The Rule of Succession
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A History of Evidence in Medical Decisions: from the Diagnostic Sign to Bayesian Inference
BRIEF REPORTS A History of Evidence in Medical Decisions: From the Diagnostic Sign to Bayesian Inference Dennis J. Mazur, MD, PhD Bayesian inference in medical decision making is a concept through the development of probability theory based on con- that has a long history with 3 essential developments: 1) the siderations of games of chance, and ending with the work of recognition of the need for data (demonstrable scientific Jakob Bernoulli, Laplace, and others, we will examine how evidence), 2) the development of probability, and 3) the Bayesian inference developed. Key words: evidence; games development of inverse probability. Beginning with the of chance; history of evidence; inference; probability. (Med demonstrative evidence of the physician’s sign, continuing Decis Making 2012;32:227–231) here are many senses of the term evidence in the Hacking argues that when humans began to examine Thistory of medicine other than scientifically things pointing beyond themselves to other things, gathered (collected) evidence. Historically, evidence we are examining a new type of evidence to support was first based on testimony and opinion by those the truth or falsehood of a scientific proposition respected for medical expertise. independent of testimony or opinion. This form of evidence can also be used to challenge the data themselves in supporting the truth or falsehood of SIGN AS EVIDENCE IN MEDICINE a proposition. In this treatment of the evidence contained in the Ian Hacking singles out the physician’s sign as the 1 physician’s diagnostic sign, Hacking is examining first example of demonstrable scientific evidence. evidence as a phenomenon of the ‘‘low sciences’’ Once the physician’s sign was recognized as of the Renaissance, which included alchemy, astrol- a form of evidence, numbers could be attached to ogy, geology, and medicine.1 The low sciences were these signs. -
The Interpretation of Probability: Still an Open Issue? 1
philosophies Article The Interpretation of Probability: Still an Open Issue? 1 Maria Carla Galavotti Department of Philosophy and Communication, University of Bologna, Via Zamboni 38, 40126 Bologna, Italy; [email protected] Received: 19 July 2017; Accepted: 19 August 2017; Published: 29 August 2017 Abstract: Probability as understood today, namely as a quantitative notion expressible by means of a function ranging in the interval between 0–1, took shape in the mid-17th century, and presents both a mathematical and a philosophical aspect. Of these two sides, the second is by far the most controversial, and fuels a heated debate, still ongoing. After a short historical sketch of the birth and developments of probability, its major interpretations are outlined, by referring to the work of their most prominent representatives. The final section addresses the question of whether any of such interpretations can presently be considered predominant, which is answered in the negative. Keywords: probability; classical theory; frequentism; logicism; subjectivism; propensity 1. A Long Story Made Short Probability, taken as a quantitative notion whose value ranges in the interval between 0 and 1, emerged around the middle of the 17th century thanks to the work of two leading French mathematicians: Blaise Pascal and Pierre Fermat. According to a well-known anecdote: “a problem about games of chance proposed to an austere Jansenist by a man of the world was the origin of the calculus of probabilities”2. The ‘man of the world’ was the French gentleman Chevalier de Méré, a conspicuous figure at the court of Louis XIV, who asked Pascal—the ‘austere Jansenist’—the solution to some questions regarding gambling, such as how many dice tosses are needed to have a fair chance to obtain a double-six, or how the players should divide the stakes if a game is interrupted. -
Chapter 1: the Objective and the Subjective in Mid-Nineteenth-Century British Probability Theory
UvA-DARE (Digital Academic Repository) "A terrible piece of bad metaphysics"? Towards a history of abstraction in nineteenth- and early twentieth-century probability theory, mathematics and logic Verburgt, L.M. Publication date 2015 Document Version Final published version Link to publication Citation for published version (APA): Verburgt, L. M. (2015). "A terrible piece of bad metaphysics"? Towards a history of abstraction in nineteenth- and early twentieth-century probability theory, mathematics and logic. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:27 Sep 2021 chapter 1 The objective and the subjective in mid-nineteenth-century British probability theory 1. Introduction 1.1 The emergence of ‘objective’ and ‘subjective’ probability Approximately at the middle of the nineteenth century at least six authors – Simeon-Denis Poisson, Bernard Bolzano, Robert Leslie Ellis, Jakob Friedrich Fries, John Stuart Mill and A.A. -
