Showing papers on "Pathwidth published in 2011"

Weisfeiler-Lehman Graph Kernels

Abstract: In this article, we propose a family of efficient kernels for large graphs with discrete node labels. Key to our method is a rapid feature extraction scheme based on the Weisfeiler-Lehman test of isomorphism on graphs. It maps the original graph to a sequence of graphs, whose node attributes capture topological and label information. A family of kernels can be defined based on this Weisfeiler-Lehman sequence of graphs, including a highly efficient kernel comparing subtree-like patterns. Its runtime scales only linearly in the number of edges of the graphs and the length of the Weisfeiler-Lehman graph sequence. In our experimental evaluation, our kernels outperform state-of-the-art graph kernels on several graph classification benchmark data sets in terms of accuracy and runtime. Our kernels open the door to large-scale applications of graph kernels in various disciplines such as computational biology and social network analysis.

A sequential importance sampling algorithm for generating random graphs with prescribed degrees

Abstract: Random graphs with given degrees are a natural next step in complexity beyond the Erdős–Renyi model, yet the degree constraint greatly complicates simulation and estimation. We use an extension of a combinatorial characterization due to Erdős and Gallai to develop a sequential algorithm for generating a random labeled graph with a given degree sequence. The algorithm is easy to implement and allows for surprisingly efficient sequential importance sampling. The resulting probabilities are easily computed on the fly, allowing the user to reweight estimators appropriately, in contrast to some ad hoc approaches that generate graphs with the desired degrees but with completely unknown probabilities. Applications are given, including simulating an ecological network and estimating the number of graphs with a given degree sequence.

Ricci curvature of graphs

Abstract: We modify the definition of Ricci curvature of Ollivier of Markov chains on graphs to study the properties of the Ricci curvature of general graphs, Cartesian product of graphs, random graphs, and some special class of graphs.

Estimating and understanding exponential random graph models

Abstract: We introduce a method for the theoretical analysis of exponential random graph models. The method is based on a large-deviations approximation to the normalizing constant shown to be consistent using theory developed by Chatterjee and Varadhan [European J. Combin. 32 (2011) 1000-1017]. The theory explains a host of difficulties encountered by applied workers: many distinct models have essentially the same MLE, rendering the problems ``practically'' ill-posed. We give the first rigorous proofs of ``degeneracy'' observed in these models. Here, almost all graphs have essentially no edges or are essentially complete. We supplement recent work of Bhamidi, Bresler and Sly [2008 IEEE 49th Annual IEEE Symposium on Foundations of Computer Science (FOCS) (2008) 803-812 IEEE] showing that for many models, the extra sufficient statistics are useless: most realizations look like the results of a simple Erd\H{o}s-R\'{e}nyi model. We also find classes of models where the limiting graphs differ from Erd\H{o}s-R\'{e}nyi graphs. A limitation of our approach, inherited from the limitation of graph limit theory, is that it works only for dense graphs.

Keyword search in graphs: finding r-cliques

Abstract: Keyword search over a graph finds a substructure of the graph containing all or some of the input keywords. Most of previous methods in this area find connected minimal trees that cover all the query keywords. Recently, it has been shown that finding subgraphs rather than trees can be more useful and informative for the users. However, the current tree or graph based methods may produce answers in which some content nodes (i.e., nodes that contain input keywords) are not very close to each other. In addition, when searching for answers, these methods may explore the whole graph rather than only the content nodes. This may lead to poor performance in execution time. To address the above problems, we propose the problem of finding r-cliques in graphs. An r-clique is a group of content nodes that cover all the input keywords and the distance between each two nodes is less than or equal to r. An exact algorithm is proposed that finds all r-cliques in the input graph. In addition, an approximation algorithm that produces r-cliques with 2-approximation in polynomial delay is proposed. Extensive performance studies using two large real data sets confirm the efficiency and accuracy of finding r-cliques in graphs.

