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    H. Djidjev

    An architecture of a parallel computing system for matrix computations based on a systolic array of processors is considered and a version of incomplete block-factorizations of sparse matrices that arise in finite difference solution of... more
    An architecture of a parallel computing system for matrix computations based on a systolic array of processors is considered and a version of incomplete block-factorizations of sparse matrices that arise in finite difference solution of three dimensional elliptic differential equations of second order is studied. The parallelization, both of factorization and solution processes, is investigated and the implementation of a stationary preconditioned iterative method on the considered computer architecture is described. Representative numerical tests for the efficiency of the consecutive version of the method for solving three-dimensional finite difference approximations to the Poisson equation are presented.
    ABSTRACT We study the design and implementation of algorithms...
    ... 2. Guiseppe Di Battista, Roberto Tamassia, and Luca Vismara, On-line convez planarzty testing, Proc. ... Math. Soc., vol. 2, pp. 464-466, 1951. 15. C. Thomassen, Planarity and duality of finite and infinite planar graphs, J.... more
    ... 2. Guiseppe Di Battista, Roberto Tamassia, and Luca Vismara, On-line convez planarzty testing, Proc. ... Math. Soc., vol. 2, pp. 464-466, 1951. 15. C. Thomassen, Planarity and duality of finite and infinite planar graphs, J. Combinatorial Theory, Series B 29, 1980, pp. 244-271. 16. ...
    One of the most useful measures of cluster quality is the modularity of a partition, which measures the difference between the number of the edges joining vertices from the same cluster and the expected number of such edges in a random... more
    One of the most useful measures of cluster quality is the modularity of a partition, which measures the difference between the number of the edges joining vertices from the same cluster and the expected number of such edges in a random (unstructured) graph. In this paper we show that the problem of finding a partition maximizing the modularity of a given graph G can be reduced to a minimum weighted cut problem on a complete graph with the same vertices as G. We then show that the resulted minimum cut problem can be efficiently solved with existing software for graph partitioning and that our algorithm finds clusterings of a better quality and much faster than the existing clustering algorithms.
    ABSTRACT We prove separator theorems in which the size of the separator is minimized with respect to non-negative vertex costs. We show that for any planar graph G there exists a vertex separator of total sum of vertex costs at most cÖ{åv... more
    ABSTRACT We prove separator theorems in which the size of the separator is minimized with respect to non-negative vertex costs. We show that for any planar graph G there exists a vertex separator of total sum of vertex costs at most cÖ{åv Î V(G)( cost (v))2}c\sqrt{\sum_{v\in V(G)}( cost (v))^2} and that this bound is optimal to within a constant factor. Moreover, such a separator can be found in linear time. This theorem implies a variety of other separation results. We describe applications of our separator theorems to graph embedding problems, to graph pebbling, and to multicommodity flow problems. Key words. Graph separators, Divide and conquer, Graph embeddings, Pebbling, Multicommodity flow.
    ABSTRACT It is known that the set of vertices of any toroidal graph (graph of orientable genus 1) can be divided into two edge-disjoint sets of size no greater than 2/3 times the size of the original graph by deleting no more than 18 n... more
    ABSTRACT It is known that the set of vertices of any toroidal graph (graph of orientable genus 1) can be divided into two edge-disjoint sets of size no greater than 2/3 times the size of the original graph by deleting no more than 18 n vertices [2]. The paper improves the constant before n in the above theorem to 12 by using the structure separation graph and gives a lower bound on the optimal constant that can replace 12.
    ABSTRACT The crossing number of a graph G = (V,E), denoted by cr(G), is the smallest number of edge crossings in any drawing of G in the plane. Leighton [14] proved that for any n-vertex graph G of bounded degree, its crossing number... more
    ABSTRACT The crossing number of a graph G = (V,E), denoted by cr(G), is the smallest number of edge crossings in any drawing of G in the plane. Leighton [14] proved that for any n-vertex graph G of bounded degree, its crossing number satisfies cr(G) + n = Ω(bw2(G)), where bw(G) is the bisection width of G. The lower bound method was extended for graphs of arbitrary vertex degrees to cr (G) + \tfrac116åu Î G du 2 = W(bw2 (G)) (G) + \tfrac{1} {{16}}\sum _{\upsilon \in G} d_\upsilon ^2 = \Omega (bw^2 (G)) in [15],[19], where d ν is the degree of any vertex ν. We improve this bound by showing that the bisection width can be replaced by a larger parameter — the cutwidth of the graph. Our result also yields an upper bound for the path-width of G in term of its crossing number.
    ABSTRACT Finding similarities between protein structures is a crucial task in molecular biology. Most of the existing tools require proteins to be aligned in order-preserving way and only find single alignments even when multiple similar... more
    ABSTRACT Finding similarities between protein structures is a crucial task in molecular biology. Most of the existing tools require proteins to be aligned in order-preserving way and only find single alignments even when multiple similar regions exist. We propose a new seed-based approach that discovers multiple pairs of similar regions. Its computational complexity is polynomial and it comes with a quality guarantee—the returned alignments have both root mean squared deviations (coordinate-based as well as internal-distances based) lower than a given threshold, if such exist. We do not require the alignments to be order preserving (i.e., we consider nonsequential alignments), which makes our algorithm suitable for detecting similar domains when comparing multidomain proteins as well as to detect structural repetitions within a single protein. Because the search space for nonsequential alignments is much larger than for sequential ones, the computational burden is addressed by extensive use of parallel computing techniques: a coarse-grain level parallelism making use of available CPU cores for computation and a fine-grain level parallelism exploiting bit-level concurrency as well as vector instructions.
    ABSTRACT We describe a new algorithm for solving the all-pairs shortest-path (APSP) problem for planar graphs and graphs with small separators that exploits the massive on-chip parallelism available in today's Graphics Processing... more
    ABSTRACT We describe a new algorithm for solving the all-pairs shortest-path (APSP) problem for planar graphs and graphs with small separators that exploits the massive on-chip parallelism available in today's Graphics Processing Units (GPUs). Our algorithm, based on the Floyd-War shall algorithm, has near optimal complexity in terms of the total number of operations, while its matrix-based structure is regular enough to allow for efficient parallel implementation on the GPUs. By applying a divide-and-conquer approach, we are able to make use of multi-node GPU clusters, resulting in more than an order of magnitude speedup over the fastest known Dijkstra-based GPU implementation and a two-fold speedup over a parallel Dijkstra-based CPU implementation.
    ... of that analysis is to discover patterns in the network traffic data that ... Keywords Networks, Protocol Graphs, Graph Decomposition, Patterns, Statistical Modeling, Anomaly Detection ... approaches for detecting malware and attacks... more
    ... of that analysis is to discover patterns in the network traffic data that ... Keywords Networks, Protocol Graphs, Graph Decomposition, Patterns, Statistical Modeling, Anomaly Detection ... approaches for detecting malware and attacks in computer systems: signature based, where a ...
    This project focused on the development of methods for simulation of multi-phase and multicomponent fluid flows in porous media that combine recent advances in numerical methods with techniques for partitioning and load balancing based on... more
    This project focused on the development of methods for simulation of multi-phase and multicomponent fluid flows in porous media that combine recent advances in numerical methods with techniques for partitioning and load balancing based on graph theory and graph algorithms. According to the research plan, we have concentrated our efforts and achieved our goals in the following interrelated groups of problems, which combine theoretical investigations with computational experimental work: