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

Hybrid model predictive control for freeway traffic using discrete speed limit signals

HYCON2 Show day - Traffic modeling, Estimation and Control 13/05/2014 GrenobleIn this paper, two hybrid Model Predictive Control (MPC) approaches for freeway traffic control are proposed considering variable speed limits (VSL) as discrete variables as in current real world implementations. These discrete characteristics of the speed limits values and some necessary constraints for the actual operation of VSL are usually underestimated in the literature, so we propose a way to include them using a macroscopic traffic model within an MPC framework. For obtaining discrete signals, the MPC controller has to solve a highly non-linear optimization problem, including mixed-integer variables. Since solving such a problem is complex and difficult to execute in real-time, we propose some methods to obtain reasonable control actions in a limited computation time. The first two methods (-exhaustive and -genetic discretization) consist of first relaxing the discrete constraints for the VSL inputs; and then, based on this continuous solution and using a genetic or an exhaustive algorithm, to find discrete solutions within a distance of the continuous solution that provide a good performance. The second class of methods split the problem in a continuous optimization for the ramp metering signals and in a discrete optimization for speed limits. The speed limits optimization, which is much more time-consuming than the ramp metering one, is solved by a genetic or an exhaustive algorithm in communication with a non-linear solver for the ramp metering. The proposed methods are tested by simulation, showing not only a good performance, but also keeping the computation time reduced.Unión Europea FP7/2007–201

Multi-objective discrete particle swarm optimisation algorithm for integrated assembly sequence planning and assembly line balancing

In assembly optimisation, assembly sequence planning and assembly line balancing have been extensively studied because both activities are directly linked with assembly efficiency that influences the final assembly costs. Both activities are categorised as NP-hard and usually performed separately. Assembly sequence planning and assembly line balancing optimisation presents a good opportunity to be integrated, considering the benefits such as larger search space that leads to better solution quality, reduces error rate in planning and speeds up time-to-market for a product. In order to optimise an integrated assembly sequence planning and assembly line balancing, this work proposes a multi-objective discrete particle swarm optimisation algorithm that used discrete procedures to update its position and velocity in finding Pareto optimal solution. A computational experiment with 51 test problems at different difficulty levels was used to test the multi-objective discrete particle swarm optimisation performance compared with the existing algorithms. A statistical test of the algorithm performance indicates that the proposed multi-objective discrete particle swarm optimisation algorithm presents significant improvement in terms of the quality of the solution set towards the Pareto optimal set