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 generic domains beyond the multivariate Euclidean spaces. The proposed procedure results in a posterior inference scheme that allows an automatic selection of the kernel parameters relevant to the problem at hand. In a series of synthetic experiments and two real data experiments (i.e. testing network heterogeneity from high-dimensional data and six-membered monocyclic ring conformation comparison), we illustrate the advantages of our approach.
Inference in popular nonparametric Bayesian models typically relies on sampling or other approximations. This paper presents a general methodology for constructing novel tractable nonparametric Bayesian methods by applying the kernel trick to inference in a parametric Bayesian model. For example, Gaussian process regression can be derived this way from Bayesian linear regression. Despite the success of the Gaussian process framework, the kernel trick is rarely explicitly considered in the Bayesian literature. In this paper, we aim to fill this gap and demonstrate the potential of applying the …
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 …
Kernel Bayesian inference is a principled approach to nonparametric inference in probabilistic graphical models, where probabilistic relationships between variables are learned from data in a nonparametric manner. Various algorithms of kernel Bayesian inference have been developed by combining kernelized basic probabilistic operations such as the kernel sum rule and kernel Bayes' rule. However, the current framework is fully nonparametric, and it does not allow a user to flexibly combine nonparametric and model-based inferences. This is inefficient when there are good probabilistic models (or …
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…
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 $ρ_s$.
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…
Marginalising over families of Gaussian Process kernels produces flexible model classes with well-calibrated uncertainty estimates. Existing approaches require likelihood evaluations of many kernels, rendering them prohibitively expensive for larger datasets. We propose a Bayesian Quadrature scheme to make this marginalisation more efficient and thereby more practical. Through use of the maximum mean discrepancies between distributions, we define a kernel over kernels that captures invariances between Spectral Mixture (SM) Kernels. Kernel samples are selected by generalising an information-the…
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 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…
Performing exact posterior inference in complex generative models is often difficult or impossible due to an expensive to evaluate or intractable likelihood function. Approximate Bayesian computation (ABC) is an inference framework that constructs an approximation to the true likelihood based on the similarity between the observed and simulated data as measured by a predefined set of summary statistics. Although the choice of appropriate problem-specific summary statistics crucially influences the quality of the likelihood approximation and hence also the quality of the posterior sample in ABC…
In practical Bayesian optimization, we must often search over structures with differing numbers of parameters. For instance, we may wish to search over neural network architectures with an unknown number of layers. To relate performance data gathered for different architectures, we define a new kernel for conditional parameter spaces that explicitly includes information about which parameters are relevant in a given structure. We show that this kernel improves model quality and Bayesian optimization results over several simpler baseline kernels.
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 res…
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…
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…
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 …
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 …
We propose a vector-valued regression problem whose solution is equivalent to the reproducing kernel Hilbert space (RKHS) embedding of the Bayesian posterior distribution. This equivalence provides a new understanding of kernel Bayesian inference. Moreover, the optimization problem induces a new regularization for the posterior embedding estimator, which is faster and has comparable performance to the squared regularization in kernel Bayes' rule. This regularization coincides with a former thresholding approach used in kernel POMDPs whose consistency remains to be established. Our theoretical …
We generalise an existing construction of Bayesian Lenses to admit lenses between pairs of objects where the backwards object is dependent on states on the forwards object (interpreted as probability distributions). This gives a natural setting for studying stochastic maps with Bayesian inverses restricted to the points supported by a given prior. In order to state this formally we develop a proposed definition by Fritz of a support object in a Markov category and show that these give rise to a section into the category of dependent Bayesian lenses encoding a more canonical notion of Bayesian …
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…
Bosch Center for Artificial Intelligence（博世人工智能中心）
Despite recent advances in automated machine learning, model selection is still a complex and computationally intensive process. For Gaussian processes (GPs), selecting the kernel is a crucial task, often done manually by the expert. Additionally, evaluating the model selection criteria for Gaussian processes typically scales cubically in the sample size, rendering kernel search particularly computationally expensive. We propose a novel, efficient search method through a general, structured kernel space. Previous methods solved this task via Bayesian optimization and relied on measuring the di…
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.
