Compression via Matroids: A Randomized Polynomial Kernel for Odd Cycle Transversal

The Odd Cycle Transversal problem (OCT) asks whether a given graph can be made bipartite by deleting at most $k$ of its vertices. In a breakthrough result Reed, Smith, and Vetta (Operations Research Letters, 2004) gave a \BigOh(4^kkmn) time algorithm for it, the first algorithm with polynomial runtime of uniform degree for every fixed $k$. It is known that this implies a polynomial-time compression algorithm that turns OCT instances into equivalent instances of size at most \BigOh(4^k), a so-called kernelization. Since then the existence of a polynomial kernel for OCT, i.e., a kernelization with size bounded polynomially in $k$, has turned into one of the main open questions in the study of kernelization. This work provides the first (randomized) polynomial kernelization for OCT. We introduce a novel kernelization approach based on matroid theory, where we encode all relevant information about a problem instance into a matroid with a representation of size polynomial in $k$. For OCT, the matroid is built to allow us to simulate the computation of the iterative compression step of the algorithm of Reed, Smith, and Vetta, applied (for only one round) to an approximate odd cycle transversal which it is aiming to shrink to size $k$. The process is randomized with one-sided error exponentially small in $k$, where the result can contain false positives but no false negatives, and the size guarantee is cubic in the size of the approximate solution. Combined with an \BigOh(\sqrt{\log n})-approximation (Agarwal et al., STOC 2005), we get a reduction of the instance to size \BigOh(k^{4.5}), implying a randomized polynomial kernelization.Comment: Minor changes to agree with SODA 2012 version of the pape

Linear Time Parameterized Algorithms via Skew-Symmetric Multicuts

A skew-symmetric graph $(D=(V,A),\sigma)$ is a directed graph $D$ with an involution $\sigma$ on the set of vertices and arcs. In this paper, we introduce a separation problem, $d$-Skew-Symmetric Multicut, where we are given a skew-symmetric graph $D$, a family of $\cal T$ of $d$-sized subsets of vertices and an integer $k$. The objective is to decide if there is a set $X\subseteq A$ of $k$ arcs such that every set $J$ in the family has a vertex $v$ such that $v$ and $\sigma(v)$ are in different connected components of $D'=(V,A\setminus (X\cup \sigma(X))$. In this paper, we give an algorithm for this problem which runs in time $O((4d)^{k}(m+n+\ell))$, where $m$ is the number of arcs in the graph, $n$ the number of vertices and $\ell$ the length of the family given in the input. Using our algorithm, we show that Almost 2-SAT has an algorithm with running time $O(4^kk^4\ell)$ and we obtain algorithms for {\sc Odd Cycle Transversal} and {\sc Edge Bipartization} which run in time $O(4^kk^4(m+n))$ and $O(4^kk^5(m+n))$ respectively. This resolves an open problem posed by Reed, Smith and Vetta [Operations Research Letters, 2003] and improves upon the earlier almost linear time algorithm of Kawarabayashi and Reed [SODA, 2010]. We also show that Deletion q-Horn Backdoor Set Detection is a special case of 3-Skew-Symmetric Multicut, giving us an algorithm for Deletion q-Horn Backdoor Set Detection which runs in time $O(12^kk^5\ell)$. This gives the first fixed-parameter tractable algorithm for this problem answering a question posed in a paper by a superset of the authors [STACS, 2013]. Using this result, we get an algorithm for Satisfiability which runs in time $O(12^kk^5\ell)$ where $k$ is the size of the smallest q-Horn deletion backdoor set, with $\ell$ being the length of the input formula

A spectral method for bipartizing a network and detecting a large anti-community

Relations between discrete quantities such as people, genes, or streets can be described by networks, which consist of nodes that are connected by edges. Network analysis aims to identify important nodes in a network and to uncover structural properties of a network. A network is said to be bipartite if its nodes can be subdivided into two nonempty sets such that there are no edges between nodes in the same set. It is a difficult task to determine the closest bipartite network to a given network. This paper describes how a given network can be approximated by a bipartite one by solving a sequence of fairly simple optimization problems. The algorithm also produces a node permutation which makes the possible bipartite nature of the initial adjacency matrix evident, and identifies the two sets of nodes. We finally show how the same procedure can be used to detect the presence of a large anti-community in a network and to identify it.Comment: 30 page

Wavelength Conversion in All-Optical Networks with Shortest-Path Routing

We consider all-optical networks with shortest-path routing that use wavelength-division multiplexing and employ wavelength conversion at specific nodes in order to maximize their capacity usage. We present efficient algorithms for deciding whether a placement of wavelength converters allows the network to run at maximum capacity, and for finding an optimal wavelength assignment when such a placement of converters is known. Our algorithms apply to both undirected and directed networks. Furthermore, we show that the problem of designing such networks, i.e., finding an optimal placement of converters, is MAX SNP-hard in both the undirected and the directed case. Finally, we give a linear-time algorithm for finding an optimal placement of converters in undirected triangle-free networks, and show that the problem remains NP-hard in bidirected triangle-free planar network

Edge Bipartization Faster Than 2^k

In the Edge Bipartization problem one is given an undirected graph $G$ and an integer $k$, and the question is whether $k$ edges can be deleted from $G$ so that it becomes bipartite. In 2006, Guo et al. [J. Comput. Syst. Sci., 72(8):1386-1396, 2006] proposed an algorithm solving this problem in time $O(2^k m^2)$; today, this algorithm is a textbook example of an application of the iterative compression technique. Despite extensive progress in the understanding of the parameterized complexity of graph separation problems in the recent years, no significant improvement upon this result has been yet reported. We present an algorithm for Edge Bipartization that works in time $O(1.977^k nm)$, which is the first algorithm with the running time dependence on the parameter better than $2^k$. To this end, we combine the general iterative compression strategy of Guo et al. [J. Comput. Syst. Sci., 72(8):1386-1396, 2006], the technique proposed by Wahlstrom [SODA 2014, 1762-1781] of using a polynomial-time solvable relaxation in the form of a Valued Constraint Satisfaction Problem to guide a bounded-depth branching algorithm, and an involved Measure & Conquer analysis of the recursion tree

An FPT haplotyping algorithm on pedigrees with a small number of sites

<p>Abstract</p> <p>Background</p> <p>Genetic disease studies investigate relationships between changes in chromosomes and genetic diseases. Single haplotypes provide useful information for these studies but extracting single haplotypes directly by biochemical methods is expensive. A computational method to infer haplotypes from genotype data is therefore important. We investigate the problem of computing the minimum number of recombination events for general pedigrees with a small number of sites for all members.</p> <p>Results</p> <p>We show that this NP-hard problem can be parametrically reduced to the Bipartization by Edge Removal problem with additional parity constraints. We solve this problem with an exact algorithm that runs in <inline-formula><graphic file="1748-7188-6-8-i1.gif"/></inline-formula> time, where <it>n </it>is the number of members, <it>m </it>is the number of sites, and <it>k </it>is the number of recombination events.</p> <p>Conclusions</p> <p>This algorithm infers haplotypes for a small number of sites, which can be useful for genetic disease studies to track down how changes in haplotypes such as recombinations relate to genetic disease.</p