Generalized Linear Models
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Generalized Linear Models and Generalized Additive Models
00:34 Friday 27th February, 2015 Copyright ©Cosma Rohilla Shalizi; do not distribute without permission updates at http://www.stat.cmu.edu/~cshalizi/ADAfaEPoV/ Chapter 13 Generalized Linear Models and Generalized Additive Models [[TODO: Merge GLM/GAM and Logistic Regression chap- 13.1 Generalized Linear Models and Iterative Least Squares ters]] [[ATTN: Keep as separate Logistic regression is a particular instance of a broader kind of model, called a gener- chapter, or merge with logis- alized linear model (GLM). You are familiar, of course, from your regression class tic?]] with the idea of transforming the response variable, what we’ve been calling Y , and then predicting the transformed variable from X . This was not what we did in logis- tic regression. Rather, we transformed the conditional expected value, and made that a linear function of X . This seems odd, because it is odd, but it turns out to be useful. Let’s be specific. Our usual focus in regression modeling has been the condi- tional expectation function, r (x)=E[Y X = x]. In plain linear regression, we try | to approximate r (x) by β0 + x β. In logistic regression, r (x)=E[Y X = x] = · | Pr(Y = 1 X = x), and it is a transformation of r (x) which is linear. The usual nota- tion says | ⌘(x)=β0 + x β (13.1) · r (x) ⌘(x)=log (13.2) 1 r (x) − = g(r (x)) (13.3) defining the logistic link function by g(m)=log m/(1 m). The function ⌘(x) is called the linear predictor. − Now, the first impulse for estimating this model would be to apply the transfor- mation g to the response. -
A Generalized Linear Model for Principal Component Analysis of Binary Data
A Generalized Linear Model for Principal Component Analysis of Binary Data Andrew I. Schein Lawrence K. Saul Lyle H. Ungar Department of Computer and Information Science University of Pennsylvania Moore School Building 200 South 33rd Street Philadelphia, PA 19104-6389 {ais,lsaul,ungar}@cis.upenn.edu Abstract they are not generally appropriate for other data types. Recently, Collins et al.[5] derived generalized criteria We investigate a generalized linear model for for dimensionality reduction by appealing to proper- dimensionality reduction of binary data. The ties of distributions in the exponential family. In their model is related to principal component anal- framework, the conventional PCA of real-valued data ysis (PCA) in the same way that logistic re- emerges naturally from assuming a Gaussian distribu- gression is related to linear regression. Thus tion over a set of observations, while generalized ver- we refer to the model as logistic PCA. In this sions of PCA for binary and nonnegative data emerge paper, we derive an alternating least squares respectively by substituting the Bernoulli and Pois- method to estimate the basis vectors and gen- son distributions for the Gaussian. For binary data, eralized linear coefficients of the logistic PCA the generalized model's relationship to PCA is anal- model. The resulting updates have a simple ogous to the relationship between logistic and linear closed form and are guaranteed at each iter- regression[12]. In particular, the model exploits the ation to improve the model's likelihood. We log-odds as the natural parameter of the Bernoulli dis- evaluate the performance of logistic PCA|as tribution and the logistic function as its canonical link. -
Generalized Linear Models (Glms)
San Jos´eState University Math 261A: Regression Theory & Methods Generalized Linear Models (GLMs) Dr. Guangliang Chen This lecture is based on the following textbook sections: • Chapter 13: 13.1 – 13.3 Outline of this presentation: • What is a GLM? • Logistic regression • Poisson regression Generalized Linear Models (GLMs) What is a GLM? In ordinary linear regression, we assume that the response is a linear function of the regressors plus Gaussian noise: 0 2 y = β0 + β1x1 + ··· + βkxk + ∼ N(x β, σ ) | {z } |{z} linear form x0β N(0,σ2) noise The model can be reformulate in terms of • distribution of the response: y | x ∼ N(µ, σ2), and • dependence of the mean on the predictors: µ = E(y | x) = x0β Dr. Guangliang Chen | Mathematics & Statistics, San Jos´e State University3/24 Generalized Linear Models (GLMs) beta=(1,2) 5 4 3 β0 + β1x b y 2 y 1 0 −1 0.0 0.2 0.4 0.6 0.8 1.0 x x Dr. Guangliang Chen | Mathematics & Statistics, San Jos´e State University4/24 Generalized Linear Models (GLMs) Generalized linear models (GLM) extend linear regression by allowing the response variable to have • a general distribution (with mean µ = E(y | x)) and • a mean that depends on the predictors through a link function g: That is, g(µ) = β0x or equivalently, µ = g−1(β0x) Dr. Guangliang Chen | Mathematics & Statistics, San Jos´e State University5/24 Generalized Linear Models (GLMs) In GLM, the response is typically assumed to have a distribution in the exponential family, which is a large class of probability distributions that have pdfs of the form f(x | θ) = a(x)b(θ) exp(c(θ) · T (x)), including • Normal - ordinary linear regression • Bernoulli - Logistic regression, modeling binary data • Binomial - Multinomial logistic regression, modeling general cate- gorical data • Poisson - Poisson regression, modeling count data • Exponential, Gamma - survival analysis Dr. -
