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  Fast Protein Classification with Multiple Networks

Tsuda, K., Shin, H., & Schölkopf, B. (2005). Fast Protein Classification with Multiple Networks. Bioinformatics, 21(Supplement 2), 59-65.

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 Creators:
Tsuda, K1, 2, Author              
Shin, H1, 2, Author              
Schölkopf, B1, 2, Author              
Affiliations:
1Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497795              
2Max Planck Institute for Biological Cybernetics, Max Planck Society, Spemannstrasse 38, 72076 Tübingen, DE, ou_1497794              

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 Abstract: Support vector machines (SVM) have been successfully used to classify proteins into functional categories. Recently, to integrate multiple data sources, a semidefinite programming (SDP) based SVM method was introduced Lanckriet et al (2004). In SDP/SVM, multiple kernel matrices corresponding to each of data sources are combined with weights obtained by solving an SDP. However, when trying to apply SDP/SVM to large problems, the computational cost can become prohibitive, since both converting the data to a kernel matrix for the SVM and solving the SDP are time and memory demanding. Another application-specific drawback arises when some of the data sources are protein networks. A common method of converting the network to a kernel matrix is the diffusion kernel method, which has time complexity of O(n^3), and produces a dense matrix of size n x n. We propose an efficient method of protein classification using multiple protein networks. Available protein networks, such as a physical interaction network or a metabolic network, can be directly incorporated. Vectorial data can also be incorporated after conversion into a network by means of neighbor point connection. Similarly to the SDP/SVM method, the combination weights are obtained by convex optimization. Due to the sparsity of network edges, the computation time is nearly linear in the number of edges of the combined network. Additionally, the combination weights provide information useful for discarding noisy or irrelevant networks. Experiments on function prediction of 3588 yeast proteins show promising results: the computation time is enormously reduced, while the accuracy is still comparable to the SDP/SVM method.

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 Dates: 2005-09
 Publication Status: Published in print
 Pages: -
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 Identifiers: DOI: 10.1093/bioinformatics/bti1110
BibTex Citekey: 3507
 Degree: -

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Title: Fourth European Conference on Computational Biology / Sixth Meeting of the Spanish Bioinformatics Network (ECCB/JBI 2005)
Place of Event: Madrid, Spain
Start-/End Date: 2005-09-28 - 2005-10-01

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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 21 (Supplement 2) Sequence Number: - Start / End Page: 59 - 65 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991