Joint response graphs and separation induced by triangular systems

Summary.  We consider joint probability distributions generated recursively in terms of univariate conditional distributions satisfying conditional independence restrictions. The independences are captured by missing edges in a directed graph. A matrix form of such a graph, called the generating edge matrix, is triangular so the distributions that are generated over such graphs are called triangular systems. We study consequences of triangular systems after grouping or reordering of the variables for analyses as chain graph models, i.e. for alternative recursive factorizations of the given density using joint conditional distributions. For this we introduce families of linear triangular equations which do not require assumptions of distributional form. The strength of the associations that are implied by such linear families for chain graph models is derived. The edge matrices of chain graphs that are implied by any triangular system are obtained by appropriately transforming the generating edge matrix. It is shown how induced independences and dependences can be studied by graphs, by edge matrix calculations and via the properties of densities. Some ways of using the results are illustrated.     

Graphs in Scientific Publications

Graphical communication in scientific publications can be improved; a detailed analysis of all graphs in one volume of Science revealed that 30% had errors. Graphs are used more in some disciplines than in others; a survey of 57 journals revealed natural science journals use far more graphs than mathematical or social science journals. Usage studies such as these provide important information for developing four other areas: new graphical methods for data presentation, guidelines, software, and human graphical perception.     

Degree-based goodness-of-fit tests for heterogeneous random graph models: Independent and exchangeable cases

The degrees are a classical and relevant way to study the topology of a network. They can be used to assess the goodness of fit for a given random graph model. In this paper, we introduce goodness-of-fit tests for two classes of models. First, we consider the case of independent graph models such as the heterogeneous Erdös-Rényi model in which the edges have different connection probabilities. Second, we consider a generic model for exchangeable random graphs called the W-graph. The stochastic block model and the expected degree distribution model fall within this framework. We prove the asymptotic normality of the degree mean square under these independent and exchangeable models and derive formal tests. We study the power of the proposed tests and we prove the asymptotic normality under specific sparsity regimes. The tests are illustrated on real networks from social sciences and ecology, and their performances are assessed via a simulation study.     

SEMIPARAMETRIC REGRESSION AND GRAPHICAL MODELS

Semiparametric regression models that use spline basis functions with penalization have graphical model representations. This link is more powerful than previously established mixed model representations of semiparametric regression, as a larger class of models can be accommodated. Complications such as missingness and measurement error are more naturally handled within the graphical model architecture. Directed acyclic graphs, also known as Bayesian networks, play a prominent role. Graphical model-based Bayesian 'inference engines', such as bugs and vibes , facilitate fitting and inference. Underlying these are Markov chain Monte Carlo schemes and recent developments in variational approximation theory and methodology.     

A course in constructing effective displays of data for pharmaceutical research personnel

Interpreting data and communicating effectively through graphs and tables are requisite skills for statisticians and non‐statisticians in the pharmaceutical industry. However, the quality of visual displays of data in the medical and pharmaceutical literature and at scientific conferences is severely lacking. We describe an interactive, workshop‐driven, 2‐day short course that we constructed for pharmaceutical research personnel to learn these skills. The examples in the course and the workshop datasets source from our professional experiences, the scientific literature, and the mass media. During the course, the participants are exposed to and gain hands‐on experience with the principles of visual and graphical perception, design, and construction of both graphic and tabular displays of quantitative and qualitative information. After completing the course, with a critical eye, the participants are able to construct, revise, critique, and interpret graphic and tabular displays according to an extensive set of guidelines. Copyright © 2013 John Wiley & Sons, Ltd.     

Tree consistency and bounds on the performance of the max-product algorithm and its generalizations

Finding the maximum a posteriori (MAP) assignment of a discrete-state distribution specified by a graphical model requires solving an integer program. The max-product algorithm, also known as the max-plus or min-sum algorithm, is an iterative method for (approximately) solving such a problem on graphs with cycles. We provide a novel perspective on the algorithm, which is based on the idea of reparameterizing the distribution in terms of so-called pseudo-max-marginals on nodes and edges of the graph. This viewpoint provides conceptual insight into the max-product algorithm in application to graphs with cycles. First, we prove the existence of max-product fixed points for positive distributions on arbitrary graphs. Next, we show that the approximate max-marginals computed by max-product are guaranteed to be consistent, in a suitable sense to be defined, over every tree of the graph. We then turn to characterizing the nature of the approximation to the MAP assignment computed by max-product. We generalize previous work by showing that for any graph, the max-product assignment satisfies a particular optimality condition with respect to any subgraph containing at most one cycle per connected component. We use this optimality condition to derive upper bounds on the difference between the log probability of the true MAP assignment, and the log probability of a max-product assignment. Finally, we consider extensions of the max-product algorithm that operate over higher-order cliques, and show how our reparameterization analysis extends in a natural manner.     

