Image-based quantitative analysis of gold immunochromatographic strip via cellular neural network approach

"(c) 2014 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works."Gold immunochromatographic strip assay provides a rapid, simple, single-copy and on-site way to detect the presence or absence of the target analyte. This paper aims to develop a method for accurately segmenting the test line and control line of the gold immunochromatographic strip (GICS) image for quantitatively determining the trace concentrations in the specimen, which can lead to more functional information than the traditional qualitative or semi-quantitative strip assay. The canny operator as well as the mathematical morphology method is used to detect and extract the GICS reading-window. Then, the test line and control line of the GICS reading-window are segmented by the cellular neural network (CNN) algorithm, where the template parameters of the CNN are designed by the switching particle swarm optimization (SPSO) algorithm for improving the performance of the CNN. It is shown that the SPSO-based CNN offers a robust method for accurately segmenting the test and control lines, and therefore serves as a novel image methodology for the interpretation of GICS. Furthermore, quantitative comparison is carried out among four algorithms in terms of the peak signal-to-noise ratio. It is concluded that the proposed CNN algorithm gives higher accuracy and the CNN is capable of parallelism and analog very-large-scale integration implementation within a remarkably efficient time

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

Where Should We Place LiDARs on the Autonomous Vehicle? - An Optimal Design Approach

Autonomous vehicle manufacturers recognize that LiDAR provides accurate 3D views and precise distance measures under highly uncertain driving conditions. Its practical implementation, however, remains costly. This paper investigates the optimal LiDAR configuration problem to achieve utility maximization. We use the perception area and non-detectable subspace to construct the design procedure as solving a min-max optimization problem and propose a bio-inspired measure -- volume to surface area ratio (VSR) -- as an easy-to-evaluate cost function representing the notion of the size of the non-detectable subspaces of a given configuration. We then adopt a cuboid-based approach to show that the proposed VSR-based measure is a well-suited proxy for object detection rate. It is found that the Artificial Bee Colony evolutionary algorithm yields a tractable cost function computation. Our experiments highlight the effectiveness of our proposed VSR measure in terms of cost-effectiveness configuration as well as providing insightful analyses that can improve the design of AV systems.Comment: 7 pages including the references, accepted by International Conference on Robotics and Automation (ICRA), 201

Training deep neural density estimators to identify mechanistic models of neural dynamics

Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators-- trained using model simulations-- to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features, and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin-Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics

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