PDF
(360KB)
Abstract
Background: Since biological systems are complex and often involve multiple types of genomic relationships, tensor analysis methods can be utilized to elucidate these hidden complex relationships. There is a pressing need for this, as the interpretation of the results of high-throughput experiments has advanced at a much slower pace than the accumulation of data.
Results: In this review we provide an overview of some tensor analysis methods for biological systems.
Conclusions: Tensors are natural and powerful generalizations of vectors and matrices to higher dimensions and play a fundamental role in physics, mathematics and many other areas. Tensor analysis methods can be used to provide the foundations of systematic approaches to distinguish significant higher order correlations among the elements of a complex systems via finding ensembles of a small number of reduced systems that provide a concise and representative summary of these correlations.
Keywords
biological systems
/
tensor analysis
/
biological and statistical validation
Cite this article
Download citation ▾
Farzane Yahyanejad, Réka Albert, Bhaskar DasGupta.
A survey of some tensor analysis techniques for biological systems.
Quant. Biol., 2019, 7(4): 266-277 DOI:10.1007/s40484-019-0186-5
| [1] |
DasGupta, B. and Liang, J. (2016) Models and Algorithms for Biomolecules and Molecular Networks. John Wiley and Sons, Inc.
|
| [2] |
Alter, O. and Golub, G. H. (2005) Reconstructing the pathways of a cellular system from genome-scale signals by using matrix and tensor computations. Proc. Natl. Acad. Sci. USA, 102, 17559–17564
|
| [3] |
Dyrby, M., Baunsgaard, D., Bro, R. and Engelsen, S. B. (2005) Multiway chemometric analysis of the metabolic response to toxins monitored by NMR. Chemom. Intell. Lab. Syst., 76, 79–89
|
| [4] |
Hore, V., Viñuela, A., Buil, A., Knight, J., McCarthy, M. I., Small, K. and Marchini, J. (2016) Tensor decomposition for multiple-tissue gene expression experiments. Nat. Genet., 48, 1094–1100
|
| [5] |
Omberg, L., Golub, G. H. and Alter, O. (2007) A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies. Proc. Natl. Acad. Sci. USA, 104, 18371–18376
|
| [6] |
Yener, B., Acar, E., Aguis, P., Bennett, K., Vandenberg, S. L. and Plopper, G. E. (2008) Multiway modeling and analysis in stem cell systems biology. BMC Syst. Biol., 2, 63
|
| [7] |
Harshman, R. A. (1970) Foundations of the PARAFAC procedure: Models and conditions for an “explanatory” multi-modal factor analysis. UCLA Working Papers in Phonetics, 16, 1–84
|
| [8] |
Miwakeichi, F., Martínez-Montes, E., Valdés-Sosa, P. A., Nishiyama, N., Mizuhara, H. and Yamaguchi, Y. (2004) Decomposing EEG data into space-time-frequency components using Parallel Factor Analysis. Neuroimage, 22, 1035–1045
|
| [9] |
Mørup. M. (2011) Applications of tensor (multiway array) factorizations and decompositions in data mining. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, 1, 24–40
|
| [10] |
Mørup, M., Hansen, L. K. and Arnfred, S. M. (2007) ERPWAVELAB a toolbox for multi-channel analysis of time-frequency transformed event related potentials. J. Neurosci. Methods, 161, 361–368
|
| [11] |
Carroll, J. D. and Chang, J. J. (1970) Analysis of individual differences in multidimensional scaling via an N-way generalization of “Eckart-Young” decomposition. Psychometrika, 35, 283–319
|
| [12] |
Kroonenberg, P. M. (2008) Applied Multiway Data Analysis. John Wiley & Sons
|
| [13] |
Murakami, T. and Kroonenberg, P. M. (2003) Three-mode models and individual differences in semantic differential data. Multivariate Behav. Res., 38, 247–283
|
| [14] |
Appellof, C. J. and Davidson, E. R. (1981) Strategies for analyzing data from video fluorometric monitoring of liquid chromatographic effluents. Anal. Chem., 53, 2053–2056
|
| [15] |
Kolda, T. G. and Bader, B. W. (2009) Tensor decompositions and applications. SIAM Rev., 51, 455–500
|
| [16] |
De Lathauwer, L., De Moor, B. and Vandewalle, J. (2000) A multilinear singular value decomposition. SIAM J. Matrix Anal. Appl., 21, 1253–1278
|
| [17] |
Miettinen, P. (2011) Boolean tensor factorizations. In: 11th IEEE International Conference on Data Mining, 447–456
