. Our technique is based on Ridge estimation with an additional correction term due to a substantial projection bias in high dimensions. We prove strong error control for our p-values and provide sufficient conditions f…
The goal of mediation analysis is to study the effect of exposure on an outcome interceded by a mediator. Two simple hypotheses are tested: the effect of the exposure on the mediator, and the effect of the mediator on the outcome. When either of these hypotheses is true, a predetermined significance level can be assured. When both nulls are true, the same test becomes conservative. Adaptively finding the correct scenario enables customizing the tests and consequently enlarges their efficiency, which is most important in a multiple testing framework. In this work, we link between adaptive two-s…
Although the log-likelihood is widely used in model selection, the log-likelihood ratio has had few applications in this area. We develop a log-likelihood ratio based method for selecting regression models by focusing on the set of models deemed plausible by the likelihood ratio test. We show that when the sample size is large and the significance level of the test is small, there is a high probability that the smallest model in the set is the true model; thus, we select this smallest model. The significance level of the test serves as a parameter for this method. We consider three levels of t…
Nagoya Institute of Technology（名古屋工业大学）；RIKEN（理化学研究所）；Nagoya University（名古屋大学）
Although a vast body of literature relates to image segmentation methods that use deep neural networks (DNNs), less attention has been paid to assessing the statistical reliability of segmentation results. In this study, we interpret the segmentation results as hypotheses driven by DNN (called DNN-driven hypotheses) and propose a method by which to quantify the reliability of these hypotheses within a statistical hypothesis testing framework. Specifically, we consider a statistical hypothesis test for the difference between the object and background regions. This problem is challenging, as the…
Bayes factors represent the ratio of probabilities assigned to data by competing scientific hypotheses. Drawbacks of Bayes factors are their dependence on prior specifications that define null and alternative hypotheses and difficulties encountered in their computation. To address these problems, we define Bayes factor functions (BFF) directly from common test statistics. BFFs depend on a single non-centrality parameter that can be expressed as a function of standardized effect sizes, and plots of BFFs versus effect size provide informative summaries of hypothesis tests that can be easily aggr…
Genetic investigations often involve the testing of vast numbers of related hypotheses simultaneously. To control the overall error rate, a substantial penalty is required, making it difficult to detect signals of moderate strength. To improve the power in this setting, a number of authors have considered using weighted $p$-values, with the motivation often based upon the scientific plausibility of the hypotheses. We review this literature, derive optimal weights and show that the power is remarkably robust to misspecification of these weights. We consider two methods for choosing weights in p…
Researchers often misinterpret and misrepresent statistical outputs. This abuse has led to a large literature on modification or replacement of testing thresholds and $P$-values with confidence intervals, Bayes factors, and other devices. Because the core problems appear cognitive rather than statistical, we review simple aids to statistical interpretations. These aids emphasize logical and information concepts over probability, and thus may be more robust to common misinterpretations than are traditional descriptions. We use the Shannon transform of the $P$-value $p$, also known as the binary…
Multiple testing literature contains ample research on controlling false discoveries for hypotheses classified according to one criterion, which we refer to as one-way classified hypotheses. Although simultaneous classification of hypotheses according to two different criteria, resulting in two-way classified hypotheses, do often occur in scientific studies, no such research has taken place yet, as far as we know, under this structure. This article produces procedures, both in their oracle and data-adaptive forms, for controlling the overall false discovery rate (FDR) across all hypotheses eff…
The asymptotic efficiency of a generalized likelihood ratio test proposed by Cox is studied under the large deviations framework for error probabilities developed by Chernoff. In particular, two separate parametric families of hypotheses are considered [Cox, 1961, 1962]. The significance level is set such that the maximal type I and type II error probabilities for the generalized likelihood ratio test decay exponentially fast with the same rate. We derive the analytic form of such a rate that is also known as the Chernoff index [Chernoff, 1952], a relative efficiency measure when there is no p…
Standard statistical methods that do not take proper account of the complexity of survey design can lead to erroneous inferences when applied to survey data due to unequal selection probabilities, clustering, and other design features. In particular, the actual type I error rates of tests of hypotheses using standard methods can be much bigger than the nominal significance level. Methods that take account of survey design features in testing hypotheses have been proposed, including Wald tests and quasi-score tests that involve the estimated covariance matrices of parameter estimates. In this p…
