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Volumn 14, Issue 127, 2017, Pages

Fundamental limitations of network reconstruction from temporal data

Author keywords

Network reconstruction; Networked systems; System identification

Indexed keywords

BIOPHYSICS; BIOTECHNOLOGY; IDENTIFICATION (CONTROL SYSTEMS);

EID: 85015180773     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2016.0966     Document Type: Article
Times cited : (61)

References (46)
  • 1
    • 84889682976 scopus 로고    scopus 로고
    • Cambridge, UK: Cambridge University Press
    • Barabási A-L. 2016 Network science. Cambridge, UK: Cambridge University Press.
    • (2016) Network Science
    • Barabási, A.-L.1
  • 2
    • 0038718854 scopus 로고    scopus 로고
    • The structure and function of complex networks
    • Newman ME. 2003 The structure and function of complex networks. SIAM Rev. 45, 167-256. (doi:10.1137/S003614450342480)
    • (2003) SIAM Rev , vol.45 , pp. 167-256
    • Newman, M.E.1
  • 3
  • 4
    • 0035794256 scopus 로고    scopus 로고
    • Epidemic spreading in scale-free networks
    • Pastor-Satorras R, Vespignani A. 2001 Epidemic spreading in scale-free networks. Phys. Rev. Lett. 86, 3200-3203. (doi:10.1103/PhysRevLett.86.3200)
    • (2001) Phys. Rev. Lett , vol.86 , pp. 3200-3203
    • Pastor-Satorras, R.1    Vespignani, A.2
  • 5
    • 0034323311 scopus 로고    scopus 로고
    • Resilience of the internet to random breakdowns
    • Cohen R, Erez K, ben Avraham D, Havlin S. 2000 Resilience of the internet to random breakdowns. Phys. Rev. Lett. 85, 4626-4628. (doi:10.1103/ PhysRevLett.85.4626)
    • (2000) Phys. Rev. Lett , vol.85 , pp. 4626-4628
    • Cohen, R.1    Erez, K.2    Ben Avraham, D.3    Havlin, S.4
  • 6
    • 0041707963 scopus 로고    scopus 로고
    • Heterogeneity in oscillator networks: Are smaller worlds easier to synchronize?
    • Nishikawa T, Motter AE, Lai Y-C, Hoppensteadt FC. 2003 Heterogeneity in oscillator networks: are smaller worlds easier to synchronize? Phys. Rev. Lett. 91, 014101. (doi:10.1103/PhysRevLett.91. 014101)
    • (2003) Phys. Rev. Lett , vol.91 , pp. 014101
    • Nishikawa, T.1    Motter, A.E.2    Lai, Y.-C.3    Hoppensteadt, F.C.4
  • 7
    • 12344327544 scopus 로고    scopus 로고
    • On partial contraction analysis for coupled nonlinear oscillators
    • Wang W, Slotine J-J. 2005 On partial contraction analysis for coupled nonlinear oscillators. Biol. Cybernetics 92, 38-53. (doi:10.1007/s00422- 004-0527-x)
    • (2005) Biol. Cybernetics , vol.92 , pp. 38-53
    • Wang, W.1    Slotine, J.-J.2
  • 8
    • 79955879494 scopus 로고    scopus 로고
    • Controllability of complex networks
    • Liu Y-Y, Slotine J-J, Barabási A-L. 2011 Controllability of complex networks. Nature 473, 167-173. (doi:10.1038/nature10011)
    • (2011) Nature , vol.473 , pp. 167-173
    • Liu, Y.-Y.1    Slotine, J.-J.2    Barabási, A.-L.3
  • 9
    • 84863449762 scopus 로고    scopus 로고
    • Controlling edge dynamics in complex networks
    • Nepusz T, Vicsek T. 2012 Controlling edge dynamics in complex networks. Nat. Phys. 8, 568-573. (doi:10.1038/nphys2327)
    • (2012) Nat. Phys , vol.8 , pp. 568-573
    • Nepusz, T.1    Vicsek, T.2
  • 11
    • 11244309139 scopus 로고    scopus 로고
    • Visualization of wormholes in sensor networks
    • Philadelphia, PA, 1 October 2004, New York, NY: ACM
