Journal Article

An unsupervised conditional random fields approach for clustering gene expression time series

Chang-Tsun Li, Yinyin Yuan and Roland Wilson

in Bioinformatics

Volume 24, issue 21, pages 2467-2473
Published in print November 2008 | ISSN: 1367-4803
Published online August 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn375
An unsupervised conditional random fields approach for clustering gene expression time series

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Motivation: There is a growing interest in extracting statistical patterns from gene expression time-series data, in which a key challenge is the development of stable and accurate probabilistic models. Currently popular models, however, would be computationally prohibitive unless some independence assumptions are made to describe large-scale data. We propose an unsupervised conditional random fields (CRF) model to overcome this problem by progressively infusing information into the labelling process through a small variable voting pool.

Results: An unsupervised CRF model is proposed for efficient analysis of gene expression time series and is successfully applied to gene class discovery and class prediction. The proposed model treats each time series as a random field and assigns an optimal cluster label to each time series, so as to partition the time series into clusters without a priori knowledge about the number of clusters and the initial centroids. Another advantage of the proposed method is the relaxation of independence assumptions.

Contact: ctli@dcs.warwick.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6067 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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