Bayesian Inference Chapter 4: Regression and Hierarchical Models
Bayesian Inference Chapter 4: Regression and Hierarchical Models Conchi Aus´ınand Mike Wiper Department of Statistics Universidad Carlos III de Madrid Master in Business Administration and Quantitative Methods Master in Mathematical Engineering Conchi Aus´ınand Mike Wiper Regression and hierarchical models Masters Programmes 1 / 35 Objective AFM Smith Dennis Lindley We analyze the Bayesian approach to fitting normal and generalized linear models and introduce the Bayesian hierarchical modeling approach. Also, we study the modeling and forecasting of time series. Conchi Aus´ınand Mike Wiper Regression and hierarchical models Masters Programmes 2 / 35 Contents 1 Normal linear models 1.1. ANOVA model 1.2. Simple linear regression model 2 Generalized linear models 3 Hierarchical models 4 Dynamic models Conchi Aus´ınand Mike Wiper Regression and hierarchical models Masters Programmes 3 / 35 Normal linear models A normal linear model is of the following form: y = Xθ + ; 0 where y = (y1;:::; yn) is the observed data, X is a known n × k matrix, called 0 the design matrix, θ = (θ1; : : : ; θk ) is the parameter set and follows a multivariate normal distribution. Usually, it is assumed that: 1 ∼ N 0 ; I : k φ k A simple example of normal linear model is the simple linear regression model T 1 1 ::: 1 where X = and θ = (α; β)T . x1 x2 ::: xn Conchi Aus´ınand Mike Wiper Regression and hierarchical models Masters Programmes 4 / 35 Normal linear models Consider a normal linear model, y = Xθ + . A conjugate prior distribution is a normal-gamma distribution: -
Stochastic Process - Introduction
Stochastic Process - Introduction • Stochastic processes are processes that proceed randomly in time. • Rather than consider fixed random variables X, Y, etc. or even sequences of i.i.d random variables, we consider sequences X0, X1, X2, …. Where Xt represent some random quantity at time t. • In general, the value Xt might depend on the quantity Xt-1 at time t-1, or even the value Xs for other times s < t. • Example: simple random walk . week 2 1 Stochastic Process - Definition • A stochastic process is a family of time indexed random variables Xt where t belongs to an index set. Formal notation, { t : ∈ ItX } where I is an index set that is a subset of R. • Examples of index sets: 1) I = (-∞, ∞) or I = [0, ∞]. In this case Xt is a continuous time stochastic process. 2) I = {0, ±1, ±2, ….} or I = {0, 1, 2, …}. In this case Xt is a discrete time stochastic process. • We use uppercase letter {Xt } to describe the process. A time series, {xt } is a realization or sample function from a certain process. • We use information from a time series to estimate parameters and properties of process {Xt }. week 2 2 Probability Distribution of a Process • For any stochastic process with index set I, its probability distribution function is uniquely determined by its finite dimensional distributions. •The k dimensional distribution function of a process is defined by FXX x,..., ( 1 x,..., k ) = P( Xt ≤ 1 ,..., xt≤ X k) x t1 tk 1 k for anyt 1 ,..., t k ∈ I and any real numbers x1, …, xk . -
Variance Function Regressions for Studying Inequality
Variance Function Regressions for Studying Inequality The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Western, Bruce and Deirdre Bloome. 2009. Variance function regressions for studying inequality. Working paper, Department of Sociology, Harvard University. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:2645469 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#OAP Variance Function Regressions for Studying Inequality Bruce Western1 Deirdre Bloome Harvard University January 2009 1Department of Sociology, 33 Kirkland Street, Cambridge MA 02138. E-mail: [email protected]. This research was supported by a grant from the Russell Sage Foundation. Abstract Regression-based studies of inequality model only between-group differ- ences, yet often these differences are far exceeded by residual inequality. Residual inequality is usually attributed to measurement error or the in- fluence of unobserved characteristics. We present a regression that in- cludes covariates for both the mean and variance of a dependent variable. In this model, the residual variance is treated as a target for analysis. In analyses of inequality, the residual variance might be interpreted as mea- suring risk or insecurity. Variance function regressions are illustrated in an analysis of panel data on earnings among released prisoners in the Na- tional Longitudinal Survey of Youth. We extend the model to a decomposi- tion analysis, relating the change in inequality to compositional changes in the population and changes in coefficients for the mean and variance. -