Compression of weighted graphs

Abstract: We propose to compress weighted graphs (networks), motivated by the observation that large networks of social, biological, or other relations can be complex to handle and visualize In the process also known as graph simplification, nodes and (unweighted) edges are grouped to supernodes and superedges, respectively, to obtain a smaller graph We propose models and algorithms for weighted graphs The interpretation (ie decompression) of a compressed, weighted graph is that a pair of original nodes is connected by an edge if their supernodes are connected by one, and that the weight of an edge is approximated to be the weight of the superedge The compression problem now consists of choosing supernodes, superedges, and superedge weights so that the approximation error is minimized while the amount of compression is maximizedIn this paper, we formulate this task as the 'simple weighted graph compression problem' We then propose a much wider class of tasks under the name of 'generalized weighted graph compression problem' The generalized task extends the optimization to preserve longer-range connectivities between nodes, not just individual edge weights We study the properties of these problems and propose a range of algorithms to solve them, with different balances between complexity and quality of the result We evaluate the problems and algorithms experimentally on real networks The results indicate that weighted graphs can be compressed efficiently with relatively little compression error

Components in time-varying graphs

Abstract: Real complex systems are inherently time-varying. Thanks to new communication systems and novel technologies, it is today possible to produce and analyze social and biological networks with detailed information on the time of occurrence and duration of each link. However, standard graph metrics introduced so far in complex network theory are mainly suited for static graphs, i.e., graphs in which the links do not change over time, or graphs built from time-varying systems by aggregating all the links as if they were concurrent in time. In this paper, we extend the notion of connectedness, and the definitions of node and graph components, to the case of time-varying graphs, which are represented as time-ordered sequences of graphs defined over a fixed set of nodes. We show that the problem of finding strongly connected components in a time-varying graph can be mapped into the problem of discovering the maximal-cliques in an opportunely constructed static graph, which we name the affine graph. It is therefore an NP-complete problem. As a practical example, we have performed a temporal component analysis of time-varying graphs constructed from three data sets of human interactions. The results show that taking time into account in the definition of graph components allows to capture important features of real systems. In particular, we observe a large variability in the size of node temporal in- and out-components. This is due to intrinsic fluctuations in the activity patterns of individuals, which cannot be detected by static graph analysis.

Approximation Schemes for Steiner Forest on Planar Graphs and Graphs of Bounded Treewidth

Abstract: We give the first polynomial-time approximation scheme (PTAS) for the Steiner forest problem on planar graphs and, more generally, on graphs of bounded genus. As a first step, we show how to build a Steiner forest spanner for such graphs. The crux of the process is a clustering procedure called prize-collecting clustering that breaks down the input instance into separate subinstances which are easier to handle; moreover, the terminals in different subinstances are far from each other. Each subinstance has a relatively inexpensive Steiner tree connecting all its terminals, and the subinstances can be solved (almost) separately. Another building block is a PTAS for Steiner forest on graphs of bounded treewidth. Surprisingly, Steiner forest is NP-hard even on graphs of treewidth 3. Therefore, our PTAS for bounded-treewidth graphs needs a nontrivial combination of approximation arguments and dynamic programming on the tree decomposition. We further show that Steiner forest can be solved in polynomial time for series-parallel graphs (graphs of treewidth at most two) by a novel combination of dynamic programming and minimum cut computations, completing our thorough complexity study of Steiner forest in the range of bounded-treewidth graphs, planar graphs, and bounded-genus graphs.

Capturing topology in graph pattern matching

Abstract: Graph pattern matching is often defined in terms of subgraph isomorphism, an np-complete problem. To lower its complexity, various extensions of graph simulation have been considered instead. These extensions allow pattern matching to be conducted in cubic-time. However, they fall short of capturing the topology of data graphs, i.e., graphs may have a structure drastically different from pattern graphs they match, and the matches found are often too large to understand and analyze. To rectify these problems, this paper proposes a notion of strong simulation, a revision of graph simulation, for graph pattern matching. (1) We identify a set of criteria for preserving the topology of graphs matched. We show that strong simulation preserves the topology of data graphs and finds a bounded number of matches. (2) We show that strong simulation retains the same complexity as earlier extensions of simulation, by providing a cubic-time algorithm for computing strong simulation. (3) We present the locality property of strong simulation, which allows us to effectively conduct pattern matching on distributed graphs. (4) We experimentally verify the effectiveness and efficiency of these algorithms, using real-life data and synthetic data.

