Posterior Propriety and Admissibility of Hyperpriors in Normal
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DSA 5403 Bayesian Statistics: an Advancing Introduction 16 Units – Each Unit a Week’S Work
DSA 5403 Bayesian Statistics: An Advancing Introduction 16 units – each unit a week’s work. The following are the contents of the course divided into chapters of the book Doing Bayesian Data Analysis . by John Kruschke. The course is structured around the above book but will be embellished with more theoretical content as needed. The book can be obtained from the library : http://www.sciencedirect.com/science/book/9780124058880 Topics: This is divided into three parts From the book: “Part I The basics: models, probability, Bayes' rule and r: Introduction: credibility, models, and parameters; The R programming language; What is this stuff called probability?; Bayes' rule Part II All the fundamentals applied to inferring a binomial probability: Inferring a binomial probability via exact mathematical analysis; Markov chain Monte C arlo; J AG S ; Hierarchical models; Model comparison and hierarchical modeling; Null hypothesis significance testing; Bayesian approaches to testing a point ("Null") hypothesis; G oals, power, and sample size; S tan Part III The generalized linear model: Overview of the generalized linear model; Metric-predicted variable on one or two groups; Metric predicted variable with one metric predictor; Metric predicted variable with multiple metric predictors; Metric predicted variable with one nominal predictor; Metric predicted variable with multiple nominal predictors; Dichotomous predicted variable; Nominal predicted variable; Ordinal predicted variable; C ount predicted variable; Tools in the trunk” Part 1: The Basics: Models, Probability, Bayes’ Rule and R Unit 1 Chapter 1, 2 Credibility, Models, and Parameters, • Derivation of Bayes’ rule • Re-allocation of probability • The steps of Bayesian data analysis • Classical use of Bayes’ rule o Testing – false positives etc o Definitions of prior, likelihood, evidence and posterior Unit 2 Chapter 3 The R language • Get the software • Variables types • Loading data • Functions • Plots Unit 3 Chapter 4 Probability distributions. -
Assessing Fairness with Unlabeled Data and Bayesian Inference
Can I Trust My Fairness Metric? Assessing Fairness with Unlabeled Data and Bayesian Inference Disi Ji1 Padhraic Smyth1 Mark Steyvers2 1Department of Computer Science 2Department of Cognitive Sciences University of California, Irvine [email protected] [email protected] [email protected] Abstract We investigate the problem of reliably assessing group fairness when labeled examples are few but unlabeled examples are plentiful. We propose a general Bayesian framework that can augment labeled data with unlabeled data to produce more accurate and lower-variance estimates compared to methods based on labeled data alone. Our approach estimates calibrated scores for unlabeled examples in each group using a hierarchical latent variable model conditioned on labeled examples. This in turn allows for inference of posterior distributions with associated notions of uncertainty for a variety of group fairness metrics. We demonstrate that our approach leads to significant and consistent reductions in estimation error across multiple well-known fairness datasets, sensitive attributes, and predictive models. The results show the benefits of using both unlabeled data and Bayesian inference in terms of assessing whether a prediction model is fair or not. 1 Introduction Machine learning models are increasingly used to make important decisions about individuals. At the same time it has become apparent that these models are susceptible to producing systematically biased decisions with respect to sensitive attributes such as gender, ethnicity, and age [Angwin et al., 2017, Berk et al., 2018, Corbett-Davies and Goel, 2018, Chen et al., 2019, Beutel et al., 2019]. This has led to a significant amount of recent work in machine learning addressing these issues, including research on both (i) definitions of fairness in a machine learning context (e.g., Dwork et al. -
Bayesian Inference Chapter 4: Regression and Hierarchical Models
