Dataset Information

Generation of 2-mode scale-free graphs for link-level internet topology modeling.

ABSTRACT: Comprehensive analysis that aims to understand the topology of real-world networks and the development of algorithms that replicate their characteristics has been significant research issues. Although the accuracy of newly developed network protocols or algorithms does not depend on the underlying topology, the performance generally depends on the topology. As a result, network practitioners have concentrated on generating representative synthetic topologies and utilize them to investigate the performance of their design in simulation or emulation environments. Network generators typically represent the Internet topology as a graph composed of point-to-point links. In this study, we discuss the implications of multi-access links on the synthetic network generation and modeling of the networks as bi-partite graphs to represent both subnetworks and routers. We then analyze the characteristics of sampled Internet topology data sets from backbone Autonomous Systems (AS) and observe that in addition to the commonly recognized power-law node degree distribution, the subnetwork size and the router interface distributions often exhibit power-law characteristics. We introduce a SubNetwork Generator (SubNetG) topology generation approach that incorporates the observed measurements to produce bipartite network topologies. In particular, generated topologies capture the 2-mode relation between the layer-2 (i.e., the subnetwork and interface distributions) and the layer-3 (i.e., the degree distribution) that is missing from the current network generators that produce 1-mode graphs. The SubNetG source code and experimental data is available at https://github.com/netml/sonet.

SUBMITTER: Bakhshaliyev K

PROVIDER: S-EPMC7652253 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Generation of 2-mode scale-free graphs for link-level internet topology modeling.

Bakhshaliyev Khalid K Gunes Mehmet Hadi MH

PloS one 20201109 11

Comprehensive analysis that aims to understand the topology of real-world networks and the development of algorithms that replicate their characteristics has been significant research issues. Although the accuracy of newly developed network protocols or algorithms does not depend on the underlying topology, the performance generally depends on the topology. As a result, network practitioners have concentrated on generating representative synthetic topologies and utilize them to investigate the p ...[more]

PMID: 33166286

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Project description:BackgroundIn rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system.ResultsFor purposes of model annotation, we propose the use of hierarchical graphs to represent structural relationships among components and subcomponents of molecules. We illustrate how hierarchical graphs can be used to naturally document the structural organization of the functional components and subcomponents of two proteins: the protein tyrosine kinase Lck and the T cell receptor (TCR) complex. We also show that computational methods developed for regular graphs can be applied to hierarchical graphs. In particular, we describe a generalization of Nauty, a graph isomorphism and canonical labeling algorithm. The generalized version of the Nauty procedure, which we call HNauty, can be used to assign canonical labels to hierarchical graphs or more generally to graphs with multiple edge types. The difference between the Nauty and HNauty procedures is minor, but for completeness, we provide an explanation of the entire HNauty algorithm.ConclusionsHierarchical graphs provide more intuitive formal representations of proteins and other structured molecules with multiple functional components than do the regular graphs of current languages for specifying rule-based models, such as the BioNetGen language (BNGL). Thus, the proposed use of hierarchical graphs should promote clarity and better understanding of rule-based models.

Dataset Information

Generation of 2-mode scale-free graphs for link-level internet topology modeling.

Publications

Generation of 2-mode scale-free graphs for link-level internet topology modeling.

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