3,127 research outputs found
On combinatorial optimisation in analysis of protein-protein interaction and protein folding networks
Abstract: Protein-protein interaction networks and protein folding networks represent prominent research topics at the intersection of bioinformatics and network science. In this paper, we present a study of these networks from combinatorial optimisation point of view. Using a combination of classical heuristics and stochastic optimisation techniques, we were able to identify several interesting combinatorial properties of biological networks of the COSIN project. We obtained optimal or near-optimal solutions to maximum clique and chromatic number problems for these networks. We also explore patterns of both non-overlapping and overlapping cliques in these networks. Optimal or near-optimal solutions to partitioning of these networks into non-overlapping cliques and to maximum independent set problem were discovered. Maximal cliques are explored by enumerative techniques. Domination in these networks is briefly studied, too. Applications and extensions of our findings are discussed
Massively Parallel Algorithms for Distance Approximation and Spanners
Over the past decade, there has been increasing interest in
distributed/parallel algorithms for processing large-scale graphs. By now, we
have quite fast algorithms -- usually sublogarithmic-time and often
-time, or even faster -- for a number of fundamental graph
problems in the massively parallel computation (MPC) model. This model is a
widely-adopted theoretical abstraction of MapReduce style settings, where a
number of machines communicate in an all-to-all manner to process large-scale
data. Contributing to this line of work on MPC graph algorithms, we present
round MPC algorithms for computing
-spanners in the strongly sublinear regime of local memory. To
the best of our knowledge, these are the first sublogarithmic-time MPC
algorithms for spanner construction. As primary applications of our spanners,
we get two important implications, as follows:
-For the MPC setting, we get an -round algorithm for
approximation of all pairs shortest paths (APSP) in the
near-linear regime of local memory. To the best of our knowledge, this is the
first sublogarithmic-time MPC algorithm for distance approximations.
-Our result above also extends to the Congested Clique model of distributed
computing, with the same round complexity and approximation guarantee. This
gives the first sub-logarithmic algorithm for approximating APSP in weighted
graphs in the Congested Clique model
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