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

Propagators and Violation Functions for Geometric and Workload Constraints Arising in Airspace Sectorisation

Airspace sectorisation provides a partition of a given airspace into sectors, subject to geometric constraints and workload constraints, so that some cost metric is minimised. We make a study of the constraints that arise in airspace sectorisation. For each constraint, we give an analysis of what algorithms and properties are required under systematic search and stochastic local search

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

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