Flexible Signal Denoising Via Flexible Empirical Bayes Shrinkage
Journal of Machine Learning Research 22 (2021) 1-28 Submitted 1/19; Revised 9/20; Published 5/21 Flexible Signal Denoising via Flexible Empirical Bayes Shrinkage Zhengrong Xing [email protected] Department of Statistics University of Chicago Chicago, IL 60637, USA Peter Carbonetto [email protected] Research Computing Center and Department of Human Genetics University of Chicago Chicago, IL 60637, USA Matthew Stephens [email protected] Department of Statistics and Department of Human Genetics University of Chicago Chicago, IL 60637, USA Editor: Edo Airoldi Abstract Signal denoising—also known as non-parametric regression—is often performed through shrinkage estima- tion in a transformed (e.g., wavelet) domain; shrinkage in the transformed domain corresponds to smoothing in the original domain. A key question in such applications is how much to shrink, or, equivalently, how much to smooth. Empirical Bayes shrinkage methods provide an attractive solution to this problem; they use the data to estimate a distribution of underlying “effects,” hence automatically select an appropriate amount of shrinkage. However, most existing implementations of empirical Bayes shrinkage are less flexible than they could be—both in their assumptions on the underlying distribution of effects, and in their ability to han- dle heteroskedasticity—which limits their signal denoising applications. Here we address this by adopting a particularly flexible, stable and computationally convenient empirical Bayes shrinkage method and apply- ing it to several signal denoising problems. These applications include smoothing of Poisson data and het- eroskedastic Gaussian data. We show through empirical comparisons that the results are competitive with other methods, including both simple thresholding rules and purpose-built empirical Bayes procedures. -
Linear, Ridge Regression, and Principal Component Analysis
Linear, Ridge Regression, and Principal Component Analysis Linear, Ridge Regression, and Principal Component Analysis Jia Li Department of Statistics The Pennsylvania State University Email: [email protected] http://www.stat.psu.edu/∼jiali Jia Li http://www.stat.psu.edu/∼jiali Linear, Ridge Regression, and Principal Component Analysis Introduction to Regression I Input vector: X = (X1, X2, ..., Xp). I Output Y is real-valued. I Predict Y from X by f (X ) so that the expected loss function E(L(Y , f (X ))) is minimized. I Square loss: L(Y , f (X )) = (Y − f (X ))2 . I The optimal predictor ∗ 2 f (X ) = argminf (X )E(Y − f (X )) = E(Y | X ) . I The function E(Y | X ) is the regression function. Jia Li http://www.stat.psu.edu/∼jiali Linear, Ridge Regression, and Principal Component Analysis Example The number of active physicians in a Standard Metropolitan Statistical Area (SMSA), denoted by Y , is expected to be related to total population (X1, measured in thousands), land area (X2, measured in square miles), and total personal income (X3, measured in millions of dollars). Data are collected for 141 SMSAs, as shown in the following table. i : 1 2 3 ... 139 140 141 X1 9387 7031 7017 ... 233 232 231 X2 1348 4069 3719 ... 1011 813 654 X3 72100 52737 54542 ... 1337 1589 1148 Y 25627 15389 13326 ... 264 371 140 Goal: Predict Y from X1, X2, and X3. Jia Li http://www.stat.psu.edu/∼jiali Linear, Ridge Regression, and Principal Component Analysis Linear Methods I The linear regression model p X f (X ) = β0 + Xj βj . -
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. -
Generalized Linear Models
Generalized Linear Models A generalized linear model (GLM) consists of three parts. i) The first part is a random variable giving the conditional distribution of a response Yi given the values of a set of covariates Xij. In the original work on GLM’sby Nelder and Wedderburn (1972) this random variable was a member of an exponential family, but later work has extended beyond this class of random variables. ii) The second part is a linear predictor, i = + 1Xi1 + 2Xi2 + + ··· kXik . iii) The third part is a smooth and invertible link function g(.) which transforms the expected value of the response variable, i = E(Yi) , and is equal to the linear predictor: g(i) = i = + 1Xi1 + 2Xi2 + + kXik. ··· As shown in Tables 15.1 and 15.2, both the general