Spanning trees of 3-uniform hypergraphs

Masbaum and Vaintrob's "Pfaffian matrix tree theorem" implies that counting spanning trees of a 3-uniform hypergraph (abbreviated to 3-graph) can be done in polynomial time for a class of "3-Pfaffian" 3-graphs, comparable to and related to the class of Pfaffian graphs. We prove a complexity result for recognizing a 3-Pfaffian 3-graph and describe two large classes of 3-Pfaffian 3-graphs -- one of these is given by a forbidden subgraph characterization analogous to Little's for bipartite Pfaffian graphs, and the other consists of a class of partial Steiner triple systems for which the property of being 3-Pfaffian can be reduced to the property of an associated graph being Pfaffian. We exhibit an infinite set of partial Steiner triple systems that are not 3-Pfaffian, none of which can be reduced to any other by deletion or contraction of triples. We also find some necessary or sufficient conditions for the existence of a spanning tree of a 3-graph (much more succinct than can be obtained by the currently fastest polynomial-time algorithm of Gabow and Stallmann for finding a spanning tree) and a superexponential lower bound on the number of spanning trees of a Steiner triple system.Comment: 34 pages, 9 figure

Minimal forbidden sets for degree sequence characterizations

Given a set F of graphs, a graph G is F-free if G does not contain any member of as an induced subgraph. A set F is degree-sequence-forcing (DSF) if, for each graph G in the class C of -free graphs, every realization of the degree sequence of G is also in C. A DSF set is minimal if no proper subset is also DSF. In this paper, we present new properties of minimal DSF sets, including that every graph is in a minimal DSF set and that there are only finitely many DSF sets of cardinality k. Using these properties and a computer search, we characterize the minimal DSF triples

The Parameterized Complexity of Finding Point Sets with Hereditary Properties

We consider problems where the input is a set of points in the plane and an integer k, and the task is to find a subset S of the input points of size k such that S satisfies some property. We focus on properties that depend only on the order type of the points and are monotone under point removals. We exhibit a property defined by three forbidden patterns for which finding a k-point subset with the property is W[1]-complete and (assuming the exponential time hypothesis) cannot be solved in time n^{o(k/log k)}. However, we show that problems of this type are fixed-parameter tractable for all properties that include all collinear point sets, properties that exclude at least one convex polygon, and properties defined by a single forbidden pattern

Hybrid tractability of soft constraint problems

The constraint satisfaction problem (CSP) is a central generic problem in computer science and artificial intelligence: it provides a common framework for many theoretical problems as well as for many real-life applications. Soft constraint problems are a generalisation of the CSP which allow the user to model optimisation problems. Considerable effort has been made in identifying properties which ensure tractability in such problems. In this work, we initiate the study of hybrid tractability of soft constraint problems; that is, properties which guarantee tractability of the given soft constraint problem, but which do not depend only on the underlying structure of the instance (such as being tree-structured) or only on the types of soft constraints in the instance (such as submodularity). We present several novel hybrid classes of soft constraint problems, which include a machine scheduling problem, constraint problems of arbitrary arities with no overlapping nogoods, and the SoftAllDiff constraint with arbitrary unary soft constraints. An important tool in our investigation will be the notion of forbidden substructures.Comment: A full version of a CP'10 paper, 26 page

The Erd\H{o}s-Rothschild problem on edge-colourings with forbidden monochromatic cliques

Let $\mathbf{k} := (k_1,\dots,k_s)$ be a sequence of natural numbers. For a graph $G$, let $F(G;\mathbf{k})$ denote the number of colourings of the edges of $G$ with colours $1,\dots,s$ such that, for every $c \in \{1,\dots,s\}$, the edges of colour $c$ contain no clique of order $k_c$. Write $F(n;\mathbf{k})$ to denote the maximum of $F(G;\mathbf{k})$ over all graphs $G$ on $n$ vertices. This problem was first considered by Erd\H{o}s and Rothschild in 1974, but it has been solved only for a very small number of non-trivial cases. We prove that, for every $\mathbf{k}$ and $n$, there is a complete multipartite graph $G$ on $n$ vertices with $F(G;\mathbf{k}) = F(n;\mathbf{k})$. Also, for every $\mathbf{k}$ we construct a finite optimisation problem whose maximum is equal to the limit of $\log_2 F(n;\mathbf{k})/{n\choose 2}$ as $n$ tends to infinity. Our final result is a stability theorem for complete multipartite graphs $G$, describing the asymptotic structure of such $G$ with $F(G;\mathbf{k}) = F(n;\mathbf{k}) \cdot 2^{o(n^2)}$ in terms of solutions to the optimisation problem.Comment: 16 pages, to appear in Math. Proc. Cambridge Phil. So

The history of degenerate (bipartite) extremal graph problems

This paper is a survey on Extremal Graph Theory, primarily focusing on the case when one of the excluded graphs is bipartite. On one hand we give an introduction to this field and also describe many important results, methods, problems, and constructions.Comment: 97 pages, 11 figures, many problems. This is the preliminary version of our survey presented in Erdos 100. In this version 2 only a citation was complete

Gene Family Histories: Theory and Algorithms

Detailed gene family histories and reconciliations with species trees are a prerequisite for studying associations between genetic and phenotypic innovations. Even though the true evolutionary scenarios are usually unknown, they impose certain constraints on the mathematical structure of data obtained from simple yes/no questions in pairwise comparisons of gene sequences. Recent advances in this field have led to the development of methods for reconstructing (aspects of) the scenarios on the basis of such relation data, which can most naturally be represented by graphs on the set of considered genes. We provide here novel characterizations of best match graphs (BMGs) which capture the notion of (reciprocal) best hits based on sequence similarities. BMGs provide the basis for the detection of orthologous genes (genes that diverged after a speciation event). There are two main sources of error in pipelines for orthology inference based on BMGs. Firstly, measurement errors in the estimation of best matches from sequence similarity in general lead to violations of the characteristic properties of BMGs. The second issue concerns the reconstruction of the orthology relation from a BMG. We show how to correct estimated BMG to mathematically valid ones and how much information about orthologs is contained in BMGs. We then discuss implicit methods for horizontal gene transfer (HGT) inference that focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of an undirected graph, the later-divergence-time (LDT) graph. We explore the mathematical structure of LDT graphs and show how much information about all HGT events is contained in such LDT graphs

A sharp threshold for random graphs with a monochromatic triangle in every edge coloring

Let $\R$ be the set of all finite graphs $G$ with the Ramsey property that every coloring of the edges of $G$ by two colors yields a monochromatic triangle. In this paper we establish a sharp threshold for random graphs with this property. Let $G(n,p)$ be the random graph on $n$ vertices with edge probability $p$. We prove that there exists a function $\hat c=\hat c(n)$ with $0 0$, as $n$ tends to infinity Pr[G(n,(1-\eps)\hat c/\sqrt{n}) \in \R ] \to 0 and Pr [ G(n,(1+\eps)\hat c/\sqrt{n}) \in \R ] \to 1. A crucial tool that is used in the proof and is of independent interest is a generalization of Szemer\'edi's Regularity Lemma to a certain hypergraph setting.Comment: 101 pages, Final version - to appear in Memoirs of the A.M.