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Showing papers on "Null graph published in 2011"


Book
04 Aug 2011
TL;DR: Graph Algorithms in the Language of Linear Algebra as discussed by the authors is the first book to cover graph algorithms accessible to engineers and scientists not trained in computer science but having a strong linear algebra background, enabling them to quickly understand and apply graph algorithms.
Abstract: Graphs are among the most important abstract data types in computer science, and the algorithms that operate on them are critical to modern life. Graphs have been shown to be powerful tools for modeling complex problems because of their simplicity and generality. Graph algorithms are one of the pillars of mathematics, informing research in such diverse areas as combinatorial optimization, complexity theory, and topology. Algorithms on graphs are applied in many ways in today s world - from Web rankings to metabolic networks, from finite element meshes to semantic graphs. The current exponential growth in graph data has forced a shift to parallel computing for executing graph algorithms. Implementing parallel graph algorithms and achieving good parallel performance have proven difficult. This book addresses these challenges by exploiting the well-known duality between a canonical representation of graphs as abstract collections of vertices and edges and a sparse adjacency matrix representation. This linear algebraic approach is widely accessible to scientists and engineers who may not be formally trained in computer science. The authors show how to leverage existing parallel matrix computation techniques and the large amount of software infrastructure that exists for these computations to implement efficient and scalable parallel graph algorithms. The benefits of this approach are reduced algorithmic complexity, ease of implementation, and improved performance. Graph Algorithms in the Language of Linear Algebra is the first book to cover graph algorithms accessible to engineers and scientists not trained in computer science but having a strong linear algebra background, enabling them to quickly understand and apply graph algorithms. It also covers array-based graph algorithms, showing readers how to express canonical graph algorithms using a highly elegant and efficient array notation and how to tap into the large range of tools and techniques that have been built for matrices and tensors; parallel array-based algorithms, demonstrating with examples how to easily implement parallel graph algorithms using array-based approaches, which enables readers to address much larger graph problems; and array-based theory for analyzing graphs, providing a template for using array-based constructs to develop new theoretical approaches for graph analysis. Audience: This book is suitable as the primary text for a class on linear algebraic graph algorithms and as either the primary or supplemental text for a class on graph algorithms for engineers and scientists without training in computer science. Contents: List of Figures; List of Tables; List of Algorithms; Preface; Acknowledgments; Part I: Algorithms: Chapter 1: Graphs and Matrices; Chapter 2: Linear Algebraic Notation and Definitions; Chapter 3: Connected Components and Minimum Paths; Chapter 4: Some Graph Algorithms in an Array-Based Language; Chapter 5: Fundamental Graph Algorithms; Chapter 6: Complex Graph Algorithms; Chapter 7: Multilinear Algebra for Analyzing Data with Multiple Linkages; Chapter 8: Subgraph Detection; Part II: Data: Chapter 9: Kronecker Graphs; Chapter 10: The Kronecker Theory of Power Law Graphs; Chapter 11: Visualizing Large Kronecker Graphs; Part III: Computation: Chapter 12: Large-Scale Network Analysis; Chapter 13: Implementing Sparse Matrices for Graph Algorithms; Chapter 14: New Ideas in Sparse Matrix-Matrix Multiplication; Chapter 15: Parallel Mapping of Sparse Computations; Chapter 16: Fundamental Questions in the Analysis of Large Graphs; Index.

283 citations


Proceedings ArticleDOI
24 Jan 2011
TL;DR: An open-source toolbox for drawing large-scale undirected graphs based on a previously implemented closed-source algorithm known as VxOrd, which is extended by incorporating edge-cutting, a multi-level approach, average-link clustering, and a parallel implementation.
Abstract: We document an open-source toolbox for drawing large-scale undirected graphs. This toolbox is based on a previously implemented closed-source algorithm known as VxOrd. Our toolbox, which we call OpenOrd, extends the capabilities of VxOrd to large graph layout by incorporating edge-cutting, a multi-level approach, average-link clustering, and a parallel implementation. At each level, vertices are grouped using force-directed layout and average-link clustering. The clustered vertices are then re-drawn and the process is repeated. When a suitable drawing of the coarsened graph is obtained, the algorithm is reversed to obtain a drawing of the original graph. This approach results in layouts of large graphs which incorporate both local and global structure. A detailed description of the algorithm is provided in this paper. Examples using datasets with over 600K nodes are given. Code is available at www.cs.sandia.gov/~smartin.

