14,111 research outputs found
Immunization of networks with community structure
In this study, an efficient method to immunize modular networks (i.e.,
networks with community structure) is proposed. The immunization of networks
aims at fragmenting networks into small parts with a small number of removed
nodes. Its applications include prevention of epidemic spreading, intentional
attacks on networks, and conservation of ecosystems. Although preferential
immunization of hubs is efficient, good immunization strategies for modular
networks have not been established. On the basis of an immunization strategy
based on the eigenvector centrality, we develop an analytical framework for
immunizing modular networks. To this end, we quantify the contribution of each
node to the connectivity in a coarse-grained network among modules. We verify
the effectiveness of the proposed method by applying it to model and real
networks with modular structure.Comment: 3 figures, 1 tabl
The failure tolerance of mechatronic software systems to random and targeted attacks
This paper describes a complex networks approach to study the failure
tolerance of mechatronic software systems under various types of hardware
and/or software failures. We produce synthetic system architectures based on
evidence of modular and hierarchical modular product architectures and known
motifs for the interconnection of physical components to software. The system
architectures are then subject to various forms of attack. The attacks simulate
failure of critical hardware or software. Four types of attack are
investigated: degree centrality, betweenness centrality, closeness centrality
and random attack. Failure tolerance of the system is measured by a 'robustness
coefficient', a topological 'size' metric of the connectedness of the attacked
network. We find that the betweenness centrality attack results in the most
significant reduction in the robustness coefficient, confirming betweenness
centrality, rather than the number of connections (i.e. degree), as the most
conservative metric of component importance. A counter-intuitive finding is
that "designed" system architectures, including a bus, ring, and star
architecture, are not significantly more failure-tolerant than interconnections
with no prescribed architecture, that is, a random architecture. Our research
provides a data-driven approach to engineer the architecture of mechatronic
software systems for failure tolerance.Comment: Proceedings of the 2013 ASME International Design Engineering
Technical Conferences & Computers and Information in Engineering Conference
IDETC/CIE 2013 August 4-7, 2013, Portland, Oregon, USA (In Print
Modular design of data-parallel graph algorithms
Amorphous Data Parallelism has proven to be a suitable vehicle for implementing concurrent graph algorithms effectively on multi-core architectures. In view of the growing complexity of graph algorithms for information analysis, there is a need to facilitate modular design techniques in the context of Amorphous Data Parallelism. In this paper, we investigate what it takes to formulate algorithms possessing Amorphous Data Parallelism in a modular fashion enabling a large degree of code re-use. Using the betweenness centrality algorithm, a widely popular algorithm in the analysis of social networks, we demonstrate that a single optimisation technique can suffice to enable a modular programming style without loosing the efficiency of a tailor-made monolithic implementation
ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality
Summary: The ModuLand plug-in provides Cytoscape users an algorithm for
determining extensively overlapping network modules. Moreover, it identifies
several hierarchical layers of modules, where meta-nodes of the higher
hierarchical layer represent modules of the lower layer. The tool assigns
module cores, which predict the function of the whole module, and determines
key nodes bridging two or multiple modules. The plug-in has a detailed
JAVA-based graphical interface with various colouring options. The ModuLand
tool can run on Windows, Linux, or Mac OS. We demonstrate its use on protein
structure and metabolic networks. Availability: The plug-in and its user guide
can be downloaded freely from: http://www.linkgroup.hu/modules.php. Contact:
[email protected] Supplementary information: Supplementary
information is available at Bioinformatics online.Comment: 39 pages, 1 figure and a Supplement with 9 figures and 10 table
Chaperones as integrators of cellular networks: Changes of cellular integrity in stress and diseases
Cellular networks undergo rearrangements during stress and diseases. In
un-stressed state the yeast protein-protein interaction network (interactome)
is highly compact, and the centrally organized modules have a large overlap.
During stress several original modules became more separated, and a number of
novel modules also appear. A few basic functions, such as the proteasome
preserve their central position. However, several functions with high energy
demand, such the cell-cycle regulation loose their original centrality during
stress. A number of key stress-dependent protein complexes, such as the
disaggregation-specific chaperone, Hsp104, gain centrality in the stressed
yeast interactome. Molecular chaperones, heat shock, or stress proteins form
complex interaction networks (the chaperome) with each other and their
partners. Here we show that the human chaperome recovers the segregation of
protein synthesis-coupled and stress-related chaperones observed in yeast
recently. Examination of yeast and human interactomes shows that (1) chaperones
are inter-modular integrators of protein-protein interaction networks, which
(2) often bridge hubs and (3) are favorite candidates for extensive
phosphorylation. Moreover, chaperones (4) become more central in the
organization of the isolated modules of the stressed yeast protein-protein
interaction network, which highlights their importance in the de-coupling and
re-coupling of network modules during and after stress. Chaperone-mediated
evolvability of cellular networks may play a key role in cellular adaptation
during stress and various polygenic and chronic diseases, such as cancer,
diabetes or neurodegeneration.Comment: 13 pages, 3 figures, 1 glossar
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