Hazem N. Nounou

Robust dissipative control for internet-based switching systems

Abstract A class of hybrid multi-rate control models with time-delay and switching controllers are formulated based on combined remote control and local control strategies. The problem of robust dissipative control for this discrete system is investigated. An improved Lyapunov–Krasovskii functional is constructed and the subsequent analysis provides some new sufficient conditions in the form of LMIs for both nominal and uncertain representations. Several special cases of practical interests are derived. A numerical simulation example is given to illustrate the effectiveness of the theoretical result.

Inferring Gene Regulatory Networks via Nonlinear State-Space Models and Exploiting Sparsity

This paper considers the problem of learning the structure of gene regulatory networks from gene expression time series data. A more realistic scenario when the state space model representing a gene network evolves nonlinearly is considered while a linear model is assumed for the microarray data. To capture the nonlinearity, a particle filter-based state estimation algorithm is considered instead of the contemporary linear approximation-based approaches. The parameters characterizing the regulatory relations among various genes are estimated online using a Kalman filter. Since a particular gene interacts with a few other genes only, the parameter vector is expected to be sparse. The state estimates delivered by the particle filter and the observed microarray data are then subjected to a LASSO-based least squares regression operation which yields a parsimonious and efficient description of the regulatory network by setting the irrelevant coefficients to zero. The performance of the aforementioned algorithm is compared with the extended Kalman filter (EKF) and Unscented Kalman Filter (UKF) employing the Mean Square Error (MSE) as the fidelity criterion in recovering the parameters of gene regulatory networks from synthetic data and real biological data. Extensive computer simulations illustrate that the proposed particle filter-based network inference algorithm outperforms EKF and UKF, and therefore, it can serve as a natural framework for modeling gene regulatory networks with nonlinear and sparse structure.

Joint Node Localization and Time-Varying Clock Synchronization in Wireless Sensor Networks

The problems of node localization and clock synchronization in wireless sensor networks are naturally tied from a statistical signal processing perspective. In this work, we consider the joint estimation of an unknown nodes location and clock parameters by incorporating the effect of imperfections in node oscillators, which render a time varying nature to the clock parameters. The data exchange mechanism is based on a two-way message exchange with anchor nodes. In order to alleviate the computational complexity associated with the optimal maximum a-posteriori estimator, two iterative approaches are proposed as simpler alternatives. The first approach utilizes an Expectation-Maximization (EM) based algorithm which iteratively estimates the clock parameters and the location of the unknown node. The EM algorithm is further simplified by a non-linear processing of the data to obtain a closed form solution of the location estimation problem using least squares (LS). The performance of the estimation algorithms is benchmarked by deriving the Hybrid Cramer-Rao lower bound (HCRB) on the mean square error (MSE) of the estimators. The theoretical findings are corroborated by simulation studies which reveal that the LS estimator closely matches the performance of the EM algorithm for small time of arrival measurement noise, and is well suited for implementation in low cost sensor networks.

State and parameter estimation for nonlinear biological phenomena modeled by S-systems

