Paradigms for Parameterized Enumeration

The aim of the paper is to examine the computational complexity and algorithmics of enumeration, the task to output all solutions of a given problem, from the point of view of parameterized complexity. First we define formally different notions of efficient enumeration in the context of parameterized complexity. Second we show how different algorithmic paradigms can be used in order to get parameter-efficient enumeration algorithms in a number of examples. These paradigms use well-known principles from the design of parameterized decision as well as enumeration techniques, like for instance kernelization and self-reducibility. The concept of kernelization, in particular, leads to a characterization of fixed-parameter tractable enumeration problems.Comment: Accepted for MFCS 2013; long version of the pape

Vertex and edge covers with clustering properties: complexity and algorithms

We consider the concepts of a t-total vertex cover and a t-total edge cover (t≥1), which generalise the notions of a vertex cover and an edge cover, respectively. A t-total vertex (respectively edge) cover of a connected graph G is a vertex (edge) cover S of G such that each connected component of the subgraph of G induced by S has at least t vertices (edges). These definitions are motivated by combining the concepts of clustering and covering in graphs. Moreover they yield a spectrum of parameters that essentially range from a vertex cover to a connected vertex cover (in the vertex case) and from an edge cover to a spanning tree (in the edge case). For various values of t, we present NP-completeness and approximability results (both upper and lower bounds) and FTP algorithms for problems concerned with finding the minimum size of a t-total vertex cover, t-total edge cover and connected vertex cover, in particular improving on a previous FTP algorithm for the latter problem

A list of parameterized problems in bioinformatics

In this report we present a list of problems that originated in bionformatics. Our aim is to collect information on such problems that have been analyzed from the point of view of Parameterized Complexity. For every problem we give its definition and biological motivation together with known complexity results.Postprint (published version

Towards Optimal and Expressive Kernelization for d-Hitting Set

d-Hitting Set is the NP-hard problem of selecting at most k vertices of a hypergraph so that each hyperedge, all of which have cardinality at most d, contains at least one selected vertex. The applications of d-Hitting Set are, for example, fault diagnosis, automatic program verification, and the noise-minimizing assignment of frequencies to radio transmitters. We show a linear-time algorithm that transforms an instance of d-Hitting Set into an equivalent instance comprising at most O(k^d) hyperedges and vertices. In terms of parameterized complexity, this is a problem kernel. Our kernelization algorithm is based on speeding up the well-known approach of finding and shrinking sunflowers in hypergraphs, which yields problem kernels with structural properties that we condense into the concept of expressive kernelization. We conduct experiments to show that our kernelization algorithm can kernelize instances with more than 10^7 hyperedges in less than five minutes. Finally, we show that the number of vertices in the problem kernel can be further reduced to O(k^{d-1}) with additional O(k^{1.5 d}) processing time by nontrivially combining the sunflower technique with d-Hitting Set problem kernels due to Abu-Khzam and Moser.Comment: This version gives corrected experimental results, adds additional figures, and more formally defines "expressive kernelization