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

The design and applications of the african buffalo algorithm for general optimization problems

Optimization, basically, is the economics of science. It is concerned with the need to maximize profit and minimize cost in terms of time and resources needed to execute a given project in any field of human endeavor. There have been several scientific investigations in the past several decades on discovering effective and efficient algorithms to providing solutions to the optimization needs of mankind leading to the development of deterministic algorithms that provide exact solutions to optimization problems. In the past five decades, however, the attention of scientists has shifted from the deterministic algorithms to the stochastic ones since the latter have proven to be more robust and efficient, even though they do not guarantee exact solutions. Some of the successfully designed stochastic algorithms include Simulated Annealing, Genetic Algorithm, Ant Colony Optimization, Particle Swarm Optimization, Bee Colony Optimization, Artificial Bee Colony Optimization, Firefly Optimization etc. A critical look at these ‘efficient’ stochastic algorithms reveals the need for improvements in the areas of effectiveness, the number of several parameters used, premature convergence, ability to search diverse landscapes and complex implementation strategies. The African Buffalo Optimization (ABO), which is inspired by the herd management, communication and successful grazing cultures of the African buffalos, is designed to attempt solutions to the observed shortcomings of the existing stochastic optimization algorithms. Through several experimental procedures, the ABO was used to successfully solve benchmark optimization problems in mono-modal and multimodal, constrained and unconstrained, separable and non-separable search landscapes with competitive outcomes. Moreover, the ABO algorithm was applied to solve over 100 out of the 118 benchmark symmetric and all the asymmetric travelling salesman’s problems available in TSPLIB95. Based on the successful experimentation with the novel algorithm, it is safe to conclude that the ABO is a worthy contribution to the scientific literature

Optimal Biocompatible Solvent Design by Mixed-integer Hybrid Differential Evolution

In this study, a flexible optimization approach is introduced to design an optimal biocompatible solvent for an extractive fermentation process with cell-recycling. The optimal process/solvent design problem is formulated as a mixed-integer nonlinear programming model in which performance requirements of the compounds are reflected in the objectives and the constraints. A flexible or fuzzy optimization approach is applied to soften the rigid requirement for maximization of the production rate, extraction efficiency and to consider the solvent utilization rate as the softened inequality constraint to the process/solvent design problem. Such a trade-off problem is then converted to the goal attainment problem, which is described as the constrained mixed-integer nonlinear programming (MINLP) problem. Mixed-integer hybrid differential evolution with multiplier updating method is introduced to solve the constrained MINLP problem. The adaptive penalty updating scheme is more efficient to achieve a global design

Identification of quasi-optimal regions in the design space using surrogate modeling

The use of Surrogate Based Optimization (SBO) is widely spread in engineering design to find optimal performance characteristics of expensive simulations (forward analysis: from input to optimal output). However, often the practitioner knows a priori the desired performance and is interested in finding the associated input parameters (reverse analysis: from desired output to input). A popular method to solve such reverse (inverse) problems is to minimize the error between the simulated performance and the desired goal. However, there might be multiple quasi-optimal solutions to the problem. In this paper, the authors propose a novel method to efficiently solve inverse problems and to sample Quasi-Optimal Regions (QORs) in the input (design) space more densely. The development of this technique, based on the probability of improvement criterion and kriging models, is driven by a real-life problem from bio-mechanics, i.e., determining the elasticity of the (rabbit) tympanic membrane, a membrane that converts acoustic sound wave into vibrations of the middle ear ossicular bones

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Comprehensive Taxonomies of Nature- and Bio-inspired Optimization: Inspiration Versus Algorithmic Behavior, Critical Analysis Recommendations

In recent algorithmic family simulates different biological processes observed in Nature in order to efficiently address complex optimization problems. In the last years the number of bio-inspired optimization approaches in literature has grown considerably, reaching unprecedented levels that dark the future prospects of this field of research. This paper addresses this problem by proposing two comprehensive, principle-based taxonomies that allow researchers to organize existing and future algorithmic developments into well-defined categories, considering two different criteria: the source of inspiration and the behavior of each algorithm. Using these taxonomies we review more than three hundred publications dealing with nature- inspired and bio-inspired algorithms, and proposals falling within each of these categories are examined, leading to a critical summary of design trends and similarities between them, and the identification of the most similar classical algorithm for each reviewed paper. From our analysis we conclude that a poor relationship is often found between the natural inspiration of an algorithm and its behavior. Furthermore, similarities in terms of behavior between different algorithms are greater than what is claimed in their public disclosure: specifically, we show that more than one-third of the reviewed bio-inspired solvers are versions of classical algorithms. Grounded on the conclusions of our critical analysis, we give several recommendations and points of improvement for better methodological practices in this active and growing research field