article

Predicting microbial interactions using vector autoregressive model with graph regularization

Editor: Ying Xu Authors:

Xingpeng Jiang,

E. K. ParkAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 12, Issue 2

Pages 254 - 261

https://doi.org/10.1109/TCBB.2014.2338298

Published: 01 March 2015 Publication History

Abstract

Microbial interactions play important roles on the structure and function of complex microbial communities. With the rapid accumulation of high-throughput metagenomic or 16S rRNA sequencing data, it is possible to infer complex microbial interactions. Co-occurrence patterns of microbial species among multiple samples are often utilized to infer interactions. There are few methods to consider the temporally interacting patterns among microbial species. In this paper, we present a Graph-regularized Vector Autoregressive (GVAR) model to infer causal relationships among microbial entities. The new model has advantage comparing to the original vector autoregressive (VAR) model. Specifically, GVAR can incorporate similarity information for microbial interaction inference--i.e., GVAR assumed that if two species are similar in the previous stage, they tend to have similar influence on the other species in the next stage. We apply the model on a time series dataset of human gut microbiome which was treated with repeated antibiotics. The experimental results indicate that the new approach has better performance than several other VAR-based models and demonstrate its capability of extracting relevant microbial interactions.

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Cited By

Wang YHe TJiang XYuan JShen X(2015)Weighted fusion regularisation and predicting microbial interactions with vector autoregressive modelInternational Journal of Data Mining and Bioinformatics10.1504/IJDMB.2015.07275713:4(378-394)Online publication date: 1-Oct-2015
https://dl.acm.org/doi/10.1504/IJDMB.2015.072757

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Predicting microbial interactions using vector autoregressive model with graph regularization

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Information & Contributors

Information

Published In

cover image IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 12, Issue 2

March/April 2015

247 pages

ISSN:1545-5963

Editor:
Ying Xu
Department of Biochemistry, Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA

Issue’s Table of Contents

Publisher

IEEE Computer Society Press

Washington, DC, United States

Publication History

Published: 01 March 2015

Accepted: 15 June 2014

Revised: 01 June 2014

Received: 30 March 2014

Published in TCBB Volume 12, Issue 2

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Cited By

Wang YHe TJiang XYuan JShen X(2015)Weighted fusion regularisation and predicting microbial interactions with vector autoregressive modelInternational Journal of Data Mining and Bioinformatics10.1504/IJDMB.2015.07275713:4(378-394)Online publication date: 1-Oct-2015
https://dl.acm.org/doi/10.1504/IJDMB.2015.072757

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