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Inferring causal relations from multivariate time series : a fast method for large-scale gene expression data

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Yuan, Yinyin and Li, Chang-Tsun (2009) Inferring causal relations from multivariate time series : a fast method for large-scale gene expression data. In: BioInformatics and BioEngineering (BIBE), 2009 Ninth IEEE International Conference on, Tʻai-chung shih (Taiwan), 2009 pp. 92-99.

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Abstract

Various multivariate time series analysis techniques have been developed with the aim of inferring causal relations between time series. Previously, these techniques have proved their effectiveness on economic and neurophysiological data, which normally consist of hundreds of samples. However, in their applications to gene regulatory inference, the small sample size of gene expression time series poses an obstacle. In this paper, we describe some of the most commonly used multivariate inference techniques and show the potential challenge related to gene expression analysis. In response, we propose a directed partial correlation (DPC) algorithm as an efficient and effective solution to causal/regulatory relations inference on small sample gene expression data. Comparative evaluations on the existing techniques and the proposed method are presented. To draw reliable conclusions, a comprehensive benchmarking on data sets of various setups is essential. Three experiments are designed to assess these methods in a coherent manner. Detailed analysis of experimental results not only reveals good accuracy of the proposed DPC method in large-scale prediction, but also gives much insight into all methods under evaluation.

Item Type:	Conference Item (Paper)
Subjects:	Q Science > QA Mathematics Q Science > QH Natural history > QH426 Genetics
Divisions:	Faculty of Science > Computer Science
Library of Congress Subject Headings (LCSH):	Time-series analysis, Gene expression -- Mathematical models
Date:	2009
Page Range:	pp. 92-99
Identification Number:	10.1109/BIBE.2009.8
Status:	Peer Reviewed
Access rights to Published version:	Open Access
Conference Paper Type:	Paper
Title of Event:	BioInformatics and BioEngineering (BIBE), 2009 Ninth IEEE International Conference on
Type of Event:	Conference
Location of Event:	Tʻai-chung shih (Taiwan)
Date(s) of Event:	2009
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URI:	http://wrap.warwick.ac.uk/id/eprint/3363