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, 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 Bayes factors. 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.

This paper introduces a novel class of models for binary data, which we call log-mean linear models. The characterizing feature of these models is that they are specified by linear constraints on the log-mean linear parameter, defined as a log-linear expansion of the mean parameter of the multivariate Bernoulli distribution. We show that marginal independence relationships between variables can be specified by setting certain log-mean linear interactions to zero and, more specifically, that graphical models of marginal independence are log-mean linear models. Our approach overcomes some drawbacks of the existing parameterizations of graphical models of marginal independence.

We present an objective Bayes method for covariance selection in Gaussian multivariate regression models having a sparse regression and covariance structure, the latter being Markov with respect to a directed acyclic graph (DAG). Our procedure can be easily complemented with a variable selection step, so that variable and graphical model selection can be performed jointly. In this way, we offer a solution to a problem of growing importance especially in the area of genetical genomics (eQTL analysis). The input of our method is a single default prior, essentially involving no subjective elicitation, while its output is a closed form marginal likelihood for every covariate-adjusted DAG model, which is constant over each class of Markov equivalent DAGs; our procedure thus naturally encompasses covariate-adjusted decomposable graphical models. In realistic experimental studies, our method is highly competitive, especially when the number of responses is large relative to the sample size

A well-known hypothesis, with far-reaching implications, is that biological evolution should preferentially lead to states that are dynamically critical. In previous papers, we showed that a well-known model of genetic regulatory networks, namely, that of random Boolean networks, allows one to study in depth the relationship between the dynamical regime of a living being’s gene network and its response to permanent perturbations. In this paper, we analyze a huge set of new experimental data on single gene knockouts in S. cerevisiae, laying down a statistical framework to determine its dynamical regime. We find that the S. cerevisiae network appears to be slightly ordered, but close to the critical region. Since our analysis relies on dichotomizing continuous data, we carefully consider the issue of an optimal threshold choice.

Directed acyclic graphical (DAG) models are increasingly employed in the study of physical and biological systems to model direct influences between variables. Identifying the graph from data is a challenging endeavor, which can be more reasonably tackled if the variables are assumed to satisfy a given ordering; in this case we simply have to estimate the presence or absence of each potential edge. Working under this assumption, we propose an objective Bayesian method for searching the space of Gaussian DAG models, which provides a rich output from minimal input. We base our analysis on non-local parameter priors, which are especially suited for learning sparse graphs, because they allow a faster learning rate, relative to ordinary local parameter priors, when the true unknown sampling distribution belongs to a simple model. We implement an efficient stochastic search algorithm, which deals effectively with data sets having sample size smaller than the number of variables, and apply our method to a variety of simulated and real data sets. Our approach compares favorably, in terms of the ROC curve for edge hit rate versus false alarm rate, to current state-of-the-art frequentist methods relying on the assumption of ordered variables; under this assumption it exhibits a competitive advantage over the PC-algorithm, which can be considered as a frequentist benchmark for unordered variables. Importantly, we find that our method is still at an advantage for learning the skeleton of the DAG, when the ordering of the variables is only moderately mis-specified. Prospectively, our method could be coupled with a strategy to learn the order of the variables, thus dropping the known ordering assumption.

Standard-Nutzungsbedingungen:Die Dokumente auf EconStor dürfen zu eigenen wissenschaftlichen Zwecken und zum Privatgebrauch gespeichert und kopiert werden.Sie dürfen die Dokumente nicht für öffentliche oder kommerzielle Zwecke vervielfältigen, öffentlich ausstellen, öffentlich zugänglich machen, vertreiben oder anderweitig nutzen.Sofern die Verfasser die Dokumente unter Open-Content-Lizenzen (insbesondere CC-Lizenzen) zur Verfügung gestellt haben sollten, gelten abweichend von diesen Nutzungsbedingungen die in der dort genannten Lizenz gewährten Nutzungsrechte. We propose a new method for the objective comparison of two nested models based on non-local priors. More specifically, starting with a default prior under each of the two models, we construct a moment prior under the larger model, and then use the fractional Bayes factor for a comparison. Non-local priors have been recently introduced to obtain a better separation between nested models, thus accelerating the learning behaviour, relative to currently used local priors, when the smaller model holds. Although the argument showing the superior performance of non-local priors is asymptotic, the improvement they produce is already apparent for small to moderate samples sizes, which makes them a useful and practical tool. As a by-product, it turns out that routinely used objective methods, such as ordinary fractional Bayes factors, are alarmingly slow in learning that the smaller model holds. On the downside, when the larger model holds, non-local priors exhibit a weaker discriminatory power against sampling distributions close to the smaller model. However, this drawback becomes rapidly negligible as the sample size grows, because the learning rate of the Bayes factor under the larger model is exponentially fast, whether one uses local or non-local priors. We apply our methodology to directed acyclic graph models having a Gaussian distribution. Because of the recursive nature of the joint density, and the assumption of global parameter independence embodied in our prior, calculations need only be performed for individual vertices admitting a distinct parent structure under the two graphs; additionally we obtain closed-form expressions as in the ordinary conjugate case. We provide illustrations of our method for a simple three-variable case, as well as for a more elaborate seven-variable situation. Although we concentrate on pairwise comparisons of nested models, our procedure can be implemented to carry-out a search over the space of all models. Terms of use: Documents inJune 2010.

Correlated proportions arise in longitudinal (panel) studies. A typical example is the "opinion swing" problem: "Has the proportion of people favoring a politician changed after his recent speech to the nation on TV?". Since the same group of individuals is interviewed before and after the speech, the two proportions are correlated. A natural null hypothesis to be tested is whether the corresponding population proportions are equal. A standard Bayesian approach to this problem has already been considered in the literature, based on a Dirichlet prior for the cell-probabilities of the underlying two-by-two table under the alternative hypothesis, together with an induced prior under the null.In lack of specific prior information, a diffuse (e.g. uniform) distribution may be used. We claim that this approach is not satisfactory, since in a testing problem one should make sure that the prior under the alternative be adequately centered around the region specified by the null, in order to obtain a fair comparison between the two hypotheses. Following an intrinsic prior methodology, we develop two strategies for the construction of a collection of objective priors increasingly peaked around the null. We provide a simple interpretation of their structure in terms of weighted imaginary sample scenarios. We illustrate our method by means of three examples, carrying out sensitivity analysis and providing comparison with existing results.

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 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 chain graphs in which every block may be either an undirected graph or a directed acyclic graph or, more generally, a chain graph. In this way we provide a flexible tool for specifying subsets of chain graphs, and we observe that the most relevant subsets of chain graphs considered in the literature are families of B-consistent chain graphs for the appropriate choice of B. Structural learning within a family of B-consistent chain graphs requires to deal with Markov equivalence. We provide a graphical characterisation of equivalence classes of B-consistent chain graphs, 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 chain graphs and essential graphs turn out to be special cases of B-essential graphs.