Probability Distributions
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Arcsine Laws for Random Walks Generated from Random Permutations with Applications to Genomics
Applied Probability Trust (4 February 2021) ARCSINE LAWS FOR RANDOM WALKS GENERATED FROM RANDOM PERMUTATIONS WITH APPLICATIONS TO GENOMICS XIAO FANG,1 The Chinese University of Hong Kong HAN LIANG GAN,2 Northwestern University SUSAN HOLMES,3 Stanford University HAIYAN HUANG,4 University of California, Berkeley EROL PEKOZ,¨ 5 Boston University ADRIAN ROLLIN,¨ 6 National University of Singapore WENPIN TANG,7 Columbia University 1 Email address: [email protected] 2 Email address: [email protected] 3 Email address: [email protected] 4 Email address: [email protected] 5 Email address: [email protected] 6 Email address: [email protected] 7 Email address: [email protected] 1 Postal address: Department of Statistics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 2 Postal address: Department of Mathematics, Northwestern University, 2033 Sheridan Road, Evanston, IL 60208 2 Current address: University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand 1 2 X. Fang et al. Abstract A classical result for the simple symmetric random walk with 2n steps is that the number of steps above the origin, the time of the last visit to the origin, and the time of the maximum height all have exactly the same distribution and converge when scaled to the arcsine law. Motivated by applications in genomics, we study the distributions of these statistics for the non-Markovian random walk generated from the ascents and descents of a uniform random permutation and a Mallows(q) permutation and show that they have the same asymptotic distributions as for the simple random walk. -
Package 'Distributional'
Package ‘distributional’ February 2, 2021 Title Vectorised Probability Distributions Version 0.2.2 Description Vectorised distribution objects with tools for manipulating, visualising, and using probability distributions. Designed to allow model prediction outputs to return distributions rather than their parameters, allowing users to directly interact with predictive distributions in a data-oriented workflow. In addition to providing generic replacements for p/d/q/r functions, other useful statistics can be computed including means, variances, intervals, and highest density regions. License GPL-3 Imports vctrs (>= 0.3.0), rlang (>= 0.4.5), generics, ellipsis, stats, numDeriv, ggplot2, scales, farver, digest, utils, lifecycle Suggests testthat (>= 2.1.0), covr, mvtnorm, actuar, ggdist RdMacros lifecycle URL https://pkg.mitchelloharawild.com/distributional/, https: //github.com/mitchelloharawild/distributional BugReports https://github.com/mitchelloharawild/distributional/issues Encoding UTF-8 Language en-GB LazyData true Roxygen list(markdown = TRUE, roclets=c('rd', 'collate', 'namespace')) RoxygenNote 7.1.1 1 2 R topics documented: R topics documented: autoplot.distribution . .3 cdf..............................................4 density.distribution . .4 dist_bernoulli . .5 dist_beta . .6 dist_binomial . .7 dist_burr . .8 dist_cauchy . .9 dist_chisq . 10 dist_degenerate . 11 dist_exponential . 12 dist_f . 13 dist_gamma . 14 dist_geometric . 16 dist_gumbel . 17 dist_hypergeometric . 18 dist_inflated . 20 dist_inverse_exponential . 20 dist_inverse_gamma -
Free Infinite Divisibility and Free Multiplicative Mixtures of the Wigner Distribution
FREE INFINITE DIVISIBILITY AND FREE MULTIPLICATIVE MIXTURES OF THE WIGNER DISTRIBUTION Victor Pérez-Abreu and Noriyoshi Sakuma Comunicación del CIMAT No I-09-0715/ -10-2009 ( PE/CIMAT) Free Infinite Divisibility of Free Multiplicative Mixtures of the Wigner Distribution Victor P´erez-Abreu∗ Department of Probability and Statistics, CIMAT Apdo. Postal 402, Guanajuato Gto. 36000, Mexico [email protected] Noriyoshi Sakumay Department of Mathematics, Keio University, 3-14-1, Hiyoshi, Yokohama 223-8522, Japan. [email protected] March 19, 2010 Abstract Let I∗ and I be the classes of all classical infinitely divisible distributions and free infinitely divisible distributions, respectively, and let Λ be the Bercovici-Pata bijection between I∗ and I: The class type