A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks

A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks
Title:
A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks
Other Titles:
Bioinformatics
Publication Date:
07 March 2020
Citation:
Zi-Chao Zhang, Xiao-Fei Zhang, Min Wu, Le Ou-Yang, Xing-Ming Zhao, Xiao-Li Li, A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks, Bioinformatics, , btaa157, https://doi.org/10.1093/bioinformatics/btaa157
Abstract:
Motivation: Predicting potential links in biomedical bipartite networks can provide useful insights into the diagnosis and treatment of complex diseases and the discovery of novel drug targets. Computational methods have been proposed recently to predict potential links for various biomedical bipartite networks. However, existing methods are usually rely on the coverage of known links, which may encounter difficulties when dealing with new nodes without any known link information. Results: In this study, we propose a new link prediction method, named graph regularized generalized matrix factorization (GRGMF), to identify potential links in biomedical bipartite networks. First, we formulate a generalized matrix factorization model to exploit the latent patterns behind observed links. In particular, it can take into account the neighborhood information of each node when learning the latent representation for each node, and the neighborhood information of each node can be learned adaptively. Second, we introduce two graph regularization terms to draw support from affinity information of each node derived from external databases to enhance the learning of latent representations. We conduct extensive experiments on six real datasets. Experiment results show that GRGMF can achieve competitive performance on all these datasets, which demonstrate the effectiveness of GRGMF in prediction potential links in biomedical bipartite networks.
License type:
PublisherCopyrights
Funding Info:
This work is supported by the National Natural Science Foundation of China (61602309, 11871026, 61932008, 61772368), Shenzhen Fundamental Research Program [JCYJ20170817095210760], Guangdong Basic and Applied Basic Research Foundation [2019A1515011384], Natural Science Foundation of Hubei province [ZRMS2018001337], Natural Science Foundation of Shanghai [17ZR1445600], Shanghai Municipal Science and Technology Major Project [2018SHZDZX01] and ZJLab, Chinese National-level College Students’ Innovative Entrepreneurial Training Plan Program[201710590016].
Description:
This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record Zi-Chao Zhang, Xiao-Fei Zhang, Min Wu, Le Ou-Yang, Xing-Ming Zhao, Xiao-Li Li, A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks, Bioinformatics, btaa157, https://doi.org/10.1093/bioinformatics/btaa157 is available online at: https://doi.org/10.1093/bioinformatics/btaa157.
ISSN:
1367-4803
1460-2059
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