No Arabic abstract
This article concerns a class of generalized linear mixed models for clustered data, where the random effects are mapped uniquely onto the grouping structure and are independent between groups. We derive necessary and sufficient conditions that enable the marginal likelihood of such class of models to be expressed in closed-form. Illustrations are provided using the Gaussian, Poisson, binomial and gamma distributions. These models are unified under a single umbrella of conjugate generalized linear mixed models, where conjugate refers to the fact that the marginal likelihood can be expressed in closed-form, rather than implying inference via the Bayesian paradigm. Having an explicit marginal likelihood means that these models are more computationally convenient, which can be important in big data contexts. Except for the binomial distribution, these models are able to achieve simultaneous conjugacy, and thus able to accommodate both unit and group level covariates.
Spatial generalized linear mixed models (SGLMMs) are popular and flexible models for non-Gaussian spatial data. They are useful for spatial interpolations as well as for fitting regression models that account for spatial dependence, and are commonly used in many disciplines such as epidemiology, atmospheric science, and sociology. Inference for SGLMMs is typically carried out under the Bayesian framework at least in part because computational issues make maximum likelihood estimation challenging, especially when high-dimensional spatial data are involved. Here we provide a computationally efficient projection-based maximum likelihood approach and two computationally efficient algorithms for routinely fitting SGLMMs. The two algorithms proposed are both variants of expectation maximization (EM) algorithm, using either Markov chain Monte Carlo or a Laplace approximation for the conditional expectation. Our methodology is general and applies to both discrete-domain (Gaussian Markov random field) as well as continuous-domain (Gaussian process) spatial models. Our methods are also able to adjust for spatial confounding issues that often lead to problems with interpreting regression coefficients. We show, via simulation and real data applications, that our methods perform well both in terms of parameter estimation as well as prediction. Crucially, our methodology is computationally efficient and scales well with the size of the data and is applicable to problems where maximum likelihood estimation was previously infeasible.
Field observations form the basis of many scientific studies, especially in ecological and social sciences. Despite efforts to conduct such surveys in a standardized way, observations can be prone to systematic measurement errors. The removal of systematic variability introduced by the observation process, if possible, can greatly increase the value of this data. Existing non-parametric techniques for correcting such errors assume linear additive noise models. This leads to biased estimates when applied to generalized linear models (GLM). We present an approach based on residual functions to address this limitation. We then demonstrate its effectiveness on synthetic data and show it reduces systematic detection variability in moth surveys.
Modern data sets in various domains often include units that were sampled non-randomly from the population and have a latent correlation structure. Here we investigate a common form of this setting, where every unit is associated with a latent variable, all latent variables are correlated, and the probability of sampling a unit depends on its response. Such settings often arise in case-control studies, where the sampled units are correlated due to spatial proximity, family relations, or other sources of relatedness. Maximum likelihood estimation in such settings is challenging from both a computational and statistical perspective, necessitating approximations that take the sampling scheme into account. We propose a family of approximate likelihood approaches which combine composite likelihood and expectation propagation. We demonstrate the efficacy of our solutions via extensive simulations. We utilize them to investigate the genetic architecture of several complex disorders collected in case-control genetic association studies, where hundreds of thousands of genetic variants are measured for every individual, and the underlying disease liabilities of individuals are correlated due to genetic similarity. Our work is the first to provide a tractable likelihood-based solution for case-control data with complex dependency structures.
We consider testing regression coefficients in high dimensional generalized linear models. An investigation of the test of Goeman et al. (2011) is conducted, which reveals that if the inverse of the link function is unbounded, the high dimensionality in the covariates can impose adverse impacts on the power of the test. We propose a test formation which can avoid the adverse impact of the high dimensionality. When the inverse of the link function is bounded such as the logistic or probit regression, the proposed test is as good as Goeman et al. (2011)s test. The proposed tests provide p-values for testing significance for gene-sets as demonstrated in a case study on an acute lymphoblastic leukemia dataset.
The functional linear model is a popular tool to investigate the relationship between a scalar/functional response variable and a scalar/functional covariate. We generalize this model to a functional linear mixed-effects model when repeated measurements are available on multiple subjects. Each subject has an individual intercept and slope function, while shares common population intercept and slope function. This model is flexible in the sense of allowing the slope random effects to change with the time. We propose a penalized spline smoothing method to estimate the population and random slope functions. A REML-based EM algorithm is developed to estimate the variance parameters for the random effects and the data noise. Simulation studies show that our estimation method provides an accurate estimate for the functional linear mixed-effects model with the finite samples. The functional linear mixed-effects model is demonstrated by investigating the effect of the 24-hour nitrogen dioxide on the daily maximum ozone concentrations and also studying the effect of the daily temperature on the annual precipitation.