In many fields of research null hypothesis significance tests and p values are the accepted way of assessing the degree of certainty with which research results can be extrapolated beyond the sample studied. However, there are very serious concerns about the suitability of p values for this purpose. An alternative approach is to cite confidence intervals for a statistic of interest, but this does not directly tell readers how certain a hypothesis is. Here, I suggest how the framework used for confidence intervals could easily be extended to derive confidence levels, or "tentative probabilities…
We study the switch distribution, introduced by Van Erven et al. (2012), applied to model selection and subsequent estimation. While switching was known to be strongly consistent, here we show that it achieves minimax optimal parametric risk rates up to a $\log\log n$ factor when comparing two nested exponential families, partially confirming a conjecture by Lauritzen (2012) and Cavanaugh (2012) that switching behaves asymptotically like the Hannan-Quinn criterion. Moreover, like Bayes factor model selection but unlike standard significance testing, when one of the models represents a simple h…
Null hypothesis significance tests and p values are widely used despite very strong arguments against their use in many contexts. Confidence intervals are often recommended as an alternative, but these do not achieve the objective of assessing the credibility of a hypothesis, and the distinction between confidence and probability is an unnecessary confusion. This paper proposes a more straightforward (probabilistic) definition of confidence, and suggests how the idea can be applied to whatever hypotheses are of interest to researchers. The relative merits of the different approaches are discus…
Multiple hypotheses testing is a core problem in statistical inference and arises in almost every scientific field. Given a sequence of null hypotheses $\mathcal{H}(n) = (H_1,..., H_n)$, Benjamini and Hochberg \cite{benjamini1995controlling} introduced the false discovery rate (FDR) criterion, which is the expected proportion of false positives among rejected null hypotheses, and proposed a testing procedure that controls FDR below a pre-assigned significance level. They also proposed a different criterion, called mFDR, which does not control a property of the realized set of tests; rather it …
Null Hypothesis Significance Testing (NHST) has long been of central importance to psychology as a science, guiding theory development and underlying the application of evidence-based intervention and decision-making. Recent years, however, have seen growing awareness of serious problems with NHST as it is typically used; this awareness has led to proposals to limit the use of NHST techniques, to abandon these techniques and move to alternative statistical approaches, or even to ban the use of NHST entirely. These proposals are premature, because the observed problems with NHST arise as a cons…
Higher criticism, or second-level significance testing, is a multiple-comparisons concept mentioned in passing by Tukey. It concerns a situation where there are many independent tests of significance and one is interested in rejecting the joint null hypothesis. Tukey suggested comparing the fraction of observed significances at a given α-level to the expected fraction under the joint null. In fact, he suggested standardizing the difference of the two quantities and forming a z-score; the resulting z-score tests the significance of the body of significance tests. We consider a generalization, w…
Scientists often adjust their significance threshold (alpha level) during null hypothesis significance testing in order to take into account multiple testing and multiple comparisons. This alpha adjustment has become particularly relevant in the context of the replication crisis in science. The present article considers the conditions in which this alpha adjustment is appropriate and the conditions in which it is inappropriate. A distinction is drawn between three types of multiple testing: disjunction testing, conjunction testing, and individual testing. It is argued that alpha adjustment is …
This article gives a survey of the e-value, a statistical significance measure a.k.a. the evidence rendered by observational data, X, in support of a statistical hypothesis, H, or, the other way around, the epistemic value of H given X. The $e$-value and the accompanying FBST, the Full Bayesian Significance Test, constitute the core of a research program that was started at IME-USP, is being developed by over 20 researchers worldwide, and has, so far, been referenced by over 200 publications. The e-value and the FBST comply with the best principles of Bayesian inference, including the likeliho…
This work is motivated by learning the individualized minimal clinically important difference, a vital concept to assess clinical importance in various biomedical studies. We formulate the scientific question into a high-dimensional statistical problem where the parameter of interest lies in an individualized linear threshold. The goal is to develop a hypothesis testing procedure for the significance of a single element in this parameter as well as of a linear combination of this parameter. The difficulty dues to the high-dimensional nuisance in developing such a testing procedure, and also st…
For a multivariate linear model, Wilk's likelihood ratio test (LRT) constitutes one of the cornerstone tools. However, the computation of its quantiles under the null or the alternative requires complex analytic approximations and more importantly, these distributional approximations are feasible only for moderate dimension of the dependent variable, say $p\le 20$. On the other hand, assuming that the data dimension $p$ as well as the number $q$ of regression variables are fixed while the sample size $n$ grows, several asymptotic approximations are proposed in the literature for Wilk's $\bLa$ …