Subgraphs of random graphs with specified degrees

Abstract: If a graph is chosen uniformly at random from all the graphs with a given degree sequence, what can be said about its subgraphs? The same can be asked of bipartite graphs, equivalently 0-1 matrices. These questions have been studied by many people. In this paper we provide a partial survey of the eld, with emphasis on two general techniques: the method of switchings and the multidimensional saddle-point method.

Treewidth computations II. Lower bounds

Abstract: For several applications, it is important to be able to compute the treewidth of a given graph and to find tree decompositions of small width reasonably fast. Good lower bounds on the treewidth of a graph can, amongst others, help to speed up branch and bound algorithms that compute the treewidth of a graph exactly. A high lower bound for a specific graph instance can tell that a dynamic programming approach for solving a problem is infeasible for this instance. This paper gives an overview of several recent methods that give lower bounds on the treewidth of graphs.

Sparse graphs: Metrics and random models

Abstract: Recently, Bollobas, Janson and Riordan introduced a family of random graph models producing inhomogeneous graphs with n vertices and Θ(n) edges whose distribution is characterized by a kernel, i.e., a symmetric measurable function κ: [0, 1]2 → [0, ∞). To understand these models, we should like to know when different kernels κ give rise to “similar” graphs, and, given a real-world network, how “similar” is it to a typical graph G(n, κ) derived from a given kernel κ. The analogous questions for dense graphs, with Θ(n2) edges, are answered by recent results of Borgs, Chayes, Lovasz, Sos, Szegedy and Vesztergombi, who showed that several natural metrics on graphs are equivalent, and moreover that any sequence of graphs converges in each metric to a graphon, i.e., a kernel taking values in [0, 1]. Possible generalizations of these results to graphs with o(n2) but ω(n) edges are discussed in a companion article [Bollobas and Riordan, London Math Soc Lecture Note Series 365 (2009), 211–287]; here we focus only on graphs with Θ(n) edges, which turn out to be much harder to handle. Many new phenomena occur, and there are a host of plausible metrics to consider; many of these metrics suggest new random graph models and vice versa. © 2010 Wiley Periodicals, Inc. Random Struct. Alg., 39, 1-38, 2011 © 2011 Wiley Periodicals, Inc.

Multiple-Source Multiple-Sink Maximum Flow in Directed Planar Graphs in Near-Linear Time

Abstract: We give an O(n log3 n) algorithm that, given an n-node directed planar graph with arc capacities, a set of source nodes, and a set of sink nodes, finds a maximum flow from the sources to the sinks. Previously, the fastest algorithms known for this problem were those for general graphs.

Using the Mutual k-Nearest Neighbor Graphs for Semi-supervised Classification on Natural Language Data

Abstract: The first step in graph-based semi-supervised classification is to construct a graph from input data. While the k-nearest neighbor graphs have been the de facto standard method of graph construction, this paper advocates using the less well-known mutual k-nearest neighbor graphs for high-dimensional natural language data. To compare the performance of these two graph construction methods, we run semi-supervised classification methods on both graphs in word sense disambiguation and document classification tasks. The experimental results show that the mutual k-nearest neighbor graphs, if combined with maximum spanning trees, consistently outperform the k-nearest neighbor graphs. We attribute better performance of the mutual k-nearest neighbor graph to its being more resistive to making hub vertices. The mutual k-nearest neighbor graphs also perform equally well or even better in comparison to the state-of-the-art b-matching graph construction, despite their lower computational complexity.

