Graphical Markov models: overview

We describe how graphical Markov models started to emerge in the last 40 years, based on three essential concepts that had been developed independently more than a century ago. Sequences of joint or single regressions and their regression graphs are singled out as being best suited for analyzing longitudinal data and for tracing developmental pathways. Interpretations are illustrated using two sets of data and some of the more recent, important results for sequences of regressions are summarized.Comment: 22 pages, 9 figure

Edge-Stable Equimatchable Graphs

A graph $G$ is \emph{equimatchable} if every maximal matching of $G$ has the same cardinality. We are interested in equimatchable graphs such that the removal of any edge from the graph preserves the equimatchability. We call an equimatchable graph $G$ \emph{edge-stable} if $G\setminus {e}$, that is the graph obtained by the removal of edge $e$ from $G$, is also equimatchable for any $e \in E(G)$. After noticing that edge-stable equimatchable graphs are either 2-connected factor-critical or bipartite, we characterize edge-stable equimatchable graphs. This characterization yields an $O(\min(n^{3.376}, n^{1.5}m))$ time recognition algorithm. Lastly, we introduce and shortly discuss the related notions of edge-critical, vertex-stable and vertex-critical equimatchable graphs. In particular, we emphasize the links between our work and the well-studied notion of shedding vertices, and point out some open questions

Robustness: a New Form of Heredity Motivated by Dynamic Networks

We investigate a special case of hereditary property in graphs, referred to as {\em robustness}. A property (or structure) is called robust in a graph $G$ if it is inherited by all the connected spanning subgraphs of $G$. We motivate this definition using two different settings of dynamic networks. The first corresponds to networks of low dynamicity, where some links may be permanently removed so long as the network remains connected. The second corresponds to highly-dynamic networks, where communication links appear and disappear arbitrarily often, subject only to the requirement that the entities are temporally connected in a recurrent fashion ({\it i.e.} they can always reach each other through temporal paths). Each context induces a different interpretation of the notion of robustness. We start by motivating the definition and discussing the two interpretations, after what we consider the notion independently from its interpretation, taking as our focus the robustness of {\em maximal independent sets} (MIS). A graph may or may not admit a robust MIS. We characterize the set of graphs \forallMIS in which {\em all} MISs are robust. Then, we turn our attention to the graphs that {\em admit} a robust MIS (\existsMIS). This class has a more complex structure; we give a partial characterization in terms of elementary graph properties, then a complete characterization by means of a (polynomial time) decision algorithm that accepts if and only if a robust MIS exists. This algorithm can be adapted to construct such a solution if one exists

Message passing for vertex covers

Constructing a minimal vertex cover of a graph can be seen as a prototype for a combinatorial optimization problem under hard constraints. In this paper, we develop and analyze message passing techniques, namely warning and survey propagation, which serve as efficient heuristic algorithms for solving these computational hard problems. We show also, how previously obtained results on the typical-case behavior of vertex covers of random graphs can be recovered starting from the message passing equations, and how they can be extended.Comment: 25 pages, 9 figures - version accepted for publication in PR

Joint estimation of multiple related biological networks

Graphical models are widely used to make inferences concerning interplay in multivariate systems. In many applications, data are collected from multiple related but nonidentical units whose underlying networks may differ but are likely to share features. Here we present a hierarchical Bayesian formulation for joint estimation of multiple networks in this nonidentically distributed setting. The approach is general: given a suitable class of graphical models, it uses an exchangeability assumption on networks to provide a corresponding joint formulation. Motivated by emerging experimental designs in molecular biology, we focus on time-course data with interventions, using dynamic Bayesian networks as the graphical models. We introduce a computationally efficient, deterministic algorithm for exact joint inference in this setting. We provide an upper bound on the gains that joint estimation offers relative to separate estimation for each network and empirical results that support and extend the theory, including an extensive simulation study and an application to proteomic data from human cancer cell lines. Finally, we describe approximations that are still more computationally efficient than the exact algorithm and that also demonstrate good empirical performance.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS761 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org