Polynomial kernels for 3-leaf power graph modification problems

A graph G=(V,E) is a 3-leaf power iff there exists a tree T whose leaves are V and such that (u,v) is an edge iff u and v are at distance at most 3 in T. The 3-leaf power graph edge modification problems, i.e. edition (also known as the closest 3-leaf power), completion and edge-deletion, are FTP when parameterized by the size of the edge set modification. However polynomial kernel was known for none of these three problems. For each of them, we provide cubic kernels that can be computed in linear time for each of these problems. We thereby answer an open problem first mentioned by Dom, Guo, Huffner and Niedermeier (2005).Comment: Submitte

Dark Matter Halo Structure in CDM Hydrodynamical Simulations

We have carried out a comparative analysis of the properties of dark matter halos in N-body and hydrodynamical simulations. We analyze their density profiles, shapes and kinematical properties with the aim of assessing the effects that hydrodynamical processes might produce on the evolution of the dark matter component. The simulations performed allow us to reproduce dark matter halos with high resolution, although the range of circular velocities is limited. We find that for halos with circular velocities of $[150-200] km s^{-1}$ at the virial radius, the presence of baryons affects the evolution of the dark matter component in the central region modifying the density profiles, shapes and velocity dispersions. We also analyze the rotation velocity curves of disk-like structures and compare them with observational results.Comment: 28 pages, 15 figures (figures 3ab sent by request), 2 tables. Accepted for publication MNRA

From aptamer-based biomarker discovery to diagnostic and clinical applications: an aptamer-based, streamlined multiplex proteomic assay

Recently, we reported an aptamer-based, highly multiplexed assay for the purpose of biomarker identification. To enable seamless transition from highly multiplexed biomarker discovery assays to a format suitable and convenient for diagnostic and life-science applications, we developed a streamlined, plate-based version of the assay. The plate-based version of the assay is robust, sensitive (sub-picomolar), rapid, can be highly multiplexed (upwards of 60 analytes), and fully automated. We demonstrate that quantification by microarray-based hybridization, Luminex bead-based methods, and qPCR are each compatible with our platform, further expanding the breadth of proteomic applications for a wide user community

On Structural Parameterizations of Hitting Set: Hitting Paths in Graphs Using 2-SAT

Hitting Set is a classic problem in combinatorial optimization. Its input consists of a set system F over a finite universe U and an integer t; the question is whether there is a set of t elements that intersects every set in F. The Hitting Set problem parameterized by the size of the solution is a well-known W[2]-complete problem in parameterized complexity theory. In this paper we investigate the complexity of Hitting Set under various structural parameterizations of the input. Our starting point is the folklore result that Hitting Set is polynomial-time solvable if there is a tree T on vertex set U such that the sets in F induce connected subtrees of T. We consider the case that there is a treelike graph with vertex set U such that the sets in F induce connected subgraphs; the parameter of the problem is a measure of how treelike the graph is. Our main positive result is an algorithm that, given a graph G with cyclomatic number k, a collection P of simple paths in G, and an integer t, determines in time 2^{5k} (|G| +|P|)^O(1) whether there is a vertex set of size t that hits all paths in P. It is based on a connection to the 2-SAT problem in multiple valued logic. For other parameterizations we derive W[1]-hardness and para-NP-completeness results.Comment: Presented at the 41st International Workshop on Graph-Theoretic Concepts in Computer Science, WG 2015. (The statement of Lemma 4 was corrected in this update.

Parameterized Algorithms for Modular-Width

It is known that a number of natural graph problems which are FPT parameterized by treewidth become W-hard when parameterized by clique-width. It is therefore desirable to find a different structural graph parameter which is as general as possible, covers dense graphs but does not incur such a heavy algorithmic penalty. The main contribution of this paper is to consider a parameter called modular-width, defined using the well-known notion of modular decompositions. Using a combination of ILPs and dynamic programming we manage to design FPT algorithms for Coloring and Partitioning into paths (and hence Hamiltonian path and Hamiltonian cycle), which are W-hard for both clique-width and its recently introduced restriction, shrub-depth. We thus argue that modular-width occupies a sweet spot as a graph parameter, generalizing several simpler notions on dense graphs but still evading the "price of generality" paid by clique-width.Comment: to appear in IPEC 2013. arXiv admin note: text overlap with arXiv:1304.5479 by other author

An FPT 2-Approximation for Tree-Cut Decomposition

The tree-cut width of a graph is a graph parameter defined by Wollan [J. Comb. Theory, Ser. B, 110:47-66, 2015] with the help of tree-cut decompositions. In certain cases, tree-cut width appears to be more adequate than treewidth as an invariant that, when bounded, can accelerate the resolution of intractable problems. While designing algorithms for problems with bounded tree-cut width, it is important to have a parametrically tractable way to compute the exact value of this parameter or, at least, some constant approximation of it. In this paper we give a parameterized 2-approximation algorithm for the computation of tree-cut width; for an input $n$-vertex graph $G$ and an integer $w$, our algorithm either confirms that the tree-cut width of $G$ is more than $w$ or returns a tree-cut decomposition of $G$ certifying that its tree-cut width is at most $2w$, in time $2^{O(w^2\log w)} \cdot n^2$. Prior to this work, no constructive parameterized algorithms, even approximated ones, existed for computing the tree-cut width of a graph. As a consequence of the Graph Minors series by Robertson and Seymour, only the existence of a decision algorithm was known.Comment: 17 pages, 3 figure

Approximation Algorithms for the Capacitated Domination Problem

We consider the {\em Capacitated Domination} problem, which models a service-requirement assignment scenario and is also a generalization of the well-known {\em Dominating Set} problem. In this problem, given a graph with three parameters defined on each vertex, namely cost, capacity, and demand, we want to find an assignment of demands to vertices of least cost such that the demand of each vertex is satisfied subject to the capacity constraint of each vertex providing the service. In terms of polynomial time approximations, we present logarithmic approximation algorithms with respect to different demand assignment models for this problem on general graphs, which also establishes the corresponding approximation results to the well-known approximations of the traditional {\em Dominating Set} problem. Together with our previous work, this closes the problem of generally approximating the optimal solution. On the other hand, from the perspective of parameterization, we prove that this problem is {\it W[1]}-hard when parameterized by a structure of the graph called treewidth. Based on this hardness result, we present exact fixed-parameter tractable algorithms when parameterized by treewidth and maximum capacity of the vertices. This algorithm is further extended to obtain pseudo-polynomial time approximation schemes for planar graphs

Tight Kernel Bounds for Problems on Graphs with Small Degeneracy

In this paper we consider kernelization for problems on d-degenerate graphs, i.e. graphs such that any subgraph contains a vertex of degree at most $d$. This graph class generalizes many classes of graphs for which effective kernelization is known to exist, e.g. planar graphs, H-minor free graphs, and H-topological-minor free graphs. We show that for several natural problems on d-degenerate graphs the best known kernelization upper bounds are essentially tight.Comment: Full version of ESA 201

A Multivariate Approach for Checking Resiliency in Access Control

In recent years, several combinatorial problems were introduced in the area of access control. Typically, such problems deal with an authorization policy, seen as a relation $UR \subseteq U \times R$, where $(u, r) \in UR$ means that user $u$ is authorized to access resource $r$. Li, Tripunitara and Wang (2009) introduced the Resiliency Checking Problem (RCP), in which we are given an authorization policy, a subset of resources $P \subseteq R$, as well as integers $s \ge 0$, $d \ge 1$ and $t \geq 1$. It asks whether upon removal of any set of at most $s$ users, there still exist $d$ pairwise disjoint sets of at most $t$ users such that each set has collectively access to all resources in $P$. This problem possesses several parameters which appear to take small values in practice. We thus analyze the parameterized complexity of RCP with respect to these parameters, by considering all possible combinations of $|P|, s, d, t$. In all but one case, we are able to settle whether the problem is in FPT, XP, W[2]-hard, para-NP-hard or para-coNP-hard. We also consider the restricted case where $s=0$ for which we determine the complexity for all possible combinations of the parameters

Vertex Cover Kernelization Revisited: Upper and Lower Bounds for a Refined Parameter

An important result in the study of polynomial-time preprocessing shows that there is an algorithm which given an instance (G,k) of Vertex Cover outputs an equivalent instance (G',k') in polynomial time with the guarantee that G' has at most 2k' vertices (and thus O((k')^2) edges) with k' <= k. Using the terminology of parameterized complexity we say that k-Vertex Cover has a kernel with 2k vertices. There is complexity-theoretic evidence that both 2k vertices and Theta(k^2) edges are optimal for the kernel size. In this paper we consider the Vertex Cover problem with a different parameter, the size fvs(G) of a minimum feedback vertex set for G. This refined parameter is structurally smaller than the parameter k associated to the vertex covering number vc(G) since fvs(G) <= vc(G) and the difference can be arbitrarily large. We give a kernel for Vertex Cover with a number of vertices that is cubic in fvs(G): an instance (G,X,k) of Vertex Cover, where X is a feedback vertex set for G, can be transformed in polynomial time into an equivalent instance (G',X',k') such that |V(G')| <= 2k and |V(G')| <= O(|X'|^3). A similar result holds when the feedback vertex set X is not given along with the input. In sharp contrast we show that the Weighted Vertex Cover problem does not have a polynomial kernel when parameterized by the cardinality of a given vertex cover of the graph unless NP is in coNP/poly and the polynomial hierarchy collapses to the third level.Comment: Published in "Theory of Computing Systems" as an Open Access publicatio