    • Wang W, Bhargava B. 2004 Visualization of wormholes in sensor networks. In Proc. of the 3rd ACM Workshop on Wireless Security (WiSE '04), Philadelphia, PA, 1 October 2004, pp. 51-60. New York, NY: ACM.
    • (2004) Proc. of the 3rd ACM Workshop on Wireless Security (WiSE '04) , pp. 51-60
    • Wang, W.1    Bhargava, B.2
  • 12
    • 63849233446 scopus 로고    scopus 로고
    • Power grid vulnerability: A complex network approach
    • Arianos S, Bompard E, Carbone A, Xue F. 2009 Power grid vulnerability: a complex network approach. Chaos 19, 013119. (doi:10.1063/1. 3077229)
    • (2009) Chaos , vol.19 , pp. 013119
    • Arianos, S.1    Bompard, E.2    Carbone, A.3    Xue, F.4
  • 13
  • 14
    • 54249124501 scopus 로고    scopus 로고
    • Learning biological networks: From modules to dynamics
    • Bonneau R. 2008 Learning biological networks: from modules to dynamics. Nat. Chem. Biol. 4, 658-664. (doi:10.1038/nchembio.122)
    • (2008) Nat. Chem. Biol , vol.4 , pp. 658-664
    • Bonneau, R.1
  • 15
    • 0035656416 scopus 로고    scopus 로고
    • Milestones, network dynamics and cell physiology
    • Tyson JJ, Chen K, Novak B. 2001 Milestones, network dynamics and cell physiology. Nat. Rev. Mol. Cell Biol. 2, 908-916. (doi:10.1038/35103078)
    • (2001) Nat. Rev. Mol. Cell Biol , vol.2 , pp. 908-916
    • Tyson, J.J.1    Chen, K.2    Novak, B.3
  • 16
    • 77952884274 scopus 로고    scopus 로고
    • How antibiotics kill bacteria: From targets to networks
    • Kohanski MA, Dwyer DJ, Collins JJ. 2010 How antibiotics kill bacteria: from targets to networks. Nat. Rev. Microbiol. 8, 423-435. (doi:10.1038/ nrmicro2333)
    • (2010) Nat. Rev. Microbiol , vol.8 , pp. 423-435
    • Kohanski, M.A.1    Dwyer, D.J.2    Collins, J.J.3
  • 18
    • 84885420310 scopus 로고    scopus 로고
    • Universality in network dynamics
    • Barzel B, Barabási A-L. 2013 Universality in network dynamics. Nat. Phys. 9, 673-681. (doi:10.1038/ nphys2741)
    • (2013) Nat. Phys , vol.9 , pp. 673-681
    • Barzel, B.1    Barabási, A.-L.2
  • 21
    • 85015209247 scopus 로고
    • Qualitative stability in model ecosystems
    • May RM. 1973 Qualitative stability in model ecosystems. Ecology 638, 1389-1391.
    • (1973) Ecology , vol.638 , pp. 1389-1391
    • May, R.M.1
  • 22
    • 77949398351 scopus 로고    scopus 로고
    • Structural sources of robustness in biochemical reaction networks
    • Shinar G, Feinberg M. 2010 Structural sources of robustness in biochemical reaction networks. Science 327, 1389-1391. (doi:10.1126/science.1183372)
    • (2010) Science , vol.327 , pp. 1389-1391
    • Shinar, G.1    Feinberg, M.2
  • 23
    • 84896916869 scopus 로고    scopus 로고
    • Control profiles of complex networks
    • Ruths J, Ruths D. 2014 Control profiles of complex networks. Science (New York, NY) 343, 1373-1376. (doi:10.1126/science.1242063)
    • (2014) Science (New York, NY) , vol.343 , pp. 1373-1376
    • Ruths, J.1    Ruths, D.2
  • 24
    • 0035794256 scopus 로고    scopus 로고
    • Epidemic spreading in scale-free networks
    • Pastor-Satorras R, Vespignani A. 2001 Epidemic spreading in scale-free networks. Phys. Rev. Lett. 86, 3200-3203. (doi:10.1103/PhysRevLett.86.3200)
    • (2001) Phys. Rev. Lett , vol.86 , pp. 3200-3203
    • Pastor-Satorras, R.1    Vespignani, A.2
  • 25
    • 33750599827 scopus 로고    scopus 로고
    • Estimating topology of networks
    • Yu D, Righero M, Kocarev L. 2006 Estimating topology of networks. Phys. Rev. Lett. 97, 188701. (doi:10.1103/PhysRevLett.97.188701)
