J. B. S. Haldane's Contribution to the Bayes Factor Hypothesis Test
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
National Academy Elects IMS Fellows Have You Voted Yet?
Volume 38 • Issue 5 IMS Bulletin June 2009 National Academy elects IMS Fellows CONTENTS The United States National Academy of Sciences has elected 72 new members and 1 National Academy elects 18 foreign associates from 15 countries in recognition of their distinguished and Raftery, Wong continuing achievements in original research. Among those elected are two IMS Adrian Raftery 2 Members’ News: Jianqing Fellows: , Blumstein-Jordan Professor of Statistics and Sociology, Center Fan; SIAM Fellows for Statistics and the Social Sciences, University of Washington, Seattle, and Wing Hung Wong, Professor 3 Laha Award recipients of Statistics and Professor of Health Research and Policy, 4 COPSS Fisher Lecturer: Department of Statistics, Stanford University, California. Noel Cressie The election was held April 28, during the business 5 Members’ Discoveries: session of the 146th annual meeting of the Academy. Nicolai Meinshausen Those elected bring the total number of active members 6 Medallion Lecture: Tony Cai to 2,150. Foreign associates are non-voting members of the Academy, with citizenship outside the United States. Meeting report: SSP Above: Adrian Raftery 7 This year’s election brings the total number of foreign 8 New IMS Fellows Below: Wing H. Wong associates to 404. The National Academy of Sciences is a private 10 Obituaries: Keith Worsley; I.J. Good organization of scientists and engineers dedicated to the furtherance of science and its use for general welfare. 12-3 JSM program highlights; It was established in 1863 by a congressional act of IMS sessions at JSM incorporation signed by Abraham Lincoln that calls on 14-5 JSM tours; More things to the Academy to act as an official adviser to the federal do in DC government, upon request, in any matter of science or 16 Accepting rejections technology. -
Arxiv:1803.00360V2 [Stat.CO] 2 Mar 2018 Prone to Misinterpretation [2, 3]
Computing Bayes factors to measure evidence from experiments: An extension of the BIC approximation Thomas J. Faulkenberry∗ Tarleton State University Bayesian inference affords scientists with powerful tools for testing hypotheses. One of these tools is the Bayes factor, which indexes the extent to which support for one hypothesis over another is updated after seeing the data. Part of the hesitance to adopt this approach may stem from an unfamiliarity with the computational tools necessary for computing Bayes factors. Previous work has shown that closed form approximations of Bayes factors are relatively easy to obtain for between-groups methods, such as an analysis of variance or t-test. In this paper, I extend this approximation to develop a formula for the Bayes factor that directly uses infor- mation that is typically reported for ANOVAs (e.g., the F ratio and degrees of freedom). After giving two examples of its use, I report the results of simulations which show that even with minimal input, this approximate Bayes factor produces similar results to existing software solutions. Note: to appear in Biometrical Letters. I. INTRODUCTION A. The Bayes factor Bayesian inference is a method of measurement that is Hypothesis testing is the primary tool for statistical based on the computation of P (H j D), which is called inference across much of the biological and behavioral the posterior probability of a hypothesis H, given data D. sciences. As such, most scientists are trained in classical Bayes' theorem casts this probability as null hypothesis significance testing (NHST). The scenario for testing a hypothesis is likely familiar to most readers of this journal. -
Memorial to Sir Harold Jeffreys 1891-1989 JOHN A
Memorial to Sir Harold Jeffreys 1891-1989 JOHN A. HUDSON and ALAN G. SMITH University of Cambridge, Cambridge, England Harold Jeffreys was one of this century’s greatest applied mathematicians, using mathematics as a means of under standing the physical world. Principally he was a geo physicist, although statisticians may feel that his greatest contribution was to the theory of probability. However, his interest in the latter subject stemmed from his realization of the need for a clear statistical method of analysis of data— at that time, travel-time readings from seismological stations across the world. He also made contributions to astronomy, fluid dynamics, meteorology, botany, psychol ogy, and photography. Perhaps one can identify Jeffreys’s principal interests from three major books that he wrote. His mathematical skills are displayed in Methods of Mathematical Physics, which he wrote with his wife Bertha Swirles Jeffreys and which was first published in 1946 and went through three editions. His Theory o f Probability, published in 1939 and also running to three editions, espoused Bayesian statistics, which were very unfashionable at the time but which have been taken up since by others and shown to be extremely powerful for the analysis of data and, in particular, image enhancement. However, the book for which he is probably best known is The Earth, Its Origin, History and Physical Consti tution, a broad-ranging account based on observations analyzed with care, using mathematics as a tool. Jeffreys’s scientific method (now known as Inverse Theory) was a logical process, clearly stated in another of his books, Scientific Inference. -
