Geometric tree graphs of points in convex position

Given a set $P$ of points in the plane, the geometric tree graph of $P$ is defined as the graph $T(P)$ whose vertices are non-crossing rectilinear spanning trees of $P$, and where two trees $T_1$ and $T_2$ are adjacent if $T_2 = T_1 -e+f$ for some edges $e$ and $f$. In this paper we concentrate on the geometric tree graph of a set of $n$ points in convex position, denoted by $G_n$. We prove several results about $G_n$, among them the existence of Hamilton cycles and the fact that they have maximum connectivity

Graphs of Edge-Intersecting Non-Splitting Paths in a Tree: Representations of Holes-Part II

Given a tree and a set P of non-trivial simple paths on it, VPT(P) is the VPT graph (i.e. the vertex intersection graph) of the paths P, and EPT(P) is the EPT graph (i.e. the edge intersection graph) of P. These graphs have been extensively studied in the literature. Given two (edge) intersecting paths in a graph, their split vertices is the set of vertices having degree at least 3 in their union. A pair of (edge) intersecting paths is termed non-splitting if they do not have split vertices (namely if their union is a path). We define the graph ENPT(P) of edge intersecting non-splitting paths of a tree, termed the ENPT graph, as the graph having a vertex for each path in P, and an edge between every pair of vertices representing two paths that are both edge-intersecting and non-splitting. A graph G is an ENPT graph if there is a tree T and a set of paths P of T such that G=ENPT(P), and we say that is a representation of G. Our goal is to characterize the representation of chordless ENPT cycles (holes). To achieve this goal, we first assume that the EPT graph induced by the vertices of an ENPT hole is given. In [2] we introduce three assumptions (P1), (P2), (P3) defined on EPT, ENPT pairs of graphs. In the same study, we define two problems HamiltonianPairRec, P3-HamiltonianPairRec and characterize the representations of ENPT holes that satisfy (P1), (P2), (P3). In this work, we continue our work by relaxing these three assumptions one by one. We characterize the representations of ENPT holes satisfying (P3) by providing a polynomial-time algorithm to solve P3-HamiltonianPairRec. We also show that there does not exist a polynomial-time algorithm to solve HamiltonianPairRec, unless P=NP

Geometric tree graphs of points in convex position

Given a set P of points in the plane, the geometric tree graph of P is defined as the graph T(P) whose vertices are non-crossing spanning with straight edges trees of P, and where two trees T1 and T2 are adjacent if T2 = T1 − e + f for some edges e and f. In this paper we concentrate on the geometric tree graph of a set of n points in convex position, denoted by Gn. We prove several results about Gn, among them the existence of Hamiltonian cycles and the fact that they have maximum connectivity

Lagrangian Relaxation for MAP Estimation in Graphical Models

We develop a general framework for MAP estimation in discrete and Gaussian graphical models using Lagrangian relaxation techniques. The key idea is to reformulate an intractable estimation problem as one defined on a more tractable graph, but subject to additional constraints. Relaxing these constraints gives a tractable dual problem, one defined by a thin graph, which is then optimized by an iterative procedure. When this iterative optimization leads to a consistent estimate, one which also satisfies the constraints, then it corresponds to an optimal MAP estimate of the original model. Otherwise there is a ``duality gap'', and we obtain a bound on the optimal solution. Thus, our approach combines convex optimization with dynamic programming techniques applicable for thin graphs. The popular tree-reweighted max-product (TRMP) method may be seen as solving a particular class of such relaxations, where the intractable graph is relaxed to a set of spanning trees. We also consider relaxations to a set of small induced subgraphs, thin subgraphs (e.g. loops), and a connected tree obtained by ``unwinding'' cycles. In addition, we propose a new class of multiscale relaxations that introduce ``summary'' variables. The potential benefits of such generalizations include: reducing or eliminating the ``duality gap'' in hard problems, reducing the number or Lagrange multipliers in the dual problem, and accelerating convergence of the iterative optimization procedure.Comment: 10 pages, presented at 45th Allerton conference on communication, control and computing, to appear in proceeding

Uprooted Phylogenetic Networks

The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard model of a phylogenetic tree by also allowing for cycles and have been introduced in rooted and unrooted form. In contrast to phylogenetic trees or their unrooted versions, rooted phylogenetic networks are notoriously difficult to understand. To help alleviate this, recent work on them has also centered on their “uprooted” versions. By focusing on such graphs and the combinatorial concept of a split system which underpins an unrooted phylogenetic network, we show that not only can a so-called (uprooted) 1-nested network N be obtained from the Buneman graph (sometimes also called a median network) associated with the split system  Σ(N)Σ(N)  induced on the set of leaves of N but also that that graph is, in a well-defined sense, optimal. Along the way, we establish the 1-nested analogue of the fundamental “splits equivalence theorem” for phylogenetic trees and characterize maximal circular split systems