The Deviance Information Criterion: 12 Years On
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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. -
Fast Computation of the Deviance Information Criterion for Latent Variable Models
Crawford School of Public Policy CAMA Centre for Applied Macroeconomic Analysis Fast Computation of the Deviance Information Criterion for Latent Variable Models CAMA Working Paper 9/2014 January 2014 Joshua C.C. Chan Research School of Economics, ANU and Centre for Applied Macroeconomic Analysis Angelia L. Grant Centre for Applied Macroeconomic Analysis Abstract The deviance information criterion (DIC) has been widely used for Bayesian model comparison. However, recent studies have cautioned against the use of the DIC for comparing latent variable models. In particular, the DIC calculated using the conditional likelihood (obtained by conditioning on the latent variables) is found to be inappropriate, whereas the DIC computed using the integrated likelihood (obtained by integrating out the latent variables) seems to perform well. In view of this, we propose fast algorithms for computing the DIC based on the integrated likelihood for a variety of high- dimensional latent variable models. Through three empirical applications we show that the DICs based on the integrated likelihoods have much smaller numerical standard errors compared to the DICs based on the conditional likelihoods. THE AUSTRALIAN NATIONAL UNIVERSITY Keywords Bayesian model comparison, state space, factor model, vector autoregression, semiparametric JEL Classification C11, C15, C32, C52 Address for correspondence: (E) [email protected] The Centre for Applied Macroeconomic Analysis in the Crawford School of Public Policy has been established to build strong links between professional macroeconomists. It provides a forum for quality macroeconomic research and discussion of policy issues between academia, government and the private sector. The Crawford School of Public Policy is the Australian National University’s public policy school, serving and influencing Australia, Asia and the Pacific through advanced policy research, graduate and executive education, and policy impact. -
A Generalized Linear Model for Binomial Response Data
A Generalized Linear Model for Binomial Response Data Copyright c 2017 Dan Nettleton (Iowa State University) Statistics 510 1 / 46 Now suppose that instead of a Bernoulli response, we have a binomial response for each unit in an experiment or an observational study. As an example, consider the trout data set discussed on page 669 of The Statistical Sleuth, 3rd edition, by Ramsey and Schafer. Five doses of toxic substance were assigned to a total of 20 fish tanks using a completely randomized design with four tanks per dose. Copyright c 2017 Dan Nettleton (Iowa State University) Statistics 510 2 / 46 For each tank, the total number of fish and the number of fish that developed liver tumors were recorded. d=read.delim("http://dnett.github.io/S510/Trout.txt") d dose tumor total 1 0.010 9 87 2 0.010 5 86 3 0.010 2 89 4 0.010 9 85 5 0.025 30 86 6 0.025 41 86 7 0.025 27 86 8 0.025 34 88 9 0.050 54 89 10 0.050 53 86 11 0.050 64 90 12 0.050 55 88 13 0.100 71 88 14 0.100 73 89 15 0.100 65 88 16 0.100 72 90 17 0.250 66 86 18 0.250 75 82 19 0.250 72 81 20 0.250 73 89 Copyright c 2017 Dan Nettleton (Iowa State University) Statistics 510 3 / 46 One way to analyze this dataset would be to convert the binomial counts and totals into Bernoulli responses. -
Comparison of Some Chemometric Tools for Metabonomics Biomarker Identification ⁎ Réjane Rousseau A, , Bernadette Govaerts A, Michel Verleysen A,B, Bruno Boulanger C
