Bioinformatics 20(Suppl. 1) © Oxford University Press 2004; all rights reserved.
Learning kernels from biological networks by maximizing entropy
1 Max Planck Institute for Biological Cybernetics, Spemannstrasse 38, 72076 Tübingen, Germany, 2 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-43 Aomi Koto-ku, Tokyo, Japan, 3 Department of Genome Sciences and 4 Department of Computer Science, 1705 NE Pacific Street, University of Washington, Seattle, WA 98109, USA
Received on January 15, 2004; accepted on March 1, 2004
Motivation: The diffusion kernel is a general method for computing pairwise distances among all nodes in a graph, based on the sum of weighted paths between each pair of nodes. This technique has been used successfully, in conjunction with kernel-based learning methods, to draw inferences from several types of biological networks.
Results: We show that computing the diffusion kernel is equivalent to maximizing the von Neumann entropy, subject to a global constraint on the sum of the Euclidean distances between nodes. This global constraint allows for high variance in the pairwise distances. Accordingly, we propose an alternative, locally constrained diffusion kernel, and we demonstrate that the resulting kernel allows for more accurate support vector machine prediction of protein functional classifications from metabolic and protein–protein interaction networks.
Availability: Supplementary results and data are available at noble.gs.washington.edu/proj/maxent
Contact: koji.tsuda{at}tuebingen.mpg.de
* To whom correspondence should be addressed.
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