Bayesian Inference Chapter 4: Regression and Hierarchical Models Conchi Aus´ınand Mike Wiper Department of Statistics Universidad Carlos III de Madrid Master in Business Administration and Quantitative Methods Master in Mathematical Engineering Conchi Aus´ınand Mike Wiper Regression and hierarchical models Masters Programmes 1 / 35 Objective AFM Smith Dennis Lindley We analyze the Bayesian approach to fitting normal and generalized linear models and introduce the Bayesian hierarchical modeling approach. Also, we study the modeling and forecasting of time series. Conchi Aus´ınand Mike Wiper Regression and hierarchical models Masters Programmes 2 / 35 Contents 1 Normal linear models 1.1. ANOVA model 1.2. Simple linear regression model 2 Generalized linear models 3 Hierarchical models 4 Dynamic models Conchi Aus´ınand Mike Wiper Regression and hierarchical models Masters Programmes 3 / 35 Normal linear models A normal linear model is of the following form: y = Xθ + ; 0 where y = (y1;:::; yn) is the observed data, X is a known n × k matrix, called 0 the design matrix, θ = (θ1; : : : ; θk ) is the parameter set and follows a multivariate normal distribution. Usually, it is assumed that: 1 ∼ N 0 ; I : k φ k A simple example of normal linear model is the simple linear regression model T 1 1 ::: 1 where X = and θ = (α; β)T . x1 x2 ::: xn Conchi Aus´ınand Mike Wiper Regression and hierarchical models Masters Programmes 4 / 35 Normal linear models Consider a normal linear model, y = Xθ + . A conjugate prior distribution is a normal-gamma distribution: -
The Bayesian Approach to Statistics
THE BAYESIAN APPROACH TO STATISTICS ANTHONY O’HAGAN INTRODUCTION the true nature of scientific reasoning. The fi- nal section addresses various features of modern By far the most widely taught and used statisti- Bayesian methods that provide some explanation for the rapid increase in their adoption since the cal methods in practice are those of the frequen- 1980s. tist school. The ideas of frequentist inference, as set out in Chapter 5 of this book, rest on the frequency definition of probability (Chapter 2), BAYESIAN INFERENCE and were developed in the first half of the 20th century. This chapter concerns a radically differ- We first present the basic procedures of Bayesian ent approach to statistics, the Bayesian approach, inference. which depends instead on the subjective defini- tion of probability (Chapter 3). In some respects, Bayesian methods are older than frequentist ones, Bayes’s Theorem and the Nature of Learning having been the basis of very early statistical rea- Bayesian inference is a process of learning soning as far back as the 18th century. Bayesian from data. To give substance to this statement, statistics as it is now understood, however, dates we need to identify who is doing the learning and back to the 1950s, with subsequent development what they are learning about. in the second half of the 20th century. Over that time, the Bayesian approach has steadily gained Terms and Notation ground, and is now recognized as a legitimate al- ternative to the frequentist approach. The person doing the learning is an individual This chapter is organized into three sections. -
The Bayesian Lasso
The Bayesian Lasso Trevor Park and George Casella y University of Florida, Gainesville, Florida, USA Summary. The Lasso estimate for linear regression parameters can be interpreted as a Bayesian posterior mode estimate when the priors on the regression parameters are indepen- dent double-exponential (Laplace) distributions. This posterior can also be accessed through a Gibbs sampler using conjugate normal priors for the regression parameters, with indepen- dent exponential hyperpriors on their variances. This leads to tractable full conditional distri- butions through a connection with the inverse Gaussian distribution. Although the Bayesian Lasso does not automatically perform variable selection, it does provide standard errors and Bayesian credible intervals that can guide variable selection. Moreover, the structure of the hierarchical model provides both Bayesian and likelihood methods for selecting the Lasso pa- rameter. The methods described here can also be extended to other Lasso-related estimation methods like bridge regression and robust variants. Keywords: Gibbs sampler, inverse Gaussian, linear regression, empirical