Integrating data from heterogeneous sources is often modeled as merging graphs. Given two or more 'compatible', but not-isomorphic graphs, the first step is to identify a graph alignment, where a potentially partial mapping of vertices between two graphs is computed. A significant portion of the literature on this problem only takes the global structure of the input graphs into account. Only more recent ones additionally use vertex and edge attributes to achieve a more accurate alignment. However, these methods are not designed to scale to map large graphs arising in many modern applications. We propose a new iterative graph aligner, gsaNA, that uses the global structure of the graphs to significantly reduce the problem size and align large graphs with a minimal loss of information. Concretely, we show that our proposed technique is highly flexible, can be used to achieve higher recall, and it is orders of magnitudes faster than the current state of the art techniques.
Solution methods proposed in the literature for graph alignment can be roughly classified into four basic categories @cite_4 @cite_1 : spectral methods @cite_16 @cite_17 @cite_27 @cite_7 , graph structure similarity methods @cite_36 @cite_32 @cite_19 @cite_13 @cite_20 , tree search or tabu search methods @cite_34 @cite_14 @cite_10 @cite_3 , and integer linear programming (ILP) methods @cite_22 @cite_9 @cite_31 . All of these works have scalability issues. Our algorithms leverage global graph structure and reduces the problem space and augment that with semantic information to alleviate most of the scalability issues.
@cite_14 @cite_4 @cite_22 @cite_7 @cite_36 @cite_10 @cite_9 @cite_1 @cite_32 @cite_34 @cite_3 @cite_19 @cite_27 @cite_31 @cite_16 @cite_13 @cite_20 @cite_17
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The growing popularity of graph databases has generated interesting data management problems, such as subgraph search, shortest-path query, reachability verification, and pattern match. Among these, a pattern match query is more flexible compared to a subgraph search and more informative compared to a shortest-path or reachability query. In this paper, we address pattern match problems over a large data graph G. Specifically, given a pattern graph (i.e., query Q), we want to find all matches (in G) that have the similar connections as those in Q. In order to reduce the search space significantly, we first transform the vertices into points in a vector space via graph embedding techniques, coverting a pattern match query into a distance-based multi-way join problem over the converted vector space. We also propose several pruning strategies and a join order selection method to process join processing efficiently. Extensive experiments on both real and synthetic datasets show that our method outperforms existing ones by orders of magnitude. In this paper, we propose a general framework for graph matching which is suitable for different problems of pattern recognition. The pattern representation we assume is at the same time highly structured, like for classic syntactic and structural approaches, and of subsymbolic nature with real-valued features, like for connectionist and statistic approaches. We show that random walk based models, inspired by Google's PageRank, give rise to a spectral theory that nicely enhances the graph topological features at node level. As a straightforward consequence, we derive a polynomial algorithm for the classic graph isomorphism problem, under the restriction of dealing with Markovian spectrally distinguishable graphs (MSD), a class of graphs that does not seem to be easily reducible to others proposed in the literature. The experimental results that we found on different test-beds of the TC-15 graph database show that the defined MSD class "almost always" covers the database, and that the proposed algorithm is significantly more efficient than top scoring VF algorithm on the same data. Most interestingly, the proposed approach is very well-suited for dealing with partial and approximate graph matching problems, derived for instance from image retrieval tasks. We consider the objects of the COIL-100 visual collection and provide a graph-based representation, whose node's labels contain appropriate visual features. We show that the adoption of classic bipartite graph matching algorithms offers a straightforward generalization of the algorithm given for graph isomorphism and, finally, we report very promising experimental results on the COIL-100 visual collection. Due to its wide range of applications, matching between two graphs has been extensively studied and remains an active topic. By contrast, it is still under-exploited on how to jointly match multiple graphs, partly due to its intrinsic combinatorial intractability. In this work, we address this challenging problem in a principled way under the rank-1 tensor approximation framework. In particular, we formulate multi-graph matching as a combinational optimization problem with two main ingredients: unary matching over graph vertices and structure matching over graph edges, both of which across multiple graphs. Then we propose an efficient power iteration solution for the resulting NP-hard optimization problem. The proposed algorithm has several advantages: 1) the intrinsic matching consistency across multiple graphs based on the high-order tensor optimization, 2) the free employment of powerful high-order node affinity, 3) the flexible integration between various types of node affinities and edge hyper-edge affinities. Experiments on diverse and challenging datasets validate the effectiveness of the proposed approach in comparison with state-of the-arts. Background: In addition to component-based comparative approaches, network alignments provide the means to study conserved network topology such as common pathways and more complex network motifs. Yet, unlike in classical sequence alignment, the comparison of networks becomes computationally more challenging, as