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

Algorithms for the minimum sum coloring problem: a review

The Minimum Sum Coloring Problem (MSCP) is a variant of the well-known vertex coloring problem which has a number of AI related applications. Due to its theoretical and practical relevance, MSCP attracts increasing attention. The only existing review on the problem dates back to 2004 and mainly covers the history of MSCP and theoretical developments on specific graphs. In recent years, the field has witnessed significant progresses on approximation algorithms and practical solution algorithms. The purpose of this review is to provide a comprehensive inspection of the most recent and representative MSCP algorithms. To be informative, we identify the general framework followed by practical solution algorithms and the key ingredients that make them successful. By classifying the main search strategies and putting forward the critical elements of the reviewed methods, we wish to encourage future development of more powerful methods and motivate new applications

Searching for partial Hadamard matrices

Three algorithms looking for pretty large partial Hadamard ma- trices are described. Here “large” means that hopefully about a third of a Hadamard matrix (which is the best asymptotic result known so far, [8]) is achieved. The first one performs some kind of local exhaustive search, and consequently is expensive from the time consuming point of view. The second one comes from the adaptation of the best genetic algorithm known so far searching for cliques in a graph, due to Singh and Gupta [21]. The last one consists in another heuristic search, which prioritizes the required processing time better than the final size of the partial Hadamard matrix to be obtained. In all cases, the key idea is characterizing the adjacency properties of vertices in a particular subgraph Gt of Ito’s Hadamard Graph (4t) [18], since cliques of order m in Gt can be seen as (m + 3) × 4t partial Hadamard matrices.Ministerio de Ciencia e Innovación MTM2008-06578Junta de Andalucía FQM-016Junta de Andalucía P07-FQM-0298

Boosting Haplotype Inference with Local Search

Abstract. A very challenging problem in the genetics domain is to infer haplotypes from genotypes. This process is expected to identify genes affecting health, disease and response to drugs. One of the approaches to haplotype inference aims to minimise the number of different haplotypes used, and is known as haplotype inference by pure parsimony (HIPP). The HIPP problem is computationally difficult, being NP-hard. Recently, a SAT-based method (SHIPs) has been proposed to solve the HIPP problem. This method iteratively considers an increasing number of haplotypes, starting from an initial lower bound. Hence, one important aspect of SHIPs is the lower bounding procedure, which reduces the number of iterations of the basic algorithm, and also indirectly simplifies the resulting SAT model. This paper describes the use of local search to improve existing lower bounding procedures. The new lower bounding procedure is guaranteed to be as tight as the existing procedures. In practice the new procedure is in most cases considerably tighter, allowing significant improvement of performance on challenging problem instances.

Core Decomposition in Multilayer Networks: Theory, Algorithms, and Applications

Multilayer networks are a powerful paradigm to model complex systems, where multiple relations occur between the same entities. Despite the keen interest in a variety of tasks, algorithms, and analyses in this type of network, the problem of extracting dense subgraphs has remained largely unexplored so far. In this work we study the problem of core decomposition of a multilayer network. The multilayer context is much challenging as no total order exists among multilayer cores; rather, they form a lattice whose size is exponential in the number of layers. In this setting we devise three algorithms which differ in the way they visit the core lattice and in their pruning techniques. We then move a step forward and study the problem of extracting the inner-most (also known as maximal) cores, i.e., the cores that are not dominated by any other core in terms of their core index in all the layers. Inner-most cores are typically orders of magnitude less than all the cores. Motivated by this, we devise an algorithm that effectively exploits the maximality property and extracts inner-most cores directly, without first computing a complete decomposition. Finally, we showcase the multilayer core-decomposition tool in a variety of scenarios and problems. We start by considering the problem of densest-subgraph extraction in multilayer networks. We introduce a definition of multilayer densest subgraph that trades-off between high density and number of layers in which the high density holds, and exploit multilayer core decomposition to approximate this problem with quality guarantees. As further applications, we show how to utilize multilayer core decomposition to speed-up the extraction of frequent cross-graph quasi-cliques and to generalize the community-search problem to the multilayer setting