A Bayes factor is proposed for testing whether the effect of a key predictor variable on the dependent variable is linear or nonlinear, possibly while controlling for certain covariates. The test can be used (i) when one is interested in quantifying the relative evidence in the data of a linear versus a nonlinear relationship and (ii) to quantify the evidence in the data in favor of a linear relationship (useful when building linear models based on transformed variables). Under the nonlinear model, a Gaussian process prior is employed using a parameterization similar to Zellner's $g$ prior resulting in a scale-invariant test. Moreover a Bayes factor is proposed for one-sided testing of whether the nonlinear effect is consistently positive, consistently negative, or neither. Applications are provides from various fields including social network research and education.
Hypothesis testing is an essential statistical method in psychology and the cognitive sciences. The problems of traditional null hypothesis significance testing (NHST) have been discussed widely, and among the proposed solutions to the replication problems caused by the inappropriate use of significance tests and $p$-values is a shift towards Bayesian data analysis. However, Bayesian hypothesis testing is concerned with various posterior indices for significance and the size of an effect. This complicates Bayesian hypothesis testing in practice, as the availability of multiple Bayesian alterna…
In this paper, we propose an explicit closed-form Bayes factor for the problem of two-sample hypothesis testing. The proposed approach can be regarded as a Bayesian version of the pooled-variance t-statistic and has various appealing properties in practical applications. It relies on data only through the t-statistic and can thus be calculated by using an Excel spreadsheet or a pocket calculator. It avoids several undesirable paradoxes, which may be encountered by the previous Bayesian approach of Gonen et al. (2005). Specifically, the proposed approach can be easily taught in an introductory …
Accelerated life testing (ALT) is typically used to assess the reliability of material's lifetime under desired stress levels. Recent advances in material engineering have made a variety of material alternatives readily available. To identify the most reliable material setting with efficient experimental design, a sequential test planning strategy is preferred. To guarantee a tractable statistical mechanism for information collection and update, we develop explicit model parameter update formulas via approximate Bayesian inference. Theories show that our explicit update formulas give consisten…
Bayesian inference for rank-order problems is frustrated by the absence of an explicit likelihood function. This hurdle can be overcome by assuming a latent normal representation that is consistent with the ordinal information in the data: the observed ranks are conceptualized as an impoverished reflection of an underlying continuous scale, and inference concerns the parameters that govern the latent representation. We apply this generic data-augmentation method to obtain Bayes factors for three popular rank-based tests: the rank sum test, the signed rank test, and Spearman's $ρ_s$.
COVID-19 incidence is analyzed at the provinces of some Spanish Communities during the period February-October, 2020. Two infinite-dimensional regression approaches are tested. The first one is implemented in the regression framework introduced in Ruiz-Medina, Miranda and Espejo (2019). Specifically, a bayesian framework is adopted in the estimation of the pure point spectrum of the temporal autocorrelation operator, characterizing the second-order structure of a surface sequence. The second approach is formulated in the context of spatial curve regression. A nonparametric estimator of the spe…
Bayes' Theorem confers inherent limitations on the accuracy of screening tests as a function of disease prevalence. We have shown in previous work that a testing system can tolerate significant drops in prevalence, up until a certain well-defined point known as the $prevalence$ $threshold$, below which the reliability of a positive screening test drops precipitously. Herein, we establish a mathematical model to determine whether sequential testing overcomes the aforementioned Bayesian limitations and thus improves the reliability of screening tests. We show that for a desired positive predicti…
In this paper we introduce objective proper prior distributions for hypothesis testing and model selection based on measures of divergence between the competing models; we call them divergence based (DB) priors. DB priors have simple forms and desirable properties, like information (finite sample) consistency; often, they are similar to other existing proposals like the intrinsic priors; moreover, in normal linear models scenarios, they exactly reproduce Jeffreys-Zellner-Siow priors. Most importantly, in challenging scenarios such as irregular models and mixture models, the DB priors are well …
In this paper we consider the problem of multiple testing when the hypotheses are dependent. In most of the existing literature, either Bayesian or non-Bayesian, the decision rules mainly focus on the validity of the test procedure rather than actually utilizing the dependency to increase efficiency. Moreover, the decisions regarding different hypotheses are marginal in the sense that they do not depend upon each other directly. However, in realistic situations, the hypotheses are usually dependent, and hence it is desirable that the decisions regarding the dependent hypotheses are taken joint…
