dorsal/arxiv
View SchemaDiscriminative Topological Features Reveal Biological Network Mechanisms
| Authors | Manuel Middendorf, Etay Ziv, Carter Adams, Jen Hom, Robin Koytcheff, Chaya Levovitz, Gregory Woods, Linda Chen, Chris Wiggins |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0402017 |
| URL | https://arxiv.org/abs/q-bio/0402017 |
| Journal | BMC Bioinformatics 2004, 5:181 (22 November 2004) |
Abstract
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how well it reproduces a few key features of the real-world data, such as degree distributions, mean geodesic lengths, and clustering coefficients. Often pairs of models can reproduce these features with indistinguishable fidelity despite being generated by vastly different mechanisms. In such cases, these few target features are insufficient to distinguish which of the different models best describes real world networks of interest; moreover, it is not clear a priori that any of the presently-existing algorithms for network generation offers a predictive description of the networks inspiring them. To derive discriminative classifiers, we construct a mapping from the set of all graphs to a high-dimensional (in principle infinite-dimensional) ``word space.'' This map defines an input space for classification schemes which allow us for the first time to state unambiguously which models are most descriptive of the networks they purport to describe. Our training sets include networks generated from 17 models either drawn from the literature or introduced in this work, source code for which is freely available. We anticipate that this new approach to network analysis will be of broad impact to a number of communities.
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"abstract": "Recent genomic and bioinformatic advances have motivated the development of\nnumerous random network models purporting to describe graphs of biological,\ntechnological, and sociological origin. The success of a model has been\nevaluated by how well it reproduces a few key features of the real-world data,\nsuch as degree distributions, mean geodesic lengths, and clustering\ncoefficients. Often pairs of models can reproduce these features with\nindistinguishable fidelity despite being generated by vastly different\nmechanisms. In such cases, these few target features are insufficient to\ndistinguish which of the different models best describes real world networks of\ninterest; moreover, it is not clear a priori that any of the presently-existing\nalgorithms for network generation offers a predictive description of the\nnetworks inspiring them. To derive discriminative classifiers, we construct a\nmapping from the set of all graphs to a high-dimensional (in principle\ninfinite-dimensional) ``word space.\u0027\u0027 This map defines an input space for\nclassification schemes which allow us for the first time to state unambiguously\nwhich models are most descriptive of the networks they purport to describe. Our\ntraining sets include networks generated from 17 models either drawn from the\nliterature or introduced in this work, source code for which is freely\navailable. We anticipate that this new approach to network analysis will be of\nbroad impact to a number of communities.",
"arxiv_id": "q-bio/0402017",
"authors": [
"Manuel Middendorf",
"Etay Ziv",
"Carter Adams",
"Jen Hom",
"Robin Koytcheff",
"Chaya Levovitz",
"Gregory Woods",
"Linda Chen",
"Chris Wiggins"
],
"categories": [
"q-bio.MN"
],
"journal_ref": "BMC Bioinformatics 2004, 5:181 (22 November 2004)",
"title": "Discriminative Topological Features Reveal Biological Network Mechanisms",
"url": "https://arxiv.org/abs/q-bio/0402017"
},
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