|
|
Reconstruction of dynamic structures of experimental setups based on measurable experimental data only |
Tian-Yu Chen(陈天宇)1, Yang Chen(陈阳)1, Hu-Jiang Yang(杨胡江)1, Jing-Hua Xiao(肖井华)1, Gang Hu(胡岗)2 |
1 School of Science, Beijing University of Posts and Telecommunications, Beijing 100876, China;
2 Department of Physics, Beijing Normal University, Beijing 100875, China |
|
|
Abstract Nowadays, massive amounts of data have been accumulated in various and wide fields, it has become today one of the central issues in interdisciplinary fields to analyze existing data and extract as much useful information as possible from data. It is often that the output data of systems are measurable while dynamic structures producing these data are hidden, and thus studies to reveal system structures by analyzing available data, i.e., reconstructions of systems become one of the most important tasks of information extractions. In the past, most of the works in this respect were based on theoretical analyses and numerical verifications. Direct analyses of experimental data are very rare. In physical science, most of the analyses of experimental setups were based on the first principles of physics laws, i.e., so-called top-down analyses. In this paper, we conducted an experiment of “Boer resonant instrument for forced vibration” (BRIFV) and inferred the dynamic structure of the experimental set purely from the analysis of the measurable experimental data, i.e., by applying the bottom-up strategy. Dynamics of the experimental set is strongly nonlinear and chaotic, and it's subjects to inevitable noises. We proposed to use high-order correlation computations to treat nonlinear dynamics; use two-time correlations to treat noise effects. By applying these approaches, we have successfully reconstructed the structure of the experimental setup, and the dynamic system reconstructed with the measured data reproduces good experimental results in a wide range of parameters.
|
Received: 30 November 2017
Revised: 04 January 2018
Accepted manuscript online:
|
PACS:
|
05.45.Tp
|
(Time series analysis)
|
|
05.45.-a
|
(Nonlinear dynamics and chaos)
|
|
Corresponding Authors:
Jing-Hua Xiao, Gang Hu
E-mail: jhxiao@bupt.edu.cn;ganghu@bnu.edu.cn
|
Cite this article:
Tian-Yu Chen(陈天宇), Yang Chen(陈阳), Hu-Jiang Yang(杨胡江), Jing-Hua Xiao(肖井华), Gang Hu(胡岗) Reconstruction of dynamic structures of experimental setups based on measurable experimental data only 2018 Chin. Phys. B 27 030503
|
[1] |
Butte A J, Tamayo P, Slonim D, Golub T R and Kohane I S 2000 Proc. Natl. Acad. Sci. 97 12182
|
[2] |
Kim S K, Lund J, Kiraly M, Duke K, Jiang M, Stuart J M, Eizinger A, Wylie B N and Davidson G S 2001 Science 293 2087
|
[3] |
Bar-Joseph Z, Gerber G K, Lee T I, Rinaldi N J, Yoo J Y, Robert F, Gordon D B, Fraenkel E, Jaakkola T S, Young R A and Gifford D K 2003 Nat. Biotechnol. 21 1337
|
[4] |
Bar-Joseph Z, Gitter A and Simon I 2012 Nat. Rev. Genet. 13 552
|
[5] |
Feist A M, Herrgard M J, Thiele I, Reed J L and Palsson B O 2009 Nat. Rev. Microbiol. 7 129
|
[6] |
De Smet R and Marchal K 2010 Nat. Rev. Microbiol. 8 717
|
[7] |
Yeung M S, Tegnér J and Collins J J 2002 Proc. Natl. Acad. Sci. 99 6163
|
[8] |
Stuart J M, Segal E, Koller D and Kim S K 2003 Science 302 249
|
[9] |
Segal E, Shapira M, Regev A, Peér D, Botstein D, Koller D and Friedman N 2003 Nat. Genet. 34 166
|
[10] |
Hu Z, Killion P J and Iyer V R 2007 Nat. Genet. 39 683
|
[11] |
Lezon T R, Banavar J R, Cieplak M, Maritan A and Fedoroff N V 2006 Proc. Natl. Acad. Sci. 103 19033
|
[12] |
Barzel B and Barabási A L 2013 Nat. Biotechnol. 31 720
|
[13] |
