Separation dimension of bounded degree graphs

The 'separation dimension' of a graph $G$ is the smallest natural number $k$ for which the vertices of $G$ can be embedded in $\mathbb{R}^k$ such that any pair of disjoint edges in $G$ can be separated by a hyperplane normal to one of the axes. Equivalently, it is the smallest possible cardinality of a family $\mathcal{F}$ of total orders of the vertices of $G$ such that for any two disjoint edges of $G$, there exists at least one total order in $\mathcal{F}$ in which all the vertices in one edge precede those in the other. In general, the maximum separation dimension of a graph on $n$ vertices is $\Theta(\log n)$. In this article, we focus on bounded degree graphs and show that the separation dimension of a graph with maximum degree $d$ is at most $2^{9log^{\star} d} d$. We also demonstrate that the above bound is nearly tight by showing that, for every $d$, almost all $d$-regular graphs have separation dimension at least $\lceil d/2\rceil$.Comment: One result proved in this paper is also present in arXiv:1212.675

On combinatorial optimisation in analysis of protein-protein interaction and protein folding networks

Abstract: Protein-protein interaction networks and protein folding networks represent prominent research topics at the intersection of bioinformatics and network science. In this paper, we present a study of these networks from combinatorial optimisation point of view. Using a combination of classical heuristics and stochastic optimisation techniques, we were able to identify several interesting combinatorial properties of biological networks of the COSIN project. We obtained optimal or near-optimal solutions to maximum clique and chromatic number problems for these networks. We also explore patterns of both non-overlapping and overlapping cliques in these networks. Optimal or near-optimal solutions to partitioning of these networks into non-overlapping cliques and to maximum independent set problem were discovered. Maximal cliques are explored by enumerative techniques. Domination in these networks is briefly studied, too. Applications and extensions of our findings are discussed

The Minrank of Random Graphs

The minrank of a graph $G$ is the minimum rank of a matrix $M$ that can be obtained from the adjacency matrix of $G$ by switching some ones to zeros (i.e., deleting edges) and then setting all diagonal entries to one. This quantity is closely related to the fundamental information-theoretic problems of (linear) index coding (Bar-Yossef et al., FOCS'06), network coding and distributed storage, and to Valiant's approach for proving superlinear circuit lower bounds (Valiant, Boolean Function Complexity '92). We prove tight bounds on the minrank of random Erd\H{o}s-R\'enyi graphs $G(n,p)$ for all regimes of $p\in[0,1]$. In particular, for any constant $p$, we show that $\mathsf{minrk}(G) = \Theta(n/\log n)$ with high probability, where $G$ is chosen from $G(n,p)$. This bound gives a near quadratic improvement over the previous best lower bound of $\Omega(\sqrt{n})$ (Haviv and Langberg, ISIT'12), and partially settles an open problem raised by Lubetzky and Stav (FOCS '07). Our lower bound matches the well-known upper bound obtained by the "clique covering" solution, and settles the linear index coding problem for random graphs. Finally, our result suggests a new avenue of attack, via derandomization, on Valiant's approach for proving superlinear lower bounds for logarithmic-depth semilinear circuits

From the Ising and Potts models to the general graph homomorphism polynomial

In this note we study some of the properties of the generating polynomial for homomorphisms from a graph to at complete weighted graph on $q$ vertices. We discuss how this polynomial relates to a long list of other well known graph polynomials and the partition functions for different spin models, many of which are specialisations of the homomorphism polynomial. We also identify the smallest graphs which are not determined by their homomorphism polynomials for $q=2$ and $q=3$ and compare this with the corresponding minimal examples for the $U$-polynomial, which generalizes the well known Tutte-polynomal.Comment: V2. Extended versio