Un critère de choix de variables en analyse en composantes principales fondé sur des modèles graphiques gaussiens particuliers

We focus on the problem of selection of a subset of the variables so as to preserve the multivariate data structure that a principal-components analysis of the initial variables would reveal. We propose a new method based on some adapted Gaussian graphical models. This method is then compared with those developed by Bonifas et al. (1984) and Krzanowski (1987a, b). It appears that the criteria for all methods consider the same correlation submatrices and often lead to similar results. The proposed approach offers some guidance as to the number of variables to be selected. In particular, Akaike's information criterion is used.     

Doubly sparse regression incorporating graphical structure among predictors

Recent research has demonstrated that information learned from building a graphical model on the predictor set of a regularized linear regression model can be leveraged to improve prediction of a continuous outcome. In this article, we present a new model that encourages sparsity at both the level of the regression coefficients and the level of individual contributions in a decomposed representation. This model provides parameter estimates with a finite sample error bound and exhibits robustness to errors in the input graph structure. Through a simulation study and the analysis of two real data sets, we demonstrate that our model provides a predictive benefit when compared to previously proposed models. Furthermore, it is a highly flexible model that provides a unified framework for the fitting of many commonly used regularized regression models. The Canadian Journal of Statistics 47: 729–747; 2019 © 2019 Statistical Society of Canada     

On the Markov Equivalence of Chain Graphs, Undirected Graphs, and Acyclic Digraphs

Graphical Markov models use undirected graphs (UDGs), acyclic directed graphs (ADGs), or (mixed) chain graphs to represent possible dependencies among random variables in a multivariate distribution. Whereas a UDG is uniquely determined by its associated Markov model, this is not true for ADGs or for general chain graphs (which include both UDGs and ADGs as special cases). This paper addresses three questions regarding the equivalence of graphical Markov models: when is a given chain graph Markov equivalent (1) to some UDG? (2) to some (at least one) ADG? (3) to some decomposable UDG? The answers are obtained by means of an extension of Frydenberg’s (1990) elegant graph-theoretic characterization of the Markov equivalence of chain graphs.     

A Unified Approach to the Characterization of Equivalence Classes of DAGs, Chain Graphs with no Flags and Chain Graphs

Abstract.  A Markov property associates a set of conditional independencies to a graph. Two alternative Markov properties are available for chain graphs (CGs), the Lauritzen–Wermuth–Frydenberg (LWF) and the Andersson–Madigan– Perlman (AMP) Markov properties, which are different in general but coincide for the subclass of CGs with no flags . Markov equivalence induces a partition of the class of CGs into equivalence classes and every equivalence class contains a, possibly empty, subclass of CGs with no flags itself containing a, possibly empty, subclass of directed acyclic graphs (DAGs). LWF-Markov equivalence classes of CGs can be naturally characterized by means of the so-called largest CGs , whereas a graphical characterization of equivalence classes of DAGs is provided by the essential graphs . In this paper, we show the existence of largest CGs with no flags that provide a natural characterization of equivalence classes of CGs of this kind, with respect to both the LWF- and the AMP-Markov properties. We propose a procedure for the construction of the largest CGs, the largest CGs with no flags and the essential graphs, thereby providing a unified approach to the problem. As by-products we obtain a characterization of graphs that are largest CGs with no flags and an alternative characterization of graphs which are largest CGs. Furthermore, a known characterization of the essential graphs is shown to be a special case of our more general framework. The three graphical characterizations have a common structure: they use two versions of a locally verifiable graphical rule. Moreover, in case of DAGs, an immediate comparison of three characterizing graphs is possible.     

Collapsibility of Graphical CG-Regression Models

Abstract.  CG-regressions are multivariate regression models for mixed continuous and discrete responses that result from conditioning in the class of conditional Gaussian (CG) models. Their conditional independence structure can be read off a marked graph. The property of collapsibility, in this context, means that the multivariate CG-regression can be decomposed into lower dimensional regressions that are still CG and are consistent with the corresponding subgraphs. We derive conditions for this property that can easily be checked on the graph, and indicate computational advantages of this kind of collapsibility. Further, a simple graphical condition is given for checking whether a decomposition into univariate regressions is possible.     

Bayesian networks of customer satisfaction survey data

A Bayesian network (BN) is a probabilistic graphical model that represents a set of variables and their probabilistic dependencies. Formally, BNs are directed acyclic graphs whose nodes represent variables, and whose arcs encode the conditional dependencies among the variables. Nodes can represent any kind of variable, be it a measured parameter, a latent variable, or a hypothesis. They are not restricted to represent random variables, which form the “Bayesian” aspect of a BN. Efficient algorithms exist that perform inference and learning in BNs. BNs that model sequences of variables are called dynamic BNs. In this context, [A. Harel, R. Kenett, and F. Ruggeri, Modeling web usability diagnostics on the basis of usage statistics, in Statistical Methods in eCommerce Research, W. Jank and G. Shmueli, eds., Wiley, 2008] provide a comparison between Markov Chains and BNs in the analysis of web usability from e-commerce data. A comparison of regression models, structural equation models, and BNs is presented in Anderson et al. [R.D. Anderson, R.D. Mackoy, V.B. Thompson, and G. Harrell, A bayesian network estimation of the service–profit Chain for transport service satisfaction, Decision Sciences 35(4), (2004), pp. 665–689]. In this article we apply BNs to the analysis of customer satisfaction surveys and demonstrate the potential of the approach. In particular, BNs offer advantages in implementing models of cause and effect over other statistical techniques designed primarily for testing hypotheses. Other advantages include the ability to conduct probabilistic inference for prediction and diagnostic purposes with an output that can be intuitively understood by managers.     

