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Sticky hidden Markov modeling of comparative genomic hybridization

Publication ,  Journal Article
Du, L; Chen, M; Lucas, J; Carin, L
Published in: IEEE Transactions on Signal Processing
October 1, 2010

We develop a sticky hidden Markov model (HMM) with a Dirichlet distribution (DD) prior, motivated by the problem of analyzing comparative genomic hybridization (CGH) data. As formulated the sticky DD-HMM prior is employed to infer the number of states in an HMM, while also imposing state persistence. The form of the proposed hierarchical model allows efficient variational Bayesian (VB) inference, of interest for large-scale CGH problems. We compare alternative formulations of the sticky HMM, while also examining the relative efficacy of VB and Markov chain Monte Carlo (MCMC) inference. To validate the formulation, example results are presented for an illustrative synthesized data set and our main applicationCGH, for which we consider data for breast cancer. For the latter, we also make comparisons and partially validate the CGH analysis through factor analysis of associated (but distinct) gene-expression data. © 2010 IEEE.

Duke Scholars

Published In

IEEE Transactions on Signal Processing

DOI

ISSN

1053-587X

Publication Date

October 1, 2010

Volume

58

Issue

10

Start / End Page

5353 / 5368

Related Subject Headings

  • Networking & Telecommunications
 

Citation

APA
Chicago
ICMJE
MLA
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Du, L., Chen, M., Lucas, J., & Carin, L. (2010). Sticky hidden Markov modeling of comparative genomic hybridization. IEEE Transactions on Signal Processing, 58(10), 5353–5368. https://doi.org/10.1109/TSP.2010.2053033
Du, L., M. Chen, J. Lucas, and L. Carin. “Sticky hidden Markov modeling of comparative genomic hybridization.” IEEE Transactions on Signal Processing 58, no. 10 (October 1, 2010): 5353–68. https://doi.org/10.1109/TSP.2010.2053033.
Du L, Chen M, Lucas J, Carin L. Sticky hidden Markov modeling of comparative genomic hybridization. IEEE Transactions on Signal Processing. 2010 Oct 1;58(10):5353–68.
Du, L., et al. “Sticky hidden Markov modeling of comparative genomic hybridization.” IEEE Transactions on Signal Processing, vol. 58, no. 10, Oct. 2010, pp. 5353–68. Scopus, doi:10.1109/TSP.2010.2053033.
Du L, Chen M, Lucas J, Carin L. Sticky hidden Markov modeling of comparative genomic hybridization. IEEE Transactions on Signal Processing. 2010 Oct 1;58(10):5353–5368.

Published In

IEEE Transactions on Signal Processing

DOI

ISSN

1053-587X

Publication Date

October 1, 2010

Volume

58

Issue

10

Start / End Page

5353 / 5368

Related Subject Headings

  • Networking & Telecommunications