Abstract
Inference of gene regulatory network (GRN) from gene expression data is still a challenging work. The supervised approaches perform better than unsupervised approaches. In this paper, we develop a new supervised approach based on radial basis function (RBF) neural network for inference of gene regulatory network. A new hybrid evolutionary method based on dissipative particle swarm optimization (DPSO) and firefly algorithm (FA) is proposed to optimize the parameters of RBF. The data from E.coli network is used to test our method and results reveal that our method performs than classical approaches.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ellwanger, D.C., Leonhardt, J.F., Mewes, H.W.: Large-scale modeling of condition-specific gene regulatory networks by information integration and inference. Nucleic Acids Res. 42(21), e166 (2014)
Vera-Licona, P., Jarrah, A., Garcia-Puente, L.D., McGee, J., Laubenbacher, R.: An algebra-based method for inferring gene regulatory networks. BMC Syst. Biol. 8, 37 (2014)
Xie, Y., Wang, R., Zhu, J.: Construction of breast cancer gene regulatory networks and drug target optimization. Arch. Gynecol. Obstet. 290(4), 749–755 (2014)
Penfold, C.A., Millar, J.B., Wild, D.L.: Inferring orthologous gene regulatory networks using interspecies data fusion. Bioinformatics 31(12), i97–i105 (2015)
Baur, B., Bozdag, S.: A canonical correlation analysis-based dynamic bayesian network prior to infer gene regulatory networks from multiple types of biological data. J. Comput. Biol. 22(4), 289–299 (2015)
Yang, M., Li, R., Chu, T.: Construction of a Boolean model of gene and protein regulatory network with memory. Neural Netw. 52, 18–24 (2014)
Adabor, E.S., Acquaah-Mensah, G.K., Oduro, F.T.: SAGA: a hybrid search algorithm for Bayesian Network structure learning of transcriptional regulatory networks. J. Biomed. Inform. 53, 27–35 (2015)
Sun, M., Cheng, X., Socolar, J.E.: Causal structure of oscillations in gene regulatory networks: Boolean analysis of ordinary differential equation attractors. Chaos 23(2), 025104 (2013)
Wang, J., Chen, B., Wang, Y., Wang, N., Garbey, M., Tran-Son-Tay, R., Berceli, S.A., Wu, R.: Reconstructing regulatory networks from the dynamic plasticity of gene expression by mutual information. Nucleic Acids Res. 41(8), e97 (2013)
Maetschke, S.R., Madhamshettiwar, P.B., Davis, M.J., Ragan, M.A.: Supervised, semi-supervised and unsupervised inference of gene regulatory networks. Brief Bioinform. 15(2), 195–211 (2014)
Cerulo, L., Elkan, C., Ceccarelli, M.: Learning gene regulatory networks from only positive and unlabeled data. BMC Bioinform. 11, 228 (2010)
Mordelet, F., Vert, J.P.: SIRENE: supervised inference of regulatory networks. Bioinformatics 24(16), i76–i82 (2008)
Gillani, Z., Akash, M.S., Rahaman, M.D., Chen, M.: CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks. BMC Bioinform. 15, 395 (2014)
Taher, N., Ehsan, A., Jabbari, M.: A new hybrid evolutionary algorithm based on new fuzzy adaptive PSO and NM algorithms for distribution feeder reconfiguration. Energy Convers. Manage. 54(1), 7–16 (2011)
Kuan-Cheng, L., Yi-Hsiu, H.: Classification of medical datasets using SVMs with hybrid evolutionary algorithms based on endocrine-based particle swarm optimization and artificial bee colony algorithms. J. Med. Syst. 39, 119 (2015)
Reza, M., Fatemi, G., Farzad, Z.: A new hybrid evolutionary based RBF networks method for forecasting time series: a case study of forecasting emergency supply demand time series. Eng. Appl. Artif. Intell. 36, 204–214 (2014)
Jia, W., Zhao, D., Shen, T., Su, C., Hu, C., Zhao, Y.: A new optimized GA-RBF neural network algorithm. Comput. Intell. Neurosci. 2014, 6 (2014). 982045
Xie, F.X., Zhang, W.J., Yang, Z.L.: A dissipative particle swarm optimization. In: Congress on Evolutionary Computation (CEC), pp. 1456–1461 (2002)
Yang, X.-S.: Firefly algorithms for multimodal optimization. In: Watanabe, O., Zeugmann, T. (eds.) SAGA 2009. LNCS, vol. 5792, pp. 169–178. Springer, Heidelberg (2009). doi:10.1007/978-3-642-04944-6_14
Butte, A.J., Tamayo, P., Slonim, D., Golub, T.R., Kohane, I.S.: Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc. Natl. Acad. Sci. U.S.A. 97(22), 12182–12186 (2000)
Acknowledgements
This work was supported by the PhD research startup foundation of Zaozhuang University (No. 2014BS13), and Shandong Provincial Natural Science Foundation, China (No. ZR2015PF007).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing AG
About this paper
Cite this paper
Liu, S., Yang, B., Wang, H. (2016). Inference of Gene Regulatory Network Based on Radial Basis Function Neural Network. In: Pardalos, P., Conca, P., Giuffrida, G., Nicosia, G. (eds) Machine Learning, Optimization, and Big Data. MOD 2016. Lecture Notes in Computer Science(), vol 10122. Springer, Cham. https://doi.org/10.1007/978-3-319-51469-7_39
Download citation
DOI: https://doi.org/10.1007/978-3-319-51469-7_39
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-51468-0
Online ISBN: 978-3-319-51469-7
eBook Packages: Computer ScienceComputer Science (R0)