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

“Comment on the Shigemasu’s article - Sage Statisticians in Social Sciences: Impact of Rubin’s Work”

Consider a situation with two treatments, the first of which is randomized but the second is not, and the multifactor version of this. Interest is in treatment effects, defined using standard factorial notation. We define estimators for the treatment effects and explore their properties when there is information about the nonrandomized treatment assignment and when there is no information on the assignment of the nonrandomized treatment. We show when and how hidden treatments can bias estimators and inflate their sampling variances.

Causal inference from treatment-control studies having an additional factor with unknown assignment mechanism

It was shown that the improvement on the performance of single cell Nb cavities made during the last 5 years by advanced dustfree mounting and firing techniques can be successfully transferred to multicell structures. Acceleration gradients of 22 MV/m in the best 5-cell and 16 MV/m in the first 9-cell cavity of improved cell shape have been achieved. The increase of E/sub acc/ beyond 25 MV/m needs additional investigation on single cell cavities. Nevertheless, superconducting accelerators are a promising option for building a linear collider for electrons with beam energies in excess of 300 GeV. >

Test results on 3 GHz structures for a superconducting linear collider

When the prior distributions for the grand mean, row effects, column effects and interaction effects are all independent, with that for the grand mean being flat, the posterior expectation and covariance matrix of the cell means (under a Gaussian model) in a 2-way MANOVA may be obtained via a special matrix inversion technique which offers a great saving in storage and computation time. An APL program and example are presented.

An algorithm for the posterior distribution of the cell means in a two‐way unbalanced manova

The health effects of environmental exposures have been studied for decades, typically using standard regression models to assess exposure-outcome associations found in observational non-experimental data. We propose and illustrate a different approach to examine causal effects of environmental exposures on health outcomes from observational data. Our strategy attempts to structure the observational data to approximate data from a hypothetical, but realistic, randomized experiment. This approach, based on insights from classical experimental design, involves four stages, and relies on modern computing to implement the effort in two of the four stages.More specifically, our strategy involves: 1) a conceptual stage that involves the precise formulation of the causal question in terms of a hypothetical randomized experiment where the exposure is assigned to units; 2) a design stage that attempts to reconstruct (or approximate) a randomized experiment before any outcome data are observed, 3) a statistical analysis comparing the outcomes of interest in the exposed and non-exposed units of the hypothetical randomized experiment, and 4) a summary stage providing conclusions about statistical evidence for the sizes of possible causal effects of the exposure on outcomes. We illustrate our approach using an example examining the effect of parental smoking on children's lung function collected in families living in East Boston in the 1970's. To complement the traditional purely model-based approaches, our strategy, which includes outcome free matched-sampling, provides workable tools to quantify possible detrimental exposure effects on human health outcomes especially because it also includes transparent diagnostics to assess the assumptions of the four-stage statistical approach being applied.

Donald B. Rubin

Papers

“Comment on the Shigemasu’s article - Sage Statisticians in Social Sciences: Impact of Rubin’s Work”

Causal inference from treatment-control studies having an additional factor with unknown assignment mechanism

Test results on 3 GHz structures for a superconducting linear collider

An algorithm for the posterior distribution of the cell means in a two‐way unbalanced manova

Bridging observational studies and randomized experiments by embedding the former in the latter