Marginal models involve restrictions on the conditional and marginal association structure of a set of categorical variables. They generalize log-linear models for contingency tables, which are the fundamental tools for modelling the conditional association structure. This chapter gives an overview of the development of marginal models during the past 20 years. After providing some motivating examples, the first few sections focus on the definition and characteristics of marginal models. Specifically, we show how their fundamental properties can be understood from the properties of marginal log-linear parameterizations. Algorithms for estimating marginal models are discussed, focussing on the maximum likelihood and the generalized estimating equations approaches. It is shown how marginal models can help to understand directed graphical and path models, and a description is given of marginal models with latent variables.
We present a method to infer on joint regression coefficients obtained from marginal regressions using a reference panel. This type of scenario is common in genetic fine-mapping, where the estimated marginal associations are reported in genomewide association studies (GWAS), and a reference panel is used for inference on the association in a joint regression model. We show that ignoring the uncertainty due to the use of a reference panel instead of the original design matrix, can lead to a severe inflation of false discoveries and a lack of replicable findings. We derive the asymptotic distrib…
The extended class of multiplicative row-column (RC) association models, introduced in this paper for two-way contingency tables, allows users to select both the type of logit (local, global, continuation, reverse continuation) suitable for the row and column classification variables and the scale on which interactions are measured. As in \cite{Kateri95} for the case of local logits, our extended class of bivariate interactions is linked to divergence measures and, by means of a representation theorem, we provide reconstruction formulas for the joint probabilities depending on pairs of logit t…
Large-scale hypothesis testing has become a ubiquitous problem in high-dimensional statistical inference, with broad applications in various scienfitic disciplines. One relevant application is constituted by imaging mass spectrometry (IMS) association studies, where a large number of tests are performed simultaneously in order to identify molecular masses that are associated with a particular phenotype, e. g., a cancer subtype. Mass spectra obtained from Matrix-assisted laser desorption/ionization (MALDI) experiments are dependent, when considered as statistical quantities. False discovery pro…
In his seminal paper Goodman (1996) introduced marginal-free correspondence analysis; where his principal aim was to reconcile Pearson correlation measure with Yule's association measure in the analysis of contingency tables. We show that marginal-free correspondence analysis is a particular case of correspondence analysis with prespecified weights studied in the beginning of the 1980s by Benzécri and his students. Furthermore, we show that it is also a particular first-order approximation of logratio analysis with uniform weights. Key words: Marginal-free correspondence analysis; logratio ana…
Modern high-throughput biomedical devices routinely produce data on a large scale, and the analysis of high-dimensional datasets has become commonplace in biomedical studies. However, given thousands or tens of thousands of measured variables in these datasets, extracting meaningful features poses a challenge. In this article, we propose a procedure to evaluate the strength of the associations between a nominal (categorical) response variable and multiple features simultaneously. Specifically, we propose a framework of large-scale multiple testing under arbitrary correlation dependency among t…
Bivariate ordered logistic models (BOLMs) are appealing to jointly model the marginal distribution of two ordered responses and their association, given a set of covariates. When the number of categories of the responses increases, the number of global odds ratios (or their re-parametrizations) to be estimated also increases and estimating the association structure becomes crucial for this type of data. In fact, such data could be too "rich" to be fully modelled with an ordinary BOLM while, sometimes, the well-known Dale's model could be too parsimonious to provide a good fit. In addition, whe…
Bivariate Frank Copula: Some More Results on Point Estimation of the Association Parameter from a Bayesian Perspective and Revisiting the Goodness of Fit Tests with an Application to Model Groundwater Data from Dong Thap, Vietnam
Faculty of Applied Science, Ho Chi Minh City University of Technology (HCMUT)（胡志明市理工大学应用科学学院）；Vietnam National University Ho Chi Minh City（越南国家大学胡志明市分校）；Faculty of Mathematics and Statistics, Ton Duc Thang University（Ton Duc Thang大学数学与统计学院）
In regression models for categorical data a linear model is typically related to the response variables via a transformation of probabilities called the link function. We introduce an approach based on two link functions for binary data named log-mean (LM) and log-mean linear (LML), respectively. The choice of the link function plays a key role for the interpretation of the model, and our approach is especially appealing in terms of interpretation of the effects of covariates on the association of responses. Similarly to Poisson regression, the LM and LML regression coefficients of single outc…