We consider the problem of comparing two Poisson parameters from the Bayesian perspective. Kawasaki and Miyaoka (2012b) proposed the Bayesian index $P(λ_1 < λ_2 | X_1,X_2)$ and expressed it using the hypergeometric series. In this paper, under some conditions, we give four other expressions of the Bayesian index in terms of the cumulative distribution functions of beta, $F$, binomial, and negative binomial distribution. Next, we investigate the relationship between the Bayesian index and the $p$-value of the conditional test with the null hypothesis $H_0: λ_1 \geq λ_2 $ versus an alternative h…
Our approach to Mendelian Randomization (MR) analysis is designed to increase reproducibility of causal effect "discoveries" by: (i) using a Bayesian approach to inference; (ii) replacing the point null hypothesis with a region of practical equivalence consisting of values of negligible magnitude for the effect of interest, while exploiting the ability of Bayesian analysis to quantify the evidence of the effect falling inside/outside the region; (iii) rejecting the usual binary decision logic in favour of a ternary logic where the hypothesis test may result in either an acceptance or a rejecti…
Scientific theories can often be formulated using equality and order constraints on the relative effects in a linear regression model. For example, it may be expected that the effect of the first predictor is larger than the effect of the second predictor, and the second predictor is expected to be larger than the third predictor. The goal is then to test such expectations against competing scientific expectations or theories. In this paper a simple default Bayes factor test is proposed for testing multiple hypotheses with equality and order constraints on the effects of interest. The proposed…
The new perspectives on ABC and Bayesian model criticisms presented in Ratmann et al.(2009) are challenging standard approaches to Bayesian model choice. We discuss here some issues arising from the authors' approach, including prior influence, model assessment and criticism, and the meaning of error in ABC.
The Poisson distribution is often used as a standard model for count data. Quite often, however, such data sets are not well fit by a Poisson model because they have more zeros than are compatible with this model. For these situations, a zero-inflated Poisson (ZIP) distribution is often proposed. This article addresses testing a Poisson versus a ZIP model, using Bayesian methodology based on suitable objective priors. Specific choices of objective priors are justified and their properties investigated. The methodology is extended to include covariates in regression models. Several applications…
While gravitational waves have not yet been measured directly, data analysis from detection experiments commonly includes an upper limit statement. Such upper limits may be derived via a frequentist or Bayesian approach; the theoretical implications are very different, and on the technical side, one notable difference is that one case requires maximization of the likelihood function over parameter space, while the other requires integration. Using a simple example (detection of a sinusoidal signal in white Gaussian noise), we investigate the differences in performance and interpretation, and t…
In the Bayesian approach to structure learning of graphical models, the equivalent sample size (ESS) in the Dirichlet prior over the model parameters was recently shown to have an important effect on the maximum-a-posteriori estimate of the Bayesian network structure. In our first contribution, we theoretically analyze the case of large ESS-values, which complements previous work: among other results, we find that the presence of an edge in a Bayesian network is favoured over its absence even if both the Dirichlet prior and the data imply independence, as long as the conditional empirical dist…
We present a Bayesian inference scheme for scaled Brownian motion, and investigate its performance on synthetic data for parameter estimation and model selection in a combined inference with fractional Brownian motion. We include the possibility of measurement noise in both models. We find that for trajectories of a few hundred time points the procedure is able to resolve well the true model and parameters. Using the prior of the synthetic data generation process also for the inference, the approach is optimal based on decision theory. We include a comparison with inference using a prior diffe…
Nonparametric and nonlinear measures of statistical dependence between pairs of random variables are important tools in modern data analysis. In particular the emergence of large data sets can now support the relaxation of linearity assumptions implicit in traditional association scores such as correlation. Here we describe a Bayesian nonparametric procedure that leads to a tractable, explicit and analytic quantification of the relative evidence for dependence vs independence. Our approach uses Polya tree priors on the space of probability measures which can then be embedded within a decision …
In this article, we propose a new method for the fundamental task of testing for dependence between two groups of variables. The response densities under the null hypothesis of independence and the alternative hypothesis of dependence are specified by nonparametric Bayesian models. Under the null hypothesis, the joint distribution is modeled by the product of two independent Dirichlet Process Mixture (DPM) priors; under the alternative, the full joint density is modeled by a multivariate DPM prior. The test is then based on the posterior probability of favoring the alternative hypothesis. The …
