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

This article considers causal inference for treatment contrasts from a randomized experiment using potential outcomes in a finite population setting. Adopting a Neymanian repeated sampling approach that integrates such causal inference with finite population survey sampling, an inferential framework is developed for general mechanisms of assigning experimental units to multiple treatments. This framework extends classical methods by allowing the possibility of randomization restrictions and unequal replications. Novel conditions that are "milder" than strict additivity of treatment effects, yet permit unbiased estimation of the finite population sampling variance of any treatment contrast estimator, are derived. The consequences of departures from such conditions are also studied under the criterion of minimax bias, and a new justification for using the Neymanian conservative sampling variance estimator in experiments is provided. The proposed approach can readily be extended to the case of treatments with a general factorial structure.

Causal Inference in Rebuilding and Extending the Recondite Bridge between Finite Population Sampling and Experimental Design

6639 Background: Objective criteria for measuring response to cancer treatment are critical to clinical research and practice. Many trials use imaging modalities like CT and NCI's Response Evaluati...

Radiologist-oncologist workflow analysis in application of RECIST

How big was the effect

This report presents data analyses investigating the relationship of high school final average, X, and first year university average, Y, in a Canadian university. The statistical summaries are (1) a matrix of observed “relative grading standards” of each high school in each matriculation year, and (2) a quadratic regression relating Y to X in each year. These summaries suggest that (1) the grading standards for some of the schools are changing consistently in time, and (2) the general relationship between Y and X is becoming more quadratic and less linear in time. The implication is that the high school attended is a more important predictor of university performance for students with poorer high school records than for students with better high school records, especially in recent years.

Donald B. Rubin

Papers

Causal Inference in Rebuilding and Extending the Recondite Bridge between Finite Population Sampling and Experimental Design

Radiologist-oncologist workflow analysis in application of RECIST

How big was the effect

Comparing high schools with respect to student performance in university

Multiple imputation for nonresponse in surveys (book review)