Multiple Model Adaptive controller for Partially-Observed Boolean Dynamical Systems

This paper is concerned with developing an adaptive controller for Partially-Observed Boolean Dynamical Systems (POBDS). Assuming that partial knowledge about the system can be modeled by a finite number of candidate models, then simultaneous identification and control of a POBDS is achieved using the combination of a state-feedback controller and a Multiple-Model Adaptive Estimation (MMAE) technique. The proposed method contains two main steps: first, in the offline step, the stationary control policy for the underlying Boolean dynamical system is computed for each candidate model. Then, in the online step, an optimal Bayesian estimator is modeled using a bank of Boolean Kalman Filters (BKFs), each tuned to a candidate model. The result of the offline step along with the estimated state by the bank of BKFs specify the control input that should be applied at each time point. The performance of the proposed adaptive controller is investigated using a Boolean network model constructed from melanoma gene expression data observed through RNA-seq measurements.

[1]  Ulisses Braga-Neto,et al.  Optimal Fault Detection and Diagnosis in Transcriptional Circuits Using Next-Generation Sequencing , 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[2]  Ting Chen,et al.  Bayesian estimation of the discrete coefficient of determination , 2016, EURASIP J. Bioinform. Syst. Biol..

[3]  Aniruddha Datta,et al.  Optimal infinite horizon control for probabilistic Boolean networks , 2006, 2006 American Control Conference.

[4]  S. Kauffman Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[5]  Mahdi Imani,et al.  State-feedback control of Partially-Observed Boolean Dynamical Systems using RNA-seq time series data , 2016, 2016 American Control Conference (ACC).

[6]  Xiaoning Qian,et al.  Bayesian module identification from multiple noisy networks , 2016, EURASIP J. Bioinform. Syst. Biol..

[7]  Jonas S. Almeida,et al.  Decoupling dynamical systems for pathway identification from metabolic profiles , 2004, Bioinform..

[8]  Peter S. Maybeck,et al.  Performance enhancement of a multiple model adaptive estimator , 1995 .

[9]  Ulisses Braga-Neto,et al.  Optimal state estimation for Boolean dynamical systems , 2011, 2011 Conference Record of the Forty Fifth Asilomar Conference on Signals, Systems and Computers (ASILOMAR).

[10]  Seyede Fatemeh Ghoreishi Uncertainty Analysis for Coupled Multidisciplinary Systems Using Sequential Importance Resampling , 2016 .

[11]  Dimitri P. Bertsekas,et al.  Dynamic Programming and Optimal Control, Two Volume Set , 1995 .

[12]  Jorge Cortés,et al.  Time-Varying Actuator Scheduling in Complex Networks , 2016, ArXiv.

[13]  Mahdi Imani,et al.  Control of Gene Regulatory Networks With Noisy Measurements and Uncertain Inputs , 2017, IEEE Transactions on Control of Network Systems.

[14]  Ulisses Braga-Neto,et al.  Boolean Kalman Filter with correlated observation noise , 2017, 2017 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

[15]  Michal Linial,et al.  Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..

[16]  Douglas Allaire,et al.  Compositional Uncertainty Analysis via Importance Weighted Gibbs Sampling for Coupled Multidisciplinary Systems , 2016 .

[17]  Ulisses Braga-Neto,et al.  BoolFilter Package Vignette , 2017 .

[18]  Aniruddha Datta,et al.  Adaptive intervention in Probabilistic Boolean Networks , 2009, 2009 American Control Conference.

[19]  Ulisses Braga-Neto,et al.  ParticleFilters for Partially-ObservedBooleanDynamical Systems , 2017 .

[20]  Aniruddha Datta,et al.  Stationary and structural control in gene regulatory networks: basic concepts , 2010, Int. J. Syst. Sci..

[21]  Douglas Allaire,et al.  Quantifying the Impact of Different Model Discrepancy Formulations in Coupled Multidisciplinary Systems , 2017 .

[22]  A. Datta,et al.  External Control in Markovian Genetic Regulatory Networks , 2003, Proceedings of the 2003 American Control Conference, 2003..

[23]  Zhu Mao,et al.  Statistical Modeling of Wavelet-Transform-Based Features in Structural Health Monitoring , 2016 .

[24]  Ulisses Braga-Neto,et al.  Classification of State Trajectories in Gene Regulatory Networks , 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[25]  Ulisses Braga-Neto,et al.  Optimal gene regulatory network inference using the Boolean Kalman filter and multiple model adaptive estimation , 2015, 2015 49th Asilomar Conference on Signals, Systems and Computers.

[26]  Zhu Mao,et al.  Probabilistic uncertainty quantification of wavelet-transform-based structural health monitoring features , 2016, SPIE Smart Structures and Materials + Nondestructive Evaluation and Health Monitoring.

[27]  Ulisses Braga-Neto,et al.  Point-based value iteration for partially-observed Boolean dynamical systems with finite observation space , 2016, 2016 IEEE 55th Conference on Decision and Control (CDC).

[28]  Edward R. Dougherty,et al.  From Boolean to probabilistic Boolean networks as models of genetic regulatory networks , 2002, Proc. IEEE.

[29]  Ulisses Braga-Neto,et al.  Particle filters for partially-observed Boolean dynamical systems , 2018, Autom..

[30]  Ádám M. Halász,et al.  Stochastic Modeling and Control of Biological Systems: The Lactose Regulation System of Escherichia Coli , 2008, IEEE Transactions on Automatic Control.

[31]  Ulisses Braga-Neto,et al.  Optimal state estimation for boolean dynamical systems using a boolean Kalman smoother , 2015, 2015 IEEE Global Conference on Signal and Information Processing (GlobalSIP).

[32]  Mauro Birattari,et al.  On the Design of Boolean Network Robots , 2011, EvoApplications.

[33]  David G. Messerschmitt,et al.  Synchronization in Digital System Design , 1990, IEEE J. Sel. Areas Commun..