This paper explores the intrinsic connections between the Bayesian false discovery rate (FDR) control procedures and their counterpart of frequentist procedures. We attempt to offer a unified view of FDR control within and beyond the setting of testing exchangeable hypotheses. Under the standard two-groups model and the Oracle condition, we show that the Bayesian and the frequentist methods can achieve asymptotically equivalent FDR control at arbitrary levels. Built on this result, we further illustrate that rigorous post-fitting model diagnosis is necessary and effective to ensure robust FDR …
For hypotheses of the type H_0:theta=theta_0 vs H_1:theta ne theta_0 we demonstrate the equivalence of a Bayesian hypothesis test using a Bayes factor and the corresponding classical test, for a large class of models, which are detailed in the paper. In particular, we show that the role of the prior and critical region for the Bayes factor test is only to specify the type I error. This is their only role since, as we show, the power function of the Bayes factor test coincides exactly with that of the classical test, once the type I error has been fixed. For more complex tests involving nuisanc…
Testing differences between a treatment and control group is common practice in biomedical research like randomized controlled trials (RCT). The standard two-sample t-test relies on null hypothesis significance testing (NHST) via p-values, which has several drawbacks. Bayesian alternatives were recently introduced using the Bayes factor, which has its own limitations. This paper introduces an alternative to current Bayesian two-sample t-tests by interpreting the underlying model as a two-component Gaussian mixture in which the effect size is the quantity of interest, which is most relevant in …
This paper introduces a feasible and practical Bayesian method for unit root testing in financial time series. We propose a convenient approximation of the Bayes factor in terms of the Bayesian Information Criterion as a straightforward and effective strategy for testing the unit root hypothesis. Our approximate approach relies on few assumptions, is of general applicability, and preserves a satisfactory error rate. Among its advantages, it does not require the prior distribution on model's parameters to be specified. Our simulation study and empirical application on real exchange rates show g…
This article concerns testing for equality of distribution between groups. We focus on screening variables with shared distributional features such as common support, modes and patterns of skewness. We propose a Bayesian testing method using kernel mixtures, which improves performance by borrowing information across the different variables and groups through shared kernels and a common probability of group differences. The inclusion of shared kernels in a finite mixture, with Dirichlet priors on the weights, leads to a simple framework for testing that scales well for high-dimensional data. We…
In modern data analysis, nonparametric measures of discrepancies between random variables are particularly important. The subject is well-studied in the frequentist literature, while the development in the Bayesian setting is limited where applications are often restricted to univariate cases. Here, we propose a Bayesian kernel two-sample testing procedure based on modelling the difference between kernel mean embeddings in the reproducing kernel Hilbert space utilising the framework established by Flaxman et al (2016). The use of kernel methods enables its application to random variables in ge…
We consider the problems of hypothesis testing and model comparison under a flexible Bayesian linear regression model whose formulation is closely connected with the linear mixed effect model and the parametric models for SNP set analysis in genetic association studies. We derive a class of analytic approximate Bayes factors and illustrate their connections with a variety of frequentist test statistics, including the Wald statistic and the variance component score statistic. Taking advantage of Bayesian model averaging and hierarchical modeling, we demonstrate some distinct advantages and flex…
Network data are increasingly collected along with other variables of interest. Our motivation is drawn from neurophysiology studies measuring brain connectivity networks for a sample of individuals along with their membership to a low or high creative reasoning group. It is of paramount importance to develop statistical methods for testing of global and local changes in the structural interconnections among brain regions across groups. We develop a general Bayesian procedure for inference and testing of group differences in the network structure, which relies on a nonparametric representation…
In this paper, a Bayesian accelerated life testing model is presented. The Weibull distribution is used as the life distribution and the generalised Eyring model as the time transformation function. This is a model that allows for the use of more than one stressor, whereas other commonly used acceleration models, such as the Arrhenius and power law models, allow for only one stressor. The generalised Eyring-Weibull model is used in an application, where MCMC methods are utilised to generate samples for posterior inference.
