Euclidean distance geometry and applications

Euclidean distance geometry is the study of Euclidean geometry based on the concept of distance. This is useful in several applications where the input data consists of an incomplete set of distances, and the output is a set of points in Euclidean space that realizes the given distances. We survey some of the theory of Euclidean distance geometry and some of the most important applications: molecular conformation, localization of sensor networks and statics.Comment: 64 pages, 21 figure

Parameterized Algorithmics for Computational Social Choice: Nine Research Challenges

Computational Social Choice is an interdisciplinary research area involving Economics, Political Science, and Social Science on the one side, and Mathematics and Computer Science (including Artificial Intelligence and Multiagent Systems) on the other side. Typical computational problems studied in this field include the vulnerability of voting procedures against attacks, or preference aggregation in multi-agent systems. Parameterized Algorithmics is a subfield of Theoretical Computer Science seeking to exploit meaningful problem-specific parameters in order to identify tractable special cases of in general computationally hard problems. In this paper, we propose nine of our favorite research challenges concerning the parameterized complexity of problems appearing in this context

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