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Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3192-7. Epub 2005 Feb 22.

Inferring network mechanisms: the Drosophila melanogaster protein interaction network.

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  • 1Department of Physics, College of Physicians and Surgeons, Columbia University, New York, NY 10027, USA.


Naturally occurring networks exhibit quantitative features revealing underlying growth mechanisms. Numerous network mechanisms have recently been proposed to reproduce specific properties such as degree distributions or clustering coefficients. We present a method for inferring the mechanism most accurately capturing a given network topology, exploiting discriminative tools from machine learning. The Drosophila melanogaster protein network is confidently and robustly (to noise and training data subsampling) classified as a duplication-mutation-complementation network over preferential attachment, small-world, and a duplication-mutation mechanism without complementation. Systematic classification, rather than statistical study of specific properties, provides a discriminative approach to understand the design of complex networks.

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