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

Characterizations and algorithms for generalized Cops and Robbers games

We propose a definition of generalized Cops and Robbers games where there are two players, the Pursuer and the Evader, who each move via prescribed rules. If the Pursuer can ensure that the game enters into a fixed set of final positions, then the Pursuer wins; otherwise, the Evader wins. A relational characterization of the games where the Pursuer wins is provided. A precise formula is given for the length of the game, along with an algorithm for computing if the Pursuer has a winning strategy whose complexity is a function of the parameters of the game. For games where the position of one player does not affect the available moves of he other, a vertex elimination ordering characterization, analogous to a cop-win ordering, is given for when the Pursuer has a winning strategy

Building Efficient and Compact Data Structures for Simplicial Complexes

The Simplex Tree (ST) is a recently introduced data structure that can represent abstract simplicial complexes of any dimension and allows efficient implementation of a large range of basic operations on simplicial complexes. In this paper, we show how to optimally compress the Simplex Tree while retaining its functionalities. In addition, we propose two new data structures called the Maximal Simplex Tree (MxST) and the Simplex Array List (SAL). We analyze the compressed Simplex Tree, the Maximal Simplex Tree, and the Simplex Array List under various settings.Comment: An extended abstract appeared in the proceedings of SoCG 201

Quantified CTL: Expressiveness and Complexity

While it was defined long ago, the extension of CTL with quantification over atomic propositions has never been studied extensively. Considering two different semantics (depending whether propositional quantification refers to the Kripke structure or to its unwinding tree), we study its expressiveness (showing in particular that QCTL coincides with Monadic Second-Order Logic for both semantics) and characterise the complexity of its model-checking and satisfiability problems, depending on the number of nested propositional quantifiers (showing that the structure semantics populates the polynomial hierarchy while the tree semantics populates the exponential hierarchy)

Treewidth of display graphs: bounds, brambles and applications

Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a function of many common dissimilarity measures between phylogenetic trees and this has been leveraged in fixed parameter tractability results. Here we further elucidate the properties of display graphs and their interaction with treewidth. We show that it is NP-hard to recognize display graphs, but that display graphs of bounded treewidth can be recognized in linear time. Next we show that if a phylogenetic network displays (i.e. topologically embeds) a phylogenetic tree, the treewidth of their display graph is bounded by a function of the treewidth of the original network (and also by various other parameters). In fact, using a bramble argument we show that this treewidth bound is sharp up to an additive term of 1. We leverage this bound to give an FPT algorithm, parameterized by treewidth, for determining whether a network displays a tree, which is an intensively-studied problem in the field. We conclude with a discussion on the future use of display graphs and treewidth in phylogenetics