The cavity approach for Steiner trees packing problems

The Belief Propagation approximation, or cavity method, has been recently applied to several combinatorial optimization problems in its zero-temperature implementation, the max-sum algorithm. In particular, recent developments to solve the edge-disjoint paths problem and the prize-collecting Steiner tree problem on graphs have shown remarkable results for several classes of graphs and for benchmark instances. Here we propose a generalization of these techniques for two variants of the Steiner trees packing problem where multiple "interacting" trees have to be sought within a given graph. Depending on the interaction among trees we distinguish the vertex-disjoint Steiner trees problem, where trees cannot share nodes, from the edge-disjoint Steiner trees problem, where edges cannot be shared by trees but nodes can be members of multiple trees. Several practical problems of huge interest in network design can be mapped into these two variants, for instance, the physical design of Very Large Scale Integration (VLSI) chips. The formalism described here relies on two components edge-variables that allows us to formulate a massage-passing algorithm for the V-DStP and two algorithms for the E-DStP differing in the scaling of the computational time with respect to some relevant parameters. We will show that one of the two formalisms used for the edge-disjoint variant allow us to map the max-sum update equations into a weighted maximum matching problem over proper bipartite graphs. We developed a heuristic procedure based on the max-sum equations that shows excellent performance in synthetic networks (in particular outperforming standard multi-step greedy procedures by large margins) and on large benchmark instances of VLSI for which the optimal solution is known, on which the algorithm found the optimum in two cases and the gap to optimality was never larger than 4 %

Single-Strip Triangulation of Manifolds with Arbitrary Topology

Triangle strips have been widely used for efficient rendering. It is NP-complete to test whether a given triangulated model can be represented as a single triangle strip, so many heuristics have been proposed to partition models into few long strips. In this paper, we present a new algorithm for creating a single triangle loop or strip from a triangulated model. Our method applies a dual graph matching algorithm to partition the mesh into cycles, and then merges pairs of cycles by splitting adjacent triangles when necessary. New vertices are introduced at midpoints of edges and the new triangles thus formed are coplanar with their parent triangles, hence the visual fidelity of the geometry is not changed. We prove that the increase in the number of triangles due to this splitting is 50% in the worst case, however for all models we tested the increase was less than 2%. We also prove tight bounds on the number of triangles needed for a single-strip representation of a model with holes on its boundary. Our strips can be used not only for efficient rendering, but also for other applications including the generation of space filling curves on a manifold of any arbitrary topology.Comment: 12 pages, 10 figures. To appear at Eurographics 200

Cut Tree Construction from Massive Graphs

The construction of cut trees (also known as Gomory-Hu trees) for a given graph enables the minimum-cut size of the original graph to be obtained for any pair of vertices. Cut trees are a powerful back-end for graph management and mining, as they support various procedures related to the minimum cut, maximum flow, and connectivity. However, the crucial drawback with cut trees is the computational cost of their construction. In theory, a cut tree is built by applying a maximum flow algorithm for $n$ times, where $n$ is the number of vertices. Therefore, naive implementations of this approach result in cubic time complexity, which is obviously too slow for today's large-scale graphs. To address this issue, in the present study, we propose a new cut-tree construction algorithm tailored to real-world networks. Using a series of experiments, we demonstrate that the proposed algorithm is several orders of magnitude faster than previous algorithms and it can construct cut trees for billion-scale graphs.Comment: Short version will appear at ICDM'1

B-splines in EMD and Graph Theory in Pattern Recognition

With the development of science and technology, a large amount of data is waiting for further scientific exploration. We can always build up some good mathematical models based on the given data to analyze and solve the real life problems. In this work, we propose three types of mathematical models for different applications.;In chapter 1, we use Bspline based EMD to analysis nonlinear and no-stationary signal data. A new idea about the boundary extension is introduced and applied to the Empirical Mode Decomposition(EMD) algorithm. Instead of the traditional mirror extension on the boundary, we propose a ratio extension on the boundary.;In chapter 2 we propose a weighted directed multigraph for text pattern recognition. We set up a weighted directed multigraph model using the distances between the keywords as the weights of arcs. We then developed a keyword-frequency-distance-based algorithm which not only utilizes the frequency information of keywords but also their ordering information.;In chapter 3, we propose a centrality guided clustering method. Different from traditional methods which choose a center of a cluster randomly, we start clustering from a LEADER - a vertex with highest centrality score, and a new member is added into an existing community if the new vertex meet some criteria and the new community with the new vertex maintain a certain density.;In chapter 4, we define a new graph optimization problem which is called postman tour with minimum route-pair cost. And we model the DNA sequence assembly problem as the postman tour with minimum route-pair cost problem

