2,385 research outputs found
Construction of near-optimal vertex clique covering for real-world networks
We propose a method based on combining a constructive and a bounding heuristic to solve the vertex clique covering problem (CCP), where the aim is to partition the vertices of a graph into the smallest number of classes, which induce cliques. Searching for the solution to CCP is highly motivated by analysis of social and other real-world networks, applications in graph mining, as well as by the fact that CCP is one of the classical NP-hard problems. Combining the construction and the bounding heuristic helped us not only to find high-quality clique coverings but also to determine that in the domain of real-world networks, many of the obtained solutions are optimal, while the rest of them are near-optimal. In addition, the method has a polynomial time complexity and shows much promise for its practical use. Experimental results are presented for a fairly representative benchmark of real-world data. Our test graphs include extracts of web-based social networks, including some very large ones, several well-known graphs from network science, as well as coappearance networks of literary works' characters from the DIMACS graph coloring benchmark. We also present results for synthetic pseudorandom graphs structured according to the Erdös-Renyi model and Leighton's model
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
GraphCombEx: A Software Tool for Exploration of Combinatorial Optimisation Properties of Large Graphs
We present a prototype of a software tool for exploration of multiple
combinatorial optimisation problems in large real-world and synthetic complex
networks. Our tool, called GraphCombEx (an acronym of Graph Combinatorial
Explorer), provides a unified framework for scalable computation and
presentation of high-quality suboptimal solutions and bounds for a number of
widely studied combinatorial optimisation problems. Efficient representation
and applicability to large-scale graphs and complex networks are particularly
considered in its design. The problems currently supported include maximum
clique, graph colouring, maximum independent set, minimum vertex clique
covering, minimum dominating set, as well as the longest simple cycle problem.
Suboptimal solutions and intervals for optimal objective values are estimated
using scalable heuristics. The tool is designed with extensibility in mind,
with the view of further problems and both new fast and high-performance
heuristics to be added in the future. GraphCombEx has already been successfully
used as a support tool in a number of recent research studies using
combinatorial optimisation to analyse complex networks, indicating its promise
as a research software tool
Partitioning networks into cliques: a randomized heuristic approach
In the context of community detection in social networks, the term community can be grounded in the strict way that simply everybody should know each other within the community. We consider the corresponding community detection problem. We search for a partitioning of a network into the minimum number of non-overlapping cliques, such that the cliques cover all vertices. This problem is called the clique covering problem (CCP) and is one of the classical NP-hard problems. For CCP, we propose a randomized heuristic approach. To construct a high quality solution to CCP, we present an iterated greedy (IG) algorithm. IG can also be combined with a heuristic used to determine how far the algorithm is from the optimum in the worst case. Randomized local search (RLS) for maximum independent set was proposed to find such a bound. The experimental results of IG and the bounds obtained by RLS indicate that IG is a very suitable technique for solving CCP in real-world graphs. In addition, we summarize our basic rigorous results, which were developed for analysis of IG and understanding of its behavior on several relevant graph classes
Searching for partial Hadamard matrices
Three algorithms looking for pretty large partial Hadamard ma-
trices are described. Here “large” means that hopefully about a third of a
Hadamard matrix (which is the best asymptotic result known so far, [8]) is
achieved. The first one performs some kind of local exhaustive search, and
consequently is expensive from the time consuming point of view. The second
one comes from the adaptation of the best genetic algorithm known so far
searching for cliques in a graph, due to Singh and Gupta [21]. The last one
consists in another heuristic search, which prioritizes the required processing
time better than the final size of the partial Hadamard matrix to be obtained. In
all cases, the key idea is characterizing the adjacency properties of vertices in a
particular subgraph Gt of Ito’s Hadamard Graph (4t) [18], since cliques of
order m in Gt can be seen as (m + 3) × 4t partial Hadamard matrices.Ministerio de Ciencia e Innovación MTM2008-06578Junta de Andalucía FQM-016Junta de Andalucía P07-FQM-0298
A novel evolutionary formulation of the maximum independent set problem
We introduce a novel evolutionary formulation of the problem of finding a
maximum independent set of a graph. The new formulation is based on the
relationship that exists between a graph's independence number and its acyclic
orientations. It views such orientations as individuals and evolves them with
the aid of evolutionary operators that are very heavily based on the structure
of the graph and its acyclic orientations. The resulting heuristic has been
tested on some of the Second DIMACS Implementation Challenge benchmark graphs,
and has been found to be competitive when compared to several of the other
heuristics that have also been tested on those graphs
Algorithms for the minimum sum coloring problem: a review
The Minimum Sum Coloring Problem (MSCP) is a variant of the well-known vertex
coloring problem which has a number of AI related applications. Due to its
theoretical and practical relevance, MSCP attracts increasing attention. The
only existing review on the problem dates back to 2004 and mainly covers the
history of MSCP and theoretical developments on specific graphs. In recent
years, the field has witnessed significant progresses on approximation
algorithms and practical solution algorithms. The purpose of this review is to
provide a comprehensive inspection of the most recent and representative MSCP
algorithms. To be informative, we identify the general framework followed by
practical solution algorithms and the key ingredients that make them
successful. By classifying the main search strategies and putting forward the
critical elements of the reviewed methods, we wish to encourage future
development of more powerful methods and motivate new applications
Cover-Encodings of Fitness Landscapes
The traditional way of tackling discrete optimization problems is by using
local search on suitably defined cost or fitness landscapes. Such approaches
are however limited by the slowing down that occurs when the local minima that
are a feature of the typically rugged landscapes encountered arrest the
progress of the search process. Another way of tackling optimization problems
is by the use of heuristic approximations to estimate a global cost minimum.
Here we present a combination of these two approaches by using cover-encoding
maps which map processes from a larger search space to subsets of the original
search space. The key idea is to construct cover-encoding maps with the help of
suitable heuristics that single out near-optimal solutions and result in
landscapes on the larger search space that no longer exhibit trapping local
minima. We present cover-encoding maps for the problems of the traveling
salesman, number partitioning, maximum matching and maximum clique; the
practical feasibility of our method is demonstrated by simulations of adaptive
walks on the corresponding encoded landscapes which find the global minima for
these problems.Comment: 15 pages, 4 figure
Maximum common subgraph isomorphism algorithms for the matching of chemical structures
The maximum common subgraph (MCS) problem has become increasingly important in those aspects of chemoinformatics that involve the matching of 2D or 3D chemical structures. This paper provides a classification and a review of the many MCS algorithms, both exact and approximate, that have been described in the literature, and makes recommendations regarding their applicability to typical chemoinformatics tasks
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