adaptive diffusion kernel learning from biological networks for protein function prediction自适应扩散内核从生物网络学习蛋白质功能预测.pdfVIP

BMC Bioinformatics BioMed Central Research article Open Access Adaptive diffusion kernel learning from biological networks for protein function prediction Liang Sun1,2, Shuiwang Ji1,2 and Jieping Ye*1,2 Address: 1Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA and 2Department of Computer Science and Engineering, Arizona State University, Tempe, AZ, USA Email: Liang Sun - sun.liang@; Shuiwang Ji - shuiwang.ji@; Jieping Ye* - jieping.ye@ * Corresponding author Published: 25 March 2008 Received: 30 May 2007 Accepted: 25 March 2008 BMC Bioinformatics 2008, 9:162 doi:10.1186/1471-2105-9-162 This article is available from: /1471-2105/9/162 © 2008 Sun et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Machine-learning tools have gained considerable attention during the last few years for analyzing biological networks for protein function prediction. Kernel methods are suitable for learning from graph-based data such as biological networks, as they only require the abstraction of the similarities between objects into the kernel matrix. One key issue in kernel methods is the selection of a good kernel function. Diffusion kernels, the discretization of the familiar Gaussian kernel of