Scaling and Universality in City Space Syntax: between Zipf and Matthew

We report about universality of rank-integration distributions of open spaces in city space syntax similar to the famous rank-size distributions of cities (Zipf's law). We also demonstrate that the degree of choice an open space represents for other spaces directly linked to it in a city follows a power law statistic. Universal statistical behavior of space syntax measures uncovers the universality of the city creation mechanism. We suggest that the observed universality may help to establish the international definition of a city as a specific land use pattern.Comment: 24 pages, 5 *.eps figure

Searching for network modules

When analyzing complex networks a key target is to uncover their modular structure, which means searching for a family of modules, namely node subsets spanning each a subnetwork more densely connected than the average. This work proposes a novel type of objective function for graph clustering, in the form of a multilinear polynomial whose coefficients are determined by network topology. It may be thought of as a potential function, to be maximized, taking its values on fuzzy clusterings or families of fuzzy subsets of nodes over which every node distributes a unit membership. When suitably parametrized, this potential is shown to attain its maximum when every node concentrates its all unit membership on some module. The output thus is a partition, while the original discrete optimization problem is turned into a continuous version allowing to conceive alternative search strategies. The instance of the problem being a pseudo-Boolean function assigning real-valued cluster scores to node subsets, modularity maximization is employed to exemplify a so-called quadratic form, in that the scores of singletons and pairs also fully determine the scores of larger clusters, while the resulting multilinear polynomial potential function has degree 2. After considering further quadratic instances, different from modularity and obtained by interpreting network topology in alternative manners, a greedy local-search strategy for the continuous framework is analytically compared with an existing greedy agglomerative procedure for the discrete case. Overlapping is finally discussed in terms of multiple runs, i.e. several local searches with different initializations.Comment: 10 page

Exact Distance Oracles for Planar Graphs

We present new and improved data structures that answer exact node-to-node distance queries in planar graphs. Such data structures are also known as distance oracles. For any directed planar graph on n nodes with non-negative lengths we obtain the following: * Given a desired space allocation $S\in[n\lg\lg n,n^2]$, we show how to construct in $\tilde O(S)$ time a data structure of size $O(S)$ that answers distance queries in $\tilde O(n/\sqrt S)$ time per query. As a consequence, we obtain an improvement over the fastest algorithm for k-many distances in planar graphs whenever $k\in[\sqrt n,n)$. * We provide a linear-space exact distance oracle for planar graphs with query time $O(n^{1/2+eps})$ for any constant eps>0. This is the first such data structure with provable sublinear query time. * For edge lengths at least one, we provide an exact distance oracle of space $\tilde O(n)$ such that for any pair of nodes at distance D the query time is $\tilde O(min {D,\sqrt n})$. Comparable query performance had been observed experimentally but has never been explained theoretically. Our data structures are based on the following new tool: given a non-self-crossing cycle C with $c = O(\sqrt n)$ nodes, we can preprocess G in $\tilde O(n)$ time to produce a data structure of size $O(n \lg\lg c)$ that can answer the following queries in $\tilde O(c)$ time: for a query node u, output the distance from u to all the nodes of C. This data structure builds on and extends a related data structure of Klein (SODA'05), which reports distances to the boundary of a face, rather than a cycle. The best distance oracles for planar graphs until the current work are due to Cabello (SODA'06), Djidjev (WG'96), and Fakcharoenphol and Rao (FOCS'01). For $\sigma\in(1,4/3)$ and space $S=n^\sigma$, we essentially improve the query time from $n^2/S$ to $\sqrt{n^2/S}$.Comment: To appear in the proceedings of the 23rd ACM-SIAM Symposium on Discrete Algorithms, SODA 201

Automatic Network Fingerprinting through Single-Node Motifs

Complex networks have been characterised by their specific connectivity patterns (network motifs), but their building blocks can also be identified and described by node-motifs---a combination of local network features. One technique to identify single node-motifs has been presented by Costa et al. (L. D. F. Costa, F. A. Rodrigues, C. C. Hilgetag, and M. Kaiser, Europhys. Lett., 87, 1, 2009). Here, we first suggest improvements to the method including how its parameters can be determined automatically. Such automatic routines make high-throughput studies of many networks feasible. Second, the new routines are validated in different network-series. Third, we provide an example of how the method can be used to analyse network time-series. In conclusion, we provide a robust method for systematically discovering and classifying characteristic nodes of a network. In contrast to classical motif analysis, our approach can identify individual components (here: nodes) that are specific to a network. Such special nodes, as hubs before, might be found to play critical roles in real-world networks.Comment: 16 pages (4 figures) plus supporting information 8 pages (5 figures