Probabilities, Random Variables and Distributions A
Probabilities, Random Variables and Distributions A Contents A.1 EventsandProbabilities................................ 318 A.1.1 Conditional Probabilities and Independence . ............. 318 A.1.2 Bayes’Theorem............................... 319 A.2 Random Variables . ................................. 319 A.2.1 Discrete Random Variables ......................... 319 A.2.2 Continuous Random Variables ....................... 320 A.2.3 TheChangeofVariablesFormula...................... 321 A.2.4 MultivariateNormalDistributions..................... 323 A.3 Expectation,VarianceandCovariance........................ 324 A.3.1 Expectation................................. 324 A.3.2 Variance................................... 325 A.3.3 Moments................................... 325 A.3.4 Conditional Expectation and Variance ................... 325 A.3.5 Covariance.................................. 326 A.3.6 Correlation.................................. 327 A.3.7 Jensen’sInequality............................. 328 A.3.8 Kullback–LeiblerDiscrepancyandInformationInequality......... 329 A.4 Convergence of Random Variables . 329 A.4.1 Modes of Convergence . 329 A.4.2 Continuous Mapping and Slutsky’s Theorem . 330 A.4.3 LawofLargeNumbers........................... 330 A.4.4 CentralLimitTheorem........................... 331 A.4.5 DeltaMethod................................ 331 A.5 ProbabilityDistributions............................... 332 A.5.1 UnivariateDiscreteDistributions...................... 333 A.5.2 Univariate Continuous Distributions . 335 -
Introduction to Bayesian Inference and Modeling Edps 590BAY
Introduction to Bayesian Inference and Modeling Edps 590BAY Carolyn J. Anderson Department of Educational Psychology c Board of Trustees, University of Illinois Fall 2019 Introduction What Why Probability Steps Example History Practice Overview ◮ What is Bayes theorem ◮ Why Bayesian analysis ◮ What is probability? ◮ Basic Steps ◮ An little example ◮ History (not all of the 705+ people that influenced development of Bayesian approach) ◮ In class work with probabilities Depending on the book that you select for this course, read either Gelman et al. Chapter 1 or Kruschke Chapters 1 & 2. C.J. Anderson (Illinois) Introduction Fall 2019 2.2/ 29 Introduction What Why Probability Steps Example History Practice Main References for Course Throughout the coures, I will take material from ◮ Gelman, A., Carlin, J.B., Stern, H.S., Dunson, D.B., Vehtari, A., & Rubin, D.B. (20114). Bayesian Data Analysis, 3rd Edition. Boco Raton, FL, CRC/Taylor & Francis.** ◮ Hoff, P.D., (2009). A First Course in Bayesian Statistical Methods. NY: Sringer.** ◮ McElreath, R.M. (2016). Statistical Rethinking: A Bayesian Course with Examples in R and Stan. Boco Raton, FL, CRC/Taylor & Francis. ◮ Kruschke, J.K. (2015). Doing Bayesian Data Analysis: A Tutorial with JAGS and Stan. NY: Academic Press.** ** There are e-versions these of from the UofI library. There is a verson of McElreath, but I couldn’t get if from UofI e-collection. C.J. Anderson (Illinois) Introduction Fall 2019 3.3/ 29 Introduction What Why Probability Steps Example History Practice Bayes Theorem A whole semester on this? p(y|θ)p(θ) p(θ|y)= p(y) where ◮ y is data, sample from some population. -
Harold Jeffreys's Theory of Probability Revisited
Statistical Science 2009, Vol. 24, No. 2, 141–172 DOI: 10.1214/09-STS284 c Institute of Mathematical Statistics, 2009 Harold Jeffreys’s Theory of Probability Revisited Christian P. Robert, Nicolas Chopin and Judith Rousseau Abstract. Published exactly seventy years ago, Jeffreys’s Theory of Probability (1939) has had a unique impact on the Bayesian commu- nity and is now considered to be one of the main classics in Bayesian Statistics as well as the initiator of the objective Bayes school. In par- ticular, its advances on the derivation of noninformative priors as well as on the scaling of Bayes factors have had a lasting impact on the field. However, the book reflects the characteristics of the time, especially in terms of mathematical rigor. In this paper we point out the fundamen- tal aspects of this reference work, especially the thorough coverage of testing problems and the construction of both estimation and testing noninformative priors based on functional divergences. Our major aim here is to help modern readers in navigating in this difficult text and in concentrating on passages that are still relevant today. Key words and phrases: Bayesian foundations, noninformative prior, σ-finite measure, Jeffreys’s prior, Kullback divergence, tests, Bayes fac- tor, p-values, goodness of fit. 1. INTRODUCTION Christian P. Robert is Professor of Statistics, Applied Mathematics Department, Universit´eParis Dauphine The theory of probability makes it possible to and Head of the Statistics Laboratory, Center for respect the great men on whose shoulders we stand. Research in Economics and Statistics (CREST), H. Jeffreys, Theory of Probability, Section 1.6. -