W of symmetric distributions in I that can be represented as free multiplicative convolutions of the Wigner distribution is studied. A characterization of this class under the condition that the mixing distribution is 2-divisible with respect to free multiplicative convolution is given. A correspondence between sym- metric distributions in I and the free counterpart under Λ of the positive distributions in I∗ is established. It is shown that the class type W does not include all symmetric distributions in I and that it does not coincide with the image under Λ of the mixtures of the Gaussian distribution in I∗. Similar results for free multiplicative convolutions with the symmetric arcsine measure are obtained. Several well-known and new concrete examples are presented. AMS 2000 Subject Classification: 46L54, 15A52. Keywords: Free convolutions, type G law, free stable law, free compound distribution, Bercovici-Pata bijection. -
Location-Scale Distributions
Location–Scale Distributions Linear Estimation and Probability Plotting Using MATLAB Horst Rinne Copyright: Prof. em. Dr. Horst Rinne Department of Economics and Management Science Justus–Liebig–University, Giessen, Germany Contents Preface VII List of Figures IX List of Tables XII 1 The family of location–scale distributions 1 1.1 Properties of location–scale distributions . 1 1.2 Genuine location–scale distributions — A short listing . 5 1.3 Distributions transformable to location–scale type . 11 2 Order statistics 18 2.1 Distributional concepts . 18 2.2 Moments of order statistics . 21 2.2.1 Definitions and basic formulas . 21 2.2.2 Identities, recurrence relations and approximations . 26 2.3 Functions of order statistics . 32 3 Statistical graphics 36 3.1 Some historical remarks . 36 3.2 The role of graphical methods in statistics . 38 3.2.1 Graphical versus numerical techniques . 38 3.2.2 Manipulation with graphs and graphical perception . 39 3.2.3 Graphical displays in statistics . 41 3.3 Distribution assessment by graphs . 43 3.3.1 PP–plots and QQ–plots . 43 3.3.2 Probability paper and plotting positions . 47 3.3.3 Hazard plot . 54 3.3.4 TTT–plot . 56 4 Linear estimation — Theory and methods 59 4.1 Types of sampling data . 59 IV Contents 4.2 Estimators based on moments of order statistics . 63 4.2.1 GLS estimators . 64 4.2.1.1 GLS for a general location–scale distribution . 65 4.2.1.2 GLS for a symmetric location–scale distribution . 71 4.2.1.3 GLS and censored samples . -
Fisher Information Matrix for Gaussian and Categorical Distributions
Fisher information matrix for Gaussian and categorical distributions Jakub M. Tomczak November 28, 2012 1 Notations Let x be a random variable. Consider a parametric distribution of x with parameters θ, p(xjθ). The contiuous random variable x 2 R can be modelled by normal distribution (Gaussian distribution): 1 n (x − µ)2 o p(xjθ) = p exp − 2πσ2 2σ2 = N (xjµ, σ2); (1) where θ = µ σ2T. A discrete (categorical) variable x 2 X , X is a finite set of K values, can be modelled by categorical distribution:1 K Y xk p(xjθ) = θk k=1 = Cat(xjθ); (2) P where 0 ≤ θk ≤ 1, k θk = 1. For X = f0; 1g we get a special case of the categorical distribution, Bernoulli distribution, p(xjθ) = θx(1 − θ)1−x = Bern(xjθ): (3) 2 Fisher information matrix 2.1 Definition The Fisher score is determined as follows [1]: g(θ; x) = rθ ln p(xjθ): (4) The Fisher information matrix is defined as follows [1]: T F = Ex g(θ; x) g(θ; x) : (5) 1We use the 1-of-K encoding [1]. 1 2.2 Example 1: Bernoulli distribution Let us calculate the fisher matrix for Bernoulli distribution (3). First, we need to take the logarithm: ln Bern(xjθ) = x ln θ + (1 − x) ln(1 − θ): (6) Second, we need to calculate the derivative: d x 1 − x ln Bern(xjθ) = − dθ θ 1 − θ x − θ = : (7) θ(1 − θ) Hence, we get the following Fisher score for the Bernoulli distribution: x − θ g(θ; x) = : (8) θ(1 − θ) The Fisher information matrix (here it is a scalar) for the Bernoulli distribution is as follows: F = Ex[g(θ; x) g(θ; x)] h (x − θ)2 i = Ex (θ(1 − θ))2 1 n o = [x2 − 2xθ + θ2] (θ(1 − θ))2 Ex 1 n o = [x2] − 2θ [x] + θ2 (θ(1 − θ))2 Ex Ex 1 n o = θ − 2θ2 + θ2 (θ(1 − θ))2 1 = θ(1 − θ) (θ(1 − θ))2 1 = : (9) θ(1 − θ) 2.3 Example 2: Categorical distribution Let us calculate the fisher matrix for categorical distribution (2). -
