Link communities reveal multiscale complexity in networks

Networks have become a key approach to understanding systems of interacting objects, unifying the study of diverse phenomena including biological organisms and human society. One crucial step when studying the structure and dynamics of networks is to identify communities: groups of related nodes that correspond to functional subunits such as protein complexes or social spheres. Communities in networks often overlap such that nodes simultaneously belong to several groups. Meanwhile, many networks are known to possess hierarchical organization, where communities are recursively grouped into a hierarchical structure. However, the fact that many real networks have communities with pervasive overlap, where each and every node belongs to more than one group, has the consequence that a global hierarchy of nodes cannot capture the relationships between overlapping groups. Here we reinvent communities as groups of links rather than nodes and show that this unorthodox approach successfully reconciles the antagonistic organizing principles of overlapping communities and hierarchy. In contrast to the existing literature, which has entirely focused on grouping nodes, link communities naturally incorporate overlap while revealing hierarchical organization. We find relevant link communities in many networks, including major biological networks such as protein-protein interaction and metabolic networks, and show that a large social network contains hierarchically organized community structures spanning inner-city to regional scales while maintaining pervasive overlap. Our results imply that link communities are fundamental building blocks that reveal overlap and hierarchical organization in networks to be two aspects of the same phenomenon.Comment: Main text and supplementary informatio

Exact Algorithms for Maximum Clique: a computational study

We investigate a number of recently reported exact algorithms for the maximum clique problem (MCQ, MCR, MCS, BBMC). The program code used is presented and critiqued showing how small changes in implementation can have a drastic effect on performance. The computational study demonstrates how problem features and hardware platforms influence algorithm behaviour. The minimum width order (smallest-last) is investigated, and MCS is broken into its consituent parts and we discover that one of these parts degrades performance. It is shown that the standard procedure used for rescaling published results is unsafe.Comment: 40 pages, 14 figures, 10 tables, 12 short java program listings, code afailable to download at http://www.dcs.gla.ac.uk/~pat/maxClique/distribution

Chris Cannings: A Life in Games

Chris Cannings was one of the pioneers of evolutionary game theory. His early work was inspired by the formulations of John Maynard Smith, Geoff Parker and Geoff Price; Chris recognized the need for a strong mathematical foundation both to validate stated results and to give a basis for extensions of the models. He was responsible for fundamental results on matrix games, as well as much of the theory of the important war of attrition game, patterns of evolutionarily stable strategies, multiplayer games and games on networks. In this paper we describe his work, key insights and their influence on research by others in this increasingly important field. Chris made substantial contributions to other areas such as population genetics and segregation analysis, but it was to games that he always returned. This review is written by three of his students from different stages of his career

A Partitioning Algorithm for Maximum Common Subgraph Problems

We introduce a new branch and bound algorithm for the maximum common subgraph and maximum common connected subgraph problems which is based around vertex labelling and partitioning. Our method in some ways resembles a traditional constraint programming approach, but uses a novel compact domain store and supporting inference algorithms which dramatically reduce the memory and computation requirements during search, and allow better dual viewpoint ordering heuristics to be calculated cheaply. Experiments show a speedup of more than an order of magnitude over the state of the art, and demonstrate that we can operate on much larger graphs without running out of memory

Semi-Supervised Overlapping Community Finding based on Label Propagation with Pairwise Constraints

Algorithms for detecting communities in complex networks are generally unsupervised, relying solely on the structure of the network. However, these methods can often fail to uncover meaningful groupings that reflect the underlying communities in the data, particularly when those structures are highly overlapping. One way to improve the usefulness of these algorithms is by incorporating additional background information, which can be used as a source of constraints to direct the community detection process. In this work, we explore the potential of semi-supervised strategies to improve algorithms for finding overlapping communities in networks. Specifically, we propose a new method, based on label propagation, for finding communities using a limited number of pairwise constraints. Evaluations on synthetic and real-world datasets demonstrate the potential of this approach for uncovering meaningful community structures in cases where each node can potentially belong to more than one community.Comment: Fix table