On the Validity of the Markov Interpretation of Path Diagrams of Gaussian Structural Equations Systems with Correlated Errors

Pearl's d -separation concept and the ensuing Markov property is applied to graphs which may have, between each two different vertices i and j , any subset of { i ← j , i → j , i ↔ j } as edges. The class of graphs so obtained is closed under marginalization. Furthermore, the approach permits a direct proof of this theorem: "The distribution of a multivariate normal random vector satisfying a system of linear simultaneous equations is Markov w.r.t. the path diagram of the linear system".     

A SINful approach to Gaussian graphical model selection

Multivariate Gaussian graphical models are defined in terms of Markov properties, i.e., conditional independences, corresponding to missing edges in the graph. Thus model selection can be accomplished by testing these independences, which are equivalent to zero values of corresponding partial correlation coefficients. For concentration graphs, acyclic directed graphs, and chain graphs (both LWF and AMP classes), we apply Fisher's z-transform, Šidák's correlation inequality, and Holm's step-down procedure to simultaneously test the multiple hypotheses specified by these zero values. This simple method for model selection controls the overall error rate for incorrect edge inclusion. Prior information about the presence and/or absence of particular edges can be readily incorporated.     

On Block Ordering of Variables in Graphical Modelling

Abstract.  In graphical modelling, the existence of substantive background knowledge on block ordering of variables is used to perform structural learning within the family of chain graphs (CGs) in which every block corresponds to an undirected graph and edges joining vertices in different blocks are directed in accordance with the ordering. We show that this practice may lead to an inappropriate restriction of the search space and introduce the concept of labelled block ordering B corresponding to a family of B - consistent CGs in which every block may be either an undirected graph or a directed acyclic graph or, more generally, a CG. In this way we provide a flexible tool for specifying subsets of chain graphs, and we observe that the most relevant subsets of CGs considered in the literature are families of B -consistent CGs for the appropriate choice of B . Structural learning within a family of B -consistent CGs requires to deal with Markov equivalence. We provide a graphical characterization of equivalence classes of B -consistent CGs, namely the B - essential graphs , as well as a procedure to construct the B -essential graph for any given equivalence class of B -consistent chain graphs. Both largest CGs and essential graphs turn out to be special cases of B -essential 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.     

Alternative Markov Properties for Chain Graphs

Graphical Markov models use graphs to represent possible dependences among statistical variables. Lauritzen, Wermuth, and Frydenberg (LWF) introduced a Markov property for chain graphs (CG): graphs that can be used to represent both structural and associative dependences simultaneously and that include both undirected graphs (UG) and acyclic directed graphs (ADG) as special cases. Here an alternative Markov property (AMP) for CGs is introduced and shown to be the Markov property satisfied by a block-recursive linear system with multivariate normal errors. This model can be decomposed into a collection of conditional normal models, each of which combines the features of multivariate linear regression models and covariance selection models, facilitating the estimation of its parameters. In the general case, necessary and sufficient conditions are given for the equivalence of the LWF and AMP Markov properties of a CG, for the AMP Markov equivalence of two CGs, for the AMP Markov equivalence of a CG to some ADG or decomposable UG, and for other equivalences. For CGs, in some ways the AMP property is a more direct extension of the ADG Markov property than is the LWF property.     

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.     

Collapsibility for Directed Acyclic Graphs

Abstract.  Collapsibility means that the same statistical result of interest can be obtained before and after marginalization over some variables. In this paper, we discuss three kinds of collapsibility for directed acyclic graphs (DAGs): estimate collapsibility, conditional independence collapsibility and model collapsibility. Related to collapsibility, we discuss removability of variables from a DAG. We present conditions for these three different kinds of collapsibility and relationships among them. We give algorithms to find a minimum variable set containing a variable subset of interest onto which a statistical result is collapsible.     

Generic Identifiability of Linear Structural Equation Models by Ancestor Decomposition

Linear structural equation models, which relate random variables via linear interdependencies and Gaussian noise, are a popular tool for modelling multivariate joint distributions. The models correspond to mixed graphs that include both directed and bidirected edges representing the linear relationships and correlations between noise terms, respectively. A question of interest for these models is that of parameter identifiability, whether or not it is possible to recover edge coefficients from the joint covariance matrix of the random variables. For the problem of determining generic parameter identifiability, we present an algorithm building upon the half‐trek criterion. Underlying our new algorithm is the idea that ancestral subsets of vertices in the graph can be used to extend the applicability of a decomposition technique.     

Objective Bayes Factors for Gaussian Directed Acyclic Graphical Models

Abstract. We propose an objective Bayesian method for the comparison of all Gaussian directed acyclic graphical models defined on a given set of variables. The method, which is based on the notion of fractional Bayes factor (BF), requires a single default (typically improper) prior on the space of unconstrained covariance matrices, together with a prior sample size hyper‐parameter, which can be set to its minimal value. We show that our approach produces genuine BFs. The implied prior on the concentration matrix of any complete graph is a data‐dependent Wishart distribution, and this in turn guarantees that Markov equivalent graphs are scored with the same marginal likelihood. We specialize our results to the smaller class of Gaussian decomposable undirected graphical models and show that in this case they coincide with those recently obtained using limiting versions of hyper‐inverse Wishart distributions as priors on the graph‐constrained covariance matrices.     