Given an i.i.d. sample drawn from a density $f$, we propose to test that $f$ equals some prescribed density $f_0$ or that $f$ belongs to some translation/scale family. We introduce a multiple testing procedure based on an estimation of the $\mathbb{L}_2$-distance between $f$ and $f_0$ or between $f$ and the parametric family that we consider. For each sample size $n$, our test has level of significance $α$. In the case of simple hypotheses, we prove that our test is adaptive: it achieves the optimal rates of testing established by Ingster [J. Math. Sci. 99 (2000) 1110--1119] over various class…
This paper raises concerns about the advantages of using statistical significance tests in research assessments as has recently been suggested in the debate about proper normalization procedures for citation indicators. Statistical significance tests are highly controversial and numerous criticisms have been leveled against their use. Based on examples from articles by proponents of the use statistical significance tests in research assessments, we address some of the numerous problems with such tests. The issues specifically discussed are the ritual practice of such tests, their dichotomous a…
Multiple hypothesis testing, a situation when we wish to consider many hypotheses, is a core problem in statistical inference that arises in almost every scientific field. In this setting, controlling the false discovery rate (FDR), which is the expected proportion of type I error, is an important challenge for making meaningful inferences. In this paper, we consider the problem of controlling FDR in an online manner. Concretely, we consider an ordered, possibly infinite, sequence of hypotheses, arriving one at each timestep, and for each hypothesis we observe a p-value along with a set of fea…
The Full Bayesian Significance Test (FBST) for precise hypotheses was presented by Pereira and Stern [Entropy 1(4) (1999) 99-110] as a Bayesian alternative instead of the traditional significance test using p-value. The FBST is based on the evidence in favor of the null hypothesis (H). An important practical issue for the implementation of the FBST is the determination of how large the evidence must be in order to decide for its rejection. In the Classical significance tests, it is known that p-value decreases as sample size increases, so by setting a single significance level, it usually lead…
Hypothesis testing in contingency tables is usually based on asymptotic results, thereby restricting its proper use to large samples. To study these tests in small samples, we consider the likelihood ratio test and define an accurate index, the P-value, for the celebrated hypotheses of homogeneity, independence, and Hardy-Weinberg equilibrium. The aim is to understand the use of the asymptotic results of the frequentist Likelihood Ratio Test and the Bayesian FBST -- Full Bayesian Significance Test -- under small-sample scenarios. The proposed exact P-value is used as a benchmark to understand …
We investigate the problem of testing whether $d$ random variables, which may or may not be continuous, are jointly (or mutually) independent. Our method builds on ideas of the two variable Hilbert-Schmidt independence criterion (HSIC) but allows for an arbitrary number of variables. We embed the $d$-dimensional joint distribution and the product of the marginals into a reproducing kernel Hilbert space and define the $d$-variable Hilbert-Schmidt independence criterion (dHSIC) as the squared distance between the embeddings. In the population case, the value of dHSIC is zero if and only if the $…
The Full Bayesian Significance Test (FBST) for precise hypotheses was presented by Pereira and Stern (1999) as a Bayesian alternative instead of the traditional significance test based on p-value. The FBST uses the evidence in favor of the null hypothesis ($H_0$) calculated as the complement of the posterior probability of the highest posterior density region, which is tangent to the set defined by $H_0$. An important practical issue for the implementation of the FBST is the determination of how large the evidence must be in order to decide for its rejection. In the Classical significance test…
Inferring linear relationships lies at the heart of many empirical investigations. A measure of linear dependence should correctly evaluate the strength of the relationship as well as qualify whether it is meaningful for the population. Pearson's correlation coefficient (PCC), the \textit{de-facto} measure for bivariate relationships, is known to lack in both regards. The estimated strength $r$ maybe wrong due to limited sample size, and nonnormality of data. In the context of statistical significance testing, erroneous interpretation of a $p$-value as posterior probability leads to Type I err…
Nowadays, beta and Kumaraswamy distributions are the most popular models to fit continuous bounded data. These models present some characteristics in common and to select one of them in a practical situation can be of great interest. With this in mind, in this paper we propose a method of selection between the beta and Kumaraswamy distributions. We use the logarithm of the likelihood ratio statistic (denoted by $T_n$, where $n$ is the sample size) and obtain its asymptotic distribution under the hypotheses $H_{\mathcal B}$ and $H_{\mathcal K}$, where $H_{\mathcal B}$ ($H_{\mathcal K}$) denotes…