Binomial and Multinomial Distributions
Binomial and multinomial distributions Kevin P. Murphy Last updated October 24, 2006 * Denotes more advanced sections 1 Introduction In this chapter, we study probability distributions that are suitable for modelling discrete data, like letters and words. This will be useful later when we consider such tasks as classifying and clustering documents, recognizing and segmenting languages and DNA sequences, data compression, etc. Formally, we will be concerned with density models for X ∈{1,...,K}, where K is the number of possible values for X; we can think of this as the number of symbols/ letters in our alphabet/ language. We assume that K is known, and that the values of X are unordered: this is called categorical data, as opposed to ordinal data, in which the discrete states can be ranked (e.g., low, medium and high). If K = 2 (e.g., X represents heads or tails), we will use a binomial distribution. If K > 2, we will use a multinomial distribution. 2 Bernoullis and Binomials Let X ∈{0, 1} be a binary random variable (e.g., a coin toss). Suppose p(X =1)= θ. Then − p(X|θ) = Be(X|θ)= θX (1 − θ)1 X (1) is called a Bernoulli distribution. It is easy to show that E[X] = p(X =1)= θ (2) Var [X] = θ(1 − θ) (3) The likelihood for a sequence D = (x1,...,xN ) of coin tosses is N − p(D|θ)= θxn (1 − θ)1 xn = θN1 (1 − θ)N0 (4) n=1 Y N N where N1 = n=1 xn is the number of heads (X = 1) and N0 = n=1(1 − xn)= N − N1 is the number of tails (X = 0). -
Arxiv:1808.10173V2 [Stat.AP] 30 Aug 2020
AN INTRODUCTION TO INDUCTIVE STATISTICAL INFERENCE FROM PARAMETER ESTIMATION TO DECISION-MAKING Lecture notes for a quantitative–methodological module at the Master degree (M.Sc.) level HENK VAN ELST August 30, 2020 parcIT GmbH Erftstraße 15 50672 Köln Germany ORCID iD: 0000-0003-3331-9547 E–Mail: [email protected] arXiv:1808.10173v2 [stat.AP] 30 Aug 2020 E–Print: arXiv:1808.10173v2 [stat.AP] © 2016–2020 Henk van Elst Dedicated to the good people at Karlshochschule Abstract These lecture notes aim at a post-Bachelor audience with a background at an introductory level in Applied Mathematics and Applied Statistics. They discuss the logic and methodology of the Bayes–Laplace ap- proach to inductive statistical inference that places common sense and the guiding lines of the scientific method at the heart of systematic analyses of quantitative–empirical data. Following an exposition of ex- actly solvable cases of single- and two-parameter estimation problems, the main focus is laid on Markov Chain Monte Carlo (MCMC) simulations on the basis of Hamiltonian Monte Carlo sampling of poste- rior joint probability distributions for regression parameters occurring in generalised linear models for a univariate outcome variable. The modelling of fixed effects as well as of correlated varying effects via multi-level models in non-centred parametrisation is considered. The simulation of posterior predictive distributions is outlined. The assessment of a model’s relative out-of-sample posterior predictive accuracy with information entropy-based criteria WAIC and LOOIC and model comparison with Bayes factors are addressed. Concluding, a conceptual link to the behavioural subjective expected utility representation of a single decision-maker’s choice behaviour in static one-shot decision problems is established. -
Estimation and Detection with Applications to Navigation
Linköping studies in science and technology. Dissertations. No. 1216 Estimation and Detection with Applications to Navigation David Törnqvist Department of Electrical Engineering Linköping University, SE–581 83 Linköping, Sweden Linköping 2008 Linköping studies in science and technology. Dissertations. No. 1216 Estimation and Detection with Applications to Navigation David Törnqvist [email protected] www.control.isy.liu.se Division of Automatic Control Department of Electrical Engineering Linköping University SE–581 83 Linköping Sweden ISBN 978-91-7393-785-6 ISSN 0345-7524 Copyright c 2008 David Törnqvist Parts of this thesis have been published previously. Paper A is published with permission from Springer Science and Business Media c 2008 Papers B and E are published with permission from IFAC c 2008. Paper C is published with permission from