5,286 research outputs found
Detection of the elite structure in a virtual multiplex social system by means of a generalized -core
Elites are subgroups of individuals within a society that have the ability
and means to influence, lead, govern, and shape societies. Members of elites
are often well connected individuals, which enables them to impose their
influence to many and to quickly gather, process, and spread information. Here
we argue that elites are not only composed of highly connected individuals, but
also of intermediaries connecting hubs to form a cohesive and structured
elite-subgroup at the core of a social network. For this purpose we present a
generalization of the -core algorithm that allows to identify a social core
that is composed of well-connected hubs together with their `connectors'. We
show the validity of the idea in the framework of a virtual world defined by a
massive multiplayer online game, on which we have complete information of
various social networks. Exploiting this multiplex structure, we find that the
hubs of the generalized -core identify those individuals that are high
social performers in terms of a series of indicators that are available in the
game. In addition, using a combined strategy which involves the generalized
-core and the recently introduced -core, the elites of the different
'nations' present in the game are perfectly identified as modules of the
generalized -core. Interesting sudden shifts in the composition of the elite
cores are observed at deep levels. We show that elite detection with the
traditional -core is not possible in a reliable way. The proposed method
might be useful in a series of more general applications, such as community
detection.Comment: 13 figures, 3 tables, 19 pages. Accepted for publication in PLoS ON
Network-based approaches to explore complex biological systems towards network medicine
Network medicine relies on different types of networks: from the molecular level of protein–protein interactions to gene regulatory network and correlation studies of gene expression. Among network approaches based on the analysis of the topological properties of protein–protein interaction (PPI) networks, we discuss the widespread DIAMOnD (disease module detection) algorithm. Starting from the assumption that PPI networks can be viewed as maps where diseases can be identified with localized perturbation within a specific neighborhood (i.e., disease modules), DIAMOnD performs a systematic analysis of the human PPI network to uncover new disease-associated genes by exploiting the connectivity significance instead of connection density. The past few years have witnessed the increasing interest in understanding the molecular mechanism of post-transcriptional regulation with a special emphasis on non-coding RNAs since they are emerging as key regulators of many cellular processes in both physiological and pathological states. Recent findings show that coding genes are not the only targets that microRNAs interact with. In fact, there is a pool of different RNAs—including long non-coding RNAs (lncRNAs) —competing with each other to attract microRNAs for interactions, thus acting as competing endogenous RNAs (ceRNAs). The framework of regulatory networks provides a powerful tool to gather new insights into ceRNA regulatory mechanisms. Here, we describe a data-driven model recently developed to explore the lncRNA-associated ceRNA activity in breast invasive carcinoma. On the other hand, a very promising example of the co-expression network is the one implemented by the software SWIM (switch miner), which combines topological properties of correlation networks with gene expression data in order to identify a small pool of genes—called switch genes—critically associated with drastic changes in cell phenotype. Here, we describe SWIM tool along with its applications to cancer research and compare its predictions with DIAMOnD disease genes
A Parameterized Centrality Metric for Network Analysis
A variety of metrics have been proposed to measure the relative importance of
nodes in a network. One of these, alpha-centrality [Bonacich, 2001], measures
the number of attenuated paths that exist between nodes. We introduce a
normalized version of this metric and use it to study network structure,
specifically, to rank nodes and find community structure of the network.