Bayes, penalised regression, hierarchical models, scale mixture of normals 1. Introduction The Lasso of Tibshirani (1996) is a method for simultaneous shrinkage and model selection in regression problems. It is most commonly applied to the linear regression model y = µ1n + Xβ + ; where y is the n 1 vector of responses, µ is the overall mean, X is the n p matrix × T × of standardised regressors, β = (β1; : : : ; βp) is the vector of regression coefficients to be estimated, and is the n 1 vector of independent and identically distributed normal errors with mean 0 and unknown× variance σ2. The estimate of µ is taken as the average y¯ of the responses, and the Lasso estimate β minimises the sum of the squared residuals, subject to a given bound t on its L1 norm. -
The Deviance Information Criterion: 12 Years On
J. R. Statist. Soc. B (2014) The deviance information criterion: 12 years on David J. Spiegelhalter, University of Cambridge, UK Nicola G. Best, Imperial College School of Public Health, London, UK Bradley P. Carlin University of Minnesota, Minneapolis, USA and Angelika van der Linde Bremen, Germany [Presented to The Royal Statistical Society at its annual conference in a session organized by the Research Section on Tuesday, September 3rd, 2013, Professor G. A.Young in the Chair ] Summary.The essentials of our paper of 2002 are briefly summarized and compared with other criteria for model comparison. After some comments on the paper’s reception and influence, we consider criticisms and proposals for improvement made by us and others. Keywords: Bayesian; Model comparison; Prediction 1. Some background to model comparison Suppose that we have a given set of candidate models, and we would like a criterion to assess which is ‘better’ in a defined sense. Assume that a model for observed data y postulates a density p.y|θ/ (which may include covariates etc.), and call D.θ/ =−2log{p.y|θ/} the deviance, here considered as a function of θ. Classical model choice uses hypothesis testing for comparing nested models, e.g. the deviance (likelihood ratio) test in generalized linear models. For non- nested models, alternatives include the Akaike information criterion AIC =−2log{p.y|θˆ/} + 2k where θˆ is the maximum likelihood estimate and k is the number of parameters in the model (dimension of Θ). AIC is built with the aim of favouring models that are likely to make good predictions. -
Empirical Bayes Methods for Combining Likelihoods Bradley EFRON
Empirical Bayes Methods for Combining Likelihoods Bradley EFRON Supposethat several independent experiments are observed,each one yieldinga likelihoodLk (0k) for a real-valuedparameter of interestOk. For example,Ok might be the log-oddsratio for a 2 x 2 table relatingto the kth populationin a series of medical experiments.This articleconcerns the followingempirical Bayes question:How can we combineall of the likelihoodsLk to get an intervalestimate for any one of the Ok'S, say 01? The resultsare presented in the formof a realisticcomputational scheme that allows model buildingand model checkingin the spiritof a regressionanalysis. No specialmathematical forms are requiredfor the priorsor the likelihoods.This schemeis designedto take advantageof recentmethods that produceapproximate numerical likelihoodsLk(6k) even in very complicatedsituations, with all nuisanceparameters eliminated. The empiricalBayes likelihood theoryis extendedto situationswhere the Ok'S have a regressionstructure as well as an empiricalBayes relationship.Most of the discussionis presentedin termsof a hierarchicalBayes model and concernshow such a model can be implementedwithout requiringlarge amountsof Bayesianinput. Frequentist approaches, such as bias correctionand robustness,play a centralrole in the methodology. KEY WORDS: ABC method;Confidence expectation; Generalized linear mixed models;Hierarchical Bayes; Meta-analysis for likelihoods;Relevance; Special exponential families. 1. INTRODUCTION for 0k, also appearing in Table 1, is A typical statistical analysis blends data from indepen- dent experimental units into a single combined inference for a parameter of interest 0. Empirical Bayes, or hierar- SDk ={ ak +.S + bb + .5 +k + -5 dk + .5 chical or meta-analytic analyses, involve a second level of SD13 = .61, for example. data acquisition. Several independent experiments are ob- The statistic 0k is an estimate of the true log-odds ratio served, each involving many units, but each perhaps having 0k in the kth experimental population, a different value of the parameter 0. -
