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

Multiple imputations in sample surveys

The multiple imputation of the National Medical Expenditure Survey (NMES) involved the use of two new techniques, both having potentially broad applicability. The first is to use distributionally incompatible MCMC (Markov Chain Monte Carlo), but to apply it only partially, to impute the missing values that destroy a monotone pattern, thereby limiting the extent of incompatibility. The second technique is to split the missing data into two parts, one that is much more computationally expensive to impute than the other, and create several imputations of the second part for each of the first part, thereby creating nested multiple imputations with their increased inferential efficiency.

Nested multiple imputation of NMES via partially incompatible MCMC

Should observational studies be designed to allow lack of balance in covariate distributions across treatment groups

The problem of drawing causal inferences from retrospective case-control studies is considered. A model for causal inference in prospective studies is reviewed and then applied to retrospective studies. The limitations of case-control studies are formulated in terms of the level of causally relevant parameters that can be estimated in such studies. An example using data from a large retrospective study of coffee-drinking and myocardial infarctions is used to illustrate the ideas of the article.

Donald B. Rubin

Papers

Multiple imputations in sample surveys

Nested multiple imputation of NMES via partially incompatible MCMC

Should observational studies be designed to allow lack of balance in covariate distributions across treatment groups

Causal Inference in Retrospective Studies

Adjusting for Nonignorable Drop-Out Using Semiparametric Nonresponse Models: Comment