most meaningful assumptions instantly lead to NPhard problems. Most previous algorithmic work on network alignments is heuristic in nature. Results: We introduce the graph-based maximum structural matching formulation for pairwise global network alignment. We relate the formulation to previous work and prove NP-hardness of the problem. Based on the new formulation we build upon recent results in computational structural biology and present a novel Lagrangian relaxation approach that, in combination with a branch-and-bound method, computes provably optimal network alignments. The Lagrangian algorithm alone is a powerful heuristic method, which produces solutions that are often near-optimal and – unlike those computed by pure heuristics – come with a quality guarantee. Conclusion: Computational experiments on the alignment of protein-protein interaction networks and on the classification of metabolic subnetworks demonstrate that the new method is reasonably fast and has advantages over pure heuristics. Our software tool is freely available as part of the LISA library. Network alignment is the problem of matching the nodes of two graphs, maximizing the similarity of the matched nodes and the edges between them. This problem is encountered in a wide array of applications - from biological networks to social networks to ontologies - where multiple networked data sources need to be integrated. Due to the difficulty of the task, an accurate alignment can rarely be found without human assistance. Thus, it is of great practical importance to develop network alignment algorithms that can optimally leverage experts who are able to provide the correct alignment for a small number of nodes. Yet, only a handful of existing works address this active network alignment setting. The majority of the existing active methods focus on absolute queries ("are nodes @math and @math the same or not?"), whereas we argue that it is generally easier for a human expert to answer relative queries ("which node in the set @math is the most similar to node @math ?"). This paper introduces a novel relative-query strategy, TopMatchings, which can be applied on top of any network alignment method that constructs and solves a bipartite matching problem. Our method identifies the most informative nodes to query based on the top- @math matchings of a bipartite graph. We compare the proposed approach to several commonly-used query strategies and perform experiments on both synthetic and real-world datasets. Our matching-based strategy yields the highest overall performance, outperforming all the baseline methods by more than 15 percentage points in some cases. Multiple networks naturally appear in numerous high-impact applications. Network alignment (i.e., finding the node correspondence across different networks) is often the very first step for many data mining tasks. Most, if not all, of the existing alignment methods are solely based on the topology of the underlying networks. Nonetheless, many real networks often have rich attribute information on nodes and or edges. In this paper, we propose a family of algorithms FINAL to align attributed networks. The key idea is to leverage the node edge attribute information to guide (topology-based) alignment process. We formulate this problem from an optimization perspective based on the alignment consistency principle, and develop effective and scalable algorithms to solve it. Our experiments on real networks show that (1) by leveraging the attribute information, our algorithms can significantly improve the alignment accuracy (i.e., up to a 30 improvement over the existing methods); (2) compared with the exact solution, our proposed fast alignment algorithm leads to a more than 10 times speed-up, while preserving a 95 accuracy; and (3) our on-query alignment method scales linearly, with an around 90 ranking accuracy compared with our exact full alignment method and a near real-time response time. In this paper, we study the problem of subgraph matching that extracts all subgraph isomorphic embeddings of a query graph q in a large data graph G. The existing algorithms for subgraph matching follow Ullmann's backtracking approach; that is, iteratively map query vertices to data vertices by following a matching order of query vertices. It has been shown that the matching order of query vertices is a very important aspect to the efficiency of a subgraph matching algorithm. Recently, many advanced techniques, such as enforcing connectivity and merging similar vertices in query or data graphs, have been proposed to provide an effective matching order with the aim to reduce unpromising intermediate results especially the ones caused by redundant Cartesian products. In this paper, for the first time we address the issue of unpromising results by Cartesian products from "dissimilar" vertices. We propose a new framework by postponing the Cartesian products based on the structure of a query to minimize the redundant Cartesian products. Our second contribution is proposing a new path-based auxiliary data structure, with the size O(|E(G)| x |V(q)|), to generate a matching order and conduct subgraph matching, which significantly reduces the exponential size O(|V(G)||V(q)|-1) of the existing path-based auxiliary data structure, where V (G) and E (G) are the vertex and edge sets of a data graph G, respectively, and V (q) is the vertex set of a query @math . Extensive empirical studies on real and synthetic graphs demonstrate that our techniques outperform the state-of-the-art algorithms by up to @math orders of magnitude. The problem of graph matching in general is NP-hard and approaches have been proposed for its sub optimal solution, most focusing on finding the one-to-one node mapping between two graphs. A more general and challenging problem arises when one aims to find consistent mappings across a number of graphs more than two. Conventional graph pair matching methods often result in mapping inconsistency since the mapping between