This paper studies the problem of testing whether a function is monotone from a nonparametric Bayesian perspective. Two new families of tests are constructed. The first uses constrained smoothing splines, together with a hierarchical stochastic-process prior that explicitly controls the prior probability of monotonicity. The second uses regression splines, together with two proposals for the prior over the regression coefficients. The finite-sample performance of the tests is shown via simulation to improve upon existing frequentist and Bayesian methods. The asymptotic properties of the Bayes …
Probabilistic predictions from neural networks which account for predictive uncertainty during classification is crucial in many real-world and high-impact decision making settings. However, in practice most datasets are trained on non-probabilistic neural networks which by default do not capture this inherent uncertainty. This well-known problem has led to the development of post-hoc calibration procedures, such as Platt scaling (logistic), isotonic and beta calibration, which transforms the scores into well calibrated empirical probabilities. A plausible alternative to the calibration approa…
MicroRNAs (miRNAs) are small non-coding RNAs that function as regulators of gene expression. In recent years, there has been a tremendous and growing interest among researchers to investigate the role of miRNAs in normal cellular as well as in disease processes. Thus to investigate the role of miRNAs in oral cancer, we analyse the expression levels of miRNAs to identify miRNAs with statistically significant differential expression in cancer tissues. In this article, we propose a novel Bayesian hierarchical model of miRNA expression data. Compelling evidences have demonstrated that the transcri…
In this work we apply the methodology of integral priors to handle Bayesian model selection in binomial regression models with a general link function. These models are very often used to investigate associations and risks in epidemiological studies where one goal is to exhibit whether or not an exposure is a risk factor for developing a certain disease; the purpose of the current paper is to test the effect of specific exposure factors. We formulate the problem as a Bayesian model selection case and solve it using objective Bayes factors. To construct the reference prior distributions on the …
Bayesian hypothesis testing is re-examined from the perspective of an a priori assessment of the test statistic distribution under the alternative. By assessing the distribution of an observable test statistic, rather than prior parameter values, we provide a practical default Bayes factor which is straightforward to interpret. To illustrate our methodology, we provide examples where evidence for a Bayesian strikingly supports the null, but leads to rejection under a classical test. Finally, we conclude with directions for future research.
IBM Research（IBM研究院）；Stanford University（斯坦福大学）；Columbia University（哥伦比亚大学）；University of WisconsinMadison（威斯康星大学麦迪逊分校）；University of Southern California（南加州大学）；Web3 Foundation（Web3基金会）；University of California, San Diego（加利福尼亚大学圣迭戈分校）
This work initiates a systematic investigation of testing high-dimensional structured distributions by focusing on testing Bayesian networks -- the prototypical family of directed graphical models. A Bayesian network is defined by a directed acyclic graph, where we associate a random variable with each node. The value at any particular node is conditionally independent of all the other non-descendant nodes once its parents are fixed. Specifically, we study the properties of identity testing and closeness testing of Bayesian networks. Our main contribution is the first non-trivial efficient tes…
Hypothesis testing is a central statistical method in psychology and the cognitive sciences. However, the problems of null hypothesis significance testing (NHST) and p-values have been debated widely, but few attractive alternatives exist. This article introduces the fbst R package, which implements the Full Bayesian Significance Test (FBST) to test a sharp null hypothesis against its alternative via the e-value. The statistical theory of the FBST has been introduced by Pereira et al. (1999) more than two decades ago and since then, the FBST has shown to be a Bayesian alternative to NHST and p…
The problem of testing mutually exclusive hypotheses with dependent test statistics is considered. Bayesian and frequentist approaches to multiplicity control are studied and compared to help gain understanding as to the effect of test statistic dependence on each approach. The Bayesian approach is shown to have excellent frequentist properties and is argued to be the most effective way of obtaining frequentist multiplicity control, without sacrificing power, when there is considerable test statistic dependence.
A key challenge in estimating the infection fatality rate (IFR) -- and its relation with various factors of interest -- is determining the total number of cases. The total number of cases is not known because not everyone is tested, but also, more importantly, because tested individuals are not representative of the population at large. We refer to the phenomenon whereby infected individuals are more likely to be tested than non-infected individuals, as "preferential testing." An open question is whether or not it is possible to reliably estimate the IFR without any specific knowledge about th…
There are racial disparities in the COVID-19 test positivity rate, suggesting that minorities may be under-tested. Here, drawing on the literature on statistically assessing racial disparities in policing, we 1) illuminate a statistical flaw, known as infra-marginality, in using the positivity rate as a metric for assessing racial disparities in under-testing; 2) develop a new type of Bayesian threshold test to measure disparities in COVID-19 testing and 3) apply the test to measure racial disparities in testing thresholds in a real-world COVID-19 dataset.