Specifically, we extend the modularity-maximization method [Newman and Girvan,
2004] for community detection to use this metric as the measure of node
connectivity. Normalized alpha-centrality is a powerful tool for network
analysis, since it contains a tunable parameter that sets the length scale of
interactions. By studying how rankings and discovered communities change when
this parameter is varied allows us to identify locally and globally important
nodes and structures. We apply the proposed method to several benchmark
networks and show that it leads to better insight into network structure than
alternative methods.Comment: 11 pages, submitted to Physical Review
Characterizing the community structure of complex networks
Community structure is one of the key properties of complex networks and
plays a crucial role in their topology and function. While an impressive amount
of work has been done on the issue of community detection, very little
attention has been so far devoted to the investigation of communities in real
networks. We present a systematic empirical analysis of the statistical
properties of communities in large information, communication, technological,
biological, and social networks. We find that the mesoscopic organization of
networks of the same category is remarkably similar. This is reflected in
several characteristics of community structure, which can be used as
``fingerprints'' of specific network categories. While community size
distributions are always broad, certain categories of networks consist mainly
of tree-like communities, while others have denser modules. Average path
lengths within communities initially grow logarithmically with community size,
but the growth saturates or slows down for communities larger than a
characteristic size. This behaviour is related to the presence of hubs within
communities, whose roles differ across categories. Also the community
embeddedness of nodes, measured in terms of the fraction of links within their
communities, has a characteristic distribution for each category. Our findings
are verified by the use of two fundamentally different community detection
methods.Comment: 15 pages, 20 figures, 4 table
Comparative approaches for assessing access to alcohol outlets: exploring the utility of a gravity potential approach.
BackgroundA growing body of research recommends controlling alcohol availability to reduce harm. Various common approaches, however, provide dramatically different pictures of the physical availability of alcohol. This limits our understanding of the distribution of alcohol access, the causes and consequences of this distribution, and how best to reduce harm. The aim of this study is to introduce both a gravity potential measure of access to alcohol outlets, comparing its strengths and weaknesses to other popular approaches, and an empirically-derived taxonomy of neighborhoods based on the type of alcohol access they exhibit.MethodsWe obtained geospatial data on Seattle, including the location of 2402 alcohol outlets, United States Census Bureau estimates on 567 block groups, and a comprehensive street network. We used exploratory spatial data analysis and employed a measure of inter-rater agreement to capture differences in our taxonomy of alcohol availability measures.ResultsSignificant statistical and spatial variability exists between measures of alcohol access, and these differences have meaningful practical implications. In particular, standard measures of outlet density (e.g., spatial, per capita, roadway miles) can lead to biased estimates of physical availability that over-emphasize the influence of the control variables. Employing a gravity potential approach provides a more balanced, geographically-sensitive measure of access to alcohol outlets.ConclusionsAccurately measuring the physical availability of alcohol is critical for understanding the causes and consequences of its distribution and for developing effective evidence-based policy to manage the alcohol outlet licensing process. A gravity potential model provides a superior measure of alcohol access, and the alcohol access-based taxonomy a helpful evidence-based heuristic for scholars and local policymakers
Random matrix analysis of localization properties of Gene co-expression network
We analyze gene co-expression network under the random matrix theory
framework. The nearest neighbor spacing distribution of the adjacency matrix of
this network follows Gaussian orthogonal statistics of random matrix theory
(RMT). Spectral rigidity test follows random matrix prediction for a certain
range, and deviates after wards. Eigenvector analysis of the network using
inverse participation ratio (IPR) suggests that the statistics of bulk of the
eigenvalues of network is consistent with those of the real symmetric random
matrix, whereas few eigenvalues are localized. Based on these IPR calculations,
we can divide eigenvalues in three sets; (A) The non-degenerate part that
follows RMT. (B) The non-degenerate part, at both ends and at intermediate
eigenvalues, which deviate from RMT and expected to contain information about
{\it important nodes} in the network. (C) The degenerate part with
eigenvalue, which fluctuates around RMT predicted value. We identify nodes
corresponding to the dominant modes of the corresponding eigenvectors and
analyze their structural properties
Graph Summarization
The continuous and rapid growth of highly interconnected datasets, which are
both voluminous and complex, calls for the development of adequate processing
and analytical techniques. One method for condensing and simplifying such
datasets is graph summarization. It denotes a series of application-specific
algorithms designed to transform graphs into more compact representations while
preserving structural patterns, query answers, or specific property
distributions. As this problem is common to several areas studying graph
topologies, different approaches, such as clustering, compression, sampling, or
influence detection, have been proposed, primarily based on statistical and
optimization methods. The focus of our chapter is to pinpoint the main graph
summarization methods, but especially to focus on the most recent approaches
and novel research trends on this topic, not yet covered by previous surveys.Comment: To appear in the Encyclopedia of Big Data Technologie
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