Structure of conflict graphs in constraint alignment problems and algorithms

We consider the constrained graph alignment problem which has applications in biological network analysis. Given two input graphs $G_1=(V_1,E_1), G_2=(V_2,E_2)$, a pair of vertex mappings induces an {\it edge conservation} if the vertex pairs are adjacent in their respective graphs. %In general terms The goal is to provide a one-to-one mapping between the vertices of the input graphs in order to maximize edge conservation. However the allowed mappings are restricted since each vertex from $V_1$ (resp. $V_2$) is allowed to be mapped to at most $m_1$ (resp. $m_2$) specified vertices in $V_2$ (resp. $V_1$). Most of results in this paper deal with the case $m_2=1$ which attracted most attention in the related literature. We formulate the problem as a maximum independent set problem in a related {\em conflict graph} and investigate structural properties of this graph in terms of forbidden subgraphs. We are interested, in particular, in excluding certain wheals, fans, cliques or claws (all terms are defined in the paper), which corresponds in excluding certain cycles, paths, cliques or independent sets in the neighborhood of each vertex. Then, we investigate algorithmic consequences of some of these properties, which illustrates the potential of this approach and raises new horizons for further works. In particular this approach allows us to reinterpret a known polynomial case in terms of conflict graph and to improve known approximation and fixed-parameter tractability results through efficiently solving the maximum independent set problem in conflict graphs. Some of our new approximation results involve approximation ratios that are function of the optimal value, in particular its square root; this kind of results cannot be achieved for maximum independent set in general graphs.Comment: 22 pages, 6 figure

Independent Set, Induced Matching, and Pricing: Connections and Tight (Subexponential Time) Approximation Hardnesses

We present a series of almost settled inapproximability results for three fundamental problems. The first in our series is the subexponential-time inapproximability of the maximum independent set problem, a question studied in the area of parameterized complexity. The second is the hardness of approximating the maximum induced matching problem on bounded-degree bipartite graphs. The last in our series is the tight hardness of approximating the k-hypergraph pricing problem, a fundamental problem arising from the area of algorithmic game theory. In particular, assuming the Exponential Time Hypothesis, our two main results are: - For any r larger than some constant, any r-approximation algorithm for the maximum independent set problem must run in at least 2^{n^{1-\epsilon}/r^{1+\epsilon}} time. This nearly matches the upper bound of 2^{n/r} (Cygan et al., 2008). It also improves some hardness results in the domain of parameterized complexity (e.g., Escoffier et al., 2012 and Chitnis et al., 2013) - For any k larger than some constant, there is no polynomial time min (k^{1-\epsilon}, n^{1/2-\epsilon})-approximation algorithm for the k-hypergraph pricing problem, where n is the number of vertices in an input graph. This almost matches the upper bound of min (O(k), \tilde O(\sqrt{n})) (by Balcan and Blum, 2007 and an algorithm in this paper). We note an interesting fact that, in contrast to n^{1/2-\epsilon} hardness for polynomial-time algorithms, the k-hypergraph pricing problem admits n^{\delta} approximation for any \delta >0 in quasi-polynomial time. This puts this problem in a rare approximability class in which approximability thresholds can be improved significantly by allowing algorithms to run in quasi-polynomial time.Comment: The full version of FOCS 201

Structural Rounding: Approximation Algorithms for Graphs Near an Algorithmically Tractable Class

We develop a framework for generalizing approximation algorithms from the structural graph algorithm literature so that they apply to graphs somewhat close to that class (a scenario we expect is common when working with real-world networks) while still guaranteeing approximation ratios. The idea is to edit a given graph via vertex- or edge-deletions to put the graph into an algorithmically tractable class, apply known approximation algorithms for that class, and then lift the solution to apply to the original graph. We give a general characterization of when an optimization problem is amenable to this approach, and show that it includes many well-studied graph problems, such as Independent Set, Vertex Cover, Feedback Vertex Set, Minimum Maximal Matching, Chromatic Number, (l-)Dominating Set, Edge (l-)Dominating Set, and Connected Dominating Set. To enable this framework, we develop new editing algorithms that find the approximately-fewest edits required to bring a given graph into one of a few important graph classes (in some cases these are bicriteria algorithms which simultaneously approximate both the number of editing operations and the target parameter of the family). For bounded degeneracy, we obtain an O(r log{n})-approximation and a bicriteria (4,4)-approximation which also extends to a smoother bicriteria trade-off. For bounded treewidth, we obtain a bicriteria (O(log^{1.5} n), O(sqrt{log w}))-approximation, and for bounded pathwidth, we obtain a bicriteria (O(log^{1.5} n), O(sqrt{log w} * log n))-approximation. For treedepth 2 (related to bounded expansion), we obtain a 4-approximation. We also prove complementary hardness-of-approximation results assuming P != NP: in particular, these problems are all log-factor inapproximable, except the last which is not approximable below some constant factor 2 (assuming UGC)

The Hardness of Approximation of Euclidean k-means

The Euclidean $k$-means problem is a classical problem that has been extensively studied in the theoretical computer science, machine learning and the computational geometry communities. In this problem, we are given a set of $n$ points in Euclidean space $R^d$, and the goal is to choose $k$ centers in $R^d$ so that the sum of squared distances of each point to its nearest center is minimized. The best approximation algorithms for this problem include a polynomial time constant factor approximation for general $k$ and a $(1+\epsilon)$-approximation which runs in time $poly(n) 2^{O(k/\epsilon)}$. At the other extreme, the only known computational complexity result for this problem is NP-hardness [ADHP'09]. The main difficulty in obtaining hardness results stems from the Euclidean nature of the problem, and the fact that any point in $R^d$ can be a potential center. This gap in understanding left open the intriguing possibility that the problem might admit a PTAS for all $k,d$. In this paper we provide the first hardness of approximation for the Euclidean $k$-means problem. Concretely, we show that there exists a constant $\epsilon > 0$ such that it is NP-hard to approximate the $k$-means objective to within a factor of $(1+\epsilon)$. We show this via an efficient reduction from the vertex cover problem on triangle-free graphs: given a triangle-free graph, the goal is to choose the fewest number of vertices which are incident on all the edges. Additionally, we give a proof that the current best hardness results for vertex cover can be carried over to triangle-free graphs. To show this we transform $G$, a known hard vertex cover instance, by taking a graph product with a suitably chosen graph $H$, and showing that the size of the (normalized) maximum independent set is almost exactly preserved in the product graph using a spectral analysis, which might be of independent interest

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

Reoptimization of Some Maximum Weight Induced Hereditary Subgraph Problems

The reoptimization issue studied in this paper can be described as follows: given an instance I of some problem Π, an optimal solution OPT for Π in I and an instance I′ resulting from a local perturbation of I that consists of insertions or removals of a small number of data, we wish to use OPT in order to solve Π in I', either optimally or by guaranteeing an approximation ratio better than that guaranteed by an ex nihilo computation and with running time better than that needed for such a computation. We use this setting in order to study weighted versions of several representatives of a broad class of problems known in the literature as maximum induced hereditary subgraph problems. The main problems studied are max independent set, max k-colorable subgraph and max split subgraph under vertex insertions and deletion