CHAPTER 2 Estimating Probabilities
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The Likelihood Principle
1 01/28/99 ãMarc Nerlove 1999 Chapter 1: The Likelihood Principle "What has now appeared is that the mathematical concept of probability is ... inadequate to express our mental confidence or diffidence in making ... inferences, and that the mathematical quantity which usually appears to be appropriate for measuring our order of preference among different possible populations does not in fact obey the laws of probability. To distinguish it from probability, I have used the term 'Likelihood' to designate this quantity; since both the words 'likelihood' and 'probability' are loosely used in common speech to cover both kinds of relationship." R. A. Fisher, Statistical Methods for Research Workers, 1925. "What we can find from a sample is the likelihood of any particular value of r [a parameter], if we define the likelihood as a quantity proportional to the probability that, from a particular population having that particular value of r, a sample having the observed value r [a statistic] should be obtained. So defined, probability and likelihood are quantities of an entirely different nature." R. A. Fisher, "On the 'Probable Error' of a Coefficient of Correlation Deduced from a Small Sample," Metron, 1:3-32, 1921. Introduction The likelihood principle as stated by Edwards (1972, p. 30) is that Within the framework of a statistical model, all the information which the data provide concerning the relative merits of two hypotheses is contained in the likelihood ratio of those hypotheses on the data. ...For a continuum of hypotheses, this principle -
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 -
Statistical Theory
Statistical Theory Prof. Gesine Reinert November 23, 2009 Aim: To review and extend the main ideas in Statistical Inference, both from a frequentist viewpoint and from a Bayesian viewpoint. This course serves not only as background to other courses, but also it will provide a basis for developing novel inference methods when faced with a new situation which includes uncertainty. Inference here includes estimating parameters and testing hypotheses. Overview • Part 1: Frequentist Statistics { Chapter 1: Likelihood, sufficiency and ancillarity. The Factoriza- tion Theorem. Exponential family models. { Chapter 2: Point estimation. When is an estimator a good estima- tor? Covering bias and variance, information, efficiency. Methods of estimation: Maximum likelihood estimation, nuisance parame- ters and profile likelihood; method of moments estimation. Bias and variance approximations via the delta method. { Chapter 3: Hypothesis testing. Pure significance tests, signifi- cance level. Simple hypotheses, Neyman-Pearson Lemma. Tests for composite hypotheses. Sample size calculation. Uniformly most powerful tests, Wald tests, score tests, generalised likelihood ratio tests. Multiple tests, combining independent tests. { Chapter 4: Interval estimation. Confidence sets and their con- nection with hypothesis tests. Approximate confidence intervals. Prediction sets. { Chapter 5: Asymptotic theory. Consistency. Asymptotic nor- mality of maximum likelihood estimates, score tests. Chi-square approximation for generalised likelihood ratio tests. Likelihood confidence regions. Pseudo-likelihood tests. • Part 2: Bayesian Statistics { Chapter 6: Background. Interpretations of probability; the Bayesian paradigm: prior distribution, posterior distribution, predictive distribution, credible intervals. Nuisance parameters are easy. 1 { Chapter 7: Bayesian models. Sufficiency, exchangeability. De Finetti's Theorem and its intepretation in Bayesian statistics. { Chapter 8: Prior distributions. Conjugate priors. -
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). -
On the Relation Between Frequency Inference and Likelihood
On the Relation between Frequency Inference and Likelihood Donald A. Pierce Radiation Effects Research Foundation 5-2 Hijiyama Park Hiroshima 732, Japan [email protected] 1. Introduction Modern higher-order asymptotic theory for frequency inference, as largely described in Barn- dorff-Nielsen & Cox (1994), is fundamentally likelihood-oriented. This has led to various indica- tions of more unity in frequency and Bayesian inferences than previously recognised, e.g. Sweeting (1987, 1992). A main distinction, the stronger dependence of frequency inference on the sample space—the outcomes not observed—is isolated in a single term of the asymptotic formula for P- values. We capitalise on that to consider from an asymptotic perspective the relation of frequency inferences to the likelihood principle, with results towards a quantification of that as follows. Whereas generally the conformance of frequency inference to the likelihood principle is only to first order, i.e. O(n–1/2), there is at least one major class of applications, likely more, where the confor- mance is to second order, i.e. O(n–1). There the issue is the effect of censoring mechanisms. On a more subtle point, it is often overlooked that there are few, if any, practical settings where exact frequency inferences exist broadly enough to allow precise comparison to the likelihood principle. To the extent that ideal frequency inference may only be defined to second order, there is some- times—perhaps usually—no conflict at all. The strong likelihood principle is that in even totally unrelated experiments, inferences from data yielding the same likelihood function should be the same (the weak one being essentially the sufficiency principle). -
