A polynomial algorithm for the k-cluster problem on interval graphs

This paper deals with the problem of finding, for a given graph and a given natural number k, a subgraph of k nodes with a maximum number of edges. This problem is known as the k-cluster problem and it is NP-hard on general graphs as well as on chordal graphs. In this paper, it is shown that the k-cluster problem is solvable in polynomial time on interval graphs. In particular, we present two polynomial time algorithms for the class of proper interval graphs and the class of general interval graphs, respectively. Both algorithms are based on a matrix representation for interval graphs. In contrast to representations used in most of the previous work, this matrix representation does not make use of the maximal cliques in the investigated graph.Comment: 12 pages, 5 figure

Interval scheduling and colorful independent sets

Numerous applications in scheduling, such as resource allocation or steel manufacturing, can be modeled using the NP-hard Independent Set problem (given an undirected graph and an integer k, find a set of at least k pairwise non-adjacent vertices). Here, one encounters special graph classes like 2-union graphs (edge-wise unions of two interval graphs) and strip graphs (edge-wise unions of an interval graph and a cluster graph), on which Independent Set remains NP-hard but admits constant-ratio approximations in polynomial time. We study the parameterized complexity of Independent Set on 2-union graphs and on subclasses like strip graphs. Our investigations significantly benefit from a new structural "compactness" parameter of interval graphs and novel problem formulations using vertex-colored interval graphs. Our main contributions are: 1. We show a complexity dichotomy: restricted to graph classes closed under induced subgraphs and disjoint unions, Independent Set is polynomial-time solvable if both input interval graphs are cluster graphs, and is NP-hard otherwise. 2. We chart the possibilities and limits of effective polynomial-time preprocessing (also known as kernelization). 3. We extend Halld\'orsson and Karlsson (2006)'s fixed-parameter algorithm for Independent Set on strip graphs parameterized by the structural parameter "maximum number of live jobs" to show that the problem (also known as Job Interval Selection) is fixed-parameter tractable with respect to the parameter k and generalize their algorithm from strip graphs to 2-union graphs. Preliminary experiments with random data indicate that Job Interval Selection with up to fifteen jobs and 5*10^5 intervals can be solved optimally in less than five minutes.Comment: This revision does not contain Theorem 7 of the first revision, whose proof contained an erro

Structural parameterizations for boxicity

The boxicity of a graph $G$ is the least integer $d$ such that $G$ has an intersection model of axis-aligned $d$-dimensional boxes. Boxicity, the problem of deciding whether a given graph $G$ has boxicity at most $d$, is NP-complete for every fixed $d \ge 2$. We show that boxicity is fixed-parameter tractable when parameterized by the cluster vertex deletion number of the input graph. This generalizes the result of Adiga et al., that boxicity is fixed-parameter tractable in the vertex cover number. Moreover, we show that boxicity admits an additive $1$-approximation when parameterized by the pathwidth of the input graph. Finally, we provide evidence in favor of a conjecture of Adiga et al. that boxicity remains NP-complete when parameterized by the treewidth.Comment: 19 page

Next Generation Cluster Editing

This work aims at improving the quality of structural variant prediction from the mapped reads of a sequenced genome. We suggest a new model based on cluster editing in weighted graphs and introduce a new heuristic algorithm that allows to solve this problem quickly and with a good approximation on the huge graphs that arise from biological datasets

Spanning trees short or small

We study the problem of finding small trees. Classical network design problems are considered with the additional constraint that only a specified number $k$ of nodes are required to be connected in the solution. A prototypical example is the $k$MST problem in which we require a tree of minimum weight spanning at least $k$ nodes in an edge-weighted graph. We show that the $k$MST problem is NP-hard even for points in the Euclidean plane. We provide approximation algorithms with performance ratio $2\sqrt{k}$ for the general edge-weighted case and $O(k^{1/4})$ for the case of points in the plane. Polynomial-time exact solutions are also presented for the class of decomposable graphs which includes trees, series-parallel graphs, and bounded bandwidth graphs, and for points on the boundary of a convex region in the Euclidean plane. We also investigate the problem of finding short trees, and more generally, that of finding networks with minimum diameter. A simple technique is used to provide a polynomial-time solution for finding $k$-trees of minimum diameter. We identify easy and hard problems arising in finding short networks using a framework due to T. C. Hu.Comment: 27 page

Fast Biclustering by Dual Parameterization

We study two clustering problems, Starforest Editing, the problem of adding and deleting edges to obtain a disjoint union of stars, and the generalization Bicluster Editing. We show that, in addition to being NP-hard, none of the problems can be solved in subexponential time unless the exponential time hypothesis fails. Misra, Panolan, and Saurabh (MFCS 2013) argue that introducing a bound on the number of connected components in the solution should not make the problem easier: In particular, they argue that the subexponential time algorithm for editing to a fixed number of clusters (p-Cluster Editing) by Fomin et al. (J. Comput. Syst. Sci., 80(7) 2014) is an exception rather than the rule. Here, p is a secondary parameter, bounding the number of components in the solution. However, upon bounding the number of stars or bicliques in the solution, we obtain algorithms which run in time $2^{5 \sqrt{pk}} + O(n+m)$ for p-Starforest Editing and $2^{O(p \sqrt{k} \log(pk))} + O(n+m)$ for p-Bicluster Editing. We obtain a similar result for the more general case of t-Partite p-Cluster Editing. This is subexponential in k for fixed number of clusters, since p is then considered a constant. Our results even out the number of multivariate subexponential time algorithms and give reasons to believe that this area warrants further study.Comment: Accepted for presentation at IPEC 201

Approximation Algorithms for Polynomial-Expansion and Low-Density Graphs

We study the family of intersection graphs of low density objects in low dimensional Euclidean space. This family is quite general, and includes planar graphs. We prove that such graphs have small separators. Next, we present efficient $(1+\varepsilon)$-approximation algorithms for these graphs, for Independent Set, Set Cover, and Dominating Set problems, among others. We also prove corresponding hardness of approximation for some of these optimization problems, providing a characterization of their intractability in terms of density