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

Symmetry Breaking for Answer Set Programming

In the context of answer set programming, this work investigates symmetry detection and symmetry breaking to eliminate symmetric parts of the search space and, thereby, simplify the solution process. We contribute a reduction of symmetry detection to a graph automorphism problem which allows to extract symmetries of a logic program from the symmetries of the constructed coloured graph. We also propose an encoding of symmetry-breaking constraints in terms of permutation cycles and use only generators in this process which implicitly represent symmetries and always with exponential compression. These ideas are formulated as preprocessing and implemented in a completely automated flow that first detects symmetries from a given answer set program, adds symmetry-breaking constraints, and can be applied to any existing answer set solver. We demonstrate computational impact on benchmarks versus direct application of the solver. Furthermore, we explore symmetry breaking for answer set programming in two domains: first, constraint answer set programming as a novel approach to represent and solve constraint satisfaction problems, and second, distributed nonmonotonic multi-context systems. In particular, we formulate a translation-based approach to constraint answer set solving which allows for the application of our symmetry detection and symmetry breaking methods. To compare their performance with a-priori symmetry breaking techniques, we also contribute a decomposition of the global value precedence constraint that enforces domain consistency on the original constraint via the unit-propagation of an answer set solver. We evaluate both options in an empirical analysis. In the context of distributed nonmonotonic multi-context system, we develop an algorithm for distributed symmetry detection and also carry over symmetry-breaking constraints for distributed answer set programming.Comment: Diploma thesis. Vienna University of Technology, August 201

Isomorphism Checking for Symmetry Reduction

In this paper, we show how isomorphism checking can be used as an effective technique for symmetry reduction. Reduced state spaces are equivalent to the original ones under a strong notion of bisimilarity which preserves the multiplicity of outgoing transitions, and therefore also preserves stochastic temporal logics. We have implemented this in a setting where states are arbitrary graphs. Since no efficiently computable canonical representation is known for arbitrary graphs modulo isomorphism, we define an isomorphism-predicting hash function on the basis of an existing partition refinement algorithm. As an example, we report a factorial state space reduction on a model of an ad-hoc network connectivity protocol

Decentralized Constraint Satisfaction

We show that several important resource allocation problems in wireless networks fit within the common framework of Constraint Satisfaction Problems (CSPs). Inspired by the requirements of these applications, where variables are located at distinct network devices that may not be able to communicate but may interfere, we define natural criteria that a CSP solver must possess in order to be practical. We term these algorithms decentralized CSP solvers. The best known CSP solvers were designed for centralized problems and do not meet these criteria. We introduce a stochastic decentralized CSP solver and prove that it will find a solution in almost surely finite time, should one exist, also showing it has many practically desirable properties. We benchmark the algorithm's performance on a well-studied class of CSPs, random k-SAT, illustrating that the time the algorithm takes to find a satisfying assignment is competitive with stochastic centralized solvers on problems with order a thousand variables despite its decentralized nature. We demonstrate the solver's practical utility for the problems that motivated its introduction by using it to find a non-interfering channel allocation for a network formed from data from downtown Manhattan

Exact bounds for distributed graph colouring

We prove exact bounds on the time complexity of distributed graph colouring. If we are given a directed path that is properly coloured with $n$ colours, by prior work it is known that we can find a proper 3-colouring in $\frac{1}{2} \log^*(n) \pm O(1)$ communication rounds. We close the gap between upper and lower bounds: we show that for infinitely many $n$ the time complexity is precisely $\frac{1}{2} \log^* n$ communication rounds.Comment: 16 pages, 3 figure