two graphs can either be determined by pair mapping or by an additional anchor graph. To address this issue, a novel formulation is derived which is maximized via alternating optimization. Our method enjoys several advantages: 1) the mappings are jointly optimized rather than sequentially performed by applying pair matching, allowing the global affinity information across graphs can be propagated and explored, 2) the number of concerned variables to optimize is in linear with the number of graphs, being superior to local pair matching resulting in O(n2) variables, 3) the mapping consistency constraints are analytically satisfied during optimization, and 4) off-the-shelf graph pair matching solvers can be reused under the proposed framework in an out-of-the-box' fashion. Competitive results on both the synthesized data and the real data are reported, by varying the level of deformation, outliers and edge densities. In this paper, we develop a novel paradigm, namely hypergraph shift, to find robust graph modes by probabilistic voting strategy, which are semantically sound besides the self-cohesiveness requirement in forming graph modes. Unlike the existing techniques to seek graph modes by shifting vertices based on pair-wise edges (i.e, an edge with 2 ends), our paradigm is based on shifting high-order edges (hyperedges) to deliver graph modes. Specifically, we convert the problem of seeking graph modes as the problem of seeking maximizers of a novel objective function with the aim to generate good graph modes based on sifting edges in hypergraphs. As a result, the generated graph modes based on dense subhypergraphs may more accurately capture the object semantics besides the self-cohesiveness requirement. We also formally prove that our technique is always convergent. Extensive empirical studies on synthetic and real world data sets are conducted on clustering and graph matching. They demonstrate that our techniques significantly outperform the existing techniques. The task of monolingual text alignment consists in finding similar text fragments between two given documents. It has applications in plagiarism detection, detection of text reuse, author identification, authoring aid, and information retrieval, to mention only a few. We describe our approach to the text alignment subtask of the plagiarism detection competition at PAN 2014, which resulted in the best-performing system at the PAN 2014 competition and outperforms the best-performing system of the PAN 2013 competition by the cumulative evaluation measure Plagdet. Our method relies on a sentence similarity measure based on a tf-idf-like weighting scheme that permits us to consider stopwords without increasing the rate of false positives. We introduce a recursive algorithm to extend the ranges of matching sentences to maximal length passages. We also introduce a novel filtering method to resolve overlapping plagiarism cases. Our system is available as open source. We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The algorithm allows to analyze large graphs and may find applications in fields such as computational biology. As a proof of concept we use our algorithm to align the similarity graphs of two interacting protein families involved in bacterial signal transduction, and to predict actually interacting protein partners between these families. In this paper, we show that many graph search problems can be solved quite efficiently for a geometric intersection graph of horizontal and vertical line segments. We first extract several basic operations for depth first search and breadth first search on a graph. Then we present data structures for the intersection graph in terms of which those operations can be implemented in an efficient manner. The data structures enable us to solve various graph search problems besides depth first search and breadth first search. Specifying the results obtained in this paper for an intersection graph of n horizontal and vertical segments with m pairs of intersecting segments, we obtain algorithms with the following complexity, where @math . (i) Depth first search and breadth first search can be executed in @math time and @math space. (ii) The biconnected components can be found in @math time and @math space. (iii) A maximum matching and a maximum independent set can be found in $O... References.- Technical Foundations.- 1 Introduction.- 2 Graphs and Their Representation.- 3 Graph Planarity and Embeddings.- 4 Graph Drawing Methods.- References.- WilmaScope - A 3D Graph Visualization System.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- Pajek - Analysis and Visualization of Large Networks.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- Tulip - A Huge Graph Visualization Framework.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- Graphviz and Dynagraph - Static and Dynamic Graph Drawing Tools.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- AGD - A Library of Algorithms for Graph Drawing.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- yFiles - Visualization and Automatic Layout of Graphs.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- GDS - A Graph Drawing Server on the Internet.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- BioPath - Exploration and Visualization of Biochemical Pathways.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- DBdraw - Automatic Layout of Relational Database Schemas.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- GoVisual - A Diagramming Software for UML Class Diagrams.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- CrocoCosmos - 3D Visualization of Large Object-oriented Programs.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- ViSta - Visualizing Statecharts.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- visone - Analysis and Visualization of Social Networks.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- Polyphemus and Hermes - Exploration and Visualization of Computer Networks.