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

A Parameterisation of Algorithms for Distributed Constraint Optimisation via Potential Games

This paper introduces a parameterisation of learning algorithms for distributed constraint optimisation problems (DCOPs). This parameterisation encompasses many algorithms developed in both the computer science and game theory literatures. It is built on our insight that when formulated as noncooperative games, DCOPs form a subset of the class of potential games. This result allows us to prove convergence properties of algorithms developed in the computer science literature using game theoretic methods. Furthermore, our parameterisation can assist system designers by making the pros and cons of, and the synergies between, the various DCOP algorithm components clear

An Order-based Algorithm for Minimum Dominating Set with Application in Graph Mining

Dominating set is a set of vertices of a graph such that all other vertices have a neighbour in the dominating set. We propose a new order-based randomised local search (RLS$_o$) algorithm to solve minimum dominating set problem in large graphs. Experimental evaluation is presented for multiple types of problem instances. These instances include unit disk graphs, which represent a model of wireless networks, random scale-free networks, as well as samples from two social networks and real-world graphs studied in network science. Our experiments indicate that RLS$_o$ performs better than both a classical greedy approximation algorithm and two metaheuristic algorithms based on ant colony optimisation and local search. The order-based algorithm is able to find small dominating sets for graphs with tens of thousands of vertices. In addition, we propose a multi-start variant of RLS$_o$ that is suitable for solving the minimum weight dominating set problem. The application of RLS$_o$ in graph mining is also briefly demonstrated

Efficient Data Collection in Multimedia Vehicular Sensing Platforms

Vehicles provide an ideal platform for urban sensing applications, as they can be equipped with all kinds of sensing devices that can continuously monitor the environment around the travelling vehicle. In this work we are particularly concerned with the use of vehicles as building blocks of a multimedia mobile sensor system able to capture camera snapshots of the streets to support traffic monitoring and urban surveillance tasks. However, cameras are high data-rate sensors while wireless infrastructures used for vehicular communications may face performance constraints. Thus, data redundancy mitigation is of paramount importance in such systems. To address this issue in this paper we exploit sub-modular optimisation techniques to design efficient and robust data collection schemes for multimedia vehicular sensor networks. We also explore an alternative approach for data collection that operates on longer time scales and relies only on localised decisions rather than centralised computations. We use network simulations with realistic vehicular mobility patterns to verify the performance gains of our proposed schemes compared to a baseline solution that ignores data redundancy. Simulation results show that our data collection techniques can ensure a more accurate coverage of the road network while significantly reducing the amount of transferred data

Greedy Randomized Adaptive Search and Variable Neighbourhood Search for the minimum labelling spanning tree problem

This paper studies heuristics for the minimum labelling spanning tree (MLST) problem. The purpose is to find a spanning tree using edges that are as similar as possible. Given an undirected labelled connected graph, the minimum labelling spanning tree problem seeks a spanning tree whose edges have the smallest number of distinct labels. This problem has been shown to be NP-hard. A Greedy Randomized Adaptive Search Procedure (GRASP) and a Variable Neighbourhood Search (VNS) are proposed in this paper. They are compared with other algorithms recommended in the literature: the Modified Genetic Algorithm and the Pilot Method. Nonparametric statistical tests show that the heuristics based on GRASP and VNS outperform the other algorithms tested. Furthermore, a comparison with the results provided by an exact approach shows that we may quickly obtain optimal or near-optimal solutions with the proposed heuristics