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. -
1 the Likelihood Principle
ISyE8843A, Brani Vidakovic Handout 2 1 The Likelihood Principle Likelihood principle concerns foundations of statistical inference and it is often invoked in arguments about correct statistical reasoning. Let f(xjθ) be a conditional distribution for X given the unknown parameter θ. For the observed data, X = x, the function `(θ) = f(xjθ), considered as a function of θ, is called the likelihood function. The name likelihood implies that, given x, the value of θ is more likely to be the true parameter than θ0 if f(xjθ) > f(xjθ0): Likelihood Principle. In the inference about θ, after x is observed, all relevant experimental information is contained in the likelihood function for the observed x. Furthermore, two likelihood functions contain the same information about θ if they are proportional to each other. Remark. The maximum-likelihood estimation does satisfy the likelihood principle. Figure 1: Leonard Jimmie Savage; Born: November 20, 1917, Detroit, Michigan; Died: November 1, 1971, New Haven, Connecticut The following example quoted by Lindley and Phillips (1976) is an argument of Leonard Savage dis- cussed at Purdue Symposium 1962. It shows that the inference can critically depend on the likelihood principle. Example 1: Testing fairness. Suppose we are interested in testing θ, the unknown probability of heads for possibly biased coin. Suppose, H0 : θ = 1=2 v:s: H1 : θ > 1=2: 1 An experiment is conducted and 9 heads and 3 tails are observed. This information is not sufficient to fully specify the model f(xjθ): A rashomonian analysis follows: ² Scenario 1: Number of flips, n = 12 is predetermined. -
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, -
Model Selection by Normalized Maximum Likelihood
Myung, J. I., Navarro, D. J. and Pitt, M. A. (2006). Model selection by normalized maximum likelihood. Journal of Mathematical Psychology, 50, 167-179 http://dx.doi.org/10.1016/j.jmp.2005.06.008 Model selection by normalized maximum likelihood Jay I. Myunga;c, Danielle J. Navarrob and Mark A. Pitta aDepartment of Psychology Ohio State University bDepartment of Psychology University of Adelaide, Australia cCorresponding Author Abstract The Minimum Description Length (MDL) principle is an information theoretic approach to in- ductive inference that originated in algorithmic coding theory. In this approach, data are viewed as codes to be compressed by the model. From this perspective, models are compared on their ability to compress a data set by extracting useful information in the data apart from random noise. The goal of model selection is to identify the model, from a set of candidate models, that permits the shortest description length (code) of the data. Since Rissanen originally formalized the problem using the crude `two-part code' MDL method in the 1970s, many significant strides have been made, especially in the 1990s, with the culmination of the development of the refined `universal code' MDL method, dubbed Normalized Maximum Likelihood (NML). It represents an elegant solution to the model selection problem. The present paper provides a tutorial review on these latest developments with a special focus on NML. An application example of NML in cognitive modeling is also provided. Keywords: Minimum Description Length, Model Complexity, Inductive Inference, Cognitive Modeling. Preprint submitted to Journal of Mathematical Psychology 13 August 2019 To select among competing models of a psychological process, one must decide which criterion to use to evaluate the models, and then make the best inference as to which model is preferable. -
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. -
P Values, Hypothesis Testing, and Model Selection: It’S De´Ja` Vu All Over Again1
FORUM P values, hypothesis testing, and model selection: it’s de´ja` vu all over again1 It was six men of Indostan To learning much inclined, Who went to see the Elephant (Though all of them were blind), That each by observation Might satisfy his mind. ... And so these men of Indostan Disputed loud and long, Each in his own opinion Exceeding stiff and strong, Though each was partly in the right, And all were in the wrong! So, oft in theologic wars The disputants, I ween, Rail on in utter ignorance Of what each other mean, And prate about an Elephant Not one of them has seen! —From The Blind Men and the Elephant: A Hindoo Fable, by John Godfrey Saxe (1872) Even if you didn’t immediately skip over this page (or the entire Forum in this issue of Ecology), you may still be asking yourself, ‘‘Haven’t I seen this before? Do we really need another Forum on P values, hypothesis testing, and model selection?’’ So please bear with us; this elephant is still in the room. We thank Paul Murtaugh for the reminder and the invited commentators for their varying perspectives on the current shape of statistical testing and inference in ecology. Those of us who went through graduate school in the 1970s, 1980s, and 1990s remember attempting to coax another 0.001 out of SAS’s P ¼ 0.051 output (maybe if I just rounded to two decimal places ...), raising a toast to P ¼ 0.0499 (and the invention of floating point processors), or desperately searching the back pages of Sokal and Rohlf for a different test that would cross the finish line and satisfy our dissertation committee.