278 citations


Journal ArticleDOI
TL;DR: In this article, the effective graph resistance is derived from the field of electric circuit analysis where it is defined as the accumulated effective resistance between all pairs of vertices, and the derivation of new expressions is based on the analysis of the associated random walk on the graph and applies tools from Markov chain theory.

277 citations


Proceedings ArticleDOI
11 Apr 2011
TL;DR: This paper proposes the first external-memory algorithm for core decomposition in massive graphs and demonstrates the efficiency of the algorithm on real networks with up to 52.9 million vertices and 1.65 billion edges.
Abstract: The k-core of a graph is the largest subgraph in which every vertex is connected to at least k other vertices within the subgraph. Core decomposition finds the k-core of the graph for every possible k. Past studies have shown important applications of core decomposition such as in the study of the properties of large networks (e.g., sustainability, connectivity, centrality, etc.), for solving NP-hard problems efficiently in real networks (e.g., maximum clique finding, densest subgraph approximation, etc.), and for large-scale network fingerprinting and visualization. The k-core is a well accepted concept partly because there exists a simple and efficient algorithm for core decomposition, by recursively removing the lowest degree vertices and their incident edges. However, this algorithm requires random access to the graph and hence assumes the entire graph can be kept in main memory. Nevertheless, real-world networks such as online social networks have become exceedingly large in recent years and still keep growing at a steady rate. In this paper, we propose the first external-memory algorithm for core decomposition in massive graphs. When the memory is large enough to hold the graph, our algorithm achieves comparable performance as the in-memory algorithm. When the graph is too large to be kept in the memory, our algorithm requires only O(k max ) scans of the graph, where k max is the largest core number of the graph. We demonstrate the efficiency of our algorithm on real networks with up to 52.9 million vertices and 1.65 billion edges.

248 citations


Journal ArticleDOI
TL;DR: The formulation and proof of the main result uses the recent development of the theory of graph limits by Lovasz and coauthors and Szemeredi's regularity lemma from graph theory to establish a large deviation principle under an appropriate topology.
Abstract: What does an Erdos-Renyi graph look like when a rare event happens? This paper answers this question when p is fixed and n tends to infinity by establishing a large deviation principle under an appropriate topology. The formulation and proof of the main result uses the recent development of the theory of graph limits by Lovasz and coauthors and Szemeredi's regularity lemma from graph theory. As a basic application of the general principle, we work out large deviations for the number of triangles in G(n,p). Surprisingly, even this simple example yields an interesting double phase transition.

219 citations


Book ChapterDOI
01 Jan 2011
TL;DR: It is believed that the algorithm rejects any graph that is e-far from having second eigenvalue at most λα/O(1), and proves the validity of this belief under an appealing combinatorial conjecture.
Abstract: We consider testing graph expansion in the bounded-degree graph model. Specifically, we refer to algorithms for testing whether the graph has a second eigenvalue bounded above by a given threshold or is far from any graph with such (or related) property. We present a natural algorithm aimed towards achieving the foregoing task. The algorithm is given a (normalized) eigenvalue bound λ 0. The algorithm runs in time N0.5+α/poly(e), and accepts any graph having (normalized) second eigenvalue at most λ. We believe that the algorithm rejects any graph that is e-far from having second eigenvalue at most λα/O(1), and prove the validity of this belief under an appealing combinatorial conjecture.

185 citations


Journal ArticleDOI
TL;DR: In this paper, the authors give a new proof which avoids Szemer edi's regularity lemma and gives a better bound for the directed and multicolored analogues of the graph removal lemma.
Abstract: Let H be a xed graph with h vertices. The graph removal lemma states that every graph on n vertices with o(n h ) copies of H can be made H-free by removing o(n 2 ) edges. We give a new proof which avoids Szemer edi’s regularity lemma and gives a better bound. This approach also works to give improved bounds for the directed and multicolored analogues of the graph removal lemma. This answers questions of Alon and Gowers.

