A binary matrix factorization algorithm for protein complex prediction
Refereed conference paper presented and published in conference proceedings


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AbstractWe propose a binary matrix factorization (BMF) algorithm under the Bayesian Ying-Yang (BYY) harmony learning, to detect protein complexes by clustering the proteins which share similar interactions through factorizing the binary adjacent matrix of the protein-protein interaction (PPI) network. The proposed BYY-BMF algorithm automatically determines the cluster number while this number is usually specified for most existing BMF algorithms. Also, BYY-BMF's clustering results does not depend on any parameters or thresholds, unlike the Markov Cluster Algorithm (MCL) that relies on a so-called inflation parameter. On synthetic PPI networks, the predictions evaluated by the known annotated complexes indicate that BYY-BMF is more robust than MCL for most cases. Moreover, BYY-BMF obtains a better balanced prediction accuracies than MCL and a spectral analysis method, on real PPI networks from the MIPS and DIP databases. ©2010 IEEE.
All Author(s) ListTu S., Xu L., Chen R.
Name of Conference2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010
Start Date of Conference18/12/2010
End Date of Conference21/12/2010
Place of ConferenceHongKong
Country/Region of ConferenceHong Kong
Detailed descriptionorganized by IEEE Computer Society,
Year2010
Month12
Day1
Pages113 - 118
ISBN9781424483044
LanguagesEnglish-United Kingdom

Last updated on 2020-28-03 at 00:24