Hierarchical inference in (generalized) regression problems is powerful for finding significant groups or even single covariates, especially in high-dimensional settings where identifiability of the entire regression parameter vector may be ill-posed. The general method proceeds in a fully data-driven and adaptive way from large to small groups or singletons of covariates, depending on the signal strength and the correlation structure of the design matrix. We propose a novel hierarchical multiple testing adjustment that can be used in combination with any significance test for a group of covar…
The classical binary hypothesis testing problem is revisited. We notice that when one of the hypotheses is composite, there is an inherent difficulty in defining an optimality criterion that is both informative and well-justified. For testing in the simple normal location problem (that is, testing for the mean of multivariate Gaussians), we overcome the difficulty as follows. In this problem there exists a natural hardness order between parameters as for different parameters the error-probailities curves (when the parameter is known) are either identical, or one dominates the other. We can thu…
A Formal Graphical Inference Framework for Combining Effect Size with Statistical Significance: Application to Multivariate and Functional Linear Models
Faculty of Agriculture and Technology, University of South Bohemia（南波希米亚大学农业与技术学院）；Natural Resources Institute Finland (Luke)（芬兰自然资源研究所（Luke））；University of Helsinki（赫尔辛基大学）
We interpret likelihood-based test functions from a geometric perspective where the Kullback-Leibler (KL) divergence is adopted to quantify the distance from a distribution to another. Such a test function can be seen as a sub-Gaussian random variable, and we propose a principled way to calculate its corresponding sub-Gaussian norm. Then an error bound for binary hypothesis testing can be obtained in terms of the sub-Gaussian norm and the KL divergence, which is more informative than Pinsker's bound when the significance level is prescribed. For $M$-ary hypothesis testing, we also derive an er…
University of Southern California（南加州大学）；Stanford University（斯坦福大学）
Multiple hypothesis testing is a core problem in statistical inference and arises in almost every scientific field. Given a set of null hypotheses $\mathcal{H}(n) = (H_1,\dotsc, H_n)$, Benjamini and Hochberg introduced the false discovery rate (FDR), which is the expected proportion of false positives among rejected null hypotheses, and proposed a testing procedure that controls FDR below a pre-assigned significance level. Nowadays FDR is the criterion of choice for large scale multiple hypothesis testing. In this paper we consider the problem of controlling FDR in an "online manner". Concrete…
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 …
In high throughput settings we inspect a great many candidate variables (e.g., genes) searching for associations with a primary variable (e.g., a phenotype). High throughput hypothesis testing can be made difficult by the presence of systemic effects and other latent variables. It is well known that those variables alter the level of tests and induce correlations between tests. They also change the relative ordering of significance levels among hypotheses. Poor rankings lead to wasteful and ineffective follow-up studies. The problem becomes acute for latent variables that are correlated with t…
Our purpose, is to put forward a change in the paradigm of testing by generalizing a very natural idea exposed by Morris DeGroot (1975) aiming to an approach that is attractive to all schools of statistics, in a procedure better suited for the needs of science. DeGroot's seminal idea is to base testing statistical hypothesis on minimizing the weighted sum of type I plus type II error instead of of the prevailing paradigm which is fixing type I error and minimizing type II error. DeGroot's result is that in simple vs simple hypothesis the optimal criterion is to reject, according to the likelih…
Drawing on some recent results that provide the formalism necessary to definite stationarity for infinite random graphs, this paper initiates the study of statistical and learning questions pertaining to these objects. Specifically, a criterion for the existence of a consistent test for complex hypotheses is presented, generalizing the corresponding results on time series. As an application, it is shown how one can test that a tree has the Markov property, or, more generally, to estimate its memory.
School of Mathematical and Computer Sciences, Heriot-Watt University（赫瑞斯泰学院数学与计算机科学系，赫瑞瓦特大学）；School of Mathematics, University of Edinburgh（爱丁堡大学数学学院）；Maxwell Institute for Mathematical Sciences（麦克斯韦数学科学研究所）
This paper proposes a class of origin-smooth approximators of indicators underlying the sum-of-negative-part statistic for testing multiple inequalities. The need for simulation or bootstrap to obtain test critical values is thereby obviated. A simple procedure is enabled using fixed critical values. The test is shown to have correct asymptotic size in the uniform sense that supremum finite-sample rejection probability over null-restricted data distributions tends asymptotically to nominal significance level. This applies under weak assumptions allowing for estimator covariance singularity. Th…
Logical Probability (LP) is strictly distinguished from Statistical Probability (SP). To measure semantic information or confirm hypotheses, we need to use sampling distribution (conditional SP function) to test or confirm fuzzy truth function (conditional LP function). The Semantic Information Measure (SIM) proposed is compatible with Shannon's information theory and Fisher's likelihood method. It can ensure that the less the LP of a predicate is and the larger the true value of the proposition is, the more information there is. So the SIM can be used as Popper's information criterion for fal…