|
| [18] |
Kiers, H. A. L. (2000) Towards a standardized notation and terminology in multiway analysis. J. Chemometr., 14, 105–122
|
| [19] |
Golub, G. H. and Van Loan, C. F. (1996) Matrix Computations, 3rd edition. The Johns Hopkins University Press
|
| [20] |
Kruskal, J. B. (1977) Three-way arrays: Rank and uniqueness of trilinear decompositions, with application to arithmetic complexity and statistics. Linear Algebra Appl., 18, 95–138
|
| [21] |
Kruskal, J. B. (1989) Rank, decomposition, and uniqueness for 3-way and N-way arrays. In: Multiway Data Analysis, Coppi, R. and Bolasco, S. (Eds.), pp. 7–18. North-Holland, Amsterdam
|
| [22] |
Levin, J. (1963) Three-Mode Factor Analysis. Dissertation for the Doctoral Degree, University of Illinois, Urbana
|
| [23] |
Tucker, L. R. (1963) Implications of factor analysis of three-way matrices for measurement of change. In: Problems in Measuring Change, Harris, C. W. (ed.), University of Wisconsin Press, 122–137
|
| [24] |
Tucker, L. R. (1964) The extension of factor analysis to three-dimensional matrices. In: Contributions to Mathematical Psychology, Gulliksen, H. and Frederiksen, N. (eds.), Holt, Rinehardt & Winston, New York, 110–127
|
| [25] |
Tucker, L. R. (1966) Some mathematical notes on three-mode factor analysis. Psychometrika, 31, 279–311
|
| [26] |
Kroonenberg, P. M. and De Leeuw, J. (1980) Principal component analysis of three-mode data by means of alternating least squares algorithms. Psychometrika, 45, 69–97
|
| [27] |
Håstad , H. (1990) Tensor rank is NP-complete. J. Algorithms, 11, 644–654
|
| [28] |
Hillar, C. J. and Lim, L.-H. (2013) Most tensor problems are NP-hard J. ACM, 60, 45:1–45:38
|
| [29] |
Barak, B., Kelner, J. A. and Steurer, D. (2015) Dictionary learning and tensor decomposition via the sum-of-squares method. In: Proceedings of the 47th ACM Symposium on Theory of Computing, pp. 143–151
|
| [30] |
Barak, B. and Moitra, A. (2016) Noisy tensor completion via the sum-of-squares hierarchy. In: Proceedings of Machine Learning Research, 49, 417–445
|
| [31] |
Ge, R. and Ma, T. (2015) Decomposing overcomplete 3rd order tensors using sum-of-squares algorithms. In: Proceedings of the 18th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, pp. 829–849
|
| [32] |
Hopkins, S. B., Shi, J. and Steurer, D. (2015) Tensor principal component analysis via sum-of-square proofs. Proceedings of Machine Learning Research, 40, 956–1006
|
| [33] |
Ma, T., Shi, J. and Steurer, D. (2016) Polynomial-time tensor decompositions with sum-of-squares. In: Proceedings of the 57th Annual IEEE Symposium on Foundations of Computer Science, pp. 438–446
|
| [34] |
Potechin, A. and Steurer, D. (2017) Exact tensor completion with sum-of-squares. In: Proceedings of Machine Learning Research, 65, 1–54
|
| [35] |
Barak, B. and Steurer, D. (2014) Sum-of-squares proofs and the quest toward optimal algorithms. In: Proceedings of International Congress of Mathematicians
|
| [36] |
Laurent, M. (2009) Sums of Squares, Moment Matrices and Optimization Over Polynomials. In: Emerging Applications of Algebraic Geometry, The IMA Volumes in Mathematics and its Applications, Putinar M. and Sullivant S., (eds.), 149, 157–270
|
| [37] |
Papadimitriou, C. H. and Steiglitz, K. (1988) Combinatorial Optimization: Algorithms and Complexity. Dover Publications
|
| [38] |
Sun, J., Tao, D. and Faloutsos, C. (2006) Beyond Streams and Graphs: Dynamic Tensor Analysis. In: Proceedings of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 374–383
|
| [39] |
Chelliah, V., Juty, N., Ajmera, I., Ali, R., Dumousseau, M., Glont, M., Hucka, M., Jalowicki, G., Keating, S., Knight-Schrijver, V., (2015) BioModels: ten-year anniversary. Nucleic Acids Res., 43, D542–D548
|
| [40] |
Helikar, T., Kowal, B., McClenathan, S., Bruckner, M., Rowley, T., Madrahimov, A., Wicks, B., Shrestha, M., Limbu, K. and Rogers, J. A. (2012) The Cell Collective: toward an open and collaborative approach to systems biology. BMC Syst. Biol., 6, 96
|
| [41] |
Chaouiya, C., Naldi, A. and Thieffry, D. (2012) Logical modelling of gene regulatory networks with GINsim. Methods Mol. Biol., 804, 463–479