A Parsimonious Tour of Bayesian Model Uncertainty
A Parsimonious Tour of Bayesian Model Uncertainty Pierre-Alexandre Mattei Université Côte d’Azur Inria, Maasai project-team Laboratoire J.A. Dieudonné, UMR CNRS 7351 e-mail: [email protected] Abstract: Modern statistical software and machine learning libraries are enabling semi-automated statistical inference. Within this context, it appears eas- ier and easier to try and fit many models to the data at hand, thereby reversing the Fisherian way of conducting science by collecting data after the scientific hypothesis (and hence the model) has been determined. The renewed goal of the statistician becomes to help the practitioner choose within such large and heterogeneous families of models, a task known as model selection. The Bayesian paradigm offers a systematized way of as- sessing this problem. This approach, launched by Harold Jeffreys in his 1935 book Theory of Probability, has witnessed a remarkable evolution in the last decades, that has brought about several new theoretical and methodological advances. Some of these recent developments are the focus of this survey, which tries to present a unifying perspective on work carried out by different communities. In particular, we focus on non-asymptotic out-of-sample performance of Bayesian model selection and averaging tech- niques, and draw connections with penalized maximum likelihood. We also describe recent extensions to wider classes of probabilistic frameworks in- cluding high-dimensional, unidentifiable, or likelihood-free models. Contents 1 Introduction: collecting data, fitting many models . .2 2 A brief history of Bayesian model uncertainty . .2 3 The foundations of Bayesian model uncertainty . .3 3.1 Handling model uncertainty with Bayes’s theorem . -
1 Estimation and Beyond in the Bayes Universe
ISyE8843A, Brani Vidakovic Handout 7 1 Estimation and Beyond in the Bayes Universe. 1.1 Estimation No Bayes estimate can be unbiased but Bayesians are not upset! No Bayes estimate with respect to the squared error loss can be unbiased, except in a trivial case when its Bayes’ risk is 0. Suppose that for a proper prior ¼ the Bayes estimator ±¼(X) is unbiased, Xjθ (8θ)E ±¼(X) = θ: This implies that the Bayes risk is 0. The Bayes risk of ±¼(X) can be calculated as repeated expectation in two ways, θ Xjθ 2 X θjX 2 r(¼; ±¼) = E E (θ ¡ ±¼(X)) = E E (θ ¡ ±¼(X)) : Thus, conveniently choosing either EθEXjθ or EX EθjX and using the properties of conditional expectation we have, θ Xjθ 2 θ Xjθ X θjX X θjX 2 r(¼; ±¼) = E E θ ¡ E E θ±¼(X) ¡ E E θ±¼(X) + E E ±¼(X) θ Xjθ 2 θ Xjθ X θjX X θjX 2 = E E θ ¡ E θ[E ±¼(X)] ¡ E ±¼(X)E θ + E E ±¼(X) θ Xjθ 2 θ X X θjX 2 = E E θ ¡ E θ ¢ θ ¡ E ±¼(X)±¼(X) + E E ±¼(X) = 0: Bayesians are not upset. To check for its unbiasedness, the Bayes estimator is averaged with respect to the model measure (Xjθ), and one of the Bayesian commandments is: Thou shall not average with respect to sample space, unless you have Bayesian design in mind. Even frequentist agree that insisting on unbiasedness can lead to bad estimators, and that in their quest to minimize the risk by trading off between variance and bias-squared a small dosage of bias can help. -
Hierarchical Models & Bayesian Model Selection
Hierarchical Models & Bayesian Model Selection Geoffrey Roeder Departments of Computer Science and Statistics University of British Columbia Jan. 20, 2016 Geoffrey Roeder Hierarchical Models & Bayesian Model Selection Jan. 20, 2016 Contact information Please report any typos or errors to geoff[email protected] Geoffrey Roeder Hierarchical Models & Bayesian Model Selection Jan. 20, 2016 Outline 1 Hierarchical Bayesian Modelling Coin toss redux: point estimates for θ Hierarchical models Application to clinical study 2 Bayesian Model Selection Introduction Bayes Factors Shortcut for Marginal Likelihood in Conjugate Case Geoffrey Roeder Hierarchical Models & Bayesian Model Selection Jan. 20, 2016 Outline 1 Hierarchical Bayesian Modelling Coin toss redux: point estimates for θ Hierarchical models Application to clinical study 2 Bayesian Model Selection Introduction Bayes Factors Shortcut for Marginal Likelihood in Conjugate Case Geoffrey Roeder Hierarchical Models & Bayesian Model Selection Jan. 20, 2016 Let Y be a random variable denoting number of observed heads in n coin tosses. Then, we can model Y ∼ Bin(n; θ), with probability mass function n p(Y = y j θ) = θy (1 − θ)n−y (1) y We want to estimate the parameter θ Coin toss: point estimates for θ Probability model Consider the experiment of tossing a coin n times. Each toss results in heads with probability θ and tails with probability 1 − θ Geoffrey Roeder Hierarchical Models & Bayesian Model Selection Jan. 20, 2016 We want to estimate the parameter θ Coin toss: point estimates for θ Probability model Consider the experiment of tossing a coin n times. Each toss results in heads with probability θ and tails with probability 1 − θ Let Y be a random variable denoting number of observed heads in n coin tosses. -
