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This article is part of the supplement: Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Systems Biology

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Integrating multiple networks for protein function prediction

Guoxian Yu12*, Hailong Zhu2*, Carlotta Domeniconi3 and Maozu Guo4

Author Affiliations

1 College of Computer and Information Sciences, Southwest University, Chongqing, China

2 Department of Computer Science, Hong Kong Baptist University, Hong Kong

3 Department of Computer Science, George Mason University, VA, US

4 School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China

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BMC Systems Biology 2015, 9(Suppl 1):S3  ) doi:10.1186/1752-0509-9-S1-S3

Published: 21 January 2015



High throughput techniques produce multiple functional association networks. Integrating these networks can enhance the accuracy of protein function prediction. Many algorithms have been introduced to generate a composite network, which is obtained as a weighted sum of individual networks. The weight assigned to an individual network reflects its benefit towards the protein functional annotation inference. A classifier is then trained on the composite network for predicting protein functions. However, since these techniques model the optimization of the composite network and the prediction tasks as separate objectives, the resulting composite network is not necessarily optimal for the follow-up protein function prediction.


We address this issue by modeling the optimization of the composite network and the prediction problems within a unified objective function. In particular, we use a kernel target alignment technique and the loss function of a network based classifier to jointly adjust the weights assigned to the individual networks. We show that the proposed method, called MNet, can achieve a performance that is superior (with respect to different evaluation criteria) to related techniques using the multiple networks of four example species (yeast, human, mouse, and fly) annotated with thousands (or hundreds) of GO terms.


MNet can effectively integrate multiple networks for protein function prediction and is robust to the input parameters. Supplementary data is available at The Matlab code of MNet is available upon request.