|
| [42] |
Kolesnikov, N., Hastings, E., Keays, M., Melnichuk, O., Tang, Y. A., Williams, E., Dylag, M., Kurbatova, N., Brandizi, M., Burdett, T., (2015) ArrayExpress update—simplifying data submissions. Nucleic Acids Res., 43, D1113–D1116
|
| [43] |
Cho, R. J., Campbell, M. J., Winzeler, E. A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T. G., Gabrielian, A. E., Landsman, D., Lockhart, D. J., (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65–73
|
| [44] |
Li, S., Assmann, S. M. and Albert, R. (2006) Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. PLoS Biol., 4, e312
|
| [45] |
Sun, Z., Jin, X., Albert, R. and Assmann, S. M. (2014) Multi-level modeling of light-induced stomatal opening offers new insights into its regulation by drought. PLOS Comput. Biol., 10, e1003930
|
| [46] |
Kannan, R., Tetali, P. and Vempala, S. (1999) Markov-chain algorithms for generating bipartite graphs and tournaments. Random Struct. Algor., 14, 293–308
|
| [47] |
Girvan, M. and Newman, M. E. J. (2002) Community structure in social and biological networks. Proc. Natl. Acad. Sci. USA, 99, 7821–7826
|
| [48] |
Leicht, E. A. and Newman, M. E. J. (2008) Community structure in directed networks. Phys. Rev. Lett., 100, 118703
|
| [49] |
Newman, M. E. J. (2004) Fast algorithm for detecting community structure in networks. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 69, 066133
|
| [50] |
Newman, M. E. J. (2003) The structure and function of complex networks. SIAM Rev., 45, 167–256
|
| [51] |
Newman, M. E. J. and Girvan, M. (2004) Finding and evaluating community structure in networks. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 69, 026113
|
| [52] |
Meijer, E. (2005) Matrix algebra for higher order moments. Linear Algebra Appl., 410, 112–134
|
| [53] |
Mendes, P. (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci., 22, 361–363
|
| [54] |
Larsen, R. J. and Marx, M. L. (2000) An Introduction to Mathematical Statistics and Its Applications. Third Edition, Pearson Education
|
| [55] |
Anandkumar, A., Ge, R., Hsu, D., Kakade, S. M. and Telgarsky, M. (2014) Tensor decompositions for learning latent variable models. J. Mach. Learn. Res., 15, 2773–2832
|
| [56] |
Bhaskara, A., Charikar, M., Moitra, A. and Vijayaraghavan, A. (2014) Smoothed analysis of tensor decompositions. In: Proceedings of the 46th Annual ACM Symposium on Theory of Computing, 594–603
|
| [57] |
Goyal, N., Vempala, S. and Xiao, Y. (2014) Fourier PCA and robust tensor decomposition. In: Proceedings of the 46th Annual ACM Symposium on Theory of Computing, 584–593
|
| [58] |
Spielman, D. A. and Teng, S. H. (2004) Smoothed analysis of algorithms: Why the simplex algorithm usually takes polynomial time. J. Assoc. Comput. Mach., 51, 385–463
|
| [59] |
Spielman, D. A. and Teng, S. H. (2009) Smoothed Analysis: An Attempt to Explain the Behavior of Algorithms in Practice. Commun. ACM, 52, 76–84
|
| [60] |
Albert, R., DasGupta, B., Hegde, R., Sivanathan, G. S., Gitter, A., G�rsoy, G., Paul, P. and Sontag, E. (2011) Computationally efficient measure of topological redundancy of biological and social networks. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 84, 036117
|
| [61] |
Albert, R., DasGupta, B. and Mobasheri, N. (2014) Topological implications of negative curvature for biological and social networks. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 89, 032811
|
| [62] |
Comon, P. (2004) Canonical Tensor Decompositions. Research report ISRN I3S/RR-2004-17-FR
|
| [63] |
Comon, P. and Mourrain, B. (1996) Decomposition of quantics in sums of powers of linear forms. Signal Processing, 53, 93–107
|
| [64] |
Anandkumar, A., Hsu, D. and Kakade, S. M. (2012) A method of moments for mixture models and hidden markov models. In: Proceedings of the Conference on Learning Theory, 33.1–33.34
|
| [65] |
Qi, L. (2007) Eigenvalues and invariants of tensors. J. Math. Anal. Appl., 325, 1363–1377
|
| [66] |
Reiss, D. J., Baliga, N. S. and Bonneau, R. (2006) Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics, 7, 280
|
RIGHTS & PERMISSIONS
Higher Education Press and Springer-Verlag GmbH Germany, part of Springer Nature