School of Social Sciences Economics Division University of Southampton Southampton SO17 1BJ, UK
School of Social Sciences Economics Division University of Southampton Southampton SO17 1BJ, UK Discussion Papers in Economics and Econometrics Professor A L Bowley’s Theory of the Representative Method John Aldrich No. 0801 This paper is available on our website http://www.socsci.soton.ac.uk/economics/Research/Discussion_Papers ISSN 0966-4246 Key names: Arthur L. Bowley, F. Y. Edgeworth, , R. A. Fisher, Adolph Jensen, J. M. Keynes, Jerzy Neyman, Karl Pearson, G. U. Yule. Keywords: History of Statistics, Sampling theory, Bayesian inference. Professor A. L. Bowley’s Theory of the Representative Method * John Aldrich Economics Division School of Social Sciences University of Southampton Southampton SO17 1BJ UK e-mail: [email protected] Abstract Arthur. L. Bowley (1869-1957) first advocated the use of surveys–the “representative method”–in 1906 and started to conduct surveys of economic and social conditions in 1912. Bowley’s 1926 memorandum for the International Statistical Institute on the “Measurement of the precision attained in sampling” was the first large-scale theoretical treatment of sample surveys as he conducted them. This paper examines Bowley’s arguments in the context of the statistical inference theory of the time. The great influence on Bowley’s conception of statistical inference was F. Y. Edgeworth but by 1926 R. A. Fisher was on the scene and was attacking Bayesian methods and promoting a replacement of his own. Bowley defended his Bayesian method against Fisher and against Jerzy Neyman when the latter put forward his concept of a confidence interval and applied it to the representative method. * Based on a talk given at the Sample Surveys and Bayesian Statistics Conference, Southampton, August 2008. -
The Enigma of Karl Pearson and Bayesian Inference
The Enigma of Karl Pearson and Bayesian Inference John Aldrich 1 Introduction “An enigmatic position in the history of the theory of probability is occupied by Karl Pearson” wrote Harold Jeffreys (1939, p. 313). The enigma was that Pearson based his philosophy of science on Bayesian principles but violated them when he used the method of moments and probability-values in statistics. It is not uncommon to see a divorce of practice from principles but Pearson also used Bayesian methods in some of his statistical work. The more one looks at his writings the more puzzling they seem. In 1939 Jeffreys was probably alone in regretting that Pearson had not been a bottom to top Bayesian. Bayesian methods had been in retreat in English statistics since Fisher began attacking them in the 1920s and only Jeffreys ever looked for a synthesis of logic, statistical methods and everything in between. In the 1890s, when Pearson started, everything was looser: statisticians used inverse arguments based on Bayesian principles and direct arguments based on sampling theory and a philosopher-physicist-statistician did not have to tie everything together. Pearson did less than his early guide Edgeworth or his students Yule and Gosset (Student) to tie up inverse and direct arguments and I will be look- ing to their work for clues to his position and for points of comparison. Of Pearson’s first course on the theory of statistics Yule (1938, p. 199) wrote, “A straightforward, organized, logically developed course could hardly then [in 1894] exist when the very elements of the subject were being developed.” But Pearson never produced such a course or published an exposition as integrated as Yule’s Introduction, not to mention the nonpareil Probability of Jeffreys. -
Bayes Factors in Practice Author(S): Robert E
Bayes Factors in Practice Author(s): Robert E. Kass Source: Journal of the Royal Statistical Society. Series D (The Statistician), Vol. 42, No. 5, Special Issue: Conference on Practical Bayesian Statistics, 1992 (2) (1993), pp. 551-560 Published by: Blackwell Publishing for the Royal Statistical Society Stable URL: http://www.jstor.org/stable/2348679 Accessed: 10/08/2010 18:09 Your use of the JSTOR archive indicates your acceptance of JSTOR's Terms and Conditions of Use, available at http://www.jstor.org/page/info/about/policies/terms.jsp. JSTOR's Terms and Conditions of Use provides, in part, that unless you have obtained prior permission, you may not download an entire issue of a journal or multiple copies of articles, and you may use content in the JSTOR archive only for your personal, non-commercial use. Please contact the publisher regarding any further use of this work. Publisher contact information may be obtained at http://www.jstor.org/action/showPublisher?publisherCode=black. Each copy of any part of a JSTOR transmission must contain the same copyright notice that appears on the screen or printed page of such transmission. JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact [email protected]. Blackwell Publishing and Royal Statistical Society are collaborating with JSTOR to digitize, preserve and extend access to Journal of the Royal Statistical Society. -
Bayes Factor Consistency