Available online at www.sciencedirect.com Chemometrics and Intelligent Laboratory Systems 91 (2008) 54–66 www.elsevier.com/locate/chemolab Comparison of some chemometric tools for metabonomics biomarker identification ⁎ Réjane Rousseau a, , Bernadette Govaerts a, Michel Verleysen a,b, Bruno Boulanger c a Université Catholique de Louvain, Institut de Statistique, Voie du Roman Pays 20, B-1348 Louvain-la-Neuve, Belgium b Université Catholique de Louvain, Machine Learning Group - DICE, Belgium c Eli Lilly, European Early Phase Statistics, Belgium Received 29 December 2006; received in revised form 15 June 2007; accepted 22 June 2007 Available online 29 June 2007 Abstract NMR-based metabonomics discovery approaches require statistical methods to extract, from large and complex spectral databases, biomarkers or biologically significant variables that best represent defined biological conditions. This paper explores the respective effectiveness of six multivariate methods: multiple hypotheses testing, supervised extensions of principal (PCA) and independent components analysis (ICA), discriminant partial least squares, linear logistic regression and classification trees. Each method has been adapted in order to provide a biomarker score for each zone of the spectrum. These scores aim at giving to the biologist indications on which metabolites of the analyzed biofluid are potentially affected by a stressor factor of interest (e.g. toxicity of a drug, presence of a given disease or therapeutic effect of a drug). The applications of the six methods to samples of 60 and 200 spectra issued from a semi-artificial database allowed to evaluate their respective properties. In particular, their sensitivities and false discovery rates (FDR) are illustrated through receiver operating characteristics curves (ROC) and the resulting identifications are used to show their specificities and relative advantages.The paper recommends to discard two methods for biomarker identification: the PCA showing a general low efficiency and the CART which is very sensitive to noise. -
Statistics 149 – Spring 2016 – Assignment 4 Solutions Due Monday April 4, 2016 1. for the Poisson Distribution, B(Θ) =
Statistics 149 { Spring 2016 { Assignment 4 Solutions Due Monday April 4, 2016 1. For the Poisson distribution, b(θ) = eθ and thus µ = b′(θ) = eθ. Consequently, θ = ∗ g(µ) = log(µ) and b(θ) = µ. Also, for the saturated model µi = yi. n ∗ ∗ D(µSy) = 2 Q yi(θi − θi) − b(θi ) + b(θi) i=1 n ∗ ∗ = 2 Q yi(log(µi ) − log(µi)) − µi + µi i=1 n yi = 2 Q yi log − (yi − µi) i=1 µi 2. (a) After following instructions for replacing 0 values with NAs, we summarize the data: > summary(mypima2) pregnant glucose diastolic triceps insulin Min. : 0.000 Min. : 44.0 Min. : 24.00 Min. : 7.00 Min. : 14.00 1st Qu.: 1.000 1st Qu.: 99.0 1st Qu.: 64.00 1st Qu.:22.00 1st Qu.: 76.25 Median : 3.000 Median :117.0 Median : 72.00 Median :29.00 Median :125.00 Mean : 3.845 Mean :121.7 Mean : 72.41 Mean :29.15 Mean :155.55 3rd Qu.: 6.000 3rd Qu.:141.0 3rd Qu.: 80.00 3rd Qu.:36.00 3rd Qu.:190.00 Max. :17.000 Max. :199.0 Max. :122.00 Max. :99.00 Max. :846.00 NA's :5 NA's :35 NA's :227 NA's :374 bmi diabetes age test Min. :18.20 Min. :0.0780 Min. :21.00 Min. :0.000 1st Qu.:27.50 1st Qu.:0.2437 1st Qu.:24.00 1st Qu.:0.000 Median :32.30 Median :0.3725 Median :29.00 Median :0.000 Mean :32.46 Mean :0.4719 Mean :33.24 Mean :0.349 3rd Qu.:36.60 3rd Qu.:0.6262 3rd Qu.:41.00 3rd Qu.:1.000 Max. -
Bayesian Methods: Review of Generalized Linear Models
Bayesian Methods: Review of Generalized Linear Models RYAN BAKKER University of Georgia ICPSR Day 2 Bayesian Methods: GLM [1] Likelihood and Maximum Likelihood Principles Likelihood theory is an important part of Bayesian inference: it is how the data enter the model. • The basis is Fisher’s principle: what value of the unknown parameter is “most likely” to have • generated the observed data. Example: flip a coin 10 times, get 5 heads. MLE for p is 0.5. • This is easily the most common and well-understood general estimation process. • Bayesian Methods: GLM [2] Starting details: • – Y is a n k design or observation matrix, θ is a k 1 unknown coefficient vector to be esti- × × mated, we want p(θ Y) (joint sampling distribution or posterior) from p(Y θ) (joint probabil- | | ity function). – Define the likelihood function: n L(θ Y) = p(Y θ) | i| i=1 Y which is no longer on the probability metric. – Our goal is the maximum likelihood value of θ: θˆ : L(θˆ Y) L(θ Y) θ Θ | ≥ | ∀ ∈ where Θ is the class of admissable values for θ. Bayesian Methods: GLM [3] Likelihood and Maximum Likelihood Principles (cont.) Its actually easier to work with the natural log of the likelihood function: • `(θ Y) = log L(θ Y) | | We also find it useful to work with the score function, the first derivative of the log likelihood func- • tion with respect to the parameters of interest: ∂ `˙(θ Y) = `(θ Y) | ∂θ | Setting `˙(θ Y) equal to zero and solving gives the MLE: θˆ, the “most likely” value of θ from the • | parameter space Θ treating the observed data as given. -
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. -
What I Should Have Described in Class Today
Statistics 849 Clarification 2010-11-03 (p. 1) What I should have described in class today Sorry for botching the description of the deviance calculation in a generalized linear model and how it relates to the function dev.resids in a glm family object in R. Once again Chen Zuo pointed out the part that I had missed. We need to use positive contributions to the deviance for each observation if we are later to take the square roots of these quantities. To ensure that these are all positive we establish a baseline level for the deviance, which is the lowest possible value of the deviance, corresponding to a saturated model in which each observation has one parameter associated with it. Another value quoted in the summary output is the null deviance, which is the deviance for the simplest possible model (the \null model") corresponding to a formula like > data(Contraception, package = "mlmRev") > summary(cm0 <- glm(use ~ 1, binomial, Contraception)) Call: glm(formula = use ~ 1, family = binomial, data = Contraception) Deviance Residuals: Min 1Q Median 3Q Max -0.9983 -0.9983 -0.9983 1.3677 1.3677 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.43702 0.04657 -9.385 <2e-16 (Dispersion parameter for binomial family taken to be 1) Null deviance: 2590.9 on 1933 degrees of freedom Residual deviance: 2590.9 on 1933 degrees of freedom AIC: 2592.9 Number of Fisher Scoring iterations: 4 Notice that the coefficient estimate, -0.437022, is the logit transformation of the proportion of positive responses > str(y <- as.integer(Contraception[["use"]]) - 1L) int [1:1934] 0 0 0 0 0 0 0 0 0 0 .. -
Posterior Propriety and Admissibility of Hyperpriors in Normal
The Annals of Statistics 2005, Vol. 33, No. 2, 606–646 DOI: 10.1214/009053605000000075 c Institute of Mathematical Statistics, 2005 POSTERIOR PROPRIETY AND ADMISSIBILITY OF HYPERPRIORS IN NORMAL HIERARCHICAL MODELS1 By James O. Berger, William Strawderman and Dejun Tang Duke University and SAMSI, Rutgers University and Novartis Pharmaceuticals Hierarchical modeling is wonderful and here to stay, but hyper- parameter priors are often chosen in a casual fashion. Unfortunately, as the number of hyperparameters grows, the effects of casual choices can multiply, leading to considerably inferior performance. As an ex- treme, but not uncommon, example use of the wrong hyperparameter priors can even lead to impropriety of the posterior. For exchangeable hierarchical multivariate normal models, we first determine when a standard class of hierarchical priors results in proper or improper posteriors. We next determine which elements of this class lead to admissible estimators of the mean under quadratic loss; such considerations provide one useful guideline for choice among hierarchical priors. Finally, computational issues with the resulting posterior distributions are addressed. 1. Introduction. 1.1. The model and the problems. Consider the block multivariate nor- mal situation (sometimes called the “matrix of means problem”) specified by the following hierarchical Bayesian model: (1) X ∼ Np(θ, I), θ ∼ Np(B, Σπ), where X1 θ1 X2 θ2 Xp×1 = . , θp×1 = . , arXiv:math/0505605v1 [math.ST] 27 May 2005 . X θ m m Received February 2004; revised July 2004. 1Supported by NSF Grants DMS-98-02261 and DMS-01-03265. AMS 2000 subject classifications. Primary 62C15; secondary 62F15. Key words and phrases. Covariance matrix, quadratic loss, frequentist risk, posterior impropriety, objective priors, Markov chain Monte Carlo. -
