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

Best Response Games on Regular Graphs

With the growth of the internet it is becoming increasingly important to understand how the behaviour of players is affected by the topology of the network interconnecting them. Many models which involve networks of interacting players have been proposed and best response games are amongst the simplest. In best response games each vertex simultaneously updates to employ the best response to their current surroundings. We concentrate upon trying to understand the dynamics of best response games on regular graphs with many strategies. When more than two strategies are present highly complex dynamics can ensue. We focus upon trying to understand exactly how best response games on regular graphs sample from the space of possible cellular automata. To understand this issue we investigate convex divisions in high dimensional space and we prove that almost every division of $k-1$ dimensional space into $k$ convex regions includes a single point where all regions meet. We then find connections between the convex geometry of best response games and the theory of alternating circuits on graphs. Exploiting these unexpected connections allows us to gain an interesting answer to our question of when cellular automata are best response games

Using Differential Evolution for the Graph Coloring

Differential evolution was developed for reliable and versatile function optimization. It has also become interesting for other domains because of its ease to use. In this paper, we posed the question of whether differential evolution can also be used by solving of the combinatorial optimization problems, and in particular, for the graph coloring problem. Therefore, a hybrid self-adaptive differential evolution algorithm for graph coloring was proposed that is comparable with the best heuristics for graph coloring today, i.e. Tabucol of Hertz and de Werra and the hybrid evolutionary algorithm of Galinier and Hao. We have focused on the graph 3-coloring. Therefore, the evolutionary algorithm with method SAW of Eiben et al., which achieved excellent results for this kind of graphs, was also incorporated into this study. The extensive experiments show that the differential evolution could become a competitive tool for the solving of graph coloring problem in the future

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

Decomposition, Reformulation, and Diving in University Course Timetabling

In many real-life optimisation problems, there are multiple interacting components in a solution. For example, different components might specify assignments to different kinds of resource. Often, each component is associated with different sets of soft constraints, and so with different measures of soft constraint violation. The goal is then to minimise a linear combination of such measures. This paper studies an approach to such problems, which can be thought of as multiphase exploitation of multiple objective-/value-restricted submodels. In this approach, only one computationally difficult component of a problem and the associated subset of objectives is considered at first. This produces partial solutions, which define interesting neighbourhoods in the search space of the complete problem. Often, it is possible to pick the initial component so that variable aggregation can be performed at the first stage, and the neighbourhoods to be explored next are guaranteed to contain feasible solutions. Using integer programming, it is then easy to implement heuristics producing solutions with bounds on their quality. Our study is performed on a university course timetabling problem used in the 2007 International Timetabling Competition, also known as the Udine Course Timetabling Problem. In the proposed heuristic, an objective-restricted neighbourhood generator produces assignments of periods to events, with decreasing numbers of violations of two period-related soft constraints. Those are relaxed into assignments of events to days, which define neighbourhoods that are easier to search with respect to all four soft constraints. Integer programming formulations for all subproblems are given and evaluated using ILOG CPLEX 11. The wider applicability of this approach is analysed and discussed.Comment: 45 pages, 7 figures. Improved typesetting of figures and table

Anagram-free Graph Colouring

An anagram is a word of the form $WP$ where $W$ is a non-empty word and $P$ is a permutation of $W$. We study anagram-free graph colouring and give bounds on the chromatic number. Alon et al. (2002) asked whether anagram-free chromatic number is bounded by a function of the maximum degree. We answer this question in the negative by constructing graphs with maximum degree 3 and unbounded anagram-free chromatic number. We also prove upper and lower bounds on the anagram-free chromatic number of trees in terms of their radius and pathwidth. Finally, we explore extensions to edge colouring and $k$-anagram-free colouring.Comment: Version 2: Changed 'abelian square' to 'anagram' for consistency with 'Anagram-free colourings of graphs' by Kam\v{c}ev, {\L}uczak, and Sudakov. Minor changes based on referee feedbac