The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization

Conor J. Kelton; Waishing Lee; Matthew Rusay; Ondrej Maxian; Elana J. Fertig; Michael F. Ochs

doi:10.1109/BIBM.2015.7359922

The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization

Conor J. Kelton, Waishing Lee, Matthew Rusay, Ondrej Maxian, Elana J. Fertig, Michael F. Ochs

School of Medicine

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Scopus citations

Abstract

Nonnegative matrix factorization and other decomposition methods have proven to offer significant advantages for the interpretation of genome-wide gene expression data. However, unlike analytic methods, they suffer from instability in the inferred factors or patterns as the dimensionality is changed. We present here two statistics, one mathematical and one biological, that estimate the dimensionality. We show that they provide close though not identical estimates, and that they provide strong evidence for elimination of some potential factorizations.

Original language	English (US)
Title of host publication	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editors	lng. Matthieu Schapranow, Jiayu Zhou, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Satoru Miyano, Illhoi Yoo, Brian Pierce, Amarda Shehu, Vijay K. Gombar, Brian Chen, Vinay Pai, Jun Huan
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1642-1649
Number of pages	8
ISBN (Electronic)	9781467367981
DOIs	https://doi.org/10.1109/BIBM.2015.7359922
State	Published - Dec 16 2015
Event	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States Duration: Nov 9 2015 → Nov 12 2015

Publication series

Name	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Other

Other	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Country/Territory	United States
City	Washington
Period	11/9/15 → 11/12/15

ASJC Scopus subject areas

Software
Artificial Intelligence
Health Informatics
Biomedical Engineering

Access to Document

10.1109/BIBM.2015.7359922

Cite this

Kelton, C. J., Lee, W., Rusay, M., Maxian, O., Fertig, E. J., & Ochs, M. F. (2015). The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization. In L. M. Schapranow, J. Zhou, X. T. Hu, B. Ma, S. Rajasekaran, S. Miyano, I. Yoo, B. Pierce, A. Shehu, V. K. Gombar, B. Chen, V. Pai, & J. Huan (Eds.), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 1642-1649). Article 7359922 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2015.7359922

The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization. / Kelton, Conor J.; Lee, Waishing; Rusay, Matthew et al.
Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. ed. / lng. Matthieu Schapranow; Jiayu Zhou; Xiaohua Tony Hu; Bin Ma; Sanguthevar Rajasekaran; Satoru Miyano; Illhoi Yoo; Brian Pierce; Amarda Shehu; Vijay K. Gombar; Brian Chen; Vinay Pai; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. p. 1642-1649 7359922 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Kelton, CJ, Lee, W, Rusay, M, Maxian, O, Fertig, EJ & Ochs, MF 2015, The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization. in LM Schapranow, J Zhou, XT Hu, B Ma, S Rajasekaran, S Miyano, I Yoo, B Pierce, A Shehu, VK Gombar, B Chen, V Pai & J Huan (eds), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015., 7359922, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Institute of Electrical and Electronics Engineers Inc., pp. 1642-1649, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, United States, 11/9/15. https://doi.org/10.1109/BIBM.2015.7359922

Kelton CJ, Lee W, Rusay M, Maxian O, Fertig EJ, Ochs MF. The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization. In Schapranow LM, Zhou J, Hu XT, Ma B, Rajasekaran S, Miyano S, Yoo I, Pierce B, Shehu A, Gombar VK, Chen B, Pai V, Huan J, editors, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc. 2015. p. 1642-1649. 7359922. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). doi: 10.1109/BIBM.2015.7359922

Kelton, Conor J. ; Lee, Waishing ; Rusay, Matthew et al. / The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization. Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. editor / lng. Matthieu Schapranow ; Jiayu Zhou ; Xiaohua Tony Hu ; Bin Ma ; Sanguthevar Rajasekaran ; Satoru Miyano ; Illhoi Yoo ; Brian Pierce ; Amarda Shehu ; Vijay K. Gombar ; Brian Chen ; Vinay Pai ; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. pp. 1642-1649 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

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abstract = "Nonnegative matrix factorization and other decomposition methods have proven to offer significant advantages for the interpretation of genome-wide gene expression data. However, unlike analytic methods, they suffer from instability in the inferred factors or patterns as the dimensionality is changed. We present here two statistics, one mathematical and one biological, that estimate the dimensionality. We show that they provide close though not identical estimates, and that they provide strong evidence for elimination of some potential factorizations.",

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AU - Ochs, Michael F.

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The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization

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