Biological pathways can be modeled as a nonlinear system described by a set of nonlinear ordinary differential equations (ODEs). A central challenge in computational modeling of biological systems is the determination of the model parameters. In such cases, estimating these variables or parameters from other easily obtained measurements can be extremely useful. For example, time-series dynamic genomic data can be used to develop models representing dynamic genetic regulatory networks, which can be used to design intervention strategies to cure major diseases and to better understand the behavior of biological systems. Unfortunately, biological measurements are usually highly affected by errors that hide the important characteristics in the data. Therefore, these noisy measurements need to be filtered to enhance their usefulness in practice. This paper addresses the problem of state and parameter estimation of biological phenomena modeled by S-systems using Bayesian approaches, where the nonlinear observed system is assumed to progress according to a probabilistic state space model. The performances of various conventional and state-of-the-art state estimation techniques are compared. These techniques include the extended Kalman filter (EKF), unscented Kalman filter (UKF), particle filter (PF), and the developed improved particle filter (IPF). Specifically, two comparative studies are performed. In the first comparative study, the state variables (the enzyme CadA, the transport protein CadB, the regulatory protein CadC and lysine Lys for a model of the Cad System in E. coli (CSEC)) are estimated from noisy measurements of these variables, and the various estimation techniques are compared by computing the estimation root mean square error (RMSE) with respect to the noise-free data. In the second comparative study, the state variables as well as the model parameters are simultaneously estimated. In this case, in addition to comparing the performances of the various state estimation techniques, the effect of the number of estimated model parameters on the accuracy and convergence of these techniques is also assessed. The results of both comparative studies show that the UKF provides a higher accuracy than the EKF due to the limited ability of EKF to accurately estimate the mean and covariance matrix of the estimated states through lineralization of the nonlinear process model. The results also show that the IPF provides a significant improvement over PF because, unlike the PF which depends on the choice of sampling distribution used to estimate the posterior distribution, the IPF yields an optimum choice of the sampling distribution, which also accounts for the observed data. The results of the second comparative study show that, for all techniques, estimating more model parameters affects the estimation accuracy as well as the convergence of the estimated states and parameters. However, the IPF can still provide both convergence as well as accuracy related advantages over other estimation methods.

Intervention in Biological Phenomena Modeled by S-Systems

Recent years have witnessed extensive research activity in modeling biological phenomena as well as in developing intervention strategies for such phenomena. S-systems, which offer a good compromise between accuracy and mathematical flexibility, are a promising framework for modeling the dynamical behavior of biological phenomena. In this paper, two different intervention strategies, namely direct and indirect, are proposed for the S-system model. In the indirect approach, the prespecified desired values for the target variables are used to compute the reference values for the control inputs, and two control algorithms, namely simple sampled-data control and model predictive control (MPC), are developed for transferring the control variables from their initial values to the computed reference ones. In the direct approach, a MPC algorithm is developed that directly guides the target variables to their desired values. The proposed intervention strategies are applied to the glycolytic-glycogenolytic pathway and the simulation results presented demonstrate the effectiveness of the proposed schemes.

Iterated Robust kernel Fuzzy Principal Component Analysis and application to fault detection

Abstract In this paper, we propose an Iterated Robust kernel Fuzzy Principal Component Analysis (IRkFPCA), which is the method that attempts to combine the advantages of the state of art methods and use a more accurate multi-objective function for jointly reducing the modeling errors, optimizing the robustness to outliers and improving the time complexity since it does not require the storage and inversion of the covariance matrix to obtain a memory-efficient approximation of kernel PCA. This proposed technique computes iteratively the principal components, which are used for modeling and fault detection. The detection stage is related to the evaluation of residuals, also known as detection indices, which are signals that reveal the fault presence. Those indices are obtained from the analysis of the difference between the process measurements and their estimations using the IRkFPCA technique. The performance of the proposed method is illustrated and compared to Iterated kernel Principal Component Analysis (IkPCA) and Iterated Principal Component Analysis (IPCA) methods through two simulated examples, one using synthetic data and the other using simulated continuously stirred tank reactor (CSTR) data. The results of the comparative studies reveal that the developed IRkFPCA method provides a better performance in terms of modeling and fault detection accuracies than the Iterated Robust Fuzzy Principal Component Analysis (IRFPCA) and Iterated kernel Principal Component Analysis (IkPCA) methods; while both methods provide improved accuracy over the Iterated Principal Component Analysis (IPCA) method.

