메뉴 건너뛰기




Volumn 5975 LNCS, Issue , 2010, Pages 74-85

On the difficulty of inferring gene regulatory networks: A study of the fitness landscape generated by relative squared error

Author keywords

[No Author keywords available]

Indexed keywords

CONTINUOUS OPTIMIZATION; DEEP VALLEY; DYNAMIC RECURRENT NEURAL NETWORKS; ERROR MEASURES; ERROR VALUES; EXPRESSION PROFILE; FITNESS LANDSCAPE; FITNESS-DISTANCE CORRELATION; GENE REGULATORY NETWORKS; NETWORK PARAMETERS; NETWORK TOPOLOGY; OPTIMAL NETWORK TOPOLOGY; OPTIMIZATION PROBLEMS; ORDERS OF MAGNITUDE; POOR PERFORMANCE; REGULATORY INTERACTIONS; SHORT DISTANCES; SQUARED ERRORS;

EID: 77954713702     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-14156-0_7     Document Type: Conference Paper
Times cited : (1)

References (28)
  • 5
    • 34547788797 scopus 로고    scopus 로고
    • Bayesian approaches to reverse engineer cellular systems: A simulation study on nonlinear gaussian networks
    • Ferrazzi, F., Sebastiani, P., Ramoni, M.F., Bellazzi, R.: Bayesian approaches to reverse engineer cellular systems: a simulation study on nonlinear gaussian networks. BMC Bioinformatics 8(suppl. 5) (2007)
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 5
    • Ferrazzi, F.1    Sebastiani, P.2    Ramoni, M.F.3    Bellazzi, R.4
  • 6
    • 62549093118 scopus 로고    scopus 로고
    • Benchmarks for identification of ordinary differential equations from time series data
    • Gennemark, P., Wedelin, D.: Benchmarks for identification of ordinary differential equations from time series data. Bioinformatics 25(6), 780-786 (2009)
    • (2009) Bioinformatics , vol.25 , Issue.6 , pp. 780-786
    • Gennemark, P.1    Wedelin, D.2
  • 8
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker, T., Ozier, O., Schwikowski, B., Siegel, A.F.: Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18(suppl. 1), 233-240 (2002)
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1 , pp. 233-240
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 10
    • 0003155122 scopus 로고
    • Fitness distance correlation as a measure of problem difficulty for genetic algorithms
    • Morgan Kaufmann, San Francisco
    • Jones, T., Forrest, S.: Fitness distance correlation as a measure of problem difficulty for genetic algorithms. In: Proceedings of the 6th International Conference on Genetic Algorithms, pp. 184-192. Morgan Kaufmann, San Francisco (1995)
    • (1995) Proceedings of the 6th International Conference on Genetic Algorithms , pp. 184-192
    • Jones, T.1    Forrest, S.2
  • 11
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review
    • de Jong, H.: Modeling and simulation of genetic regulatory systems: A literature review. Journal of Computational Biology 9(1), 67-103 (2002)
    • (2002) Journal of Computational Biology , vol.9 , Issue.1 , pp. 67-103
    • De Jong, H.1
  • 13
    • 56449091133 scopus 로고    scopus 로고
    • Incorporating heuristics in a swarm intelligence framework for inferring gene regulatory networks from gene expression time series
    • Dorigo, M., Birattari, M., Blum, C., Clerc, M., Stützle, T., Winfield, A.F.T. (eds.) ANTS 2008. Springer, Heidelberg
    • Kentzoglanakis, K., Poole, M.J., Adams, C.: Incorporating heuristics in a swarm intelligence framework for inferring gene regulatory networks from gene expression time series. In: Dorigo, M., Birattari, M., Blum, C., Clerc, M., Stützle, T., Winfield, A.F.T. (eds.) ANTS 2008. LNCS, vol. 5217, pp. 323-330. Springer, Heidelberg (2008)
    • (2008) LNCS , vol.5217 , pp. 323-330
    • Kentzoglanakis, K.1    Poole, M.J.2    Adams, C.3
  • 16