Categorical Distributions in Natural Language Processing Version 0.1
Categorical Distributions in Natural Language Processing Version 0.1 MURAWAKI Yugo 12 May 2016 MURAWAKI Yugo Categorical Distributions in NLP 1 / 34 Categorical distribution Suppose random variable x takes one of K values. x is generated according to categorical distribution Cat(θ), where θ = (0:1; 0:6; 0:3): RYG In many task settings, we do not know the true θ and need to infer it from observed data x = (x1; ··· ; xN). Once we infer θ, we often want to predict new variable x0. NOTE: In Bayesian settings, θ is usually integrated out and x0 is predicted directly from x. MURAWAKI Yugo Categorical Distributions in NLP 2 / 34 Categorical distributions are a building block of natural language models N-gram language model (predicting the next word) POS tagging based on a Hidden Markov Model (HMM) Probabilistic context-free grammar (PCFG) Topic model (Latent Dirichlet Allocation (LDA)) MURAWAKI Yugo Categorical Distributions in NLP 3 / 34 Example: HMM-based POS tagging BOS DT NN VBZ VBN EOS the sun has risen Let K be the number of POS tags and V be the vocabulary size (ignore BOS and EOS for simplicity). The transition probabilities can be computed using K categorical θTRANS; θTRANS; ··· distributions ( DT NN ), with the dimension K. θTRANS = : ; : ; : ; ··· DT (0 21 0 27 0 09 ) NN NNS ADJ Similarly, the emission probabilities can be computed using K θEMIT; θEMIT; ··· categorical distributions ( DT NN ), with the dimension V. θEMIT = : ; : ; : ; ··· NN (0 012 0 002 0 005 ) sun rose cat MURAWAKI Yugo Categorical Distributions in NLP 4 / 34 Outline Categorical and multinomial distributions Conjugacy and posterior predictive distribution LDA (Latent Dirichlet Applocation) as an application Gibbs sampling for inference MURAWAKI Yugo Categorical Distributions in NLP 5 / 34 Categorical distribution: 1 observation Suppose θ is known. -
Handbook on Probability Distributions
R powered R-forge project Handbook on probability distributions R-forge distributions Core Team University Year 2009-2010 LATEXpowered Mac OS' TeXShop edited Contents Introduction 4 I Discrete distributions 6 1 Classic discrete distribution 7 2 Not so-common discrete distribution 27 II Continuous distributions 34 3 Finite support distribution 35 4 The Gaussian family 47 5 Exponential distribution and its extensions 56 6 Chi-squared's ditribution and related extensions 75 7 Student and related distributions 84 8 Pareto family 88 9 Logistic distribution and related extensions 108 10 Extrem Value Theory distributions 111 3 4 CONTENTS III Multivariate and generalized distributions 116 11 Generalization of common distributions 117 12 Multivariate distributions 133 13 Misc 135 Conclusion 137 Bibliography 137 A Mathematical tools 141 Introduction This guide is intended to provide a quite exhaustive (at least as I can) view on probability distri- butions. It is constructed in chapters of distribution family with a section for each distribution. Each section focuses on the tryptic: definition - estimation - application. Ultimate bibles for probability distributions are Wimmer & Altmann (1999) which lists 750 univariate discrete distributions and Johnson et al. (1994) which details continuous distributions. In the appendix, we recall the basics of probability distributions as well as \common" mathe- matical functions, cf. section A.2. And for all distribution, we use the following notations • X a random variable following a given distribution, • x a realization of this random variable, • f the density function (if it exists), • F the (cumulative) distribution function, • P (X = k) the mass probability function in k, • M the moment generating function (if it exists), • G the probability generating function (if it exists), • φ the characteristic function (if it exists), Finally all graphics are done the open source statistical software R and its numerous packages available on the Comprehensive R Archive Network (CRAN∗). -
Field Guide to Continuous Probability Distributions
