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

Generalizing backdoors

Abstract. A powerful intuition in the design of search methods is that one wants to proactively select variables that simplify the problem instance as much as possible when these variables are assigned values. The notion of “Backdoor ” variables follows this intuition. In this work we generalize Backdoors in such a way to allow more general classes of sub-solvers, both complete and heuristic. In order to do so, Pseudo-Backdoors and Heuristic-Backdoors are formally introduced and then applied firstly to a simple Multiple Knapsack Problem and secondly to a complex combinatorial optimization problem in the area of stochastic inventory control. Our preliminary computational experience shows the effectiveness of these approaches that are able to produce very low run times and — in the case of Heuristic-Backdoors — high quality solutions by employing very simple heuristic rules such as greedy local search strategies.

A study on exponential-size neighborhoods for the bin packing problem with conflicts

We propose an iterated local search based on several classes of local and large neighborhoods for the bin packing problem with conflicts. This problem, which combines the characteristics of both bin packing and vertex coloring, arises in various application contexts such as logistics and transportation, timetabling, and resource allocation for cloud computing. We introduce $O(1)$ evaluation procedures for classical local-search moves, polynomial variants of ejection chains and assignment neighborhoods, an adaptive set covering-based neighborhood, and finally a controlled use of 0-cost moves to further diversify the search. The overall method produces solutions of good quality on the classical benchmark instances and scales very well with an increase of problem size. Extensive computational experiments are conducted to measure the respective contribution of each proposed neighborhood. In particular, the 0-cost moves and the large neighborhood based on set covering contribute very significantly to the search. Several research perspectives are open in relation to possible hybridizations with other state-of-the-art mathematical programming heuristics for this problem.Comment: 26 pages, 8 figure

Solving the minimum labelling spanning tree problem using hybrid local search

Given a connected, undirected graph whose edges are labelled (or coloured), the minimum labelling spanning tree (MLST) problem seeks a spanning tree whose edges have the smallest number of distinct labels (or colours). In recent work, the MLST problem has been shown to be NP-hard and some effective heuristics (Modified Genetic Algorithm (MGA) and Pilot Method (PILOT)) have been proposed and analyzed. A hybrid local search method, that we call Group-Swap Variable Neighbourhood Search (GS-VNS), is proposed in this paper. It is obtained by combining two classic metaheuristics: Variable Neighbourhood Search (VNS) and Simulated Annealing (SA). Computational experiments show that GS-VNS outperforms MGA and PILOT. 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 heuristic