Factorial graphical lasso for dynamic networks

Dynamic networks models describe a growing number of important scientific processes, from cell biology and epidemiology to sociology and finance. There are many aspects of dynamical networks that require statistical considerations. In this paper we focus on determining network structure. Estimating dynamic networks is a difficult task since the number of components involved in the system is very large. As a result, the number of parameters to be estimated is bigger than the number of observations. However, a characteristic of many networks is that they are sparse. For example, the molecular structure of genes make interactions with other components a highly-structured and therefore sparse process. Penalized Gaussian graphical models have been used to estimate sparse networks. However, the literature has focussed on static networks, which lack specific temporal constraints. We propose a structured Gaussian dynamical graphical model, where structures can consist of specific time dynamics, known presence or absence of links and block equality constraints on the parameters. Thus, the number of parameters to be estimated is reduced and accuracy of the estimates, including the identification of the network, can be tuned up. Here, we show that the constrained optimization problem can be solved by taking advantage of an efficient solver, logdetPPA, developed in convex optimization. Moreover, model selection methods for checking the sensitivity of the inferred networks are described. Finally, synthetic and real data illustrate the proposed methodologies.Comment: 30 pp, 5 figure

A joint regression modeling framework for analyzing bivariate binary data in R

We discuss some of the features of the R add-on package GJRM which implements a flexible joint modeling framework for fitting a number of multivariate response regression models under various sampling schemes. In particular,we focus on the case inwhich the user wishes to fit bivariate binary regression models in the presence of several forms of selection bias. The framework allows for Gaussian and non-Gaussian dependencies through the use of copulae, and for the association and mean parameters to depend on flexible functions of covariates. We describe some of the methodological details underpinning the bivariate binary models implemented in the package and illustrate them by fitting interpretable models of different complexity on three data-sets

Mixed Cumulative Distribution Networks

Directed acyclic graphs (DAGs) are a popular framework to express multivariate probability distributions. Acyclic directed mixed graphs (ADMGs) are generalizations of DAGs that can succinctly capture much richer sets of conditional independencies, and are especially useful in modeling the effects of latent variables implicitly. Unfortunately there are currently no good parameterizations of general ADMGs. In this paper, we apply recent work on cumulative distribution networks and copulas to propose one one general construction for ADMG models. We consider a simple parameter estimation approach, and report some encouraging experimental results.Comment: 11 pages, 4 figure

Gene Copy Number Analysis for Family Data Using Semiparametric Copula Model

Gene copy number changes are common characteristics of many genetic disorders. A new technology, array comparative genomic hybridization (a-CGH), is widely used today to screen for gains and losses in cancers and other genetic diseases with high resolution at the genome level or for specific chromosomal region. Statistical methods for analyzing such a-CGH data have been developed. However, most of the existing methods are for unrelated individual data and the results from them provide explanation for horizontal variations in copy number changes. It is potentially meaningful to develop a statistical method that will allow for the analysis of family data to investigate the vertical kinship effects as well. Here we consider a semiparametric model based on clustering method in which the marginal distributions are estimated nonparametrically, and the familial dependence structure is modeled by copula. The model is illustrated and evaluated using simulated data. Our results show that the proposed method is more robust than the commonly used multivariate normal model. Finally, we demonstrated the utility of our method using a real dataset

Adaptive Basis Sampling for Smoothing Splines

Smoothing splines provide flexible nonparametric regression estimators. Penalized likelihood method is adopted when responses are from exponential families and multivariate models are constructed with certain analysis of variance decomposition. However, the high computational cost of smoothing splines for large data sets has hindered their wide application. We develop a new method, named adaptive basis sampling, for efficient computation of smoothing splines in super-large samples. Generally, a smoothing spline for a regression problem with sample size n can be expressed as a linear combination of n basis functions and its computational complexity is O(n³). We achieve a more scalable computation in the multivariate case by evaluating the smoothing spline using a smaller set of basis functions, obtained by an adaptive sampling scheme that uses values of the response variable. Our asymptotic analysis shows that smoothing splines computed via adaptive basis sampling converge to the true function at the same rate as full basis smoothing splines. We show that the proposed method outperforms a sampling method that does not use the values of response variable by simulation studies, and apply it to several real data examples

Assessing the relationship between markers of glycemic control through flexible copula regression models

Glycated haemoglobin (HbA1c) is a sensitive marker of blood glucose in patientswith diabetes. However, levels can vary considerably, even among individualswith similar mean blood glucose concentrations. Other glycated proteins, such asfructosamine, can also act as blood sugar markers, but estimating HbA1c and fruc-tosamine via independent models may lead to errors of interpretation regardingdisease severity. From a clinical standpoint, it would be of great interest to knowthe factors that affect the mean concentration of both HbA1c and fructosamine,that influence the variability in the concentrations of these glycated markers, andthat cause HbA1c/fructosamine discordance. Flexible models are required that illus-trate the behaviour of these variables as well as the association between them. Thepresent work reviews existing models that might serve in this regard. Flexible cop-ula regression models using P-splines, were used to provide a better understandingof the behaviour of both glycated proteins, and the relationship between them underthe possible influence of different covariates. This work shows the usefulness ofthis type of models in practice, and provides a basis for its clinical interpretation bymeans of an understandable case study. Ultimately, to better understand the effectsof each continuous covariate, they were represented at the true scale of the response variables