177 citations


Proceedings ArticleDOI
01 Jun 2011
TL;DR: This talk surveys recent progress on the design of provably fast algorithms for solving linear equations in the Laplacian matrices of graphs.
Abstract: The Laplacian matrices of graphs are fundamental. In addition to facilitating the application of linear algebra to graph theory, they arise in many practical problems. In this talk we survey recent progress on the design of provably fast algorithms for solving linear equations in the Laplacian matrices of graphs. These algorithms motivate and rely upon fascinating primitives in graph theory, including low-stretch spanning trees, graph sparsifiers, ultra-sparsifiers, and local graph clustering. These are all connected by a definition of what it means for one graph to approximate another. While this definition is dictated by Numerical Linear Algebra, it proves useful and natural from a graph theoretic perspective. Mathematics Subject Classification (2010). Primary 68Q25; Secondary 65F08.

163 citations


Journal ArticleDOI
01 Feb 2011
TL;DR: This work provides the first formal algorithmic study of the optimization of human computation for graph search by asking an omniscient human questions of the form "Is there a target node that is reachable from the current node?".
Abstract: We consider the problem of human-assisted graph search: given a directed acyclic graph with some (unknown) target node(s), we consider the problem of finding the target node(s) by asking an omniscient human questions of the form "Is there a target node that is reachable from the current node?". This general problem has applications in many domains that can utilize human intelligence, including curation of hierarchies, debugging workflows, image segmentation and categorization, interactive search and filter synthesis. To our knowledge, this work provides the first formal algorithmic study of the optimization of human computation for this problem. We study various dimensions of the problem space, providing algorithms and complexity results. We also compare the performance of our algorithm against other algorithms, for the problem of webpage categorization on a real taxonomy. Our framework and algorithms can be used in the design of an optimizer for crowd-sourcing platforms such as Mechanical Turk.

155 citations


Journal ArticleDOI
TL;DR: A novel graph clustering algorithm, SA-Cluster, which achieves a good balance between structural and attribute similarities through a unified distance measure and an effective method is proposed to automatically learn the degree of contributions of structural similarity and attribute similarity.
Abstract: Social networks, sensor networks, biological networks, and many other information networks can be modeled as a large graph. Graph vertices represent entities, and graph edges represent their relationships or interactions. In many large graphs, there is usually one or more attributes associated with every graph vertex to describe its properties. In many application domains, graph clustering techniques are very useful for detecting densely connected groups in a large graph as well as for understanding and visualizing a large graph. The goal of graph clustering is to partition vertices in a large graph into different clusters based on various criteria such as vertex connectivity or neighborhood similarity. Many existing graph clustering methods mainly focus on the topological structure for clustering, but largely ignore the vertex properties, which are often heterogenous. In this article, we propose a novel graph clustering algorithm, SA-Cluster, which achieves a good balance between structural and attribute similarities through a unified distance measure. Our method partitions a large graph associated with attributes into k clusters so that each cluster contains a densely connected subgraph with homogeneous attribute values. An effective method is proposed to automatically learn the degree of contributions of structural similarity and attribute similarity. Theoretical analysis is provided to show that SA-Cluster is converging quickly through iterative cluster refinement. Some optimization techniques on matrix computation are proposed to further improve the efficiency of SA-Cluster on large graphs. Extensive experimental results demonstrate the effectiveness of SA-Cluster through comparisons with the state-of-the-art graph clustering and summarization methods.