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.     

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。     

Signed directed acyclic graphs for causal inference

Summary.  Formal rules governing signed edges on causal directed acyclic graphs are described and it is shown how these rules can be useful in reasoning about causality. Specifically, the notions of a monotonic effect, a weak monotonic effect and a signed edge are introduced. Results are developed relating these monotonic effects and signed edges to the sign of the causal effect of an intervention in the presence of intermediate variables. The incorporation of signed edges in the directed acyclic graph causal framework furthermore allows for the development of rules governing the relationship between monotonic effects and the sign of the covariance between two variables. It is shown that when certain assumptions about monotonic effects can be made then these results can be used to draw conclusions about the presence of causal effects even when data are missing on confounding variables.     

Scatter Plot and Additional Variables

We often want to complete the interpretation of the usual graphs (x, y) with additional quantitative variables. The Prefmap method (vectorial model) proposes a representation of these additional variables but this representation has some drawbacks when the variables x and y are correlated. To solve this problem, we propose to substitute the coefficients of the linear regression by the coefficient of the PLS regression in the Prefmap method. The graph obtained is made operational thanks to contour lines of quality of representation and it becomes richer than the Prefmap one.     

Characterization of discrete distributions using expected values

In this paper we study characterization problems for discrete distributions using the doubly truncated mean function m(xy)=E(h(X)|x≤X≤y), for a monotonic function h(x). We obtain the distribution function F(x) from m(x,y) and we give the necessary and sufficient conditions for any real function to be the doubly truncated mean function for a discrete distribution.     

Maximum Likelihood Estimation in Gaussian Chain Graph Models under the Alternative Markov Property

Abstract.  The Andersson–Madigan–Perlman (AMP) Markov property is a recently proposed alternative Markov property (AMP) for chain graphs. In the case of continuous variables with a joint multivariate Gaussian distribution, it is the AMP rather than the earlier introduced Lauritzen–Wermuth–Frydenberg Markov property that is coherent with data-generation by natural block-recursive regressions. In this paper, we show that maximum likelihood estimates in Gaussian AMP chain graph models can be obtained by combining generalized least squares and iterative proportional fitting to an iterative algorithm. In an appendix, we give useful convergence results for iterative partial maximization algorithms that apply in particular to the described algorithm.     

On the problem of augmented fractional factorial designs

Let D be a saturated fractional factorial design of the general K₁ x K₂ ...x K_t factorial such that it consists of m distinct treatment combinations and it is capable of providing an unbiased estimator of a subvector of m factorial parameters under the assumption that the remaining k-m,t (k = H it ) factorial parameters are negligible. Such a design will not provide an unbiased estimator of the varianceσ² Suppose that D is an optimal design with respect to some optimality criterion (e.g. d-optimality, a-optimality or e-optimality) and it is desirable to augment D with c treatmentcombinations with the aim to estimate ² Suppose that D is an optimal design with respect to some optimality criterion (e.g. d-optimality, a-optimality or e-optimality) and it is desirable to augment D with c treatment combinations with the aim to estimate σ² unbiasedly. The problem then is how to select the c treatment combinations such that the augmented design D retains its optimality property. This problem, in all its generality is extremely complex. The objective of this paper is to provide some insight in the problem by providing a partial answer in the case of the 2^tfactorial, using the d-optimality criterion.     

Bayesian analysis of directed graphs data with applications to social networks

Summary.  A fully Bayesian analysis of directed graphs, with particular emphasis on applica- tions in social networks, is explored. The model is capable of incorporating the effects of covariates, within and between block ties and multiple responses. Inference is straightforward by using software that is based on Markov chain Monte Carlo methods. Examples are provided which highlight the variety of data sets that can be entertained and the ease with which they can be analysed.     

Confidence Intervals and the Within-the-Bar Bias

Bar graphs displaying means have been shown to bias interpretations of the underlying distributions: viewers typically report higher likelihoods for values within a bar than outside of a bar. One explanation is that viewer attention is driven by the whole bar, rather than only the edge that provides information about an average. This study explored several approaches to correcting this bias. Bar graphs with 95% confidence intervals were used with different levels of contrast to manipulate attention directed to the bar. Viewers showed less bias when the salience of the bar itself was reduced. Response latencies were lowest and bias was eliminated when participants were presented with only a confidence interval and no bar.     

Copula directed acyclic graphs

A new methodology for selecting a Bayesian network for continuous data outside the widely used class of multivariate normal distributions is developed. The ‘copula DAGs’ combine directed acyclic graphs and their associated probability models with copula C/D-vines. Bivariate copula densities introduce flexibility in the joint distributions of pairs of nodes in the network. An information criterion is studied for graph selection tailored to the joint modeling of data based on graphs and copulas. Examples and simulation studies show the flexibility and properties of the method.