Bayes Factor Consistency Siddhartha Chib John M. Olin School of Business, Washington University in St. Louis and Todd A. Kuffner Department of Mathematics, Washington University in St. Louis July 1, 2016 Abstract Good large sample performance is typically a minimum requirement of any model selection criterion. This article focuses on the consistency property of the Bayes fac- tor, a commonly used model comparison tool, which has experienced a recent surge of attention in the literature. We thoroughly review existing results. As there exists such a wide variety of settings to be considered, e.g. parametric vs. nonparametric, nested vs. non-nested, etc., we adopt the view that a unified framework has didactic value. Using the basic marginal likelihood identity of Chib (1995), we study Bayes factor asymptotics by decomposing the natural logarithm of the ratio of marginal likelihoods into three components. These are, respectively, log ratios of likelihoods, prior densities, and posterior densities. This yields an interpretation of the log ra- tio of posteriors as a penalty term, and emphasizes that to understand Bayes factor consistency, the prior support conditions driving posterior consistency in each respec- tive model under comparison should be contrasted in terms of the rates of posterior contraction they imply. Keywords: Bayes factor; consistency; marginal likelihood; asymptotics; model selection; nonparametric Bayes; semiparametric regression. 1 1 Introduction Bayes factors have long held a special place in the Bayesian inferential paradigm, being the criterion of choice in model comparison problems for such Bayesian stalwarts as Jeffreys, Good, Jaynes, and others. An excellent introduction to Bayes factors is given by Kass & Raftery (1995). -
Mathematical Statistics and the ISI (1885-1939)
Mathematical Statistics and the ISI (1885-1939) Stephen M. Stigler University of Chicago, Department of Statistics 5734 University Avenue Chicago IL 60637, USA [email protected] 1. Introduction From its inception in 1885, the International Statistical Institute took all of statistics as its province. But the understood meaning of “statistics” has undergone significant change over the life of the Institute, and it is of interest to inquire how that change, whether evolutionary or revolutionary, has been reflected in the business of the Institute, in its meetings and its membership. I propose to consider this question in regard to one particular dimension, that of mathematical statistics, and one particular period, that from the rebirth of international statistics in 1885 until the eve of World War II. Mathematical statistics has been a recognized division of statistics at least since the 1860s, when Quetelet at the Congress in the Hague admonished the assembled statisticians not to divide the école mathématique from the école historique, but to take statistics whole, to open the doors to statistics in the broadest sense in all its flavors (Stigler, 2000). But even with this recognition, mathematical statistics only emerged as a discipline later. I have argued elsewhere that this emergence can be dated to the year 1933, and even if one thinks that date absurdly precise, there was a distinct and palpable change that was evident around that time (Stigler, 1999, Ch. 8). It was then that changes initiated a half-century earlier by Galton and Edgeworth and developed subsequently by Karl Pearson and Udny Yule, were seized upon and transformed by Ronald Fisher and Jerzy Neyman and Egon S. -
Bayesian Data-Analysis Toolbox User Manual
Bayesian Data-Analysis Toolbox Release 4.23, Manual Version 3 G. Larry Bretthorst Biomedical MR Laboratory Washington University School Of Medicine, Campus Box 8227 Room 2313, East Bldg., 4525 Scott Ave. St. Louis MO 63110 http://bayes.wustl.edu Email: [email protected] September 18, 2018 Appendix C Thermodynamic Integration Thermodynamic Integration is a technique used in Bayesian probability theory to compute the posterior probability for a model. As a reminder, if a set of m models is designated as M 2 f1; 2; : : : ; mg, then one can compute the posterior probability for the models by an application of Bayes' Theorem [1] P (MjDI) / P (MjI)P (DjMI) (C.1) where we have dropped a normalization constant, M = 1 means we are computing the posterior probability for model 1, M = 2 the probability for model 2, etc. The three terms in this equation, going from left to right, are the posterior probability for the model indicator given the data and the prior information, P (MjDI), the prior probability for the model given only the prior information, P (MjI), and the marginal direct probability for the data given the model and the prior information, P (DjMI). The marginal direct probability for the data given a model can be computed from the joint posterior probability for the data and the model parameters, which we will call Ω, given the Model and the prior information Z P (DjMI) = dΩP (ΩjMI)P (DjΩMI): (C.2) Unfortunately, the integrals on the right-hand side of this equation can be very high dimensional. Consequently, although we know exactly what calculation must be done to compute the marginal direct probability, in most applications the integrals are not tractable.