Topological Cluster Analysis Reveals the Systemic Organization of the Caenorhabditis elegans Connectome

The modular organization of networks of individual neurons interwoven through synapses has not been fully explored due to the incredible complexity of the connectivity architecture. Here we use the modularity-based community detection method for directed, weighted networks to examine hierarchically organized modules in the complete wiring diagram (connectome) of Caenorhabditis elegans (C. elegans) and to investigate their topological properties. Incorporating bilateral symmetry of the network as an important cue for proper cluster assignment, we identified anatomical clusters in the C. elegans connectome, including a body-spanning cluster, which correspond to experimentally identified functional circuits. Moreover, the hierarchical organization of the five clusters explains the systemic cooperation (e.g., mechanosensation, chemosensation, and navigation) that occurs among the structurally segregated biological circuits to produce higher-order complex behaviors

Wiring

cost in the organization of a biological neuronal networ

Massive multi-agent data-driven simulations of the github ecosystem

Simulating and predicting planetary-scale techno-social systems poses heavy computational and modeling challenges. The DARPA SocialSim program set the challenge to model the evolution of GitHub, a large collaborative software-development ecosystem, using massive multiagent simulations. We describe our best performing models and our agent-based simulation framework, which we are currently extending to allow simulating other planetary-scale techno-social systems. The challenge problem measured participant’s ability, given 30 months of metadata on user activity on GitHub, to predict the next months’ activity as measured by a broad range of metrics applied to ground truth, using agent-based simulation. The challenge required scaling to a simulation of roughly 3 million agents producing a combined 30 million actions, acting on 6 million repositories with commodity hardware. It was also important to use the data optimally to predict the agent’s next moves. We describe the agent framework and the data analysis employed by one of the winning teams in the challenge. Six different agent models were tested based on a variety of machine learning and statistical methods. While no single method proved the most accurate on every metric, the broadly most successful sampled from a stationary probability distribution of actions and repositories for each agent. Two reasons for the success of these agents were their use of a distinct characterization of each agent, and that GitHub users change their behavior relatively slowl

Googling social interactions : web search engine based social network construction

Social network analysis has long been an untiring topic of sociology. However, until the era of information technology, the availability of data, mainly collected by the traditional method of personal survey, was highly limited and prevented large-scale analysis. Recently, the exploding amount of automatically generated data has completely changed the pattern of research. For instance, the enormous amount of data from so-called high-throughput biological experiments has introduced a systematic or network viewpoint to traditional biology. Then, is “high-throughput” sociological data generation possible? Google, which has become one of the most influential symbols of the new Internet paradigm within the last ten years, might provide torrents of data sources for such study in this (now and forthcoming) digital era. We investigate social networks between people by extracting information on the Web and introduce new tools of analysis of such networks in the context of statistical physics of complex systems or socio-physics. As a concrete and illustrative example, the members of the 109th United States Senate are analyzed and it is demonstrated that the methods of construction and analysis are applicable to various other weighted networks