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References. We study approaches for the exact solution of the NP-hard minimum spanning tree problem under conflict constraints. Given a graph (G(V,E) ) and a set (C E E ) of conflicting edge pairs, the problem consists of finding a conflict-free minimum spanning tree, i.e. feasible solutions are allowed to include at most one of the edges from each pair in (C ). The problem was introduced recently in the literature, with several results on its complexity and approximability. Some formulations and both exact and heuristic algorithms were also discussed, but computational results indicate considerably large duality gaps and a lack of optimality certificates for benchmark instances. In this paper, we build on the representation of conflict constraints using an auxiliary conflict graph ( G (E,C) ), where stable sets correspond to conflict-free subsets of (E ). We introduce a general preprocessing method and a branch and cut algorithm using an IP formulation with exponentially sized classes of valid inequalities for both the spanning tree and the stable set polytopes. Encouraging computational results indicate that the dual bounds of our approach are significantly stronger than those previously available, already in the initial LP relaxation, and we are able to provide new feasibility and optimality certificates. Abstract Alignment-free approaches are gaining persistent interest in many sequence analysis applications such as phylogenetic inference and metagenomic classification clustering, especially for large-scale sequence datasets. Besides the widely used k-mer methods, the average common substring (ACS) approach has emerged to be one of the well-known alignment-free approaches. Two recent works further generalize this ACS approach by allowing a bounded number k of mismatches in the common substrings, relying on approximation (linear time) and exact computation, respectively. Albeit having a good worst-case time complexity aastex amsbsy amsfonts amssymb bm mathrsfs pifont stmaryrd textcomp portland, xspace amsmath, amsxtra empty 10 9 7 6 @math log ^ ... A 5 4-approximation algorithm is presented for the minimum cardinality 2-edge-connected spanning subgraph problem in undirected graphs. This improves the previous best approximation ratio of 4 3. It is shown that our ratio is tight with respect to current lower bounds, and any further improvement is possible only if new lower bounds are discovered. Given an arc-weighted directed graph G = (V, A, spl lscr ) and a pair of nodes s, t, we seek to find an s-t walk of length at most B that maximizes some given function f of the set of nodes visited by the walk. The simplest case is when we seek to maximize the number of nodes visited: this is called the orienteering problem. Our main result is a quasi-polynomial time algorithm that yields an O(log OPT) approximation for this problem when f is a given submodular set function. We then extend it to the case when a node v is counted as visited only if the walk reaches v in its time window [R(v), D(v)]. We apply the algorithm to obtain several new results. First, we obtain an O(log OPT) approximation for a generalization of the orienteering problem in which the profit for visiting each node may vary arbitrarily with time. This captures the time window problem considered earlier for which, even in undirected graphs, the best approximation ratio known [Bansal, (2004)] is O(log sup 2 OPT). The second application is an O(log sup 2 k) approximation for the k-TSP problem in directed graphs (satisfying asymmetric triangle inequality). This is the first non-trivial approximation algorithm for this problem. The third application is an O(log sup 2 k) approximation (in quasi-poly time) for the group Steiner problem in undirected graphs where k is the number of groups. This improves earlier ratios (Garg, ) by a logarithmic factor and almost matches the inapproximability threshold on trees (Halperin and Krauthgamer, 2003). This connection to group Steiner trees also enables us to prove that the problem we consider is hard to approximate to a ratio better than spl Omega (log sup 1- spl epsi OPT), even in undirected graphs. Even though our algorithm runs in quasi-poly time, we believe that the implications for the approximability of several basic optimization problems are interesting. Graph matching has a wide spectrum of computer vision applications such as finding feature point correspondences across images. The problem of graph matching is generally NP-hard, so most existing work pursues suboptimal solutions between two graphs. This paper investigates a more general problem of matching N attributed graphs to each other, i.e. labeling their common node correspondences such that a certain compatibility affinity objective is optimized. This multi-graph matching problem involves two key ingredients affecting the overall accuracy: a) the pairwise affinity matching score between two local graphs, and b) global matching consistency that measures the uniqueness and consistency of the pairwise matching results by different sequential matching orders. Previous work typically either enforces the matching consistency constraints in the beginning of iterative optimization, which may propagate matching error both over iterations and across different graph pairs; or separates score optimizing and consistency synchronization in two steps. This paper is motivated by the observation that affinity score and consistency are mutually affected and shall be tackled jointly to capture their correlation behavior. As such, we propose a novel multi-graph matching algorithm to incorporate the two aspects by iteratively approximating the global-optimal affinity score, meanwhile gradually infusing the consistency as a regularizer, which improves the performance of the initial solutions obtained by existing pairwise graph matching solvers. The proposed algorithm with a theoretically proven convergence shows notable efficacy on both synthetic and public image datasets.