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  Graph kernels for disease outcome prediction from protein-protein interaction networks

Borgwardt, K., Kriegel, H.-P., Vishwanathan, S., & Schraudolph, N. (2007). Graph kernels for disease outcome prediction from protein-protein interaction networks. In R. Altman, A. Dunker, L. Hunter, T. Murray, & T. Klein (Eds.), Biocomputing 2007, Proceedings of the Pacific Symposium, Maui, Hawaii, USA, 3-7 January 2007 (pp. 4-15). Hackensack, NJ, USA: World Scientific.

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Item Permalink: https://hdl.handle.net/11858/00-001M-0000-0013-CEF9-5 Version Permalink: https://hdl.handle.net/21.11116/0000-0003-E8D0-C
Genre: Conference Paper

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http://psb.stanford.edu/psb-online/proceedings/psb07/borgwardt.pdf (Publisher version)
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 Creators:
Borgwardt, KM1, Author           
Kriegel, H-P, Author
Vishwanathan, SVN, Author
Schraudolph, NN, Author
Affiliations:
1External Organizations, ou_persistent22              

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 Abstract: It is widely believed that comparing discrepancies in the protein-protein interaction (PPI) networks of individuals will become an important tool in understanding and
preventing diseases. Currently PPI networks for individuals are not available, but gene expression data is becoming easier to obtain and allows us to represent individuals by a co-integrated gene expression/protein interaction network. Two major problems hamper the application of graph kernels – state-of-the-art methods for whole-graph comparison – to compare PPI networks. First, these methods do not scale to graphs of the size of a PPI network. Second, missing edges in these interaction networks are biologically relevant for detecting discrepancies, yet, these methods do not take this into account. In this article we present graph kernels for biological network comparison that are fast to compute and take into account
missing interactions. We evaluate their practical performance on two datasets of co-integrated gene expression/PPI networks.

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 Dates: 2007-01
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: ISBN: 978-981-270417-7
BibTex Citekey: BorgwardtVSK2007
 Degree: -

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Title: 12. Pacific Symposium on Biocomputing (PSB 2007)
Place of Event: Maui, HI, USA
Start-/End Date: 2007-01-03 - 2007-01-07

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Title: Biocomputing 2007, Proceedings of the Pacific Symposium, Maui, Hawaii, USA, 3-7 January 2007
Source Genre: Proceedings
 Creator(s):
Altman, RB, Editor
Dunker, AK, Editor
Hunter, L, Editor
Murray, T, Editor
Klein, TE, Editor
Affiliations:
-
Publ. Info: Hackensack, NJ, USA : World Scientific
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: 4 - 15 Identifier: ISBN: 981-270-417-5