Substantial statistical research has recently been devoted to the analysis of large-scale microarray experiments which provide a measure of the simultaneous expression of thousands of genes in a particular condition. A typical goal is the comparison of gene expression between two conditions (e.g., diseased vs. nondiseased) to detect genes which show differential expression. Classical hypothesis testing procedures have been applied to this problem and more recent work has employed sophisticated models that allow for the sharing of information across genes. However, many recent gene expression s…
We compared Bayes factors to normalized maximum likelihood for the simple case of selecting between an order-constrained versus a full binomial model. This comparison revealed two qualitative differences in testing order constraints regarding data dependence and model preference.
A/B testing is one of the most successful applications of statistical theory in modern Internet age. One problem of Null Hypothesis Statistical Testing (NHST), the backbone of A/B testing methodology, is that experimenters are not allowed to continuously monitor the result and make decision in real time. Many people see this restriction as a setback against the trend in the technology toward real time data analytics. Recently, Bayesian Hypothesis Testing, which intuitively is more suitable for real time decision making, attracted growing interest as an alternative to NHST. While corrections of…
A new computation method of frequentist $p$-values and Bayesian posterior probabilities based on the bootstrap probability is discussed for the multivariate normal model with unknown expectation parameter vector. The null hypothesis is represented as an arbitrary-shaped region. We introduce new parametric models for the scaling-law of bootstrap probability so that the multiscale bootstrap method, which was designed for one-sided test, can also computes confidence measures of two-sided test, extending applicability to a wider class of hypotheses. Parameter estimation is improved by the two-step…
Network data often exhibit block structures characterized by clusters of nodes with similar patterns of edge formation. When such relational data are complemented by additional information on exogenous node partitions, these sources of knowledge are typically included in the model to supervise the cluster assignment mechanism or to improve inference on edge probabilities. Although these solutions are routinely implemented, there is a lack of formal approaches to test if a given external node partition is in line with the endogenous clustering structure encoding stochastic equivalence patterns …
We study the following independence testing problem: given access to samples from a distribution $P$ over $\{0,1\}^n$, decide whether $P$ is a product distribution or whether it is $\varepsilon$-far in total variation distance from any product distribution. For arbitrary distributions, this problem requires $\exp(n)$ samples. We show in this work that if $P$ has a sparse structure, then in fact only linearly many samples are required. Specifically, if $P$ is Markov with respect to a Bayesian network whose underlying DAG has in-degree bounded by $d$, then $\tildeΘ(2^{d/2}\cdot n/\varepsilon^2)$…
When we use the normal mixture model, the optimal number of the components describing the data should be determined. Testing homogeneity is good for this purpose; however, to construct its theory is challenging, since the test statistic does not converge to the $χ^{2}$ distribution even asymptotically. The reason for such asymptotic behavior is that the parameter set describing the null hypothesis (N.H.) contains singularities in the space of the alternative hypothesis (A.H.). Recently, a $\it{Bayesian}$ theory for singular models was developed, and it has elucidated various problems of statis…
Continuous time Bayesian networks are investigated with a special focus on their ability to express causality. A framework is presented for doing inference in these networks. The central contributions are a representation of the intensity matrices for the networks and the introduction of a causality measure. A new model for high-frequency financial data is presented. It is calibrated to market data and by the new causality measure it performs better than older models.
Given the well-known and fundamental problems with hypothesis testing via classical (point-form) significance tests, there has been a general move to alternative approaches, often focused on the Bayesian t-test. We show that the Bayesian t-test approach does not address the observed problems with classical significance testing, that Bayesian and classical t-tests are mathematically equivalent and linearly related in order of magnitude (so that the Bayesian t-test providing no further information beyond that given by point-form significance tests), and that Bayesian t-tests are subject to serio…
In this article, we propose a novel Bayesian multiple testing formulation for model and variable selection in inverse setups, judiciously embedding the idea of inverse reference distributions proposed by Bhattacharya (2013) in a mixture framework consisting of the competing models. We develop the theory and methods in the general context encompassing parametric and nonparametric competing models, dependent data, as well as misspecifications. Our investigation shows that asymptotically the multiple testing procedure almost surely selects the best possible inverse model that minimizes the minimu…
The following zero-sum game between nature and a statistician blends Bayesian methods with frequentist methods such as p-values and confidence intervals. Nature chooses a posterior distribution consistent with a set of possible priors. At the same time, the statistician selects a parameter distribution for inference with the goal of maximizing the minimum Kullback-Leibler information gained over a confidence distribution or other benchmark distribution. An application to testing a simple null hypothesis leads the statistician to report a posterior probability of the hypothesis that is informed…