Heteroscedastic Errors
Heteroscedastic Errors ◮ Sometimes plots and/or tests show that the error variances 2 σi = Var(ǫi ) depend on i ◮ Several standard approaches to fixing the problem, depending on the nature of the dependence. ◮ Weighted Least Squares. ◮ Transformation of the response. ◮ Generalized Linear Models. Richard Lockhart STAT 350: Heteroscedastic Errors and GLIM Weighted Least Squares ◮ Suppose variances are known except for a constant factor. 2 2 ◮ That is, σi = σ /wi . ◮ Use weighted least squares. (See Chapter 10 in the text.) ◮ This usually arises realistically in the following situations: ◮ Yi is an average of ni measurements where you know ni . Then wi = ni . 2 ◮ Plots suggest that σi might be proportional to some power of 2 γ γ some covariate: σi = kxi . Then wi = xi− . Richard Lockhart STAT 350: Heteroscedastic Errors and GLIM Variances depending on (mean of) Y ◮ Two standard approaches are available: ◮ Older approach is transformation. ◮ Newer approach is use of generalized linear model; see STAT 402. Richard Lockhart STAT 350: Heteroscedastic Errors and GLIM Transformation ◮ Compute Yi∗ = g(Yi ) for some function g like logarithm or square root. ◮ Then regress Yi∗ on the covariates. ◮ This approach sometimes works for skewed response variables like income; ◮ after transformation we occasionally find the errors are more nearly normal, more homoscedastic and that the model is simpler. ◮ See page 130ff and check under transformations and Box-Cox in the index. Richard Lockhart STAT 350: Heteroscedastic Errors and GLIM Generalized Linear Models ◮ Transformation uses the model T E(g(Yi )) = xi β while generalized linear models use T g(E(Yi )) = xi β ◮ Generally latter approach offers more flexibility. -
And the Winner Is…? How to Pick a Better Model Part 2 – Goodness-Of-Fit and Internal Stability
And The Winner Is…? How to Pick a Better Model Part 2 – Goodness-of-Fit and Internal Stability Dan Tevet, FCAS, MAAA Goodness-of-Fit • Trying to answer question: How well does our model fit the data? • Can be measured on training data or on holdout data • By identifying areas of poor model fit, we may be able to improve our model • A few ways to measure goodness-of-fit – Squared or absolute error – Likelihood/log-likelihood – AIC/BIC – Deviance/deviance residuals – Plot of actual versus predicted target Liberty Mutual Insurance Squared Error & Absolute Error • For each record, calculate the squared or absolute difference between actual and predicted target variable • Easy and intuitive, but generally inappropriate for insurance data, and can lead to selection of wrong model • Squared error appropriate for Normal data, but insurance data generally not Normal Liberty Mutual Insurance Residuals • Raw residual = yi – μi, where y is actual value of target variable and μ is predicted value • In simple linear regression, residuals are supposed to be Normally distributed, and departure from Normality indicates poor fit • For insurance data, raw residuals are highly skewed and generally not useful Liberty Mutual Insurance Likelihood • The probability, as predicted by our model, that what actually did occur would occur • A GLM calculates the parameters that maximize likelihood • Higher likelihood better model fit (very simple terms) • Problem with likelihood – adding a variable always improves likelihood Liberty Mutual Insurance AIC & BIC – penalized -
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.