Label‐ and Level‐Invariant Graphical Log‐Linear Models

We introduce two types of graphical log‐linear models: label‐ and level‐invariant models for triangle‐free graphs. These models generalise symmetry concepts in graphical log‐linear models and provide a tool with which to model symmetry in the discrete case. A label‐invariant model is category‐invariant and is preserved after permuting some of the vertices according to transformations that maintain the graph, whereas a level‐invariant model equates expected frequencies according to a given set of permutations. These new models can both be seen as instances of a new type of graphical log‐linear model termed the restricted graphical log‐linear model, or RGLL, in which equality restrictions on subsets of main effects and first‐order interactions are imposed. Their likelihood equations and graphical representation can be obtained from those derived for the RGLL models.     

Generic reversible jump MCMC using graphical models

Markov chain Monte Carlo techniques have revolutionized the field of Bayesian statistics. Their power is so great that they can even accommodate situations in which the structure of the statistical model itself is uncertain. However, the analysis of such trans-dimensional (TD) models is not easy and available software may lack the flexibility required for dealing with the complexities of real data, often because it does not allow the TD model to be simply part of some bigger model. In this paper we describe a class of widely applicable TD models that can be represented by a generic graphical model, which may be incorporated into arbitrary other graphical structures without significantly affecting the mechanism of inference. We also present a decomposition of the reversible jump algorithm into abstract and problem-specific components, which provides infrastructure for applying the method to all models in the class considered. These developments represent a first step towards a context-free method for implementing TD models that will facilitate their use by applied scientists for the practical exploration of model uncertainty. Our approach makes use of the popular WinBUGS framework as a sampling engine and we illustrate its use via two simple examples in which model uncertainty is a key feature.     

时间序列的图模型及其在股市相关性中的应用

图模型方法是高维数据统计分析的重要工具,时间序列的图模型方法有链图、因果图和偏相关图,将基于VAR模型的时间序列链图和因果图应用于国际股票市场,研究主要股指的动态相关性,结果表明：美国股市对周边股市的影响较大。将偏相关图应用于亚洲股票市场,研究亚洲主要股指的交互作用,结果表明：中国内地是相对独立的市场,中国香港、台湾以及新加坡、日本股票市场之间存在显著的信息流动。     

Graphs for Margins of Bayesian Networks

Directed acyclic graph (DAG) models—also called Bayesian networks—are widely used in probabilistic reasoning, machine learning and causal inference. If latent variables are present, then the set of possible marginal distributions over the remaining (observed) variables is generally not represented by any DAG. Larger classes of mixed graphical models have been introduced to overcome this; however, as we show, these classes are not sufficiently rich to capture all the marginal models that can arise. We introduce a new class of hyper‐graphs, called mDAGs, and a latent projection operation to obtain an mDAG from the margin of a DAG. We show that each distinct marginal of a DAG model is represented by at least one mDAG and provide graphical results towards characterizing equivalence of these models. Finally, we show that mDAGs correctly capture the marginal structure of causally interpreted DAGs under interventions on the observed variables.     

On Some Properties of Autopersistence Functions and Autopersistence Graphs

The classical autocorrelation function might not be very informative when measuring a dependence in binary time series. Recently, alternative tools, namely the autopersistence functions (APF) and their sample counterparts, the autpersistence graphs (APG), have been proposed for the analysis of dependent dichotomous variables. In this article, we summarize properties of the autopersistence functions for general binary series as well as for some important particular cases. We suggest a normalized version of APF which might be more convenient for a practical use. The asymptotic properties of autopersistence graphs are investigated. The consistency and asymptotic normality is discussed. The theoretical results are illustrated by a simulation study.     

Graphical evaluation of robust parameter designs based on extended scaled prediction variance and extended spherical average prediction variance

For any response surface design, there are locations in the design region where responses are estimated well and locations where estimation is relatively poor. Consequently, graphical evaluation—such as variance dispersion graphs and the fraction of design space—is used as an alternative to a single-valued criterion. Such plots are used to investigate and compare the prediction capabilities of certain response surface designs currently available to the researcher. In this article, we propose the extended scaled prediction variance and extended spherical average prediction variance as prediction methods. We also illustrate how graphical methods can be employed to evaluate robust parameter designs.     

Accuracy of variational estimates for random graph mixture models

Variational and variational Bayes techniques are popular approaches for statistical inference of complex models but their theoretical properties are still not well known. Because of both unobserved variables and intricate dependency structures, mixture models for random graphs constitute a good case study. We first present four different variational estimates for the parameters of these models. We then compare their accuracy through simulation studies and show that the variational Bayes estimates seem the most accurate for moderate graph size. We finally re-analyse the regulatory network of Escherichia coli with this approach.