Efficient Algorithms for Node Disjoint Subgraph Homeomorphism Determination

Recently, great efforts have been dedicated to researches on the management of large scale graph based data such as WWW, social networks, biological networks. In the study of graph based data management, node disjoint subgraph homeomorphism relation between graphs is more suitable than (sub)graph isomorphism in many cases, especially in those cases that node skipping and node mismatching are allowed. However, no efficient node disjoint subgraph homeomorphism determination (ndSHD) algorithms have been available. In this paper, we propose two computationally efficient ndSHD algorithms based on state spaces searching with backtracking, which employ many heuristics to prune the search spaces. Experimental results on synthetic data sets show that the proposed algorithms are efficient, require relative little time in most of the testing cases, can scale to large or dense graphs, and can accommodate to more complex fuzzy matching cases.Comment: 15 pages, 11 figures, submitted to DASFAA 200

Dynamics of surface diffeomorphisms relative to homoclinic and heteroclinic orbits

The Nielsen-Thurston theory of surface diffeomorphisms shows that useful dynamical information can be obtained about a surface diffeomorphism from a finite collection of periodic orbits.In this paper, we extend these results to homoclinic and heteroclinic orbits of saddle points. These orbits are most readily computed and studied as intersections of unstable and stable manifolds comprising homoclinic or heteroclinic tangles in the surface. We show how to compute a map of a one-dimensional space similar to a train-track which represents the isotopy-stable dynamics of the surface diffeomorphism relative to a tangle. All orbits of this one-dimensional representative are globally shadowed by orbits of the surface diffeomorphism, and periodic, homoclinic and heteroclinic orbits of the one-dimensional representative are shadowed by similar orbits in the surface.By constructing suitable surface diffeomorphisms, we prove that these results are optimal in the sense that the topological entropy of the one-dimensional representative is the greatest lower bound for the entropies of diffeomorphisms in the isotopy class.Comment: Version submitted to "Dynamical Systems: An International Journal" Section 7 has been further revised; the method for pA maps is new. Notation has been standardised throughou

Exact Localisations of Feedback Sets

The feedback arc (vertex) set problem, shortened FASP (FVSP), is to transform a given multi digraph $G=(V,E)$ into an acyclic graph by deleting as few arcs (vertices) as possible. Due to the results of Richard M. Karp in 1972 it is one of the classic NP-complete problems. An important contribution of this paper is that the subgraphs $G_{\mathrm{el}}(e)$, $G_{\mathrm{si}}(e)$ of all elementary cycles or simple cycles running through some arc $e \in E$, can be computed in $\mathcal{O}\big(|E|^2\big)$ and $\mathcal{O}(|E|^4)$, respectively. We use this fact and introduce the notion of the essential minor and isolated cycles, which yield a priori problem size reductions and in the special case of so called resolvable graphs an exact solution in $\mathcal{O}(|V||E|^3)$. We show that weighted versions of the FASP and FVSP possess a Bellman decomposition, which yields exact solutions using a dynamic programming technique in times $\mathcal{O}\big(2^{m}|E|^4\log(|V|)\big)$ and $\mathcal{O}\big(2^{n}\Delta(G)^4|V|^4\log(|E|)\big)$, where $m \leq |E|-|V| +1$, $n \leq (\Delta(G)-1)|V|-|E| +1$, respectively. The parameters $m,n$ can be computed in $\mathcal{O}(|E|^3)$, $\mathcal{O}(\Delta(G)^3|V|^3)$, respectively and denote the maximal dimension of the cycle space of all appearing meta graphs, decoding the intersection behavior of the cycles. Consequently, $m,n$ equal zero if all meta graphs are trees. Moreover, we deliver several heuristics and discuss how to control their variation from the optimum. Summarizing, the presented results allow us to suggest a strategy for an implementation of a fast and accurate FASP/FVSP-SOLVER

Dynamics of shear homeomorphisms of tori and the Bestvina-Handel algorithm

Sharkovskii proved that the existence of a periodic orbit in a one-dimensional dynamical system implies existence of infinitely many periodic orbits. We obtain an analog of Sharkovskii's theorem for periodic orbits of shear homeomorphisms of the torus. This is done by obtaining a dynamical order relation on the set of simple orbits and simple pairs. We then use this order relation for a global analysis for a quantum chaotic physical system called the kicked accelerated particle.Comment: 31 pages, 24 figures, to appear in Topological Methods in Nonlinear Analysi

Quantifying the Extent of Lateral Gene Transfer Required to Avert a `Genome of Eden'

The complex pattern of presence and absence of many genes across different species provides tantalising clues as to how genes evolved through the processes of gene genesis, gene loss and lateral gene transfer (LGT). The extent of LGT, particularly in prokaryotes, and its implications for creating a `network of life' rather than a `tree of life' is controversial. In this paper, we formally model the problem of quantifying LGT, and provide exact mathematical bounds, and new computational results. In particular, we investigate the computational complexity of quantifying the extent of LGT under the simple models of gene genesis, loss and transfer on which a recent heuristic analysis of biological data relied. Our approach takes advantage of a relationship between LGT optimization and graph-theoretical concepts such as tree width and network flow

Simple realizability of complete abstract topological graphs simplified

An abstract topological graph (briefly an AT-graph) is a pair $A=(G,\mathcal{X})$ where $G=(V,E)$ is a graph and $\mathcal{X}\subseteq {E \choose 2}$ is a set of pairs of its edges. The AT-graph $A$ is simply realizable if $G$ can be drawn in the plane so that each pair of edges from $\mathcal{X}$ crosses exactly once and no other pair crosses. We show that simply realizable complete AT-graphs are characterized by a finite set of forbidden AT-subgraphs, each with at most six vertices. This implies a straightforward polynomial algorithm for testing simple realizability of complete AT-graphs, which simplifies a previous algorithm by the author. We also show an analogous result for independent $\mathbb{Z}_2$-realizability, where only the parity of the number of crossings for each pair of independent edges is specified.Comment: 26 pages, 17 figures; major revision; original Section 5 removed and will be included in another pape

On retracts, absolute retracts, and folds in cographs

Let G and H be two cographs. We show that the problem to determine whether H is a retract of G is NP-complete. We show that this problem is fixed-parameter tractable when parameterized by the size of H. When restricted to the class of threshold graphs or to the class of trivially perfect graphs, the problem becomes tractable in polynomial time. The problem is also soluble when one cograph is given as an induced subgraph of the other. We characterize absolute retracts of cographs.Comment: 15 page