Maximum likelihood or restricted maximum likelihood (REML) estimates of the parameters in linear mixed-effects models can be determined using the lmer function in the lme4 package for R. As for most model-fitting functions in R, the model is described in an lmer call by a formula, in this case including both fixed- and random-effects terms. The formula and data together determine a numerical representation of the model from which the profiled deviance or the profiled REML criterion can be evaluated as a function of some of the model parameters. The appropriate criterion is optimized, using one of the constrained optimization functions in R, to provide the parameter estimates. We describe the structure of the model, the steps in evaluating the profiled deviance or REML criterion, and the structure of classes or types that represents such a model. Sufficient detail is included to allow specialization of these structures by users who wish to write functions to fit specialized linear mixed models, such as models incorporating pedigrees or smoothing splines, that are not easily expressible in the formula language used by lmer.

/pdf/fitting-linear-mixed-effects-models-using-lme4-4zzrpoy9lh.pdf

Fitting Linear Mixed-Effects Models Using lme4

https://rss.onlinelibrary.wiley.com/doi/pdf/10.1111/j.2517-6161.1977.tb01600.x

Maximum likelihood from incomplete data via the EM algorithm

Deep learning is a form of machine learning that enables computers to learn from experience and understand the world in terms of a hierarchy of concepts. Because the computer gathers knowledge from experience, there is no need for a human computer operator to formally specify all the knowledge that the computer needs. The hierarchy of concepts allows the computer to learn complicated concepts by building them out of simpler ones; a graph of these hierarchies would be many layers deep. This book introduces a broad range of topics in deep learning. The text offers mathematical and conceptual background, covering relevant concepts in linear algebra, probability theory and information theory, numerical computation, and machine learning. It describes deep learning techniques used by practitioners in industry, including deep feedforward networks, regularization, optimization algorithms, convolutional networks, sequence modeling, and practical methodology; and it surveys such applications as natural language processing, speech recognition, computer vision, online recommendation systems, bioinformatics, and videogames. Finally, the book offers research perspectives, covering such theoretical topics as linear factor models, autoencoders, representation learning, structured probabilistic models, Monte Carlo methods, the partition function, approximate inference, and deep generative models. Deep Learning can be used by undergraduate or graduate students planning careers in either industry or research, and by software engineers who want to begin using deep learning in their products or platforms. A website offers supplementary material for both readers and instructors.

Deep Learning

Meta-Analysis in Clinical Trials*

We describe latent Dirichlet allocation (LDA), a generative probabilistic model for collections of discrete data such as text corpora. LDA is a three-level hierarchical Bayesian model, in which each item of a collection is modeled as a finite mixture over an underlying set of topics. Each topic is, in turn, modeled as an infinite mixture over an underlying set of topic probabilities. In the context of text modeling, the topic probabilities provide an explicit representation of a document. We present efficient approximate inference techniques based on variational methods and an EM algorithm for empirical Bayes parameter estimation. We report results in document modeling, text classification, and collaborative filtering, comparing to a mixture of unigrams model and the probabilistic LSI model.

/pdf/latent-dirichlet-allocation-4gmscb06en.pdf

Latent dirichlet allocation

: The results of observational studies are often disputed because of nonrandom treatment assignment. For example, patients at greater risk may be overrepresented in some treatment group. This paper discusses the central role of propensity scores and balancing scores in the analysis of observational studies. The propensity score is the (estimated) conditional probability of assignment to a particular treatment given a vector of observed covariates. Both large and small sample theory show that adjustment for the scalar propensity score is sufficient to remove bias due to all observed covariates. Applications include: matched sampling on the univariate propensity score which is equal percent bias reducing under more general conditions than required for discriminant matching, multivariate adjustment by subclassification on balancing scores where the same subclasses are used to estimate treatment effects for all outcome variables and in all subpopulations, and visual representation of multivariate adjustment by a two-dimensional plot. (Author)

/pdf/the-central-role-of-the-propensity-score-in-observational-hqdiv01vha.pdf

The central role of the propensity score in observational studies for causal effects

Preface.PART I: OVERVIEW AND BASIC APPROACHES.Introduction.Missing Data in Experiments.Complete-Case and Available-Case Analysis, Including Weighting Methods.Single Imputation Methods.Estimation of Imputation Uncertainty.PART II: LIKELIHOOD-BASED APPROACHES TO THE ANALYSIS OF MISSING DATA.Theory of Inference Based on the Likelihood Function.Methods Based on Factoring the Likelihood, Ignoring the Missing-Data Mechanism.Maximum Likelihood for General Patterns of Missing Data: Introduction and Theory with Ignorable Nonresponse.Large-Sample Inference Based on Maximum Likelihood Estimates.Bayes and Multiple Imputation.PART III: LIKELIHOOD-BASED APPROACHES TO THE ANALYSIS OF MISSING DATA: APPLICATIONS TO SOME COMMON MODELS.Multivariate Normal Examples, Ignoring the Missing-Data Mechanism.Models for Robust Estimation.Models for Partially Classified Contingency Tables, Ignoring the Missing-Data Mechanism.Mixed Normal and Nonnormal Data with Missing Values, Ignoring the Missing-Data Mechanism.Nonignorable Missing-Data Models.References.Author Index.Subject Index.