    • (2006) Phys. Rev. Lett , vol.97 , pp. 188701
    • Yu, D.1    Righero, M.2    Kocarev, L.3
  • 26
    • 80053292377 scopus 로고    scopus 로고
    • Inferring network connectivity by delayed feedback control
    • Yu D, Parlitz U. 2011 Inferring network connectivity by delayed feedback control. PLoS ONE 6, e24333. (doi:10.1371/journal.pone.0024333)
    • (2011) PLoS ONE , vol.6 , pp. e24333
    • Yu, D.1    Parlitz, U.2
  • 28
    • 70449529712 scopus 로고    scopus 로고
    • Reverse engineering and verification of gene networks: Principles, assumptions, and limitations of present methods and future perspectives
    • He F, Balling R, Zeng A-P. 2009 Reverse engineering and verification of gene networks: principles, assumptions, and limitations of present methods and future perspectives. J. Biotechnol. 144, 190-203. (doi:10.1016/j.jbiotec.2009.07.013)
    • (2009) J. Biotechnol , vol.144 , pp. 190-203
    • He, F.1    Balling, R.2    Zeng, A.-P.3
  • 31
    • 84891892050 scopus 로고    scopus 로고
    • Reverse engineering and identification in systems biology: Strategies, perspectives and challenges
    • Villaverde AF, Banga JR. 2014 Reverse engineering and identification in systems biology: strategies, perspectives and challenges. J. R. Soc. Interface 11, 20130505. (doi:10.1098/rsif.2013.0505)
    • (2014) J. R. Soc. Interface , vol.11 , pp. 20130505
    • Villaverde, A.F.1    Banga, J.R.2
  • 32
    • 84906535595 scopus 로고    scopus 로고
    • Revealing networks from dynamics: An introduction
    • Timme M, Casadiego J. 2014 Revealing networks from dynamics: an introduction. J. Phys. A Math. Theor. 47, 343001. (doi:10.1088/1751-8113/47/34/ 343001)
    • (2014) J. Phys. A Math. Theor , vol.47 , pp. 343001
    • Timme, M.1    Casadiego, J.2
  • 34
    • 0041627865 scopus 로고    scopus 로고
    • Influence of network topology and data collection on network inference
    • (eds RB Altman, AK Dunker, L Hunter, TA Jung, TE Klien), Singapore: World Scientific
    • Smith VA, Jarvis ED, Hartemink AJ. 2003 Influence of network topology and data collection on network inference. In Pacific symposium on biocomputing (eds RB Altman, AK Dunker, L Hunter, TA Jung, TE Klien), pp. 164-175. Singapore: World Scientific.
    • (2003) Pacific Symposium on Biocomputing , pp. 164-175
    • Smith, V.A.1    Jarvis, E.D.2    Hartemink, A.J.3
  • 35
    • 38349055557 scopus 로고    scopus 로고
    • Indeterminacy of reverse engineering of gene regulatory networks: The curse of gene elasticity
    • Krishnan A, Giuliani A, Tomita M. 2007 Indeterminacy of reverse engineering of gene regulatory networks: the curse of gene elasticity. PLoS ONE 2, e562. (doi:10. 1371/journal.pone.0000562)
    • (2007) PLoS ONE , vol.2 , pp. e562
    • Krishnan, A.1    Giuliani, A.2    Tomita, M.3
  • 36
    • 81555207959 scopus 로고    scopus 로고
    • Structural identifiability of systems biology models: A critical comparison of methods
    • Chis O-T, Banga JR, Balsa-Canto E. 2011 Structural identifiability of systems biology models: a critical comparison of methods. PLoS ONE 6, e27755. (doi:10.1371/journal.pone.0027755)
    • (2011) PLoS ONE , vol.6 , pp. e27755
    • Chis, O.-T.1    Banga, J.R.2    Balsa-Canto, E.3
  • 37
    • 43249126563 scopus 로고    scopus 로고
    • Identifiability of chemical reaction networks
    • Craciun G, Pantea C. 2008 Identifiability of chemical reaction networks. J. Math. Chem. 44, 244-259. (doi:10.1007/s10910-007-9307-x)
