64,824 research outputs found
Comparison and improvement of algorithms for computing minimal cut sets
BACKGROUND: Constrained minimal cut sets (cMCSs) have recently been introduced as a framework to enumerate minimal genetic intervention strategies for targeted optimization of metabolic networks. Two different algorithmic schemes (adapted Berge algorithm and binary integer programming) have been proposed to compute cMCSs from elementary modes. However, in their original formulation both algorithms are not fully comparable. RESULTS: Here we show that by a small extension to the integer program both methods become equivalent. Furthermore, based on well-known preprocessing procedures for integer programming we present efficient preprocessing steps which can be used for both algorithms. We then benchmark the numerical performance of the algorithms in several realistic medium-scale metabolic models. The benchmark calculations reveal (i) that these preprocessing steps can lead to an enormous speed-up under both algorithms, and (ii) that the adapted Berge algorithm outperforms the binary integer approach. CONCLUSIONS: Generally, both of our new implementations are by at least one order of magnitude faster than other currently available implementations
Tree-based Coarsening and Partitioning of Complex Networks
Many applications produce massive complex networks whose analysis would
benefit from parallel processing. Parallel algorithms, in turn, often require a
suitable network partition. For solving optimization tasks such as graph
partitioning on large networks, multilevel methods are preferred in practice.
Yet, complex networks pose challenges to established multilevel algorithms, in
particular to their coarsening phase.
One way to specify a (recursive) coarsening of a graph is to rate its edges
and then contract the edges as prioritized by the rating. In this paper we (i)
define weights for the edges of a network that express the edges' importance
for connectivity, (ii) compute a minimum weight spanning tree with
respect to these weights, and (iii) rate the network edges based on the
conductance values of 's fundamental cuts. To this end, we also (iv)
develop the first optimal linear-time algorithm to compute the conductance
values of \emph{all} fundamental cuts of a given spanning tree. We integrate
the new edge rating into a leading multilevel graph partitioner and equip the
latter with a new greedy postprocessing for optimizing the maximum
communication volume (MCV). Experiments on bipartitioning frequently used
benchmark networks show that the postprocessing already reduces MCV by 11.3%.
Our new edge rating further reduces MCV by 10.3% compared to the previously
best rating with the postprocessing in place for both ratings. In total, with a
modest increase in running time, our new approach reduces the MCV of complex
network partitions by 20.4%
Incremental complexity of a bi-objective hypergraph transversal problem
The hypergraph transversal problem has been intensively studied, from both a
theoretical and a practical point of view. In particular , its incremental
complexity is known to be quasi-polynomial in general and polynomial for
bounded hypergraphs. Recent applications in computational biology however
require to solve a generalization of this problem, that we call bi-objective
transversal problem. The instance is in this case composed of a pair of
hypergraphs (A, B), and the aim is to find minimal sets which hit all the
hyperedges of A while intersecting a minimal set of hyperedges of B. In this
paper, we formalize this problem, link it to a problem on monotone boolean
-- formulae of depth 3 and study its incremental complexity
Put three and three together: Triangle-driven community detection
Community detection has arisen as one of the most relevant topics in the field of graph data mining due to its applications in many fields such as biology, social networks, or network traffic analysis. Although the existing metrics used to quantify the quality of a community work well in general, under some circumstances, they fail at correctly capturing such notion. The main reason is that these metrics consider the internal community edges as a set, but ignore how these actually connect the vertices of the community. We propose the Weighted Community Clustering (WCC), which is a new community metric that takes the triangle instead of the edge as the minimal structural motif indicating the presence of a strong relation in a graph. We theoretically analyse WCC in depth and formally prove, by means of a set of properties, that the maximization of WCC guarantees communities with cohesion and structure. In addition, we propose Scalable Community Detection (SCD), a community detection algorithm based on WCC, which is designed to be fast and scalable on SMP machines, showing experimentally that WCC correctly captures the concept of community in social networks using real datasets. Finally, using ground-truth data, we show that SCD provides better quality than the best disjoint community detection algorithms of the state of the art while performing faster.Peer ReviewedPostprint (author's final draft
Parallel Graph Partitioning for Complex Networks
Processing large complex networks like social networks or web graphs has
recently attracted considerable interest. In order to do this in parallel, we
need to partition them into pieces of about equal size. Unfortunately, previous
parallel graph partitioners originally developed for more regular mesh-like
networks do not work well for these networks. This paper addresses this problem
by parallelizing and adapting the label propagation technique originally
developed for graph clustering. By introducing size constraints, label
propagation becomes applicable for both the coarsening and the refinement phase
of multilevel graph partitioning. We obtain very high quality by applying a
highly parallel evolutionary algorithm to the coarsened graph. The resulting
system is both more scalable and achieves higher quality than state-of-the-art
systems like ParMetis or PT-Scotch. For large complex networks the performance
differences are very big. For example, our algorithm can partition a web graph
with 3.3 billion edges in less than sixteen seconds using 512 cores of a high
performance cluster while producing a high quality partition -- none of the
competing systems can handle this graph on our system.Comment: Review article. Parallelization of our previous approach
arXiv:1402.328
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