    • 0031616241 scopus 로고    scopus 로고
    • Reveal: A general reverse engineering algorithm for inference of genetic network architectures
    • Liang, S., Fuhrman, S., Somogyi, R.: Reveal: a general reverse engineering algorithm for inference of genetic network architectures. In: Pacific Symposium on Biocomputing, pp. 18-29 (1998)
    • (1998) Pacific Symposium on Biocomputing , pp. 18-29
    • Liang, S.1    Fuhrman, S.2    Somogyi, R.3
  • 18
    • 0003144777 scopus 로고    scopus 로고
    • Fitness landscapes and memetic algorithm design
    • Corne, D., Dorigo, M., Glover, F. (eds.) McGraw Hill, London
    • Merz, P., Freisleben, B.: Fitness landscapes and memetic algorithm design. In: Corne, D., Dorigo, M., Glover, F. (eds.) New Ideas in Optimization, pp. 244-260. McGraw Hill, London (1999)
    • (1999) New Ideas in Optimization , pp. 244-260
    • Merz, P.1    Freisleben, B.2
  • 20
    • 68949099095 scopus 로고    scopus 로고
    • Benchmarking derivative-free optimization algorithms
    • Moré, J.J., Wild, S.M.: Benchmarking derivative-free optimization algorithms. SIAM Journal on Optimization 20(1), 172-191 (2009)
    • (2009) SIAM Journal on Optimization , vol.20 , Issue.1 , pp. 172-191
    • Moré, J.J.1    Wild, S.M.2
  • 21
    • 33748530630 scopus 로고    scopus 로고
    • Reverse engineering genetic networks using evolutionary computation
    • Noman, N., Iba, I.: Reverse engineering genetic networks using evolutionary computation. Genome Informatics 16(2), 205-214 (2005)
    • (2005) Genome Informatics , vol.16 , Issue.2 , pp. 205-214
    • Noman, N.1    Iba, I.2
  • 25
    • 33846703173 scopus 로고    scopus 로고
    • Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of saccharomyces cerevisiae
    • Vu, T.T., Vohradsky, J.: Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of saccharomyces cerevisiae. Nucleic Acids Research 35(1), 279-287 (2007)
    • (2007) Nucleic Acids Research , vol.35 , Issue.1 , pp. 279-287
    • Vu, T.T.1    Vohradsky, J.2
  • 26
    • 10944233884 scopus 로고    scopus 로고
    • Inference of genetic regulatory networks from time series gene expression data
    • IEEE Press, Los Alamitos
    • Xu, R., Hu, X., Wunsch II, D.: Inference of genetic regulatory networks from time series gene expression data. In: Proceedings of the International Joint Conference on Neural Networks, vol. 2, pp. 1215-1220. IEEE Press, Los Alamitos (2004)
    • (2004) Proceedings of the International Joint Conference on Neural Networks , vol.2 , pp. 1215-1220
    • Xu, R.1    Hu, X.2    Wunsch II, D.3
  • 27
    • 34848893948 scopus 로고    scopus 로고
    • Modeling of gene regulatory networks with hybrid differential evolution and particle swarm optimization
    • Xu, R., Venayagamoorthy, G.K., Wunsch II, D.C.: Modeling of gene regulatory networks with hybrid differential evolution and particle swarm optimization. Neural Networks 20(8), 917-927 (2007)
    • (2007) Neural Networks , vol.20 , Issue.8 , pp. 917-927
    • Xu, R.1    Venayagamoorthy, G.K.2    Wunsch II, D.C.3
  • 28
    • 36248944068 scopus 로고    scopus 로고
    • Inference of genetic regulatory networks with recurrent neural network models using particle swarm optimization
    • Xu, R., Wunsch II, D., Frank, R.: Inference of genetic regulatory networks with recurrent neural network models using particle swarm optimization. IEEE/ACM Trans. Comput. Biol. Bioinformatics 4(4), 681-692 (2007)
    • (2007) IEEE/ACM Trans. Comput. Biol. Bioinformatics , vol.4 , Issue.4 , pp. 681-692
    • Xu, R.1    Wunsch II, D.2    Frank, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.