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

Approximation Algorithms for Union and Intersection Covering Problems

In a classical covering problem, we are given a set of requests that we need to satisfy (fully or partially), by buying a subset of items at minimum cost. For example, in the k-MST problem we want to find the cheapest tree spanning at least k nodes of an edge-weighted graph. Here nodes and edges represent requests and items, respectively. In this paper, we initiate the study of a new family of multi-layer covering problems. Each such problem consists of a collection of h distinct instances of a standard covering problem (layers), with the constraint that all layers share the same set of requests. We identify two main subfamilies of these problems: - in a union multi-layer problem, a request is satisfied if it is satisfied in at least one layer; - in an intersection multi-layer problem, a request is satisfied if it is satisfied in all layers. To see some natural applications, consider both generalizations of k-MST. Union k-MST can model a problem where we are asked to connect a set of users to at least one of two communication networks, e.g., a wireless and a wired network. On the other hand, intersection k-MST can formalize the problem of connecting a subset of users to both electricity and water. We present a number of hardness and approximation results for union and intersection versions of several standard optimization problems: MST, Steiner tree, set cover, facility location, TSP, and their partial covering variants

Approximation Algorithms for the Joint Replenishment Problem with Deadlines

The Joint Replenishment Problem (JRP) is a fundamental optimization problem in supply-chain management, concerned with optimizing the flow of goods from a supplier to retailers. Over time, in response to demands at the retailers, the supplier ships orders, via a warehouse, to the retailers. The objective is to schedule these orders to minimize the sum of ordering costs and retailers' waiting costs. We study the approximability of JRP-D, the version of JRP with deadlines, where instead of waiting costs the retailers impose strict deadlines. We study the integrality gap of the standard linear-program (LP) relaxation, giving a lower bound of 1.207, a stronger, computer-assisted lower bound of 1.245, as well as an upper bound and approximation ratio of 1.574. The best previous upper bound and approximation ratio was 1.667; no lower bound was previously published. For the special case when all demand periods are of equal length we give an upper bound of 1.5, a lower bound of 1.2, and show APX-hardness

Quantified Conjunctive Queries on Partially Ordered Sets

We study the computational problem of checking whether a quantified conjunctive query (a first-order sentence built using only conjunction as Boolean connective) is true in a finite poset (a reflexive, antisymmetric, and transitive directed graph). We prove that the problem is already NP-hard on a certain fixed poset, and investigate structural properties of posets yielding fixed-parameter tractability when the problem is parameterized by the query. Our main algorithmic result is that model checking quantified conjunctive queries on posets of bounded width is fixed-parameter tractable (the width of a poset is the maximum size of a subset of pairwise incomparable elements). We complement our algorithmic result by complexity results with respect to classes of finite posets in a hierarchy of natural poset invariants, establishing its tightness in this sense.Comment: Accepted at IPEC 201

The architecture of the protein domain universe

Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain universe, which has been found to poses peculiar scale-free properties (Dokholyan et al., Proc. Natl. Acad. Sci. USA 99: 14132-14136 (2002)). We examine the origin of these scale-free properties of the graph of protein domain structures (PDUG) and determine that that the PDUG is not modular, i.e. it does not consist of modules with uniform properties. Instead, we find the PDUG to be self-similar at all scales. We further characterize the PDUG architecture by studying the properties of the hub nodes that are responsible for the scale-free connectivity of the PDUG. We introduce a measure of the betweenness centrality of protein domains in the PDUG and find a power-law distribution of the betweenness centrality values. The scale-free distribution of hubs in the protein universe suggests that a set of specific statistical mechanics models, such as the self-organized criticality model, can potentially identify the principal driving forces of molecular evolution. We also find a gatekeeper protein domain, removal of which partitions the largest cluster into two large sub-clusters. We suggest that the loss of such gatekeeper protein domains in the course of evolution is responsible for the creation of new fold families.Comment: 14 pages, 3 figure

Streaming Verification of Graph Properties

Streaming interactive proofs (SIPs) are a framework for outsourced computation. A computationally limited streaming client (the verifier) hands over a large data set to an untrusted server (the prover) in the cloud and the two parties run a protocol to confirm the correctness of result with high probability. SIPs are particularly interesting for problems that are hard to solve (or even approximate) well in a streaming setting. The most notable of these problems is finding maximum matchings, which has received intense interest in recent years but has strong lower bounds even for constant factor approximations. In this paper, we present efficient streaming interactive proofs that can verify maximum matchings exactly. Our results cover all flavors of matchings (bipartite/non-bipartite and weighted). In addition, we also present streaming verifiers for approximate metric TSP. In particular, these are the first efficient results for weighted matchings and for metric TSP in any streaming verification model.Comment: 26 pages, 2 figure, 1 tabl

Approximating Upper Degree-Constrained Partial Orientations

In the Upper Degree-Constrained Partial Orientation problem we are given an undirected graph $G=(V,E)$, together with two degree constraint functions $d^-,d^+ : V \to \mathbb{N}$. The goal is to orient as many edges as possible, in such a way that for each vertex $v \in V$ the number of arcs entering $v$ is at most $d^-(v)$, whereas the number of arcs leaving $v$ is at most $d^+(v)$. This problem was introduced by Gabow [SODA'06], who proved it to be MAXSNP-hard (and thus APX-hard). In the same paper Gabow presented an LP-based iterative rounding $4/3$-approximation algorithm. Since the problem in question is a special case of the classic 3-Dimensional Matching, which in turn is a special case of the $k$-Set Packing problem, it is reasonable to ask whether recent improvements in approximation algorithms for the latter two problems [Cygan, FOCS'13; Sviridenko & Ward, ICALP'13] allow for an improved approximation for Upper Degree-Constrained Partial Orientation. We follow this line of reasoning and present a polynomial-time local search algorithm with approximation ratio $5/4+\varepsilon$. Our algorithm uses a combination of two types of rules: improving sets of bounded pathwidth from the recent $4/3+\varepsilon$-approximation algorithm for 3-Set Packing [Cygan, FOCS'13], and a simple rule tailor-made for the setting of partial orientations. In particular, we exploit the fact that one can check in polynomial time whether it is possible to orient all the edges of a given graph [Gy\'arf\'as & Frank, Combinatorics'76].Comment: 12 pages, 1 figur

Bi-Criteria and Approximation Algorithms for Restricted Matchings

In this work we study approximation algorithms for the \textit{Bounded Color Matching} problem (a.k.a. Restricted Matching problem) which is defined as follows: given a graph in which each edge $e$ has a color $c_e$ and a profit $p_e \in \mathbb{Q}^+$, we want to compute a maximum (cardinality or profit) matching in which no more than $w_j \in \mathbb{Z}^+$ edges of color $c_j$ are present. This kind of problems, beside the theoretical interest on its own right, emerges in multi-fiber optical networking systems, where we interpret each unique wavelength that can travel through the fiber as a color class and we would like to establish communication between pairs of systems. We study approximation and bi-criteria algorithms for this problem which are based on linear programming techniques and, in particular, on polyhedral characterizations of the natural linear formulation of the problem. In our setting, we allow violations of the bounds $w_j$ and we model our problem as a bi-criteria problem: we have two objectives to optimize namely (a) to maximize the profit (maximum matching) while (b) minimizing the violation of the color bounds. We prove how we can "beat" the integrality gap of the natural linear programming formulation of the problem by allowing only a slight violation of the color bounds. In particular, our main result is \textit{constant} approximation bounds for both criteria of the corresponding bi-criteria optimization problem