Universidad Carlos III de Madrid（马德里卡洛斯三世大学）；Universidad Rey Juan Carlos（胡安卡洛斯国王大学）
This is an up-to-date introduction to, and overview of, marginal likelihood computation for model selection and hypothesis testing. Computing normalizing constants of probability models (or ratio of constants) is a fundamental issue in many applications in statistics, applied mathematics, signal processing and machine learning. This article provides a comprehensive study of the state-of-the-art of the topic. We highlight limitations, benefits, connections and differences among the different techniques. Problems and possible solutions with the use of improper priors are also described. Some of …
For the analysis of clustered survival data, two different types of models that take the association into account, are commonly used: frailty models and copula models. Frailty models assume that conditional on a frailty term for each cluster, the hazard functions of individuals within that cluster are independent. These unknown frailty terms with their imposed distribution are used to express the association between the different individuals in a cluster. Copula models on the other hand assume that the joint survival function of the individuals within a cluster is given by a copula function, e…
This paper proposes a maximum-likelihood approach to jointly estimate marginal conditional quantiles of multivariate response variables in a linear regression framework. We consider a slight reparameterization of the Multivariate Asymmetric Laplace distribution proposed by Kotz et al (2001) and exploit its location-scale mixture representation to implement a new EM algorithm for estimating model parameters. The idea is to extend the link between the Asymmetric Laplace distribution and the well-known univariate quantile regression model to a multivariate context, i.e. when a multivariate depend…
We extend the log-mean linear parameterization introduced by Roverato et al. (2013) for binary data to discrete variables with arbitrary number of levels, and show that also in this case it can be used to parameterize bi-directed graph models. Furthermore, we show that the log-mean linear parameterization allows one to simultaneously represent marginal independencies among variables and marginal independencies that only appear when certain levels are collapsed into a single one. We illustrate the application of this property by means of an example based on genetic association studies involving…
Estimating marginal association between paired outcomes in clustered data with an application to analyzing caries and periodontal disease data from the National Health and Nutrition Examination Survey
Marginal association summary statistics have attracted great attention in statistical genetics, mainly because the primary results of most genome-wide association studies (GWAS) are produced by marginal screening. In this paper, we study the prediction accuracy of marginal estimator in dense (or sparsity free) high-dimensional settings with $(n,p,m) \to \infty$, $m/n \to γ\in (0,\infty)$, and $p/n \to ω\in (0,\infty)$. We consider a general correlation structure among the $p$ features and allow an unknown subset $m$ of them to be signals. As the marginal estimator can be viewed as a ridge esti…
The Yule-Simpson paradox notes that an association between random variables can be reversed when averaged over a background variable. Cox and Wermuth (2003) introduced the concept of distribution dependence between two random variables X and Y, and developed two dependence conditions, each of which guarantees that reversal cannot occur. Ma, Xie and Geng (2006) studied the collapsibility of distribution dependence over a background variable W, under a rather strong homogeneity condition. Collapsibility ensures the association remains the same for conditional and marginal models, so that Yule-Si…
Models for dependent data are distinguished by their targets of inference. Marginal models are useful when interest lies in quantifying associations averaged across a population of clusters. When the functional form of a covariate-outcome association is unknown, flexible regression methods are needed to allow for potentially non-linear relationships. We propose a novel marginal additive model (MAM) for modelling cluster-correlated data with non-linear population-averaged associations. The proposed MAM is a unified framework for estimation and uncertainty quantification of a marginal mean model…
The association between two random variables is often of primary interest in statistical research. In this paper semiparametric models for the association between random vectors X and Y are considered which leave the marginal distributions arbitrary. Given that the odds ratio function comprises the whole information about the association the focus is on bilinear log-odds ratio models and in particular on the odds ratio parameter vector θ. The covariance structure of the maximum likelihood estimator θ^ of θ is of major importance for asymptotic inference. To this end different representations o…
Independence screening methods such as the two sample $t$-test and the marginal correlation based ranking are among the most widely used techniques for variable selection in ultrahigh dimensional data sets. In this short note, simple examples are used to demonstrate potential problems with the independence screening methods in the presence of correlated predictors. Also, an example is considered where all important variables are independent among themselves and all but one important variables are independent with the unimportant variables. Furthermore, a real data example from a genome wide as…
