Noniterative convex optimization methods for network component analysis

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 5, 2012, Pages 1472-1481

  Jacklin, Neil ^a   Ding, Zhi ^a   Chen, Wei ^b   Chang, Chunqi ^c  

^a University of California Davis   (United States)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

^c UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

bilinear model; network component analysis; total least squares; Transcriptional network reconstruction

Indexed keywords

BILINEAR MODELS; ERROR METRICS; ESTIMATION PROCEDURES; GENE EXPRESSION DATA; GENE REGULATORY NETWORKS; NETWORK COMPONENT ANALYSIS; NETWORK CONNECTIVITY; NON-ITERATIVE; OPTIMIZATION METHOD; ORDERS OF MAGNITUDE; SIMULATED DATA; SOURCE ESTIMATION; STRENGTH ESTIMATION; SUBSPACE BASED METHODS; TOTAL LEAST SQUARES; TRANSCRIPTIONAL NETWORKS; WORK STUDY; YEAST SACCHAROMYCES CEREVISIAE;

ALGORITHMS; COMPRESSIVE STRENGTH; CONVEX OPTIMIZATION; ESTIMATION; GENES; LEAST SQUARES APPROXIMATIONS; STATISTICAL TESTS; TRANSCRIPTION FACTORS; YEAST;

NETWORK COMPONENTS;

TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; METHODOLOGY; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; GENE EXPRESSION PROFILING; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION FACTORS;

EID: 84864955664     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2012.81     Document Type: Article

References (35)