153 citations


Proceedings ArticleDOI
12 Jun 2011
TL;DR: Under this new measure, it is proved that subgraph similarity search is NP hard, while graph similarity match is polynomial, and an information propagation model is found that is able to convert a large network into a set of multidimensional vectors, where sophisticated indexing and similarity search algorithms are available.
Abstract: Complex social and information network search becomes important with a variety of applications. In the core of these applications, lies a common and critical problem: Given a labeled network and a query graph, how to efficiently search the query graph in the target network. The presence of noise and the incomplete knowledge about the structure and content of the target network make it unrealistic to find an exact match. Rather, it is more appealing to find the top-k approximate matches.In this paper, we propose a neighborhood-based similarity measure that could avoid costly graph isomorphism and edit distance computation. Under this new measure, we prove that subgraph similarity search is NP hard, while graph similarity match is polynomial. By studying the principles behind this measure, we found an information propagation model that is able to convert a large network into a set of multidimensional vectors, where sophisticated indexing and similarity search algorithms are available. The proposed method, called Ness (Neighborhood Based Similarity Search), is appropriate for graphs with low automorphism and high noise, which are common in many social and information networks. Ness is not only efficient, but also robust against structural noise and information loss. Empirical results show that it can quickly and accurately find high-quality matches in large networks, with negligible cost.

Proceedings ArticleDOI
16 May 2011
TL;DR: A novel approach to graph partitioning based on the notion of natural cuts, called PUNCH, which obtains the best known partitions for continental-sized networks, significantly improving on previous results.
Abstract: We present a novel approach to graph partitioning based on the notion of \emph{natural cuts}. Our algorithm, called PUNCH, has two phases. The first phase performs a series of minimum-cut computations to identify and contract dense regions of the graph. This reduces the graph size, but preserves its general structure. The second phase uses a combination of greedy and local search heuristics to assemble the final partition. The algorithm performs especially well on road networks, which have an abundance of natural cuts (such as bridges, mountain passes, and ferries). In a few minutes, it obtains the best known partitions for continental-sized networks, significantly improving on previous results.

Proceedings ArticleDOI
11 Apr 2011
TL;DR: A class of reachability queries and a class of graph patterns, in which an edge is specified with a regular expression of a certain form, expressing the connectivity in a data graph via edges of various types are proposed.
Abstract: It is increasingly common to find graphs in which edges bear different types, indicating a variety of relationships. For such graphs we propose a class of reachability queries and a class of graph patterns, in which an edge is specified with a regular expression of a certain form, expressing the connectivity in a data graph via edges of various types. In addition, we define graph pattern matching based on a revised notion of graph simulation. On graphs in emerging applications such as social networks, we show that these queries are capable of finding more sensible information than their traditional counterparts. Better still, their increased expressive power does not come with extra complexity. Indeed, (1) we investigate their containment and minimization problems, and show that these fundamental problems are in quadratic time for reachability queries and are in cubic time for pattern queries. (2) We develop an algorithm for answering reachability queries, in quadratic time as for their traditional counterpart. (3) We provide two cubic-time algorithms for evaluating graph pattern queries based on extended graph simulation, as opposed to the NP-completeness of graph pattern matching via subgraph isomorphism. (4) The effectiveness, efficiency and scalability of these algorithms are experimentally verified using real-life data and synthetic data.

Proceedings ArticleDOI
11 Dec 2011
TL;DR: This work proposes the Slash Burn method (burn the hubs, and slash the remaining graph into smaller connected components), which avoids the `no good cuts' problem, gives better compression, and leads to faster execution times for matrix-vector operations, which are the back-bone of most graph processing tools.
Abstract: Given a real world graph, how should we lay-out its edges? How can we compress it? These questions are closely related, and the typical approach so far is to find clique-like communities, like the `cavemen graph', and compress them. We show that the block-diagonal mental image of the `cavemen graph' is the wrong paradigm, in full agreement with earlier results that real world graphs have no good cuts. Instead, we propose to envision graphs as a collection of hubs connecting spokes, with super-hubs connecting the hubs, and so on, recursively. Based on the idea, we propose the Slash Burn method (burn the hubs, and slash the remaining graph into smaller connected components). Our view point has several advantages: (a) it avoids the `no good cuts' problem, (b) it gives better compression, and (c) it leads to faster execution times for matrix-vector operations, which are the back-bone of most graph processing tools. Experimental results show that our Slash Burn method consistently outperforms other methods on all datasets, giving good compression and faster running time.