Recently more and more evidence suggests that rare variants with much lower minor allele frequencies play significant roles in disease etiology. Advances in next-generation sequencing technologies will lead to many more rare variants association studies. Several statistical methods have been proposed to assess the effect of rare variants by aggregating information from multiple loci across a genetic region and testing the association between the phenotype and aggregated genotype. One limitation of existing methods is that they only look into the marginal effects of rare variants but do not sys…
Estimating large covariance and precision matrices are fundamental in modern multivariate analysis. The problems arise from statistical analysis of large panel economics and finance data. The covariance matrix reveals marginal correlations between variables, while the precision matrix encodes conditional correlations between pairs of variables given the remaining variables. In this paper, we provide a selective review of several recent developments on estimating large covariance and precision matrices. We focus on two general approaches: rank based method and factor model based method. Theorie…
Motivated by genome-wide association screening studies (GWAS), we study high-dimensional marginal screenings of categorical variables where test statistics have approximate chi-square distributions. We characterize four new phase transitions in high-dimensional chi-square models, and derive the signal sizes necessary and sufficient for statistical procedures to simultaneously control false discovery (in terms of family-wise error rate or false discovery rate) and missed detection (in terms of family-wise non-discovery rate or false non-discovery rate) in large dimensions. Remarkably, degrees o…
The proposal of Reshef et al. (2011) is an interesting new approach for discovering non-linear dependencies among pairs of measurements in exploratory data mining. However, it has a potentially serious drawback. The authors laud the fact that MIC has no preference for some alternatives over others, but as the authors know, there is no free lunch in Statistics: tests which strive to have high power against all alternatives can have low power in many important situations. To investigate this, we ran simulations to compare the power of MIC to that of standard Pearson correlation and distance corr…
In genome-wide association studies (GWAS), penalization is an important approach for identifying genetic markers associated with trait while mixed model is successful in accounting for a complicated dependence structure among samples. Therefore, penalized linear mixed model is a tool that combines the advantages of penalization approach and linear mixed model. In this study, a GWAS with multiple highly correlated traits is analyzed. For GWAS with multiple quantitative traits that are highly correlated, the analysis using traits marginally inevitably lose some essential information among multip…
Bivariate observations of binary and ordinal data arise frequently and require a bivariate modelling approach in cases where one is interested in aspects of the marginal distributions as separate outcomes along with the association between the two. We consider methods for constructing such bivariate models with logistic marginals and propose a model based on the Ali-Mikhail-Haq bivariate logistic distribution. We motivate the model as an extension of that based on the Gumbel type 2 distribution as considered by other authors and as a bivariate extension of the logistic distribution which prese…
As the sequencing costs are decreasing, there is great incentive to perform large scale association studies to increase power of detecting new variants. Federated association testing among different institutions is a viable solution for increasing sample sizes by sharing the intermediate testing statistics that are aggregated by a central server. There are, however, standing challenges to performing federated association testing. Association tests are known to be confounded by numerous factors such as population stratification, which can be especially important in multiancestral studies and in…
The central aim in this paper is to address variable selection questions in nonlinear and nonparametric regression. Motivated by statistical genetics, where nonlinear interactions are of particular interest, we introduce a novel and interpretable way to summarize the relative importance of predictor variables. Methodologically, we develop the "RelATive cEntrality" (RATE) measure to prioritize candidate genetic variants that are not just marginally important, but whose associations also stem from significant covarying relationships with other variants in the data. We illustrate RATE through Bay…
Phylogenetic trait evolution models allow for the estimation of evolutionary correlations between a set of traits observed in a sample of related organisms. By directly modeling the evolution of the traits along an estimable phylogenetic tree, the model's structure effectively controls for shared evolutionary history. In these models, relevant correlations are usually assessed through the high posterior density interval of their marginal distributions. However, the selected correlations alone may not provide the full picture regarding trait relationships. Their association structure, expressed…
