Header logo is ei

Learning kernels from biological networks by maximizing entropy




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.

Author(s): Tsuda, K. and Noble, WS.
Journal: Bioinformatics
Volume: 20
Number (issue): Suppl. 1
Pages: i326-i333
Year: 2004
Month: August
Day: 0

Department(s): Empirical Inference
Bibtex Type: Article (article)

Digital: 0
Language: en
Organization: Max-Planck-Gesellschaft
School: Biologische Kybernetik

Links: PDF


  title = {Learning kernels from biological networks by maximizing entropy},
  author = {Tsuda, K. and Noble, WS.},
  journal = {Bioinformatics},
  volume = {20},
  number = {Suppl. 1},
  pages = {i326-i333},
  organization = {Max-Planck-Gesellschaft},
  school = {Biologische Kybernetik},
  month = aug,
  year = {2004},
  month_numeric = {8}