IEEE c 2008. Paper D is published with permission from EURASIP c 2007. Printed by LiU-Tryck, Linköping, Sweden 2008 To my family! Abstract The ability to navigate in an unknown environment is an enabler for truly autonomous systems. Such a system must be aware of its relative position to the surroundings using sensor measurements. It is instrumental that these measurements are monitored for distur- bances and faults. Having correct measurements, the challenging problem for a robot is to estimate its own position and simultaneously build a map of the environment. This prob- lem is referred to as the Simultaneous Localization and Mapping (SLAM) problem. This thesis studies several topics related to SLAM, on-board sensor processing, exploration and disturbance detection. The particle filter (PF) solution to the SLAM problem is commonly referred to as FastSLAM and has been used extensively for ground robot applications. -
On Non-Informativeness in a Classical Bayesian Inference Problem
On non-informativeness in a classical Bayesian inference problem Citation for published version (APA): Coolen, F. P. A. (1992). On non-informativeness in a classical Bayesian inference problem. (Memorandum COSOR; Vol. 9235). Technische Universiteit Eindhoven. Document status and date: Published: 01/01/1992 Document Version: Publisher’s PDF, also known as Version of Record (includes final page, issue and volume numbers) Please check the document version of this publication: • A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal. -
31 Aug 2021 What Is the Probability That a Vaccinated Person Is Shielded
What is the probability that a vaccinated person is shielded from Covid-19? A Bayesian MCMC based reanalysis of published data with emphasis on what should be reported as ‘efficacy’ Giulio D’Agostini1 and Alfredo Esposito2 Abstract Based on the information communicated in press releases, and finally pub- lished towards the end of 2020 by Pfizer, Moderna and AstraZeneca, we have built up a simple Bayesian model, in which the main quantity of interest plays the role of vaccine efficacy (‘ǫ’). The resulting Bayesian Network is processed by a Markov Chain Monte Carlo (MCMC), implemented in JAGS interfaced to R via rjags. As outcome, we get several probability density functions (pdf’s) of ǫ, each conditioned on the data provided by the three pharma companies. The result is rather stable against large variations of the number of people participating in the trials and it is ‘somehow’ in good agreement with the re- sults provided by the companies, in the sense that their values correspond to the most probable value (‘mode’) of the pdf’s resulting from MCMC, thus reassuring us about the validity of our simple model. However we maintain that the number to be reported as vaccine efficacy should be the mean of the distribution, rather than the mode, as it was already very clear to Laplace about 250 years ago (its ‘rule of succession’ follows from the simplest problem of the kind). This is particularly important in the case in which the number of successes equals the numbers of trials, as it happens with the efficacy against ‘severe forms’ of infection, claimed by Moderna to be 100%. -
Inverse Probability, Entropy
Copyright Cambridge University Press 2003. On-screen viewing permitted. Printing not permitted. http://www.cambridge.org/0521642981 You can buy this book for 30 pounds or $50. See http://www.inference.phy.cam.ac.uk/mackay/itila/ for links. 2.3: Forward probabilities and inverse probabilities 27 Bayesians also use probabilities to describe inferences. 2.3 Forward probabilities and inverse probabilities Probability calculations often fall into one of two categories: forward prob- ability and inverse probability. Here is an example of a forward probability problem: Exercise 2.4.[2, p.40] An urn contains K balls, of which B are black and W = K B are white. Fred draws a ball at random from the urn and replaces − it, N times. (a) What is the probability distribution of the number of times a black ball is drawn, nB? (b) What is the expectation of nB? What is the variance of nB? What is the standard deviation of nB? Give numerical answers for the cases N = 5 and N = 400, when B = 2 and K = 10. Forward probability problems involve a generative model that describes a pro- cess that is assumed to give rise to some data; the task is to compute the probability distribution or expectation of some quantity that depends on the data. Here is another example of a forward probability problem: Exercise 2.5.[2, p.40] An urn contains K balls, of which B are black and W = K B are white. We define the fraction f B/K. Fred draws N − B ≡ times from the urn, exactly as in exercise 2.4, obtaining nB blacks, and computes the quantity (n f N)2 z = B − B .