Proceedings ArticleDOI
10 Apr 2011
TL;DR: It is shown that, using O(k log(n)) path measurements, it is able to recover any k-sparse link vector (with no more than k nonzero elements), even though the measurements have to follow the graph path constraints.
Abstract: In this paper, motivated by network inference and tomography applications, we study the problem of compressive sensing for sparse signal vectors over graphs. In particular, we are interested in recovering sparse vectors representing the properties of the edges from a graph. Unlike existing compressive sensing results, the collective additive measurements we are allowed to take must follow connected paths over the underlying graph. For a sufficiently connected graph with n nodes, it is shown that, using O(k log(n)) path measurements, we are able to recover any k-sparse link vector (with no more than k nonzero elements), even though the measurements have to follow the graph path constraints. We mainly show that the computationally efficient l 1 minimization can provide theoretical guarantees for inferring such k-sparse vectors with O(k log(n)) path measurements from the graph.

Book ChapterDOI
18 May 2011
TL;DR: This paper proposes a novel approach for the efficient computation of graph edit distance based on bipartite graph matching by means of the Volgenant-Jonker assignment algorithm, which provides only suboptimal edit distances, but runs in polynomial time.
Abstract: In the field of structural pattern recognition graphs constitute a very common and powerful way of representing objects. The main drawback of graph representations is that the computation of various graph similarity measures is exponential in the number of involved nodes. Hence, such computations are feasible for rather small graphs only. One of the most flexible graph similarity measures is graph edit distance. In this paper we propose a novel approach for the efficient computation of graph edit distance based on bipartite graph matching by means of the Volgenant-Jonker assignment algorithm. Our proposed algorithm provides only suboptimal edit distances, but runs in polynomial time. The reason for its sub-optimality is that edge information is taken into account only in a limited fashion during the process of finding the optimal node assignment between two graphs. In experiments on diverse graph representations we demonstrate a high speed up of our proposed method over a traditional algorithm for graph edit distance computation and over two other sub-optimal approaches that use the Hungarian and Munkres algorithm. Also, we show that classification accuracy remains nearly unaffected by the suboptimal nature of the algorithm.

Journal ArticleDOI
TL;DR: A highly effective multilevel memetic algorithm, which integrates a new multiparent crossover operator and a powerful perturbation-based tabu search algorithm that performs far better than any of the existing graph partitioning algorithms in terms of solution quality.
Abstract: Graph partitioning is one of the most studied NP-complete problems. Given a graph G=(V, E) , the task is to partition the vertex set V into k disjoint subsets of about the same size, such that the number of edges with endpoints in different subsets is minimized. In this paper, we present a highly effective multilevel memetic algorithm, which integrates a new multiparent crossover operator and a powerful perturbation-based tabu search algorithm. The proposed crossover operator tends to preserve the backbone with respect to a certain number of parent individuals, i.e., the grouping of vertices which is common to all parent individuals. Extensive experimental studies on numerous benchmark instances from the graph partitioning archive show that the proposed approach, within a time limit ranging from several minutes to several hours, performs far better than any of the existing graph partitioning algorithms in terms of solution quality.

Journal ArticleDOI
01 Aug 2011
TL;DR: This paper considers the problem of answering threshold-based probabilistic queries over a large uncertain graph database with the possible world semantics and adopts a filtering-and-verification strategy to speed up the search.
Abstract: Retrieving graphs containing a query graph from a large graph database is a key task in many graph-based applications, including chemical compounds discovery, protein complex prediction, and structural pattern recognition. However, graph data handled by these applications is often noisy, incomplete, and inaccurate because of the way the data is produced. In this paper, we study subgraph queries over uncertain graphs. Specifically, we consider the problem of answering threshold-based probabilistic queries over a large uncertain graph database with the possible world semantics. We prove that problem is #P-complete, therefore, we adopt a filtering-and-verification strategy to speed up the search. In the filtering phase, we use a probabilistic inverted index, PIndex, based on subgraph features obtained by an optimal feature selection process. During the verification phase, we develop exact and bound algorithms to validate the remaining candidates. Extensive experimental results demonstrate the effectiveness of the proposed algorithms.

