A hybrid EKF and switching PSO algorithm for joint state and parameter estimation of lateral flow immunoassay models

This is the post-print version of the Article. The official published can be accessed from the link below - Copyright @ 2012 IEEEIn this paper, a hybrid extended Kalman filter (EKF) and switching particle swarm optimization (SPSO) algorithm is proposed for jointly estimating both the parameters and states of the lateral flow immunoassay model through available short time-series measurement. Our proposed method generalizes the well-known EKF algorithm by imposing physical constraints on the system states. Note that the state constraints are encountered very often in practice that give rise to considerable difficulties in system analysis and design. The main purpose of this paper is to handle the dynamic modeling problem with state constraints by combining the extended Kalman filtering and constrained optimization algorithms via the maximization probability method. More specifically, a recently developed SPSO algorithm is used to cope with the constrained optimization problem by converting it into an unconstrained optimization one through adding a penalty term to the objective function. The proposed algorithm is then employed to simultaneously identify the parameters and states of a lateral flow immunoassay model. It is shown that the proposed algorithm gives much improved performance over the traditional EKF method.This work was supported in part by the International Science and Technology Cooperation Project of China under Grant 2009DFA32050, Natural Science Foundation of China under Grants 61104041, International Science and Technology Cooperation Project of Fujian Province of China under Grant 2009I0016

Informative and misinformative interactions in a school of fish

It is generally accepted that, when moving in groups, animals process information to coordinate their motion. Recent studies have begun to apply rigorous methods based on Information Theory to quantify such distributed computation. Following this perspective, we use transfer entropy to quantify dynamic information flows locally in space and time across a school of fish during directional changes around a circular tank, i.e. U-turns. This analysis reveals peaks in information flows during collective U-turns and identifies two different flows: an informative flow (positive transfer entropy) based on fish that have already turned about fish that are turning, and a misinformative flow (negative transfer entropy) based on fish that have not turned yet about fish that are turning. We also reveal that the information flows are related to relative position and alignment between fish, and identify spatial patterns of information and misinformation cascades. This study offers several methodological contributions and we expect further application of these methodologies to reveal intricacies of self-organisation in other animal groups and active matter in general

Extending the Modern Synthesis: The evolution of ecosystems

The Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of information theory, that instantiates the punctuated dynamic relations of organisms and their embedding environments. The mathematical overhead is considerable, and we conclude that the model must itself be extended even further to allow the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis

Modeling and Estimation of Biological Plants

Estimating the state of a dynamic system is an essential task for achieving important objectives such as process monitoring, identification, and control. Unlike linear systems, no systematic method exists for the design of observers for nonlinear systems. Although many researchers have devoted their attention to these issues for more than 30 years, there are still many open questions. We envisage that estimation plays a crucial role in biology because of the possibility of creating new avenues for biological studies and for the development of diagnostic, management, and treatment tools. To this end, this thesis aims to address two types of nonlinear estimation techniques, namely, the high-gain observer and the moving-horizon estimator with application to three different biological plants. After recalling basic definitions of stability and observability of dynamical systems and giving a bird's-eye survey of the available state estimation techniques, we are interested in the high-gain observers. These observers may be used when the system dynamics can be expressed in specific a coordinate under the so-called observability canonical form with the possibility to assign the rate of convergence arbitrarily by acting on a single parameter called the high-gain parameter. Despite the evident benefits of this class of observers, their use in real applications is questionable due to some drawbacks: numerical problems, the peaking phenomenon, and high sensitivity to measurement noise. The first part of the thesis aims to enrich the theory of high-gain observers with novel techniques to overcome or attenuate these challenging performance issues that arise when implementing such observers. The validity and applicability of our proposed techniques have been shown firstly on a simple one-gene regulatory network, and secondly on an SI epidemic model. The second part of the thesis studies the problem of state estimation using the moving horizon approach. The main advantage of MHE is that information about the system can be explicitly considered in the form of constraints and hence improve the estimates. In this work, we focus on estimation for nonlinear plants that can be rewritten in the form of quasi-linear parameter-varying systems with bounded unknown parameters. Moving-horizon estimators are proposed to estimate the state of such systems according to two different formulations, i.e., "optimistic" and "pessimistic". In the former case, we perform estimation by minimizing the least-squares moving-horizon cost with respect to both state variables and parameters simultaneously. In the latter, we minimize such a cost with respect to the state variables after picking up the maximum of the parameters. Under suitable assumptions, the stability of the estimation error given by the exponential boundedness is proved in both scenarios. Finally, the validity of our obtained results has been demonstrated through three different examples from biological and biomedical fields, namely, an example of one gene regulatory network, a two-stage SI epidemic model, and Amnioserosa cell's mechanical behavior during Dorsal closure

Mathematical models of cellular signaling and supramolecular self-assembly

Synthetic biologists endeavor to predict how the increasing complexity of multi-step signaling cascades impacts the fidelity of molecular signaling, whereby cellular state information is often transmitted with proteins diffusing by a pseudo-one-dimensional stochastic process. We address this problem by using a one-dimensional drift-diffusion model to derive an approximate lower bound on the degree of facilitation needed to achieve single-bit informational efficiency in signaling cascades as a function of their length. We find that a universal curve of the Shannon-Hartley form describes the information transmitted by a signaling chain of arbitrary length and depends upon only a small number of physically measurable parameters. This enables our model to be used in conjunction with experimental measurements to aid in the selective design of biomolecular systems. Another important concept in the cellular world is molecular self-assembly. As manipulating the self-assembly of supramolecular and nanoscale constructs at the single-molecule level increasingly becomes the norm, new theoretical scaffolds must be erected to replace the classical thermodynamic and kinetics-based models. The models we propose use state probabilities as its fundamental objects and directly model the transition probabilities between the initial and final states of a trajectory. We leverage these probabilities in the context of molecular self-assembly to compute the overall likelihood that a specified experimental condition leads to a desired structural outcome. We also investigated a larger complex self-assembly system, the heterotypic interactions between amyloid-beta and fatty acids by an independent ensemble kinetic simulation using an underlying differential equation-based system which was validated by biophysical experiments