This works extends the Random Embedding Bayesian Optimization approach by integrating a warping of the high dimensional subspace within the covariance kernel. The proposed warping, that relies on elementary geometric considerations, allows mitigating the drawbacks of the high extrinsic dimensionality while avoiding the algorithm to evaluate points giving redundant information. It also alleviates constraints on bound selection for the embedded domain, thus improving the robustness, as illustrated with a test case with 25 variables and intrinsic dimension 6.
Asymptotic theory of tail index estimation has been studied extensively in the frequentist literature on extreme values, but rarely in the Bayesian context. We investigate whether popular Bayesian kernel mixture models are able to support heavy tailed distributions and consistently estimate the tail index. We show that posterior inconsistency in tail index is surprisingly common for both parametric and nonparametric mixture models. We then present a set of sufficient conditions under which posterior consistency in tail index can be achieved, and verify these conditions for Pareto mixture model…
We propose Bayesian extensions of two nonparametric regression methods which are kernel and mutual $k$-nearest neighbor regression methods. Derived based on Gaussian process models for regression, the extensions provide distributions for target value estimates and the framework to select the hyperparameters. It is shown that both the proposed methods asymptotically converge to kernel and mutual $k$-nearest neighbor regression methods, respectively. The simulation results show that the proposed methods can select proper hyperparameters and are better than or comparable to the former methods for…
In this article we perform an asymptotic analysis of Bayesian parallel kernel density estimators introduced by Neiswanger, Wang and Xing (2014). We derive the asymptotic expansion of the mean integrated squared error for the full data posterior estimator and investigate the properties of asymptotically optimal bandwidth parameters. Our analysis demonstrates that partitioning data into subsets requires a non-trivial choice of bandwidth parameters that optimizes the estimation error.
Kernel methods are ubiquitous tools in machine learning. However, there is often little reason for the common practice of selecting a kernel a priori. Even if a universal approximating kernel is selected, the quality of the finite sample estimator may be greatly affected by the choice of kernel. Furthermore, when directly applying kernel methods, one typically needs to compute a $N \times N$ Gram matrix of pairwise kernel evaluations to work with a dataset of $N$ instances. The computation of this Gram matrix precludes the direct application of kernel methods on large datasets, and makes kerne…
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.
Helsinki Institute for Information Technology HIIT（赫尔辛基信息技术研究所）；Aalto University School of Science（阿尔托大学理工学院）
Multiple kernel learning algorithms are proposed to combine kernels in order to obtain a better similarity measure or to integrate feature representations coming from different data sources. Most of the previous research on such methods is focused on the computational efficiency issue. However, it is still not feasible to combine many kernels using existing Bayesian approaches due to their high time complexity. We propose a fully conjugate Bayesian formulation and derive a deterministic variational approximation, which allows us to combine hundreds or thousands of kernels very efficiently. We …
University of Queensland（昆士兰大学）；University of Cambridge（剑桥大学）
A simple, flexible approach to creating expressive priors in Gaussian process (GP) models makes new kernels from a combination of basic kernels, e.g. summing a periodic and linear kernel can capture seasonal variation with a long term trend. Despite a well-studied link between GPs and Bayesian neural networks (BNNs), the BNN analogue of this has not yet been explored. This paper derives BNN architectures mirroring such kernel combinations. Furthermore, it shows how BNNs can produce periodic kernels, which are often useful in this context. These ideas provide a principled approach to designing …
Kernel methods are one of the mainstays of machine learning, but the problem of kernel learning remains challenging, with only a few heuristics and very little theory. This is of particular importance in methods based on estimation of kernel mean embeddings of probability measures. For characteristic kernels, which include most commonly used ones, the kernel mean embedding uniquely determines its probability measure, so it can be used to design a powerful statistical testing framework, which includes nonparametric two-sample and independence tests. In practice, however, the performance of thes…
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…
In this paper, we propose an outlier-robust regularized kernel-based method for linear system identification. The unknown impulse response is modeled as a zero-mean Gaussian process whose covariance (kernel) is given by the recently proposed stable spline kernel, which encodes information on regularity and exponential stability. To build robustness to outliers, we model the measurement noise as realizations of independent Laplacian random variables. The identification problem is cast in a Bayesian framework, and solved by a new Markov Chain Monte Carlo (MCMC) scheme. In particular, exploiting …
