Parallel Community Detection Based on Distance Dynamics for Large-Scale Network

© 2013 IEEE. Data mining task is a challenge on finding a high-quality community structure from large-scale networks. The distance dynamics model was proved to be active on regular-size network community, but it is difficult to discover the community structure effectively from the large-scale network (0.1-1 billion edges), due to the limit of machine hardware and high time complexity. In this paper, we proposed a parallel community detection algorithm based on the distance dynamics model called P-Attractor, which is capable of handling the detection problem of large networks community. Our algorithm first developed a graph partitioning method to divide large network into lots of sub-networks, yet maintaining the complete neighbor structure of the original network. Then, the traditional distance dynamics model was improved by the dynamic interaction process to simulate the distance evolution of each sub-network. Finally, we discovered the real community structure by removing all external edges after evolution process. In our extensive experiments on multiple synthetic networks and real-world networks, the results showed the effectiveness and efficiency of P-Attractor, and the execution time on 4 threads and 32 threads are around 10 and 2 h, respectively. Our proposed algorithm is potential to discover community from a billion-scale network, such as Uk-2007

A Modified Distance Dynamics Model for Improvement of Community Detection

© 2018 IEEE. Community detection is a key technique for identifying the intrinsic community structures of complex networks. The distance dynamics model has been proven effective in finding communities with arbitrary size and shape and identifying outliers. However, to simulate distance dynamics, the model requires manual parameter specification and is sensitive to the cohesion threshold parameter, which is difficult to determine. Furthermore, it has difficulty handling rough outliers and ignores hubs (nodes that bridge communities). In this paper, we propose a robust distance dynamics model, namely, Attractor++, which uses a dynamic membership degree. In Attractor++, the dynamic membership degree is used to determine the influence of exclusive neighbors on the distance instead of setting the cohesion threshold. In addition, considering its inefficiency and low accuracy in handling outliers and identifying hubs, we design an outlier optimization model that is based on triangle adjacency. By using optimization rules, a postprocessing method further judges whether a singleton node should be merged into the same community as its triangles or regarded as a hub or an outlier. Extensive experiments on both real-world and synthetic networks demonstrate that our algorithm more accurately identifies nodes that have special roles (hubs and outliers) and more effectively identifies community structures

Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors.

Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD) simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach designed to reduce the large MD simulation spatiotemporal datasets into a manageable set in order to guide our understanding of how protein mechanics emerge from side chain organization and dynamic reorganization. We focus on the detection of side chain interactions that undergo rearrangements mediating global domain motions and vice versa. Side chain rearrangements are extracted from side chain interactions that undergo well-defined abrupt and persistent changes in distance time series using Gaussian mixture models, whereas global domain motions are detected using dynamic cross-correlation. Both side chain rearrangements and global domain motions represent the dynamic components of the protein MD simulation, and are both mapped into a network where they are connected based on their degree of coupling. This method allows for the study of allosteric communication in proteins by mapping out the protein dynamics into an intramolecular network to reduce the large simulation data into a manageable set of communities composed of coupled side chain rearrangements and global domain motions. This computational framework is suitable for the study of tightly packed proteins, such as G protein-coupled receptors, and we present an application on a seven microseconds MD trajectory of CC chemokine receptor 7 (CCR7) bound to its ligand CCL21

Fundamental structures of dynamic social networks

Social systems are in a constant state of flux with dynamics spanning from minute-by-minute changes to patterns present on the timescale of years. Accurate models of social dynamics are important for understanding spreading of influence or diseases, formation of friendships, and the productivity of teams. While there has been much progress on understanding complex networks over the past decade, little is known about the regularities governing the micro-dynamics of social networks. Here we explore the dynamic social network of a densely-connected population of approximately 1000 individuals and their interactions in the network of real-world person-to-person proximity measured via Bluetooth, as well as their telecommunication networks, online social media contacts, geo-location, and demographic data. These high-resolution data allow us to observe social groups directly, rendering community detection unnecessary. Starting from 5-minute time slices we uncover dynamic social structures expressed on multiple timescales. On the hourly timescale, we find that gatherings are fluid, with members coming and going, but organized via a stable core of individuals. Each core represents a social context. Cores exhibit a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores are preceded by coordination behavior in the communication networks, and demonstrating that social behavior can be predicted with high precision.Comment: Main Manuscript: 16 pages, 4 figures. Supplementary Information: 39 pages, 34 figure