Exponential state estimation for competitive neural network via stochastic sampled-data control with packet losses

This paper investigates the exponential state estimation problem for competitive neural networks via stochastic sampled-data control with packet losses. Based on this strategy, a switched system model is used to describe packet dropouts for the error system. In addition, transmittal delays between neurons are also considered. Instead of the continuous measurement, the sampled measurement is used to estimate the neuron states, and a sampled-data estimator with probabilistic sampling in two sampling periods is proposed. Then the estimator is designed in terms of the solution to a set of linear matrix inequalities (LMIs), which can be solved by using available software. When the missing of control packet occurs, some sufficient conditions are obtained to guarantee that the exponentially stable of the error system by means of constructing an appropriate Lyapunov function and using the average dwell-time technique. Finally, a numerical example is given to show the effectiveness of the proposed method

Bio-inspired Dynamic Control Systems with Time Delays

The world around us exhibits a rich and ever changing environment of startling, bewildering and fascinating complexity. Almost everything is never as simple as it seems, but through the chaos we may catch fleeting glimpses of the mechanisms within. Throughout the history of human endeavour we have mimicked nature to harness it for our own ends. Our attempts to develop truly autonomous and intelligent machines have however struggled with the limitations of our human ability. This has encouraged some to shirk this responsibility and instead model biological processes and systems to do it for us. This Thesis explores the introduction of continuous time delays into biologically inspired dynamic control systems. We seek to exploit rich temporal dynamics found in physical and biological systems for modelling complex or adaptive behaviour through the artificial evolution of networks to control robots. Throughout, arguments have been presented for the modelling of delays not only to better represent key facets of physical and biological systems, but to increase the computational potential of such systems for the synthesis of control. The thorough investigation of the dynamics of small delayed networks with a wide range of time delays has been undertaken, with a detailed mathematical description of the fixed points of the system and possible oscillatory modes developed to fully describe the behaviour of a single node. Exploration of the behaviour for even small delayed networks illustrates the range of complex behaviour possible and guides the development of interesting solutions. To further exploit the potential of the rich dynamics in such systems, a novel approach to the 3D simulation of locomotory robots has been developed focussing on minimising the computational cost. To verify this simulation tool a simple quadruped robot was developed and the motion of the robot when undergoing a manually designed gait evaluated. The results displayed a high degree of agreement between the simulation and laser tracker data, verifying the accuracy of the model developed. A new model of a dynamic system which includes continuous time delays has been introduced, and its utility demonstrated in the evolution of networks for the solution of simple learning behaviours. A range of methods has been developed for determining the time delays, including the novel concept of representing the time delays as related to the distance between nodes in a spatial representation of the network. The application of these tools to a range of examples has been explored, from Gene Regulatory Networks (GRNs) to robot control and neural networks. The performance of these systems has been compared and contrasted with the efficacy of evolutionary runs for the same task over the whole range of network and delay types. It has been shown that delayed dynamic neural systems are at least as capable as traditional Continuous Time Recurrent Neural Networks (CTRNNs) and show significant performance improvements in the control of robot gaits. Experiments in adaptive behaviour, where there is not such a direct link between the enhanced system dynamics and performance, showed no such discernible improvement. Whilst we hypothesise that the ability of such delayed networks to generate switched pattern generating nodes may be useful in Evolutionary Robotics (ER) this was not borne out here. The spatial representation of delays was shown to be more efficient for larger networks, however these techniques restricted the search to lower complexity solutions or led to a significant falloff as the network structure becomes more complex. This would suggest that for anything other than a simple genotype, the direct method for encoding delays is likely most appropriate. With proven benefits for robot locomotion and the open potential for adaptive behaviour delayed dynamic systems for evolved control remain an interesting and promising field in complex systems research

Comprehensive review of models and methods for inferences in bio-chemical reaction networks

The key processes in biological and chemical systems are described by networks of chemical reactions. From molecular biology to biotechnology applications, computational models of reaction networks are used extensively to elucidate their non-linear dynamics. The model dynamics are crucially dependent on the parameter values which are often estimated from observations. Over the past decade, the interest in parameter and state estimation in models of (bio-) chemical reaction networks (BRNs) grew considerably. The related inference problems are also encountered in many other tasks including model calibration, discrimination, identifiability, and checking, and optimum experiment design, sensitivity analysis, and bifurcation analysis. The aim of this review paper is to examine the developments in literature to understand what BRN models are commonly used, and for what inference tasks and inference methods. The initial collection of about 700 documents concerning estimation problems in BRNs excluding books and textbooks in computational biology and chemistry were screened to select over 270 research papers and 20 graduate research theses. The paper selection was facilitated by text mining scripts to automate the search for relevant keywords and terms. The outcomes are presented in tables revealing the levels of interest in different inference tasks and methods for given models in the literature as well as the research trends are uncovered. Our findings indicate that many combinations of models, tasks and methods are still relatively unexplored, and there are many new research opportunities to explore combinations that have not been considered—perhaps for good reasons. The most common models of BRNs in literature involve differential equations, Markov processes, mass action kinetics, and state space representations whereas the most common tasks are the parameter inference and model identification. The most common methods in literature are Bayesian analysis, Monte Carlo sampling strategies, and model fitting to data using evolutionary algorithms. The new research problems which cannot be directly deduced from the text mining data are also discussed