Contraction decomposition in h-minor-free graphs and algorithmic applications

Abstract: We prove that any graph excluding a fixed minor can have its edges partitioned into a desired number k of color classes such that contracting the edges in any one color class results in a graph of treewidth linear in k. This result is a natural finale to research in contraction decomposition, generalizing previous such decompositions for planar and bounded-genus graphs, and solving the main open problem in this area (posed at SODA 2007). Our decomposition can be computed in polynomial time, resulting in a general framework for approximation algorithms, particularly PTASs (with k ∼ 1/e), and fixed-parameter algorithms, for problems closed under contractions in graphs excluding a fixed minor. For example, our approximation framework gives the first PTAS for TSP in weighted H-minor-free graphs, solving a decade-old open problem of Grohe; and gives another fixed-parameter algorithm for k-cut in H-minor-free graphs, which was an open problem of Downey et al. even for planar graphs.To obtain our contraction decompositions, we develop new graph structure theory to realize virtual edges in the clique-sum decomposition by actual paths in the graph, enabling the use of the powerful Robertson--Seymour Graph Minor decomposition theorem in the context of edge contractions (without edge deletions). This requires careful construction of paths to avoid blowup in the number of required paths beyond 3. Along the way, we strengthen and simplify contraction decompositions for bounded-genus graphs, so that the partition is determined by a simple radial ball growth independent of handles, starting from a set of vertices instead of just one, as long as this set is tight in a certain sense. We show that this tightness property holds for a constant number of approximately shortest paths in the surface, introducing several new concepts such as dives and rainbows.

Mining large graphs: Algorithms, inference, and discoveries

Abstract: How do we find patterns and anomalies, on graphs with billions of nodes and edges, which do not fit in memory? How to use parallelism for such terabyte-scale graphs? In this work, we focus on inference, which often corresponds, intuitively, to “guilt by association” scenarios. For example, if a person is a drug-abuser, probably its friends are so, too; if a node in a social network is of male gender, his dates are probably females. We show how to do inference on such huge graphs through our proposed HAdoop Line graph Fixed Point (Ha-Lfp), an efficient parallel algorithm for sparse billion-scale graphs, using the Hadoop platform. Our contributions include (a) the design of Ha-Lfp, observing that it corresponds to a fixed point on a line graph induced from the original graph; (b) scalability analysis, showing that our algorithm scales up well with the number of edges, as well as with the number of machines; and (c) experimental results on two private, as well as two of the largest publicly available graphs — the Web Graphs from Yahoo! (6.6 billion edges and 0.24 Tera bytes), and the Twitter graph (3.7 billion edges and 0.13 Tera bytes). We evaluated our algorithm using M45, one of the top 50 fastest supercomputers in the world, and we report patterns and anomalies discovered by our algorithm, which would be invisible otherwise.

Linear-space approximate distance oracles for planar, bounded-genus and minor-free graphs

Abstract: A (1+e)-approximate distance oracle for a graph is a data structure that supports approximate point-to-point shortest-path-distance queries. The most relevant measures for a distance-oracle construction are: space, query time, and preprocessing time. There are strong distance-oracle constructions known for planar graphs (Thorup, JACM'04) and, subsequently, minor-excluded graphs (Abraham and Gavoille, PODC'06). However, these require Ω(e-1n lg n) space for n-node graphs. In this paper, for planar graphs, bounded-genus graphs, and minor-excluded graphs we give distance-oracle constructions that require only O(n) space. The big O hides only a fixed constant, independent of e and independent of genus or size of an excluded minor. The preprocessing times for our distance oracle are also faster than those for the previously known constructions. For planar graphs, the preprocessing time is O(nlg2 n). However, our constructions have slower query times. For planar graphs, the query time is O(e-2 lg2 n). For all our linear-space results, we can in fact ensure, for any δ > 0, that the space required is only 1 + δ times the space required just to represent the graph itself.

Markov properties for mixed graphs

Abstract: In this paper, we unify the Markov theory of a variety of different types of graphs used in graphical Markov models by introducing the class of loopless mixed graphs, and show that all independence models induced by $m$-separation on such graphs are compositional graphoids. We focus in particular on the subclass of ribbonless graphs which as special cases include undirected graphs, bidirected graphs, and directed acyclic graphs, as well as ancestral graphs and summary graphs. We define maximality of such graphs as well as a pairwise and a global Markov property. We prove that the global and pairwise Markov properties of a maximal ribbonless graph are equivalent for any independence model that is a compositional graphoid.