1. M.A. Savageau, Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology. Addison-Wesley, 1976.
2. D.M. Rocke and B. Durbin, "A Model for Measurement Error for Gene Expression Arrays," J. Computational Biology, vol. 8, no. 6, pp. 557-569, 2001. (Pubitemid 34053496)
3. X. Liu, M. Milo, N.D. Lawrence, and M. Rattray, "Probe-Level Measurement Error Improves Acuracy in Detecting Differential Gene Expression," Bioinformatics, vol. 22, no. 7, pp. 2107-2113, 2006. (Pubitemid 44390901)
4. J. Yao, C. Chang, M. Salmi, Y. Hung, A. Loraine, and S. Roux, "Genome-Scale Cluster Analysis of Replicated Microarrays Using Shrinkage Correlation Coefficient," BMC Bioinformatics, vol. 9, article 288, 2008.
5. C. Chang, Y. Hung, and M. Niranjan, "Modelling Uncertainty in Transcriptome Measurements Enhances Network Component Analysis of Yeast Metabolic Cycle," Proc. IEEE Int'l Conf. Acoustics, Speech and Signal Processing (ICASSP '09), pp. 1769-1772, 2009.
6. J.C. Liao, R. Boscolo, Y.L. Yang, L.M. Tran, C. Sabatti, and V.P. Roychowdhury, "Network Component Analysis: Reconstruction of Regulatory Signals in Biological Systems," Proc. Nat'l Academy of Sciences USA, vol. 100, no. 26, pp. 15522-15527, 2003. (Pubitemid 38021022)
7. T.D. Moloshok, R.R. Klevecz, J.D. Grant, F.J. Manion, W.F. Speier IV, and M.F. Ochs, "Application of Bayesian Decomposition for Analysing Microarray Data," Bioinformatics, vol. 18, no. 4, pp. 566-575, 2002. (Pubitemid 34521046)
8. A.V. Kossenkov and M.F. Ochs, "Matrix Factorization Methods Applied in Microarray Data Analysis," Int'l J. Data Mining and Bioinformatics, vol. 4, no. 1, pp. 72-90, 2010.
9. D.P. Kroese, T. Taimre, and Z.I. Botev, Handbook of Monte Carlo Methods. John Wiley and Sons, 2011.
10. B.C. Levy, Principles of Signal Detection and Parameter Estimation. Springer Science+Business Media, 2008.
11. C.Q. Chang, Y.S. Hung, and Z. Ding, "A New Optimization Algorithm for Network Component Analysis Based on Convex Programming," Proc. IEEE Int'l Conf. Audio Speech and Signal Processing, Mar. 2009.
12. J. Dai, C. Chang, Z. Ye, and Y. Hung, "An Efficient Convex Nonnegative Network Component Analysis for Gene Regulatory Network Reconstruction," Pattern Recognition in Bioinformatics, V. Kadirkamanathan, G. Sanguinetti, M. Girolami, M. Niranjan, and J. Noirel, eds., vol. 5780, pp. 56-66, Springer, 2009.
13. P.T. Spellman, G. Sherlock, M.Q. Zhang, V.R. Iyer, K. Anders, M.B. Eisen, P.O. Brown, D. Botstein, and B. Futcher, "Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces Cerevisiae by Microarray Hybridization," Molecular Biology of the Cell, vol. 9, no. 12, pp. 3273-3297, 1998. (Pubitemid 28551928)
14. C.Q. Chang, Z. Ding, Y.S. Hung, and P.C.W. Fung, "Fast Network Component Analysis (FastNCA) for Gene Regulatory Network Reconstruction from Microarray Data," Bioinformatics, vol. 24, no. 11, pp. 1349-1358, 2008. (Pubitemid 351737140)
15. W. Liebermeister, "Linear Modes of Gene Expression Determined by Independent Component Analysis," Bioinformatics, vol. 18, no. 1, pp. 51-60, 2002. (Pubitemid 34145031)
16. S.I. Lee and S. Batzoglou, "Application of Independent Component Analysis to Microarrays," Genome Biology, vol. 4, no. 11, p. R76, 2003.
17. O. Alter, P.O. Brown, and D. Botstein, "Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling," Proc. Nat'l Academy of Sciences USA, vol. 97, no. 18, pp. 10101-10106, 2000.
18. O. Alter and G.H. Golub, "Reconstructing the Pathways of a Cellular System from Genome-Scale Signals by Using Matrix and Tensor Computations," Proc. Nat'l Academy of Science USA, vol. 102, no. 49, pp. 17559-17564, 2005. (Pubitemid 41803536)
19. L. Omberg, G.H. Golub, and O. Alter, "A Tensor Higher-Order Singular Value Decomposition for Integrative Analysis of DNA Microarray Data from Different Studies," Proc. Nat'l Academy of Sciences USA, vol. 104, no. 47, pp. 18371-18376, 2007. (Pubitemid 350210703)
20. M. Yeung, J. Tegner, and J. Collins, "Reverse Engineering Gene Networks Using Singular Value Decomposition and Robust Regression," Proc. Nat'l Academy of Sciences USA, vol. 99, no. 9, pp. 6163-6168, 2002. (Pubitemid 34493283)
21. T.W. Yu and K.C. Li, "Inference of Transcriptional Regulatory Network by Two-Stage Constrained Space Factor Analysis," Bioinformatics, vol. 21, no. 21, pp. 4033-4038, 2005.
22. C. Sabatti and G.M. James, "Bayesian Sparse Hidden Components Analysis for Transcription Regulation Networks," Bioinformatics, vol. 22, no. 6, pp. 739-746, 2006.
23. H. Li, Y. Sun, and M. Zhan, "The Discovery of Transcriptional Modules by a Two-Stage Matrix Decomposition Approach," Bioinformatics, vol. 23, no. 4, pp. 473-479, 2007. (Pubitemid 46323128)
24. F. Abrard and Y. Deville, "Blind Separation of Dependent Sources Using the "Time-Frequency Ratio of Mixtures" Approach," Proc. Seventh Int'l Symp. Signal Processing and Its Applications, pp. 81-84, July 2003.
25. C.Q. Chang, J. Ren, P. Fung, Y. Hung, J. Shen, and F. Chan, "Novel Sparse Component Analysis Approach to Free Radical EPR Spectra Decomposition," J. Magnetic Resonance, vol. 175, no. 2, pp. 242-255, 2005. (Pubitemid 40891680)
26. T.I. Lee, N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Gerber, N.M. Hannett, C.T. Harbison, C.M. Thompson, I. Simon, J. Zeitlinger, E.G. Jennings, H.L. Murray, D.B. Gordon, B. Ren, J.J. Wyrick, J.B. Tagne, T.L. Volkert, E. Fraenkel, D.K. Gifford, and R.A. Young, "Transcriptional Regulatory Networks in Sacchar-omyces Cerevisiae," Science, vol. 298, no. 5594, pp. 799-804, 2002. (Pubitemid 35231527)
27. J. Bobin, Y. Moudden, J.-L. Starck, and M. Elad, "Morphological Diversity and Source Separation," IEEE Signal Processing Letters, vol. 13, no. 7, pp. 409-412, July 2006. (Pubitemid 43997199)
28. J. Bobin, Y. Moudden, J.-L. Starck, and J. Fadili, "Sparsity and Morphological Diversity for Hyperspectral Data Analysis," Proc. IEEE 16th Int'l Conf. Image Processing (ICIP), pp. 1481-1484, Nov. 2009.
29. I. Markovsky and M. Niranjan, "Approximate Low-Rank Factorization with Structured Factors," Computation Statistics and Data Analysis, vol. 54, pp. 3411-3420, 2010.
30. C. Wang, J. Xuan, L. Chen, P. Zhao, Y. Wang, R. Clarke, and E. Hoffman, "Motif-Directed Network Component Analysis for Regulatory Network Inference," BMC Bioinformatics, vol. 9, Suppl 1, article S21, 2008.
31. L.M. Tran, M.P. Brynildsen, K.C. Kao, J.K. Suen, and J.C. Liao, "gNCA: A Framework for Determining Transcription Factor Activity Based on Transcriptome: Identifiability and Numerical Implementation," Metabolic Eng., vol. 7, no. 2, pp. 128-141, 2005. (Pubitemid 40387560)
32. C.Q. Chang, Z. Ding, Y.S. Hung, and P.C.W. Fung, "Fast Network Component Analysis for Gene Regulation Networks," Proc. IEEE Int'l Workshop Machine Learning for Signal Processing, Aug. 2007.
33. Optimization Toolbox User's Guide, Version 5.1, Mathworks, http://www.mathworks.com/help/toolbox/optim/, 2010.
34. G.H. Golub and C.F. Van Loan, "An Analysis of the Total Least Squares Problem," SIAM J. Numerical Analysis, vol. 17, no. 6, pp. 883-893, Dec. 1980.
35. S.V. Huffel and J. Vandewalle, The Total Least Squares Problem: Computational Aspects and Analysis. SIAM Publications, 1991.