Linear kernels for outbranching problems in sparse digraphs

In the $k$-Leaf Out-Branching and $k$-Internal Out-Branching problems we are given a directed graph $D$ with a designated root $r$ and a nonnegative integer $k$. The question is to determine the existence of an outbranching rooted at $r$ that has at least $k$ leaves, or at least $k$ internal vertices, respectively. Both these problems were intensively studied from the points of view of parameterized complexity and kernelization, and in particular for both of them kernels with $O(k^2)$ vertices are known on general graphs. In this work we show that $k$-Leaf Out-Branching admits a kernel with $O(k)$ vertices on $\mathcal{H}$-minor-free graphs, for any fixed family of graphs $\mathcal{H}$, whereas $k$-Internal Out-Branching admits a kernel with $O(k)$ vertices on any graph class of bounded expansion.Comment: Extended abstract accepted for IPEC'15, 27 page

Flud: a hybrid crowd-algorithm approach for visualizing biological networks

Modern experiments in many disciplines generate large quantities of network (graph) data. Researchers require aesthetic layouts of these networks that clearly convey the domain knowledge and meaning. However, the problem remains challenging due to multiple conflicting aesthetic criteria and complex domain-specific constraints. In this paper, we present a strategy for generating visualizations that can help network biologists understand the protein interactions that underlie processes that take place in the cell. Specifically, we have developed Flud, an online game with a purpose (GWAP) that allows humans with no expertise to design biologically meaningful graph layouts with the help of algorithmically generated suggestions. Further, we propose a novel hybrid approach for graph layout wherein crowdworkers and a simulated annealing algorithm build on each other's progress. To showcase the effectiveness of Flud, we recruited crowd workers on Amazon Mechanical Turk to lay out complex networks that represent signaling pathways. Our results show that the proposed hybrid approach outperforms state-of-the-art techniques for graphs with a large number of feedback loops. We also found that the algorithmically generated suggestions guided the players when they are stuck and helped them improve their score. Finally, we discuss broader implications for mixed-initiative interactions in human computation games.Comment: This manuscript is currently under revie

Chasing the Rainbow Connection: Hardness, Algorithms, and Bounds

We study rainbow connectivity of graphs from the algorithmic and graph-theoretic points of view. The study is divided into three parts. First, we study the complexity of deciding whether a given edge-colored graph is rainbow-connected. That is, we seek to verify whether the graph has a path on which no color repeats between each pair of its vertices. We obtain a comprehensive map of the hardness landscape of the problem. While the problem is NP-complete in general, we identify several structural properties that render the problem tractable. At the same time, we strengthen the known NP-completeness results for the problem. We pinpoint various parameters for which the problem is fixed-parameter tractable, including dichotomy results for popular width parameters, such as treewidth and pathwidth. The study extends to variants of the problem that consider vertex-colored graphs and/or rainbow shortest paths. We also consider upper and lower bounds for exact parameterized algorithms. In particular, we show that when parameterized by the number of colors k, the existence of a rainbow s-t path can be decided in O∗ (2k ) time and polynomial space. For the highly related problem of finding a path on which all the k colors appear, i.e., a colorful path, we explain the modest progress over the last twenty years. Namely, we prove that the existence of an algorithm for finding a colorful path in (2 − ε)k nO(1) time for some ε > 0 disproves the so-called Set Cover Conjecture.Second, we focus on the problem of finding a rainbow coloring. The minimum number of colors for which a graph G is rainbow-connected is known as its rainbow connection number, denoted by rc(G). Likewise, the minimum number of colors required to establish a rainbow shortest path between each pair of vertices in G is known as its strong rainbow connection number, denoted by src(G). We give new hardness results for computing rc(G) and src(G), including their vertex variants. The hardness results exclude polynomial-time algorithms for restricted graph classes and also fast exact exponential-time algorithms (under reasonable complexity assumptions). For positive results, we show that rainbow coloring is tractable for e.g., graphs of bounded treewidth. In addition, we give positive parameterized results for certain variants and relaxations of the problems in which the goal is to save k colors from a trivial upper bound, or to rainbow connect only a certain number of vertex pairs.Third, we take a more graph-theoretic view on rainbow coloring. We observe upper bounds on the rainbow connection numbers in terms of other well-known graph parameters. Furthermore, despite the interest, there have been few results on the strong rainbow connection number of a graph. We give improved bounds and determine exactly the rainbow and strong rainbow connection numbers for some subclasses of chordal graphs. Finally, we pose open problems and conjectures arising from our work

EPTAS and Subexponential Algorithm for Maximum Clique on Disk and Unit Ball Graphs

A (unit) disk graph is the intersection graph of closed (unit) disks in the plane. Almost three decades ago, an elegant polynomial-time algorithm was found for Maximum Cliqe on unit disk graphs [Clark, Colbourn, Johnson; Discrete Mathematics ’90]. Since then, it has been an intriguing open question whether or not tractability can be extended to general disk graphs. We show that the disjoint union of two odd cycles is never the complement of a disk graph nor of a unit (3-dimensional) ball graph. From that fact and existing results, we derive a simple QPTAS and a subexponential algorithm running in time 2O˜(n2/3) for Maximum Cliqe on disk and unit ball graphs. We then obtain a randomized EPTAS for computing the independence number on graphs having no disjoint union of two odd cycles as an induced subgraph, bounded VC-dimension, and linear independence number. This, in combination with our structural results, yields a randomized EPTAS for Max Cliqe on disk and unit ball graphs. Max Cliqe on unit ball graphs is equivalent to finding, given a collection of points in R3, a maximum subset of points with diameter at most some fixed value. In stark contrast, Maximum Cliqe on ball graphs and unit 4-dimensional ball graphs, as well as intersection graphs of filled ellipses (even close to unit disks) or filled triangles is unlikely to have such algorithms. Indeed, we show that, for all those problems, there is a constant ratio of approximation which cannot be attained even in time 2n1−ε, unless the Exponential Time Hypothesis fails