Feizi S, Marbach D, Médard M and Kellis M 2013 Nat. Biotechnol. 31 726
|
[14] |
Marbach D, Prill R J, Schaffter T, Mattiussi C, Floreano D and Stolovitzky G 2010 Proc. Natl. Acad. Sci. 107 6286
|
[15] |
Marbach D, Costello J C, Küffner R, Vega N M, Prill R J, Camacho D M, Allison K R, The DREAM5 Consortium, Kellis M, Collins J J and Stolovitzky G 2012 Nat. Methods 9 796
|
[16] |
Bullmore E and Sporns O 2009 Nat. Rev. Neurosci. 10 186
|
[17] |
Burioni R, Casartelli M, Di Volo M, Livi R and Vezzani A 2014 Sci. Rep. 4 4336
|
[18] |
Sugihara G, May R, Ye H, Hsieh C H, Deyle E, Fogarty M and Munch S 2012 Science 338 496
|
[19] |
Glass L and Mackey M C 1988 From Clocks to Chaos:the Rhythms of Life (Princeton:Princeton University Press)
|
[20] |
Goldbeter A and Tyson J J 1996 Nature 380 213
|
[21] |
Alon U 2006 An introduction to Systems Biology:Design Principles of Biological Circuits (Boca Raton:CRC Press)
|
[22] |
Tsai T Y C, Choi Y S, Ma W, Pomerening J R, Tang C and Ferrell J E 2008 Science 321 126
|
[23] |
Basso K, Margolin A A, Stolovitzky G, Klein U, Dalla-Favera R and Califano A 2005 Nat. Genet. 37 382
|
[24] |
Bansal M, Belcastro V, Ambesi-Impiombato A and Di Bernardo D 2007 Mol. Syst. Biol. 3 78
|
[25] |
Villaverde A F, Ross J and Banga J R 2013 Cells 2 306
|
[26] |
Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan N J, Chung S B, Emili A, Snyder M, Greenblatt J F and Gerstein M 2003 Science 302 449
|
[27] |
Hao C Q, Wang J, Deng B and Wei X L 2012 Acta Phys. Sin. 61 130507 (in Chinese)
|
[28] |
Friedman N 2004 Science 303 799
|
[29] |
Gardner T S, Di Bernardo D, Lorenz D and Collins J J 2003 Science 301 102
|
[30] |
Eisen M B, Spellman P T, Brown P O and Botstein D 1998 Proc. Natl. Acad. Sci. 95 14863
|
[31] |
Faith J J, Hayete B, Thaden J T, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins J J and Gardner T S 2007 PLoS Biol. 5 e8
|
[32] |
Wang W X, Chen Q, Huang L, Lai Y C and Harrison M A F 2009 Phys. Rev. E 80 16116
|
[33] |
Ren J, Wang W X, Li B and Lai Y C 2010 Phys. Rev. Lett. 104 58701
|
[34] |
Ching E S, Lai P Y and Leung C Y 2013 Phys. Rev. E 88 42817
|
[35] |
Miao C, Luo W, Ma Y, Liu W and Xiao J 2014 Eur. J. Phys. 35 55012
|
[36] |
Stavrou D, Assimopoulos S and Skordoulis C 2013 Phys. Educ. 48 355
|
[37] |
Peters R D 1995 Am. J. Phys. 63 1128
|
[38] |
Berger J E and Nunes Jr G 1997 Am. J. Phys. 65 841
|
[39] |
Roal'd Zinnurovich Sagdeev, Daniel'Alekseevich Usikov and Zaslavskii G M 1990 Harwood Academic
|
[40] |
Tropp J A and Gilbert A C 2007 IEEE Trans. Inf. Theory 53 4655
|
[41] |
Pati Y C, Rezaiifar R and Krishnaprasad P S 1993 Conference Record of The Twenty-Seventh Asilomar Conference on Signals, Systems and Computers, November 1-3, 1993, Pacific Grove, CA, USA, p. 4846193
|
[42] |
Davis G, Mallat S and Avellaneda M 1997 Constr. Approx. 13 57
|
[43] |
Chen Y, Zhang Z Y, Chen T Y, Wang S S and Hu G 2017 Sci. Rep. 7 44639
|
No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
Altmetric
|
blogs
Facebook pages
Wikipedia page
Google+ users
|
Online attention
Altmetric calculates a score based on the online attention an article receives. Each coloured thread in the circle represents a different type of online attention. The number in the centre is the Altmetric score. Social media and mainstream news media are the main sources that calculate the score. Reference managers such as Mendeley are also tracked but do not contribute to the score. Older articles often score higher because they have had more time to get noticed. To account for this, Altmetric has included the context data for other articles of a similar age.
View more on Altmetrics
|
|
|