A tensor-based Markov chain method for module identification from multiple networks

Chenyang Shen, Shuqin Zhang, Michael K. Ng

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

The interactions among different genes, proteins and other small molecules are becoming more and more significant and have been studied intensively nowadays. One general way that helps people understand these interactions is to analyze networks constructed from genes/proteins. In particular, module structure as a common property of most biological networks has drawn much attention of researchers from different fields. In most cases, biological networks can be corrupted by noise in the data and the corruption may cause mis-identification of module structure. Besides, some structure may be destroyed when improper experimental settings are built up. Thus module structure may be unstable when one single network is employed. In this paper, we consider employing multiple networks for consistent module detection in order to reduce the effect of noise and experimental setting. Instead of considering different networks separately, our idea is to combine multiple networks together by building them into tensor structure data. Then given any node as prior label information, tensor-based Markov chains are constructed iteratively for identification of the modules shared by the multiple networks. In addition, the proposed tensor-based Markov chain algorithm is capable of simultaneously evaluating the contribution from each network. It would be useful to measure the consistency of modules in the multiple networks. In the experiments, we test our method on two groups of gene co-expression networks from human beings. We also validate the modules identified by the proposed method.

Original languageEnglish (US)
Title of host publicationInternational Conference on Systems Biology, ISB
EditorsLing-Yun Wu, Yong Wang, Luonan Chen, Xiang-Sun Zhang
PublisherIEEE Computer Society
Pages49-58
Number of pages10
ISBN (Electronic)9781479972944
DOIs
StatePublished - Dec 17 2014
Externally publishedYes
Event8th International Conference on Systems Biology, ISB 2014 - Qingdao, China
Duration: Aug 24 2014Aug 27 2014

Conference

Conference8th International Conference on Systems Biology, ISB 2014
CountryChina
CityQingdao
Period8/24/148/27/14

Fingerprint

Markov Chains
Markov processes
Tensors
Markov chain
Tensor
Genes
Module
Proteins
Noise
Research Personnel
Gene Expression
Labels
Biological Networks
Gene
Molecules
Protein
Experiments
Interaction
Data Structures
Unstable

ASJC Scopus subject areas

  • Modeling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Computer Science Applications

Cite this

Shen, C., Zhang, S., & Ng, M. K. (2014). A tensor-based Markov chain method for module identification from multiple networks. In L-Y. Wu, Y. Wang, L. Chen, & X-S. Zhang (Eds.), International Conference on Systems Biology, ISB (pp. 49-58). [6990431] IEEE Computer Society. https://doi.org/10.1109/ISB.2014.6990431

A tensor-based Markov chain method for module identification from multiple networks. / Shen, Chenyang; Zhang, Shuqin; Ng, Michael K.

International Conference on Systems Biology, ISB. ed. / Ling-Yun Wu; Yong Wang; Luonan Chen; Xiang-Sun Zhang. IEEE Computer Society, 2014. p. 49-58 6990431.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Shen, C, Zhang, S & Ng, MK 2014, A tensor-based Markov chain method for module identification from multiple networks. in L-Y Wu, Y Wang, L Chen & X-S Zhang (eds), International Conference on Systems Biology, ISB., 6990431, IEEE Computer Society, pp. 49-58, 8th International Conference on Systems Biology, ISB 2014, Qingdao, China, 8/24/14. https://doi.org/10.1109/ISB.2014.6990431
Shen C, Zhang S, Ng MK. A tensor-based Markov chain method for module identification from multiple networks. In Wu L-Y, Wang Y, Chen L, Zhang X-S, editors, International Conference on Systems Biology, ISB. IEEE Computer Society. 2014. p. 49-58. 6990431 https://doi.org/10.1109/ISB.2014.6990431
Shen, Chenyang ; Zhang, Shuqin ; Ng, Michael K. / A tensor-based Markov chain method for module identification from multiple networks. International Conference on Systems Biology, ISB. editor / Ling-Yun Wu ; Yong Wang ; Luonan Chen ; Xiang-Sun Zhang. IEEE Computer Society, 2014. pp. 49-58
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