A Widely Applicable Bayesian Information Criterion
JournalofMachineLearningResearch14(2013)867-897 Submitted 8/12; Revised 2/13; Published 3/13 A Widely Applicable Bayesian Information Criterion Sumio Watanabe [email protected] Department of Computational Intelligence and Systems Science Tokyo Institute of Technology Mailbox G5-19, 4259 Nagatsuta, Midori-ku Yokohama, Japan 226-8502 Editor: Manfred Opper Abstract A statistical model or a learning machine is called regular if the map taking a parameter to a prob- ability distribution is one-to-one and if its Fisher information matrix is always positive definite. If otherwise, it is called singular. In regular statistical models, the Bayes free energy, which is defined by the minus logarithm of Bayes marginal likelihood, can be asymptotically approximated by the Schwarz Bayes information criterion (BIC), whereas in singular models such approximation does not hold. Recently, it was proved that the Bayes free energy of a singular model is asymptotically given by a generalized formula using a birational invariant, the real log canonical threshold (RLCT), instead of half the number of parameters in BIC. Theoretical values of RLCTs in several statistical models are now being discovered based on algebraic geometrical methodology. However, it has been difficult to estimate the Bayes free energy using only training samples, because an RLCT depends on an unknown true distribution. In the present paper, we define a widely applicable Bayesian information criterion (WBIC) by the average log likelihood function over the posterior distribution with the inverse temperature 1/logn, where n is the number of training samples. We mathematically prove that WBIC has the same asymptotic expansion as the Bayes free energy, even if a statistical model is singular for or unrealizable by a statistical model. -
Bayes Theorem and Its Recent Applications
BAYES THEOREM AND ITS RECENT APPLICATIONS Nicholas Stylianides Eleni Kontou March 2020 Abstract Individuals who have studied maths to a specific level have come across Bayes’ Theorem or Bayes Formula. Bayes’ Theorem has many applications in areas such as mathematics, medicine, finance, marketing, engineering and many other. This paper covers Bayes’ Theorem at a basic level and explores how the formula was derived. We also, look at some extended forms of the formula and give an explicit example. Lastly, we discuss recent applications of Bayes’ Theorem in valuating depression and predicting water quality conditions. The goal of this expository paper is to break down the interesting topic of Bayes’ Theorem to a basic level which can be easily understood by a wide audience. What is Bayes Theorem? Thomas Bayes was an 18th-century British mathematician who developed a mathematical formula to calculate conditional probability in order to provide a way to re-examine current expectations. This mathematical formula is well known as Bayes Theorem or Bayes’ rule or Bayes’ Law. It is also the basis of a whole field of statistics known as Bayesian Statistics. For example, in finance, Bayes’ Theorem can be utilized to rate the risk of loaning cash to possible borrowers. The formula for Bayes’ Theorem is: [1] P(A) =The probability of A occurring P(B) = The probability of B occurring P(A|B) = The probability of A given B P(B|A) = The probability of B given A P(A∩B) = The probability of both A and B occurring MA3517 Mathematics Research Journal @Nicholas Stylianides, Eleni Kontou Bayes’ Theorem: , a $% &((!) > 0 %,- .// Proof: From Bayes’ Formula: (1) From the Total Probability (2) Theorem: Substituting equation (2) into equation (1) we obtain . -
A Review of Bayesian Optimization