Journal ArticleDOI
TL;DR: A complexity dichotomy is provided (polynomial-time solvable versus NP-hard) for the underlying edge modification problems, forbidden subgraph characterizations of ''cluster graphs with overlaps'', and the parameterized complexity in terms of the number of allowed edge modifications is studied.

Proceedings ArticleDOI
11 Dec 2011
TL;DR: This paper defines a novel D-core framework, extending the classic graph-theoretic notion of k-cores for undirected graphs to directed ones and devise a wealth of novel metrics used to evaluate graph collaboration features of directed graphs.
Abstract: Community detection and evaluation is an important task in graph mining. In many cases, a community is defined as a sub graph characterized by dense connections or interactions among its nodes. A large variety of measures have been proposed to evaluate the quality of such communities â€" in most cases ignoring the directed nature of edges. In this paper, we introduce novel metrics for evaluating the collaborative nature of directed graphs â€" a property not captured by the single node metrics or by other established community evaluation metrics. In order to accomplish this objective, we capitalize on the concept of graph degeneracy and define a novel D-core framework, extending the classic graph-theoretic notion of k-cores for undirected graphs to directed ones. Based on the D-core, which essentially can be seen as a measure of the robustness of a community under degeneracy, we devise a wealth of novel metrics used to evaluate graph collaboration features of directed graphs. We applied the D-core approach on large real-world graphs such as Wikipedia and DBLP and report interesting results at the graph as well at node level.

Journal ArticleDOI
TL;DR: Achlioptas, D'Souza, and Spencer as discussed by the authors showed that there exists a product rule such that with high probability the order of the largest component "jumps" from $o(n)$ to at least $delta n$ in the process, a phenomenon known as "explosive percolation".
Abstract: It is widely believed that certain simple modifications of the random graph process lead to discontinuous phase transitions. In particular, starting with the empty graph on $n$ vertices, suppose that at each step two pairs of vertices are chosen uniformly at random, but only one pair is joined, namely, one minimizing the product of the sizes of the components to be joined. Making explicit an earlier belief of Achlioptas and others, in 2009, Achlioptas, D'Souza and Spencer [Science 323 (2009) 1453-1455] conjectured that there exists a $\delta>0$ (in fact, $\delta\ge1/2$) such that with high probability the order of the largest component "jumps" from $o(n)$ to at least $\delta n$ in $o(n)$ steps of the process, a phenomenon known as "explosive percolation." We give a simple proof that this is not the case. Our result applies to all "Achlioptas processes," and more generally to any process where a fixed number of independent random vertices are chosen at each step, and (at least) one edge between these vertices is added to the current graph, according to any (online) rule. We also prove the existence and continuity of the limit of the rescaled size of the giant component in a class of such processes, settling a number of conjectures. Intriguing questions remain, however, especially for the product rule described above.

Proceedings ArticleDOI
13 Jun 2011
TL;DR: This paper introduces a new automata model for query answering with two modes of acceptance: one captures queries returning nodes, and the other queries returning paths, and introduces additional restrictions for tractability, and shows that some intractable cases can be naturally cast as instances of constraint satisfaction problem.
Abstract: Graph data appears in a variety of application domains, and many uses of it, such as querying, matching, and transforming data, naturally result in incompletely specified graph data, i.e., graph patterns. While queries need to be posed against such data, techniques for querying patterns are generally lacking, and properties of such queries are not well understood.Our goal is to study the basics of querying graph patterns. We first identify key features of patterns, such as node and label variables and edges specified by regular expressions, and define a classification of patterns based on them. We then study standard graph queries on graph patterns, and give precise characterizations of both data and combined complexity for each class of patterns. If complexity is high, we do further analysis of features that lead to intractability, as well as lower complexity restrictions. We introduce a new automata model for query answering with two modes of acceptance: one captures queries returning nodes, and the other queries returning paths. We study properties of such automata, and the key computational tasks associated with them. Finally, we provide additional restrictions for tractability, and show that some intractable cases can be naturally cast as instances of constraint satisfaction problem.