    • (2008) J. Math. Chem , vol.44 , pp. 244-259
    • Craciun, G.1    Pantea, C.2
  • 38
    • 84983300207 scopus 로고    scopus 로고
    • Network dynamics as an inverse problem
    • Berlin, Germany: Springer
    • Casadiego J, Timme M. 2015 Network dynamics as an inverse problem. In Mathematical technology of networks, pp. 39-48. Berlin, Germany: Springer.
    • (2015) Mathematical Technology of Networks , pp. 39-48
    • Casadiego, J.1    Timme, M.2
  • 39
    • 84855997910 scopus 로고    scopus 로고
    • Inference of complex biological networks: Distinguishability issues and optimization-based solutions
    • Szederkényi G, Banga JR, Alonso AA. 2011 Inference of complex biological networks: distinguishability issues and optimization-based solutions. BMC Syst. Biol. 5, 177. (doi:10.1186/1752-0509-5-177)
    • (2011) BMC Syst. Biol , vol.5 , pp. 177
    • Szederkényi, G.1    Banga, J.R.2    Alonso, A.A.3
  • 40
    • 0028441801 scopus 로고
    • Identifiability and distinguishability of general reaction systems
    • Vajda S, Rabitz H. 1994 Identifiability and distinguishability of general reaction systems. J. Phys. Chem. 98, 5265-5271. (doi:10.1021/ j100071a016)
    • (1994) J. Phys. Chem , vol.98 , pp. 5265-5271
    • Vajda, S.1    Rabitz, H.2
  • 41
    • 0010178122 scopus 로고
    • Some connections between the theory of sufficient statistics and the identifiability problem
    • Picci G. 1977 Some connections between the theory of sufficient statistics and the identifiability problem. SIAM J. Appl. Math. 33, 383-398. (doi:10. 1137/0133025)
    • (1977) SIAM J. Appl. Math , vol.33 , pp. 383-398
    • Picci, G.1
  • 42
    • 67650760503 scopus 로고    scopus 로고
    • Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
    • Raue A, Kreutz C, Maiwald T, Bachmann J, Schilling M, Klingmüller U, Timmer J. 2009 Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics 25, 1923-1929. (doi:10. 1093/bioinformatics/btp358)
    • (2009) Bioinformatics , vol.25 , pp. 1923-1929
    • Raue, A.1    Kreutz, C.2    Maiwald, T.3    Bachmann, J.4    Schilling, M.5    Klingmüller, U.6    Timmer, J.7
  • 43
    • 52249116064 scopus 로고    scopus 로고
    • Necessary and sufficient conditions for dynamical structure reconstruction of LTI networks
    • Gonçalves J, Warnick S. 2008 Necessary and sufficient conditions for dynamical structure reconstruction of LTI networks. IEEE Trans. Automat. Contr. 53, 1670-1674. (doi:10.1109/TAC.2008. 928114)
    • (2008) IEEE Trans. Automat. Contr , vol.53 , pp. 1670-1674
    • Gonçalves, J.1    Warnick, S.2
  • 45
    • 37849021822 scopus 로고    scopus 로고
    • Optimal experimental design and some related control problems
    • Pronzato L. 2008 Optimal experimental design and some related control problems. Automatica 44, 303-325. (doi:10.1016/j.automatica.2007.05.016)
    • (2008) Automatica , vol.44 , pp. 303-325
    • Pronzato, L.1
  • 46
    • 73449142148 scopus 로고    scopus 로고
    • Optimal experimental design for parameter estimation of a cell signaling model
    • Bandara S, Schlöder J, Eils R, Bock H, Meyer T. 2009 Optimal experimental design for parameter estimation of a cell signaling model. PLoS Comput. Biol. 5, e1000558. (doi:10.1371/journal.pcbi.1000558)
    • (2009) PLoS Comput. Biol , vol.5 , pp. e1000558
    • Bandara, S.1    Schlöder, J.2    Eils, R.3    Bock, H.4    Meyer, T.5


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