Taking the Human Out of the Loop: A Review of Bayesian Optimization The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Shahriari, Bobak, Kevin Swersky, Ziyu Wang, Ryan P. Adams, and Nando de Freitas. 2016. “Taking the Human Out of the Loop: A Review of Bayesian Optimization.” Proc. IEEE 104 (1) (January): 148– 175. doi:10.1109/jproc.2015.2494218. Published Version doi:10.1109/JPROC.2015.2494218 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:27769882 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#OAP 1 Taking the Human Out of the Loop: A Review of Bayesian Optimization Bobak Shahriari, Kevin Swersky, Ziyu Wang, Ryan P. Adams and Nando de Freitas Abstract—Big data applications are typically associated with and the analytics company that sits between them. The analyt- systems involving large numbers of users, massive complex ics company must develop procedures to automatically design software systems, and large-scale heterogeneous computing and game variants across millions of users; the objective is to storage architectures. The construction of such systems involves many distributed design choices. The end products (e.g., rec- enhance user experience and maximize the content provider’s ommendation systems, medical analysis tools, real-time game revenue. engines, speech recognizers) thus involves many tunable config- The preceding examples highlight the importance of au- uration parameters. -
A New Hyperprior Distribution for Bayesian Regression Model with Application in Genomics
bioRxiv preprint doi: https://doi.org/10.1101/102244; this version posted January 22, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. A New Hyperprior Distribution for Bayesian Regression Model with Application in Genomics Renato Rodrigues Silva 1,* 1 Institute of Mathematics and Statistics, Federal University of Goi´as, Goi^ania,Goi´as,Brazil *[email protected] Abstract In the regression analysis, there are situations where the model have more predictor variables than observations of dependent variable, resulting in the problem known as \large p small n". In the last fifteen years, this problem has been received a lot of attention, specially in the genome-wide context. Here we purposed the bayes H model, a bayesian regression model using mixture of two scaled inverse chi square as hyperprior distribution of variance for each regression coefficient. This model is implemented in the R package BayesH. Introduction 1 In the regression analysis, there are situations where the model have more predictor 2 variables than observations of dependent variable, resulting in the problem known as 3 \large p small n" [1]. 4 To figure out this problem, there are already exists some methods developed as ridge 5 regression [2], least absolute shrinkage and selection operator (LASSO) regression [3], 6 bridge regression [4], smoothly clipped absolute deviation (SCAD) regression [5] and 7 others. This class of regression models is known in the literature as regression model 8 with penalized likelihood [6]. In the bayesian paradigma, there are also some methods 9 purposed as stochastic search variable selection [7], and Bayesian LASSO [8]. -
Bayesian Learning
SC4/SM8 Advanced Topics in Statistical Machine Learning Bayesian Learning Dino Sejdinovic Department of Statistics Oxford Slides and other materials available at: http://www.stats.ox.ac.uk/~sejdinov/atsml/ Department of Statistics, Oxford SC4/SM8 ATSML, HT2018 1 / 14 Bayesian Learning Review of Bayesian Inference The Bayesian Learning Framework Bayesian learning: treat parameter vector θ as a random variable: process of learning is then computation of the posterior distribution p(θjD). In addition to the likelihood p(Djθ) need to specify a prior distribution p(θ). Posterior distribution is then given by the Bayes Theorem: p(Djθ)p(θ) p(θjD) = p(D) Likelihood: p(Djθ) Posterior: p(θjD) Prior: p(θ) Marginal likelihood: p(D) = Θ p(Djθ)p(θ)dθ ´ Summarizing the posterior: MAP Posterior mode: θb = argmaxθ2Θ p(θjD) (maximum a posteriori). mean Posterior mean: θb = E [θjD]. Posterior variance: Var[θjD]. Department of Statistics, Oxford SC4/SM8 ATSML, HT2018 2 / 14 Bayesian Learning Review of Bayesian Inference Bayesian Inference on the Categorical Distribution Suppose we observe the with yi 2 f1;:::; Kg, and model them as i.i.d. with pmf π = (π1; : : : ; πK): n K Y Y nk p(Djπ) = πyi = πk i=1 k=1 Pn PK with nk = i=1 1(yi = k) and πk > 0, k=1 πk = 1. The conjugate prior on π is the Dirichlet distribution Dir(α1; : : : ; αK) with parameters αk > 0, and density PK K Γ( αk) Y p(π) = k=1 παk−1 QK k k=1 Γ(αk) k=1 PK on the probability simplex fπ : πk > 0; k=1 πk = 1g.