Proceedings ArticleDOI
06 Jun 2011
TL;DR: It is shown that the proof complexities form a natural hierarchy of complexity classes: for many classical graph problems, the proof complexity is either 0, (1), (log n), or poly(n) bits per node.
Abstract: This work studies decision problems from the perspective of nondeterministic distributed algorithms. For a yes instance there must exist a proof that can be verified with a distributed algorithm: all nodes must accept a valid proof, and at least one node must reject an invalid proof. We focus on locally checkable proofs that can be verified with a constant-time distributed algorithm.For example, it is easy to prove that a graph is bipartite: the locally checkable proof gives a 2-colouring of the graph, which only takes 1 bit per node. However, it is more difficult to prove that a graph is not bipartite - it turns out that any locally checkable proof requires ©(log n) bits per node.In this work we classify graph problems according to their local proof complexity, i.e., how many bits per node are needed in a locally checkable proof. We establish tight or near-tight results for classical graph properties such as the chromatic number. We show that the proof complexities form a natural hierarchy of complexity classes: for many classical graph problems, the proof complexity is either 0, (1), (log n), or poly(n) bits per node. Among the most difficult graph properties are symmetric graphs, which require ©(n²) bits per node, and non-3-colourable graphs, which require ©(n²/log n) bits per node - any pure graph property admits a trivial proof of size O(n²).

Journal ArticleDOI
TL;DR: 3D-ASAP successfully incorporates information specific to the molecule problem in structural biology, in particular information on known substructures and their orientation, and compare favorably with similar state-of-the-art localization algorithms.
Abstract: The graph realization problem has received a great deal of attention in recent years, due to its importance in applications such as wireless sensor networks and structural biology. In this paper, we extend on previous work and propose the 3D-ASAP algorithm, for the graph realization problem in $\mathbb{R}^3$, given a sparse and noisy set of distance measurements. 3D-ASAP is a divide and conquer, non-incremental and non-iterative algorithm, which integrates local distance information into a global structure determination. Our approach starts with identifying, for every node, a subgraph of its 1-hop neighborhood graph, which can be accurately embedded in its own coordinate system. In the noise-free case, the computed coordinates of the sensors in each patch must agree with their global positioning up to some unknown rigid motion, that is, up to translation, rotation and possibly reflection. In other words, to every patch there corresponds an element of the Euclidean group Euc(3) of rigid transformations in $\mathbb{R}^3$, and the goal is to estimate the group elements that will properly align all the patches in a globally consistent way. Furthermore, 3D-ASAP successfully incorporates information specific to the molecule problem in structural biology, in particular information on known substructures and their orientation. In addition, we also propose 3D-SP-ASAP, a faster version of 3D-ASAP, which uses a spectral partitioning algorithm as a preprocessing step for dividing the initial graph into smaller subgraphs. Our extensive numerical simulations show that 3D-ASAP and 3D-SP-ASAP are very robust to high levels of noise in the measured distances and to sparse connectivity in the measurement graph, and compare favorably to similar state-of-the art localization algorithms.

Proceedings Article
27 Jul 2011
TL;DR: The method is algorithmically and conceptually simple, especially with respect to how problem-specific knowledge is incorporated into the model, and competitive with other unsupervised approaches in terms of F1 whilst attaining significantly higher cluster purity.
Abstract: In this paper we present a method for unsupervised semantic role induction which we formalize as a graph partitioning problem. Argument instances of a verb are represented as vertices in a graph whose edge weights quantify their role-semantic similarity. Graph partitioning is realized with an algorithm that iteratively assigns vertices to clusters based on the cluster assignments of neighboring vertices. Our method is algorithmically and conceptually simple, especially with respect to how problem-specific knowledge is incorporated into the model. Experimental results on the CoNLL 2008 benchmark dataset demonstrate that our model is competitive with other unsupervised approaches in terms of F1 whilst attaining significantly higher cluster purity.