Generation of Cubic graphs

Abstract: We describe a new algorithm for the efficient generation of all non-isomorphic connected cubic graphs. Our implementation of this algorithm is more than 4 times faster than previous generators. The generation can also be efficiently restricted to cubic graphs with girth at least 4 or 5.

The Laplacian eigenvalues of graphs: a survey

Abstract: The Laplacian matrix of a simple graph is the difference of the diagonal matrix of vertex degree and the (0,1) adjacency matrix. In the past decades, the Laplacian spectrum has received much more and more attention, since it has been applied to several fields, such as randomized algorithms, combinatorial optimization problems and machine learning. This paper is primarily a survey of various aspects of the eigenvalues of the Laplacian matrix of a graph for the past teens. In addition, some new unpublished results and questions are concluded. Emphasis is given on classifications of the upper and lower bounds for the Laplacian eigenvalues of graphs (including some special graphs, such as trees, bipartite graphs, triangular-free graphs, cubic graphs, etc.) as a function of other graph invariants, such as degree sequence, the average 2-degree, diameter, the maximal independence number, the maximal matching number, vertex connectivity, the domination number, the number of the spanning trees, etc.

Normalized graph Laplacians for directed graphs

Abstract: We consider the normalized Laplace operator for directed graphs with positive and negative edge weights. This generalization of the normalized Laplace operator for undirected graphs is used to characterize directed acyclic graphs. Moreover, we identify certain structural properties of the underlying graph with extremal eigenvalues of the normalized Laplace operator. We prove comparison theorems that establish a relationship between the eigenvalues of directed graphs and certain undirected graphs. This relationship is used to derive eigenvalue estimates for directed graphs. Finally we introduce the concept of neighborhood graphs for directed graphs and use it to obtain further eigenvalue estimates.

Bidimensionality and Geometric Graphs

Abstract: In this paper we use several of the key ideas from Bidimensionality to give a new generic approach to design EPTASs and subexponential time parameterized algorithms for problems on classes of graphs which are not minor closed, but instead exhibit a geometric structure. In particular we present EPTASs and subexponential time parameterized algorithms for Feedback Vertex Set, Vertex Cover, Connected Vertex Cover, Diamond Hitting Set, on map graphs and unit disk graphs, and for Cycle Packing and Minimum-Vertex Feedback Edge Set on unit disk graphs. Our results are based on the recent decomposition theorems proved by Fomin et al [SODA 2011], and our algorithms work directly on the input graph. Thus it is not necessary to compute the geometric representations of the input graph. To the best of our knowledge, these results are previously unknown, with the exception of the EPTAS and a subexponential time parameterized algorithm on unit disk graphs for Vertex Cover, which were obtained by Marx [ESA 2005] and Alber and Fiala [J. Algorithms 2004], respectively. We proceed to show that our approach can not be extended in its full generality to more general classes of geometric graphs, such as intersection graphs of unit balls in R^d, d >= 3. Specifically we prove that Feedback Vertex Set on unit-ball graphs in R^3 neither admits PTASs unless P=NP, nor subexponential time algorithms unless the Exponential Time Hypothesis fails. Additionally, we show that the decomposition theorems which our approach is based on fail for disk graphs and that therefore any extension of our results to disk graphs would require new algorithmic ideas. On the other hand, we prove that our EPTASs and subexponential time algorithms for Vertex Cover and Connected Vertex Cover carry over both to disk graphs and to unit-ball graphs in R^d for every fixed d.

Graphs Attached to Rings Revisited

Abstract: In this paper, we discuss some recent results on graphs attached to rings. In particular, we deal with comaximal graphs, unit graphs, and total graphs. We then define the notion of cototal graph and, using this graph, we characterize the rings which are additively generated by their zero divisors. Finally, we glance at graphs attached to other algebraic structures.

Distance in Graphs

Abstract: The distance between two vertices is the basis of the definition of several graph parameters including diameter, radius, average distance and metric dimension. These invariants are examined, especially how they relate to one another and to other graph invariants and their behaviour in certain graph classes. We also discuss characterizations of graph classes described in terms of distance or shortest paths. Finally, generalizations are considered.