An Algorithmic Meta-Theorem for Graph Modification to Planarity and FOL

In general, a graph modification problem is defined by a graph modification operation $\boxtimes$ and a target graph property ${\cal P}$. Typically, the modification operation $\boxtimes$ may be vertex removal}, edge removal}, edge contraction}, or edge addition and the question is, given a graph $G$ and an integer $k$, whether it is possible to transform $G$ to a graph in ${\cal P}$ after applying $k$ times the operation $\boxtimes$ on $G$. This problem has been extensively studied for particilar instantiations of $\boxtimes$ and ${\cal P}$. In this paper we consider the general property ${\cal P}_{{\phi}}$ of being planar and, moreover, being a model of some First-Order Logic sentence ${\phi}$ (an FOL-sentence). We call the corresponding meta-problem Graph $\boxtimes$-Modification to Planarity and ${\phi}$ and prove the following algorithmic meta-theorem: there exists a function $f:\Bbb{N}^{2}\to\Bbb{N}$ such that, for every $\boxtimes$ and every FOL sentence ${\phi}$, the Graph $\boxtimes$-Modification to Planarity and ${\phi}$ is solvable in $f(k,|{\phi}|)\cdot n^2$ time. The proof constitutes a hybrid of two different classic techniques in graph algorithms. The first is the irrelevant vertex technique that is typically used in the context of Graph Minors and deals with properties such as planarity or surface-embeddability (that are not FOL-expressible) and the second is the use of Gaifman's Locality Theorem that is the theoretical base for the meta-algorithmic study of FOL-expressible problems

Computing k-Modal Embeddings of Planar Digraphs

Given a planar digraph G and a positive even integer k, an embedding of G in the plane is k-modal, if every vertex of G is incident to at most k pairs of consecutive edges with opposite orientations, i.e., the incoming and the outgoing edges at each vertex are grouped by the embedding into at most k sets of consecutive edges with the same orientation. In this paper, we study the k-Modality problem, which asks for the existence of a k-modal embedding of a planar digraph. This combinatorial problem is at the very core of a variety of constrained embedding questions for planar digraphs and flat clustered networks. First, since the 2-Modality problem can be easily solved in linear time, we consider the general k-Modality problem for any value of k>2 and show that the problem is NP-complete for planar digraphs of maximum degree Delta <= k+3. We relate its computational complexity to that of two notions of planarity for flat clustered networks: Planar Intersection-Link and Planar NodeTrix representations. This allows us to answer in the strongest possible way an open question by Di Giacomo [https://doi.org/10.1007/978-3-319-73915-1_37], concerning the complexity of constructing planar NodeTrix representations of flat clustered networks with small clusters, and to address a research question by Angelini et al. [https://doi.org/10.7155/jgaa.00437], concerning intersection-link representations based on geometric objects that determine complex arrangements. On the positive side, we provide a simple FPT algorithm for partial 2-trees of arbitrary degree, whose running time is exponential in k and linear in the input size. Second, motivated by the recently-introduced planar L-drawings of planar digraphs [https://doi.org/10.1007/978-3-319-73915-1_36], which require the computation of a 4-modal embedding, we focus our attention on k=4. On the algorithmic side, we show a complexity dichotomy for the 4-Modality problem with respect to Delta, by providing a linear-time algorithm for planar digraphs with Delta <= 6. This algorithmic result is based on decomposing the input digraph into its blocks via BC-trees and each of these blocks into its triconnected components via SPQR-trees. In particular, we are able to show that the constraints imposed on the embedding by the rigid triconnected components can be tackled by means of a small set of reduction rules and discover that the algorithmic core of the problem lies in special instances of NAESAT, which we prove to be always NAE-satisfiable - a result of independent interest that improves on Porschen et al. [https://doi.org/10.1007/978-3-540-24605-3_14]. Finally, on the combinatorial side, we consider outerplanar digraphs and show that any such a digraph always admits a k-modal embedding with k=4 and that this value of k is best possible for the digraphs in this family

Numerical integration of massive two-loop Mellin-Barnes integrals in Minkowskian regions

Mellin-Barnes (MB) techniques applied to integrals emerging in particle physics perturbative calculations are summarized. New versions of AMBRE packages which construct planar and nonplanar MB representations are shortly discussed. The numerical package MBnumerics.m is presented for the first time which is able to calculate with a high precision multidimensional MB integrals in Minkowskian regions. Examples are given for massive vertex integrals which include threshold effects and several scale parameters.Comment: Proceedings for 13th DESY Workshop on Elementary Particle Physics: Loops and Legs in Quantum Field Theory (LL2016), final PoS versio

Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex

We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA segments. We analyze such experiments for the Mu protein-DNA complex. We characterize the solutions to the corresponding tangle equations by certain knotted graphs. By investigating planarity conditions on these graphs we show that there is a unique biologically relevant solution. That is, we show there is a unique rational tangle solution, which is also the unique solution with small crossing number.Comment: 60 pages, 74 figure

L-Drawings of Directed Graphs

We introduce L-drawings, a novel paradigm for representing directed graphs aiming at combining the readability features of orthogonal drawings with the expressive power of matrix representations. In an L-drawing, vertices have exclusive $x$- and $y$-coordinates and edges consist of two segments, one exiting the source vertically and one entering the destination horizontally. We study the problem of computing L-drawings using minimum ink. We prove its NP-completeness and provide a heuristics based on a polynomial-time algorithm that adds a vertex to a drawing using the minimum additional ink. We performed an experimental analysis of the heuristics which confirms its effectiveness.Comment: 11 pages, 7 figure

A compositional algorithm for parallel model checking of polygonal hybrid systems

The reachability problem as well as the computation of the phase portrait for the class of planar hybrid systems defined by constant differential inclusions (SPDI), has been shown to be decidable. The existing reachability algorithm is based on the exploitation of topological properties of the plane which are used to accelerate certain kind of cycles. The complexity of the algorithm makes the analysis of large systems generally unfeasible. In this paper we present a compositional parallel algorithm for reachability analysis of SPDIs. The parallelization is based on the qualitative information obtained from the phase portrait of an SPDI, in particular the controllability kernel.The United Nations Univ., Int. Inst. for Softw. Technol., Macau,Tunisian Ministry of Higher Education,University of New South Wales, UKpeer-reviewe