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

Randomized experiments are the "gold standard" for estimating causal effects, yet often in practice, chance imbalances exist in covariate distributions between treatment groups. If covariate data are available before units are exposed to treatments, these chance imbalances can be mitigated by first checking covariate balance before the physical experiment takes place. Provided a precise definition of imbalance has been specified in advance, unbalanced randomizations can be discarded, followed by a rerandomization, and this process can continue until a randomization yielding balance according to the definition is achieved. By improving covariate balance, rerandomization provides more precise and trustworthy estimates of treatment effects.

Rerandomization to improve covariate balance in experiments

Significance levels from repeated p-values with multiply imputed data

https://psycnet.apa.org/journals/edu/74/5/708.pdf

Further meta-analytic procedures for assessing cognitive gender differences.

A Note on Percent Variance Explained as A Measure of the Importance of Effects

A framework is given for organizing and understanding the problems of estimating the parameters of a multivariate data set which contains blocks of missing observations. The basic technique is to decompose the original estimation problem into smaller estimation problems by factoring the likelihood of the observed data into a product of likelihoods. The result is summarized in a “factorization table,” which identifies the “complete-data” factors whose parameters may be estimated using standard, well-understood complete-data techniques, and the “incomplete-data” factors whose parameters must be estimated using special missing-data methods.

Donald B. Rubin

Papers

Rerandomization to improve covariate balance in experiments

Significance levels from repeated p-values with multiply imputed data

Further meta-analytic procedures for assessing cognitive gender differences.

A Note on Percent Variance Explained as A Measure of the Importance of Effects

Characterizing the Estimation of Parameters in Incomplete-Data Problems