Field Guide to Continuous Probability Distributions Gavin E. Crooks v 1.0.0 2019 G. E. Crooks – Field Guide to Probability Distributions v 1.0.0 Copyright © 2010-2019 Gavin E. Crooks ISBN: 978-1-7339381-0-5 http://threeplusone.com/fieldguide Berkeley Institute for Theoretical Sciences (BITS) typeset on 2019-04-10 with XeTeX version 0.99999 fonts: Trump Mediaeval (text), Euler (math) 271828182845904 2 G. E. Crooks – Field Guide to Probability Distributions Preface: The search for GUD A common problem is that of describing the probability distribution of a single, continuous variable. A few distributions, such as the normal and exponential, were discovered in the 1800’s or earlier. But about a century ago the great statistician, Karl Pearson, realized that the known probabil- ity distributions were not sufficient to handle all of the phenomena then under investigation, and set out to create new distributions with useful properties. During the 20th century this process continued with abandon and a vast menagerie of distinct mathematical forms were discovered and invented, investigated, analyzed, rediscovered and renamed, all for the purpose of de- scribing the probability of some interesting variable. There are hundreds of named distributions and synonyms in current usage. The apparent diver- sity is unending and disorienting. Fortunately, the situation is less confused than it might at first appear. Most common, continuous, univariate, unimodal distributions can be orga- nized into a small number of distinct families, which are all special cases of a single Grand Unified Distribution. This compendium details these hun- dred or so simple distributions, their properties and their interrelations. -
Arcsine Laws for Random Walks Generated from Random
ARCSINE LAWS FOR RANDOM WALKS GENERATED FROM RANDOM PERMUTATIONS WITH APPLICATIONS TO GENOMICS XIAO FANG, HAN LIANG GAN, SUSAN HOLMES, HAIYAN HUANG, EROL PEKOZ,¨ ADRIAN ROLLIN,¨ AND WENPIN TANG Abstract. A classical result for the simple symmetric random walk with 2n steps is that the number of steps above the origin, the time of the last visit to the origin, and the time of the maximum height all have exactly the same distribution and converge when scaled to the arcsine law. Motivated by applications in genomics, we study the distributions of these statistics for the non-Markovian random walk generated from the ascents and descents of a uniform random permutation and a Mallows(q) permutation and show that they have the same asymptotic distributions as for the simple random walk. We also give an unexpected conjecture, along with numerical evidence and a partial proof in special cases, for the result that the number of steps above the origin by step 2n for the uniform permutation generated walk has exactly the same discrete arcsine distribution as for the simple random walk, even though the other statistics for these walks have very different laws. We also give explicit error bounds to the limit theorems using Stein’s method for the arcsine distribution, as well as functional central limit theorems and a strong embedding of the Mallows(q) permutation which is of independent interest. Key words : Arcsine distribution, Brownian motion, L´evy statistics, limiting distribu- tion, Mallows permutation, random walks, Stein’s method, strong embedding, uniform permutation. AMS 2010 Mathematics Subject Classification: 60C05, 60J65, 05A05. -
Package 'Extradistr'
Package ‘extraDistr’ September 7, 2020 Type Package Title Additional Univariate and Multivariate Distributions Version 1.9.1 Date 2020-08-20 Author Tymoteusz Wolodzko Maintainer Tymoteusz Wolodzko <[email protected]> Description Density, distribution function, quantile function and random generation for a number of univariate and multivariate distributions. This package implements the following distributions: Bernoulli, beta-binomial, beta-negative binomial, beta prime, Bhattacharjee, Birnbaum-Saunders, bivariate normal, bivariate Poisson, categorical, Dirichlet, Dirichlet-multinomial, discrete gamma, discrete Laplace, discrete normal, discrete uniform, discrete Weibull, Frechet, gamma-Poisson, generalized extreme value, Gompertz, generalized Pareto, Gumbel, half-Cauchy, half-normal, half-t, Huber