Identification of Stochastic Timed Discrete Event Systems with st-IPN

[EN] This paper presents amethod for the identification of stochastic timed discrete event systems, based on the analysis of the behavior of the input and output signals, arranged in a timeline. To achieve this goal stochastic timed interpreted Petri nets are defined.These nets link timed discrete event systems modelling with stochastic time modelling. The procedure starts with the observation of the input/output signals; these signals are converted into events, so that the sequence of events is the observed language. This language arrives to an identifier that builds a stochastic timed interpreted Petri net which generates the same language. The identified model is a deterministic generator of the observed language.The identification method also includes an algorithm that determines when the identification process is over.This work was supported by a Grant from the Universidad del Cauca, reference 2.3-31.2/05 2011.Muñoz-Añasco, DM.; Correcher Salvador, A.; García Moreno, E.; Morant Anglada, FJ. (2014). Identification of Stochastic Timed Discrete Event Systems with st-IPN. Mathematical Problems in Engineering. 2014:1-21. https://doi.org/10.1155/2014/835312S1212014Cassandras, C. G., & Lafortune, S. (Eds.). (2008). Introduction to Discrete Event Systems. doi:10.1007/978-0-387-68612-7Yingwei Zhang, Jiayu An, & Chi Ma. (2013). Fault Detection of Non-Gaussian Processes Based on Model Migration. IEEE Transactions on Control Systems Technology, 21(5), 1517-1526. doi:10.1109/tcst.2012.2217966Ichikawa, A., & Hiraishi, K. (s. f.). Analysis and control of discrete event systems represented by petri nets. Lecture Notes in Control and Information Sciences, 115-134. doi:10.1007/bfb0042308Fanti, M. P., Mangini, A. M., & Ukovich, W. (2013). Fault Detection by Labeled Petri Nets in Centralized and Distributed Approaches. IEEE Transactions on Automation Science and Engineering, 10(2), 392-404. doi:10.1109/tase.2012.2203596Cabasino, M. P., Giua, A., & Seatzu, C. (2010). Fault detection for discrete event systems using Petri nets with unobservable transitions. Automatica, 46(9), 1531-1539. doi:10.1016/j.automatica.2010.06.013Hu, H., Zhou, M., Li, Z., & Tang, Y. (2013). An Optimization Approach to Improved Petri Net Controller Design for Automated Manufacturing Systems. IEEE Transactions on Automation Science and Engineering, 10(3), 772-782. doi:10.1109/tase.2012.2201714Hu, H., Zhou, M., & Li, Z. (2011). Supervisor Optimization for Deadlock Resolution in Automated Manufacturing Systems With Petri Nets. IEEE Transactions on Automation Science and Engineering, 8(4), 794-804. doi:10.1109/tase.2011.2156783Hiraishi, K. (1992). Construction of a class of safe Petri nets by presenting firing sequences. Lecture Notes in Computer Science, 244-262. doi:10.1007/3-540-55676-1_14Estrada-Vargas, A. P., López-Mellado, E., & Lesage, J.-J. (2010). A Comparative Analysis of Recent Identification Approaches for Discrete-Event Systems. Mathematical Problems in Engineering, 2010, 1-21. doi:10.1155/2010/453254Shaolong Shu, & Feng Lin. (2013). I-Detectability of Discrete-Event Systems. IEEE Transactions on Automation Science and Engineering, 10(1), 187-196. doi:10.1109/tase.2012.2215959Li, L., & Hadjicostis, C. N. (2011). Least-Cost Transition Firing Sequence Estimation in Labeled Petri Nets With Unobservable Transitions. IEEE Transactions on Automation Science and Engineering, 8(2), 394-403. doi:10.1109/tase.2010.2070065Supavatanakul, P., Lunze, J., Puig, V., & Quevedo, J. (2006). Diagnosis of timed automata: Theory and application to the DAMADICS actuator benchmark problem. Control Engineering Practice, 14(6), 609-619. doi:10.1016/j.conengprac.2005.03.028Dotoli, M., Fanti, M. P., & Mangini, A. M. (2008). Real time identification of discrete event systems using Petri nets. Automatica, 44(5), 1209-1219. doi:10.1016/j.automatica.2007.10.014Chen, Y., Li, Z., Khalgui, M., & Mosbahi, O. (2011). Design of a Maximally Permissive Liveness- Enforcing Petri Net Supervisor for Flexible Manufacturing Systems. IEEE Transactions on Automation Science and Engineering, 8(2), 374-393. doi:10.1109/tase.2010.2060332Murata, T. (1989). Petri nets: Properties, analysis and applications. Proceedings of the IEEE, 77(4), 541-580. doi:10.1109/5.24143Ramirez-Trevino, A., Ruiz-Beltran, E., Aramburo-Lizarraga, J., & Lopez-Mellado, E. (2012). Structural Diagnosability of DES and Design of Reduced Petri Net Diagnosers. IEEE Transactions on Systems, Man, and Cybernetics - Part A: Systems and Humans, 42(2), 416-429. doi:10.1109/tsmca.2011.2169950Ramirez-Trevino, A., Ruiz-Beltran, E., Rivera-Rangel, I., & Lopez-Mellado, E. (2007). Online Fault Diagnosis of Discrete Event Systems. A Petri Net-Based Approach. IEEE Transactions on Automation Science and Engineering, 4(1), 31-39. doi:10.1109/tase.2006.872120Toutenburg, H. (1974). Fleiss, J. L.: Statistical Methods for Rates and Proportions. John Wiley & Sons, New York-London-Sydney-Toronto 1973. XIII, 233 S. Biometrische Zeitschrift, 16(8), 539-539. doi:10.1002/bimj.19740160814Livingston, E. H., & Cassidy, L. (2005). Statistical Power and Estimation of the Number of Required Subjects for a Study Based on the t-Test: A Surgeon’s Primer. Journal of Surgical Research, 126(2), 149-159. doi:10.1016/j.jss.2004.12.013Ruppert, D. (2011). Statistics and Data Analysis for Financial Engineering. Springer Texts in Statistics. doi:10.1007/978-1-4419-7787-

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