linear model that we have studied extensively and the logistic regression model from Chapter 14 are special cases of this model. One property of members of the exponential family of distributions is that the conditional variance of the response is a function of its mean, (), and possibly a dispersion parameter . The expressions for the variance functions for common members of the exponential family are shown in Table 15.2. Also, for each distribution there is a so-called canonical link function, which simplifies some of the GLM calculations, which is also shown in Table 15.2. Estimation and Testing for GLMs Parameter estimation in GLMs is conducted by the method of maximum likelihood. As with logistic regression models from the last chapter, the generalization of the residual sums of squares from the general linear model is the residual deviance, Dm 2(log Ls log Lm), where Lm is the maximized likelihood for the model of interest, and Ls is the maximized likelihood for a saturated model, which has one parameter per observation and fits the data as well as possible. -
Variance Function Estimation in Multivariate Nonparametric Regression by T
Variance Function Estimation in Multivariate Nonparametric Regression by T. Tony Cai, Lie Wang University of Pennsylvania Michael Levine Purdue University Technical Report #06-09 Department of Statistics Purdue University West Lafayette, IN USA October 2006 Variance Function Estimation in Multivariate Nonparametric Regression T. Tony Cail, Michael Levine* Lie Wangl October 3, 2006 Abstract Variance function estimation in multivariate nonparametric regression is consid- ered and the minimax rate of convergence is established. Our work uses the approach that generalizes the one used in Munk et al (2005) for the constant variance case. As is the case when the number of dimensions d = 1, and very much contrary to the common practice, it is often not desirable to base the estimator of the variance func- tion on the residuals from an optimal estimator of the mean. Instead it is desirable to use estimators of the mean with minimal bias. Another important conclusion is that the first order difference-based estimator that achieves minimax rate of convergence in one-dimensional case does not do the same in the high dimensional case. Instead, the optimal order of differences depends on the number of dimensions. Keywords: Minimax estimation, nonparametric regression, variance estimation. AMS 2000 Subject Classification: Primary: 62G08, 62G20. Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA 19104. The research of Tony Cai was supported in part by NSF Grant DMS-0306576. 'Corresponding author. Address: 250 N. University Street, Purdue University, West Lafayette, IN 47907. Email: [email protected]. Phone: 765-496-7571. Fax: 765-494-0558 1 Introduction We consider the multivariate nonparametric regression problem where yi E R, xi E S = [0, Ild C Rd while a, are iid random variables with zero mean and unit variance and have bounded absolute fourth moments: E lail 5 p4 < m. -
Variance Function Program
Variance Function Program Version 15.0 (for Windows XP and later) July 2018 W.A. Sadler 71B Middleton Road Christchurch 8041 New Zealand Ph: +64 3 343 3808 e-mail: [email protected] (formerly at Nuclear Medicine Department, Christchurch Hospital) Contents Page Variance Function Program 15.0 1 Windows Vista through Windows 10 Issues 1 Program Help 1 Gestures 1 Program Structure 2 Data Type 3 Automation 3 Program Data Area 3 User Preferences File 4 Auto-processing File 4 Graph Templates 4 Decimal Separator 4 Screen Settings 4 Scrolling through Summaries and Displays 4 The Variance Function 5 Variance Function Output Examples 8 Variance Stabilisation 11 Histogram, Error and Biological Variation Plots 12 Regression Analysis 13 Limit of Blank (LoB) and Limit of Detection (LoD) 14 Bland-Altman Analysis 14 Appendix A (Program Delivery) 16 Appendix B (Program Installation) 16 Appendix C (Program Removal) 16 Appendix D (Example Data, SD and Regression Files) 16 Appendix E (Auto-processing Example Files) 17 Appendix F (History) 17 Appendix G (Changes: Version 14.0 to Version 15.0) 18 Appendix H (Version 14.0 Bug Fixes) 19 References 20 Variance Function Program 15.0 1 Variance Function Program 15.0 The variance function (the relationship between variance and the mean) has several applications in statistical analysis of medical laboratory data (eg. Ref. 1), but the single most important use is probably the construction of (im)precision profile plots (2). This program (VFP.exe) was initially aimed at immunoassay data which exhibit relatively extreme variance relationships. It was based around the “standard” 3-parameter variance function, 2 J σ = (β1 + β2U) 2 where σ denotes variance, U denotes the mean, and β1, β2 and J are the parameters (3, 4).