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

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

On Maximum Weight Clique Algorithms, and How They Are Evaluated

Maximum weight clique and maximum weight independent set solvers are often benchmarked using maximum clique problem instances, with weights allocated to vertices by taking the vertex number mod 200 plus 1. For constraint programming approaches, this rule has clear implications, favouring weight-based rather than degree-based heuristics. We show that similar implications hold for dedicated algorithms, and that additionally, weight distributions affect whether certain inference rules are cost-effective. We look at other families of benchmark instances for the maximum weight clique problem, coming from winner determination problems, graph colouring, and error-correcting codes, and introduce two new families of instances, based upon kidney exchange and the Research Excellence Framework. In each case the weights carry much more interesting structure, and do not in any way resemble the 200 rule. We make these instances available in the hopes of improving the quality of future experiments

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

A Structured Approach to Modifying Successful Heuristics

In some cases, heuristics may be transferred easily between different optimisation problems. This is the case if these problems are equivalent or dual (e.g., maximum clique and maximum independent set) or have similar objective functions. However, the link between problems can further be defined by the constraints that define them. This refining can be achieved by organising constraints into families and translating between them using gadgets. If two problems are in the same constraint family, the gadgets tell us how to map from one problem to another and which constraints are modified. This helps better understand a problem through its constraints and how best to use domain specific heuristics. In this position paper, we argue that this allows us to understand how to map between heuristics developed for one problem to heuristics for another problem, giving an example of how this might be achieved

Delivery Time Reduction for Order-Constrained Applications using Binary Network Codes

Consider a radio access network wherein a base-station is required to deliver a set of order-constrained messages to a set of users over independent erasure channels. This paper studies the delivery time reduction problem using instantly decodable network coding (IDNC). Motivated by time-critical and order-constrained applications, the delivery time is defined, at each transmission, as the number of undelivered messages. The delivery time minimization problem being computationally intractable, most of the existing literature on IDNC propose sub-optimal online solutions. This paper suggests a novel method for solving the problem by introducing the delivery delay as a measure of distance to optimality. An expression characterizing the delivery time using the delivery delay is derived, allowing the approximation of the delivery time minimization problem by an optimization problem involving the delivery delay. The problem is, then, formulated as a maximum weight clique selection problem over the IDNC graph wherein the weight of each vertex reflects its corresponding user and message's delay. Simulation results suggest that the proposed solution achieves lower delivery and completion times as compared to the best-known heuristics for delivery time reduction