density, inverse chi-squared, inverse-gamma, Kumaraswamy, Laplace, location-scale t, logarithmic, Lomax, multivariate hypergeometric, multinomial, negative hypergeometric, non-standard beta, normal mixture, Poisson mixture, Pareto, power, reparametrized beta, Rayleigh, shifted Gompertz, Skellam, slash, triangular, truncated binomial, truncated normal, truncated Poisson, Tukey lambda, Wald, zero-inflated binomial, zero-inflated negative binomial, zero-inflated Poisson. License GPL-2 URL https://github.com/twolodzko/extraDistr BugReports https://github.com/twolodzko/extraDistr/issues Encoding UTF-8 LazyData TRUE Depends R (>= 3.1.0) LinkingTo Rcpp 1 2 R topics documented: Imports Rcpp Suggests testthat, LaplacesDemon, VGAM, evd, hoa, -
Chapter 9. Exponential Family of Distributions
Machine Learning for Engineers: Chapter 9. Exponential Family of Distributions Osvaldo Simeone King's College London January 26, 2021 Osvaldo Simeone ML4Engineers 1 / 97 This Chapter In the previous chapters, we have adopted a limited range of probabilistic models, namely Bernoulli and categorical for discrete rvs and Gaussian for continuous rvs. While these are the most common modelling choices, they clearly do not represent many important situations. Examples: I Discrete data may a priori take arbitrarily large values, making Bernoulli and categorical models not suitable F ex.: waiting times for next arrival in a queue; I Continuous data may be non-negative, making Gaussian models not suitable F ex.: measurements of weights or heights. Osvaldo Simeone ML4Engineers 2 / 97 This Chapter Furthermore, we have seen that Bernoulli, categorical, and Gaussian distributions share several common features: I The gradient of the log-loss with respect to the model parameters can be expressed in terms of a mean error that measures the difference between mean under the model and observation (see Chapters 4 and 6); I ML learning can be solved in closed form by evaluating empirical averages (see Chapters 3, 4, and 6); I Information-theoretic quantities such as (differential) entropy and KL divergence can be computed in closed form (see Chapter 3). Osvaldo Simeone ML4Engineers 3 / 97 This Chapter In this chapter, we will introduce a general family of distributions that includes Bernoulli, categorical, and Gaussian as special cases: the exponential family of distributions. The family is much larger, and it also encompasses distributions such as I Poisson and geometric distributions, whose support is discrete and includes all integers; I exponential and gamma distributions, whose support is continuous and includes only non-negative values. -
Discrete Categorical Distribution
Discrete Categorical Distribution Carl Edward Rasmussen November 11th, 2016 Carl Edward Rasmussen Discrete Categorical Distribution November 11th, 2016 1 / 8 Key concepts We generalize the concepts from binary variables to multiple discrete outcomes. • discrete and multinomial distributions • the Dirichlet distribution Carl Edward Rasmussen Discrete Categorical Distribution November 11th, 2016 2 / 8 The multinomial distribution (1) Generalisation of the binomial distribution from 2 outcomes to m outcomes. Useful for random variables that take one of a finite set of possible outcomes. Throw a die n = 60 times, and count the observed (6 possible) outcomes. Outcome Count X = x1 = 1 k1 = 12 X = x2 = 2 k2 = 7 Note that we have one parameter too many. We X = x3 = 3 k3 = 11 don’t need to know all the ki and n, because 6 X = x4 = 4 k4 = 8 i=1 ki = n. X = x5 = 5 k5 = 9 P X = x6 = 6 k6 = 13 Carl Edward Rasmussen Discrete Categorical Distribution November 11th, 2016 3 / 8 The multinomial distribution (2) Consider a discrete random variable X that can take one of m values x1,..., xm. Out of n independent trials, let ki be the number of times X = xi was observed. m It follows that i=1 ki = n. m Denote by πi the probability that X = xi, with i=1 πi = 1. P > The probability of observing a vector of occurrences k = [k1,..., km] is given by P > the multinomial distribution parametrised by π = [π1,..., πm] : n! ki p(kjπ, n) = p(k1,..., kmjπ1,..., πm, n) = πi k !k !... km! 1 2 i= Y1 • Note that we can write p(kjπ) since n is redundant.