Title: Predicting microbial interactions from time series data with network information

Authors: Yan Wang; Mingzhi Mao; Fang Li; Wenping Deng; Shaowu Shen; Xingpeng Jiang

Addresses: Information Engineering College, Hubei University of Chinese Medicine, Wuhan 430065, China ' School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China ' Information Engineering College, Jing De Zhen Ceramic Institute, JiuJiang 333403, China ' Information Engineering College, Hubei University of Chinese Medicine, Wuhan 430065, China ' Institute of Standardization and Information Technology, Information Engineering College, Hubei University of Chinese Medicine, Wuhan 430065, China ' School of Computer Science, Central China Normal University, Wuhan 430079, China

Abstract: The evolution of biotechnological knowledge poses some new challenges to study microbial interactions. Vector autoregressive (VAR) model was proved to be an efficient approach to infer dynamic interactions in biological systems. However, high-throughput metagenomics or 16S-rRNA sequencing data is high dimension, which means that the number of covariates is much larger than the number of observations. Reducing the dimension of data or selecting suitable covariates became a critical component VAR modelling. In this paper, we develop a graph-regularised vector autoregressive model incorporating network information to infer causal relationships among microbial entities. The method not only considers the signs of the network connections among any two covariates, but also constructs a network weighted matrix by microbial topology information. The coordinate descent algorithm for estimating model parameters improves the accuracy of prediction. The experimental results on a time series data set of human gut microbiomes indicate that the proposed approach has better performance than other VAR-based models with penalty functions.

Keywords: microbiome; microbial interactions; vector autoregression model; Laplacian regularisation; coordinate descent; penalty function.

DOI: 10.1504/IJDMB.2017.084260

International Journal of Data Mining and Bioinformatics, 2017 Vol.17 No.2, pp.97 - 114

Received: 02 Jan 2017
Accepted: 02 Jan 2017
Published online: 22 May 2017 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article