Journal ArticleDOI
TL;DR: A skeletal representation is introduced that generalizes the definition of the Reeb graph to arbitrary point clouds sampled from m-dimensional manifolds embedded in the d-dimensional space and yields to an effective abstraction of the data.
Abstract: This paper introduces a skeletal representation, called Point Cloud Graph, that generalizes the definition of the Reeb graph to arbitrary point clouds sampled from m-dimensional manifolds embedded in the d-dimensional space. The proposed algorithm is easy to implement and the graph representation yields to an effective abstraction of the data. Finally, we present experimental results on point-sampled surfaces and volumetric data that show the robustness of the Point Cloud Graph to non-uniform point distributions and its usefulness for shape comparison.

Proceedings Article
21 Oct 2011
TL;DR: This work shows that the parallel variant of the edgeconfiguration model given by Chung and Lu (referred to as CL) is notably similar to the Stochastic Kronecker Graph model, and suggests that users of the SKG model should consider the CL model because of its similar properties, simpler structure, and ability to fit a wider range of degree distributions.
Abstract: The analysis of massive graphs is now becoming a very important part of science and industrial research This has led to the construction of a large variety of graph models, each with their own advantages The Stochastic Kronecker Graph (SKG) model has been chosen by the Graph500 steering committee to create supercomputer benchmarks for graph algorithms The major reasons for this are its easy parallelization and ability to mirror real data Although SKG is easy to implement, there is little understanding of the properties and behavior of this model We show that the parallel variant of the edgeconfiguration model given by Chung and Lu (referred to as CL) is notably similar to the SKG model The graph properties of an SKG are extremely close to those of a CL graph generated with the appropriate parameters Indeed, the final probability matrix used by SKG is almost identical to that of a CL model This implies that the graph distribution represented by SKG is almost the same as that given by a CL model We also show that when it comes to fitting real data, CL performs as well as SKG based on empirical studies of graph properties CL has the added benefit of a trivially simple fitting procedure and exactly matching the degree distribution Our results suggest that users of the SKG model should consider the CL model because of its similar properties, simpler structure, and ability to fit a wider range of degree distributions At the very least, CL is a good control model to compare against ∗This work was funded by the applied mathematics program at the United States Department of Energy and performed at Sandia National Laboratories, a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the United States Department of Energy’s National Nuclear Security Administration under contract DE-AC04-94AL85000 †Sandia National Laboratories, CA, apinar@sandiagov ‡Sandia National Laboratories, CA, scomand@sandiagov §Sandia National Laboratories, CA, tgkolda@sandiagov

Book ChapterDOI
24 May 2011
TL;DR: In this paper, a self-test for any connected graph state is presented, where the authors give a set of non-local correlations that can only be achieved (quantumly) by that particular graph state and certain local measurements.
Abstract: We give a construction for a self-test for any connected graph state. In other words, for each connected graph state we give a set of non-local correlations that can only be achieved (quantumly) by that particular graph state and certain local measurements. The number of correlations considered is small, being linear in the number of vertices in the graph. We also prove robustness for the test.

Journal ArticleDOI
TL;DR: Lower and upper bounds on GA"1 are obtained and characterize graphs for which these bounds are best possible and the effect onGA"1 of inserting an edge into a graph is discussed.

Book ChapterDOI
04 Oct 2011
TL;DR: The integrated development environment AGG supports the specification of algebraic graph transformation systems based on attributed, typed graphs with node type inheritance, graph rules with application conditions, and graph constraints, and includes various new features added over the past two years.
Abstract: The integrated development environment AGG supports the specification of algebraic graph transformation systems based on attributed, typed graphs with node type inheritance, graph rules with application conditions, and graph constraints It offers several analysis techniques for graph transformation systems including graph parsing, consistency checking of graphs as well as conflict and dependency detection in transformations by critical pair analysis of graph rules, an important instrument to support the confluence check of graph transformation systems AGG 20 includes various new features added over the past two years It supports the specification of complex control structures for rule application comprising the definition of control and object flow for rule sequences and nested application conditions Furthermore, new possibilities for constructing rules from existing ones (eg, inverse, minimal, amalgamated, and concurrent rules) and for more flexible usability of critical pair analyses have been realized