https://leseprobe.buch.de/images-adb/61/97/61976bf3-cfac-463d-bb88-ca1ddb674cdf.pdf

Statistical Analysis with Missing Data

FUNDAMENTALS OF BAYESIAN INFERENCE Probability and Inference Single-Parameter Models Introduction to Multiparameter Models Asymptotics and Connections to Non-Bayesian Approaches Hierarchical Models FUNDAMENTALS OF BAYESIAN DATA ANALYSIS Model Checking Evaluating, Comparing, and Expanding Models Modeling Accounting for Data Collection Decision Analysis ADVANCED COMPUTATION Introduction to Bayesian Computation Basics of Markov Chain Simulation Computationally Efficient Markov Chain Simulation Modal and Distributional Approximations REGRESSION MODELS Introduction to Regression Models Hierarchical Linear Models Generalized Linear Models Models for Robust Inference Models for Missing Data NONLINEAR AND NONPARAMETRIC MODELS Parametric Nonlinear Models Basic Function Models Gaussian Process Models Finite Mixture Models Dirichlet Process Models APPENDICES A: Standard Probability Distributions B: Outline of Proofs of Asymptotic Theorems C: Computation in R and Stan Bibliographic Notes and Exercises appear at the end of each chapter.

Bayesian Data Analysis

Tables and Figures. Glossary. 1. Introduction. 1.1 Overview. 1.2 Examples of Surveys with Nonresponse. 1.3 Properly Handling Nonresponse. 1.4 Single Imputation. 1.5 Multiple Imputation. 1.6 Numerical Example Using Multiple Imputation. 1.7 Guidance for the Reader. 2. Statistical Background. 2.1 Introduction. 2.2 Variables in the Finite Population. 2.3 Probability Distributions and Related Calculations. 2.4 Probability Specifications for Indicator Variables. 2.5 Probability Specifications for (X,Y). 2.6 Bayesian Inference for a Population Quality. 2.7 Interval Estimation. 2.8 Bayesian Procedures for Constructing Interval Estimates, Including Significance Levels and Point Estimates. 2.9 Evaluating the Performance of Procedures. 2.10 Similarity of Bayesian and Randomization--Based Inferences in Many Practical Cases. 3. Underlying Bayesian Theory. 3.1 Introduction and Summary of Repeated--Imputation Inferences. 3.2 Key Results for Analysis When the Multiple Imputations are Repeated Draws from the Posterior Distribution of the Missing Values. 3.3 Inference for Scalar Estimands from a Modest Number of Repeated Completed--Data Means and Variances. 3.4 Significance Levels for Multicomponent Estimands from a Modest Number of Repeated Completed--Data Means and Variance--Covariance Matrices. 3.5 Significance Levels from Repeated Completed--Data Significance Levels. 3.6 Relating the Completed--Data and Completed--Data Posterior Distributions When the Sampling Mechanism is Ignorable. 4. Randomization--Based Evaluations. 4.1 Introduction. 4.2 General Conditions for the Randomization--Validity of Infinite--m Repeated--Imputation Inferences. 4.3Examples of Proper and Improper Imputation Methods in a Simple Case with Ignorable Nonresponse. 4.4 Further Discussion of Proper Imputation Methods. 4.5 The Asymptotic Distibution of (Qm,Um,Bm) for Proper Imputation Methods. 4.6 Evaluations of Finite--m Inferences with Scalar Estimands. 4.7 Evaluation of Significance Levels from the Moment--Based Statistics Dm and Dm with Multicomponent Estimands. 4.8 Evaluation of Significance Levels Based on Repeated Significance Levels. 5. Procedures with Ignorable Nonresponse. 5.1 Introduction. 5.2 Creating Imputed Values under an Explicit Model. 5.3 Some Explicit Imputation Models with Univariate YI and Covariates. 5.4 Monotone Patterns of Missingness in Multivariate YI. 5.5 Missing Social Security Benefits in the Current Population Survey. 5.6 Beyond Monotone Missingness. 6. Procedures with Nonignorable Nonresponse. 6.1 Introduction. 6.2 Nonignorable Nonresponse with Univariate YI and No XI. 6.3 Formal Tasks with Nonignorable Nonresponse. 6.4 Illustrating Mixture Modeling Using Educational Testing Service Data. 6.5 Illustrating Selection Modeling Using CPS Data. 6.6 Extensions to Surveys with Follow--Ups. 6.7 Follow--Up Response in a Survey of Drinking Behavior Among Men of Retirement Age. References. Author Index. Subject Index. Appendix I. Report Written for the Social Security Administration in 1977. Appendix II. Report Written for the Census Bureau in 1983.

Donald B. Rubin

Papers

Maximum likelihood from incomplete data via the EM algorithm

The central role of the propensity score in observational studies for causal effects

Statistical Analysis with Missing Data

Bayesian Data Analysis

Multiple imputation for nonresponse in surveys