We revisit Rahimi and Recht (2007)'s kernel random Fourier features (RFF) method through the lens of the PAC-Bayesian theory. While the primary goal of RFF is to approximate a kernel, we look at the Fourier transform as a prior distribution over trigonometric hypotheses. It naturally suggests learning a posterior on these hypotheses. We derive generalization bounds that are optimized by learning a pseudo-posterior obtained from a closed-form expression. Based on this study, we consider two learning strategies: The first one finds a compact landmarks-based representation of the data where each …
We propose a practical Bayesian optimization method over sets, to minimize a black-box function that takes a set as a single input. Because set inputs are permutation-invariant, traditional Gaussian process-based Bayesian optimization strategies which assume vector inputs can fall short. To address this, we develop a Bayesian optimization method with \emph{set kernel} that is used to build surrogate functions. This kernel accumulates similarity over set elements to enforce permutation-invariance, but this comes at a greater computational cost. To reduce this burden, we propose two key componen…
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…
The Gibbs reference posterior distribution provides an objective full-Bayesian solution to the problem of prediction of a stationary Gaussian process with Matérn anisotropic kernel. A full-Bayesian approach is possible, because the posterior distribution is expressed as the invariant distribution of a uniformly ergodic Markovian kernel for which we give an explicit expression. In this paper, we show that it is appropriate for the Universal Kriging framework, that is when an unknown function is added to the stationary Gaussian process. We give sufficient conditions for the existence and proprie…
University of Sydney（悉尼大学）；CSIRO（澳大利亚联邦科学与工业研究组织）；NVIDIA（英伟达）
Conditional kernel mean embeddings form an attractive nonparametric framework for representing conditional means of functions, describing the observation processes for many complex models. However, the recovery of the original underlying function of interest whose conditional mean was observed is a challenging inference task. We formalize deconditional kernel mean embeddings as a solution to this inverse problem, and show that it can be naturally viewed as a nonparametric Bayes' rule. Critically, we introduce the notion of task transformed Gaussian processes and establish deconditional kernel …
Bayesian Optimization (BO) has become a core method for solving expensive black-box optimization problems. While much research focussed on the choice of the acquisition function, we focus on online length-scale adaption and the choice of kernel function. Instead of choosing hyperparameters in view of maximum likelihood on past data, we propose to use the acquisition function to decide on hyperparameter adaptation more robustly and in view of the future optimization progress. Further, we propose a particular kernel function that includes non-stationarity and local anisotropy and thereby implici…
University of Texas at Austin（德克萨斯大学奥斯汀分校）；Helsinki Institute for Information Technology（赫尔辛基信息技术研究所）
The kernel least mean squares (KLMS) algorithm is a computationally efficient nonlinear adaptive filtering method that "kernelizes" the celebrated (linear) least mean squares algorithm. We demonstrate that the least mean squares algorithm is closely related to the Kalman filtering, and thus, the KLMS can be interpreted as an approximate Bayesian filtering method. This allows us to systematically develop extensions of the KLMS by modifying the underlying state-space and observation models. The resulting extensions introduce many desirable properties such as "forgetting", and the ability to lear…
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 $\tildeΘ(2^{d/2}\cdot n/\varepsilon^2)$…
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.
In this paper, we study error bounds for {\em Bayesian quadrature} (BQ), with an emphasis on noisy settings, randomized algorithms, and average-case performance measures. We seek to approximate the integral of functions in a {\em Reproducing Kernel Hilbert Space} (RKHS), particularly focusing on the Matérn-$ν$ and squared exponential (SE) kernels, with samples from the function potentially being corrupted by Gaussian noise. We provide a two-step meta-algorithm that serves as a general tool for relating the average-case quadrature error with the $L^2$-function approximation error. When speciali…
SIKA-GP: Accelerating Gaussian Process Inference with Sparse Inducing Kernel Approximations for Bayesian Deep Learning
Department of Electrical；Computer Engineering, Texas A\&M University, College Station, US；Department of Industrial；Systems Engineering, Texas A\&M University, College Station, US
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…
Integrating Marketing Channels into Quantile Transformation and Bayesian Optimization of Ensemble Kernels for Sales Prediction with Gaussian Process Models
