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

One approach to handling incomplete data occasionally encountered in the literature is to treat the missing data as parameters and to maximize the complete-data likelihood over the missing data and parameters. This article points out that although this approach can be useful in particular problems, it is not a generally reliable approach to the analysis of incomplete data. In particular, it does not share the optimal properties of maximum likelihood estimation, except under the trivial asymptotics in which the proportion of missing data goes to zero as the sample size increases.

On Jointly Estimating Parameters and Missing Data by Maximizing the Complete-Data Likelihood

Many double-blind placebo-controlled randomized experiments with active drugs suffer from complications beyond simple noncompliance. First, the compliance with assigned dose is often partial, with ...

Principal Stratification for Causal Inference With Extended Partial Compliance

Comment on "Causal inference without counterfactuals," by Dawid AP

Multivariate matching methods are commonly used in the behavioral and medical sciences in an attempt to control bias when randomization is not feasible. Some examples of multivariate matching methods are discussed in Althauser and Rubin (1970) and Cochran and Rubin (1973), but otherwise seem to have received little attention in the literature. Here, we present examples of multivariate matching methods that will yield the same percent reduction in bias for each matching variable for a variety of underlying distributions. Eleven distributional cases are considered, and for each one, matching methods are defined which are equal percent bias reducing. Methods discussed in Section 8, which are based on the values of the estimated best linear discriminant or which define distance by a sample based inner-product, will probably be the most generally applicable in practice.

Donald B. Rubin

Papers

On Jointly Estimating Parameters and Missing Data by Maximizing the Complete-Data Likelihood

Principal Stratification for Causal Inference With Extended Partial Compliance

Comment on "Causal inference without counterfactuals," by Dawid AP

Multivariate matching methods that are equal percent bias reducing, I : some examples

Identification of Causal Effects Using Instrumental Variables: Rejoinder