Network-Wide Clock Synchronization via Message Passing with Exponentially Distributed Link Delays

Clock synchronization has become an indispensable requirement in wireless sensor networks due to its central importance in vital network operations such as data fusion and duty cycling, and has attracted considerable research interest recently. Assuming exponentially distributed random delays in a two-way message exchange mechanism, this work proposes a network-wide clock synchronization algorithm using a factor graph representation of the network. Message passing using the max-product algorithm is adopted to derive the update rules for the proposed iterative procedure. A closed form solution is obtained for each nodes belief about its clock offset at each iteration. Simulation results show that the application of the proposed message passing-based network-wide clock synchronization algorithm provides convergent estimates for both regular cycle-free and random topologies. Moreover, the mean square error (MSE) performance of the proposed algorithm is also compared with the Cramer-Rao bound (CRB) for small example networks, which further highlights the effectiveness of the proposed algorithm.

Multiscale Denoising of Biological Data: A Comparative Analysis

Measured microarray genomic and metabolic data are a rich source of information about the biological systems they represent. For example, time-series biological data can be used to construct dynamic genetic regulatory network models, which can be used to design intervention strategies to cure or manage major diseases. Also, copy number data can be used to determine the locations and extent of aberrations in chromosome sequences. Unfortunately, measured biological data are usually contaminated with errors that mask the important features in the data. Therefore, these noisy measurements need to be filtered to enhance their usefulness in practice. Wavelet-based multiscale filtering has been shown to be a powerful denoising tool. In this work, different batch as well as online multiscale filtering techniques are used to denoise biological data contaminated with white or colored noise. The performances of these techniques are demonstrated and compared to those of some conventional low-pass filters using two case studies. The first case study uses simulated dynamic metabolic data, while the second case study uses real copy number data. Simulation results show that significant improvement can be achieved using multiscale filtering over conventional filtering techniques.

A model-free design of reduced-order controllers and application to a DC servomotor

Abstract This paper presents a new model-free technique to design fixed-structure controllers for linear unknown systems. In the current control design approaches, measured data are used to first identify a model of the plant, then a controller is designed based on the identified model. Due to errors associated with the identification process, degradation in the controller performance is expected. Hence, we use the measured data to directly design the controller without the need for model identification. Our objective here is to design measurement-based controllers for stable and unstable systems, even when the closed-loop architecture is unknown. This proposed method can be very useful for many industrial applications. The proposed control methodology is a reference model design approach which aims at finding suitable parameter values of a fixed-order controller so that the closed-loop frequency response matches a desired frequency response. This reference model design problem is formulated as a nonlinear programming problem using the concept of bounded error, which can then be solved to find suitable values of the controller parameters. In addition to the well-known advantages of data-based control methods, the main features of our proposed approach are: (1) the error is guaranteed to be bounded, (2) it enables us to avoid issues related to the use of minimization methods, (3) it can be applied to stable and unstable plants and does not require any knowledge about the closed-loop architecture, and (4) the controller structure can be selected a priori , which means that low-order controllers can be designed. The proposed technique is experimentally validated through a real position control problem of a DC servomotor, where the results demonstrate the efficacy of the proposed method.

Parameter Estimation of Biological Phenomena: An Unscented Kalman Filter Approach

Recent advances in high-throughput technologies for biological data acquisition have spurred a broad interest in the construction of mathematical models for biological phenomena. The development of such mathematical models relies on the estimation of unknown parameters of the system using the time-course profiles of different metabolites in the system. One of the main challenges in the parameter estimation of biological phenomena is the fact that the number of unknown parameters is much more than the number of metabolites in the system. Moreover, the available metabolite measurements are corrupted by noise. In this paper, a new parameter estimation algorithm is developed based on the stochastic estimation framework for nonlinear systems, namely the unscented Kalman filter (UKF). A new iterative UKF algorithm with covariance resetting is developed in which the UKF algorithm is applied iteratively to the available noisy time profiles of the metabolites. The proposed estimation algorithm is applied to noisy time-course data synthetically produced from a generic branched pathway as well as real time-course profile for the Cad system of E. coli. The simulation results demonstrate the effectiveness of the proposed scheme.