Dataset Information

Parameter Estimation of Two Spiking Neuron Models With Meta-Heuristic Optimization Algorithms.

ABSTRACT: The automatic fitting of spiking neuron models to experimental data is a challenging problem. The integrate and fire model and Hodgkin-Huxley (HH) models represent the two complexity extremes of spiking neural models. Between these two extremes lies two and three differential-equation-based models. In this work, we investigate the problem of parameter estimation of two simple neuron models with a sharp reset in order to fit the spike timing of electro-physiological recordings based on two problem formulations. Five optimization algorithms are investigated; three of them have not been used to tackle this problem before. The new algorithms show improved fitting when compared with the old ones in both problems under investigation. The improvement in fitness function is between 5 and 8%, which is achieved by using the new algorithms while also being more consistent between independent trials. Furthermore, a new problem formulation is investigated that uses a lower number of search space variables when compared to the ones reported in related literature.

SUBMITTER: AbdelAty AM

PROVIDER: S-EPMC8888432 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Publications

Parameter Estimation of Two Spiking Neuron Models With Meta-Heuristic Optimization Algorithms.

AbdelAty Amr M AM Fouda Mohammed E ME Eltawil Ahmed A

Frontiers in neuroinformatics 20220216

The automatic fitting of spiking neuron models to experimental data is a challenging problem. The integrate and fire model and Hodgkin-Huxley (HH) models represent the two complexity extremes of spiking neural models. Between these two extremes lies two and three differential-equation-based models. In this work, we investigate the problem of parameter estimation of two simple neuron models with a sharp reset in order to fit the spike timing of electro-physiological recordings based on two proble ...[more]

PMID: 35250525

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Project description:BackgroundWe address the task of parameter estimation in models of the dynamics of biological systems based on ordinary differential equations (ODEs) from measured data, where the models are typically non-linear and have many parameters, the measurements are imperfect due to noise, and the studied system can often be only partially observed. A representative task is to estimate the parameters in a model of the dynamics of endocytosis, i.e., endosome maturation, reflected in a cut-out switch transition between the Rab5 and Rab7 domain protein concentrations, from experimental measurements of these concentrations. The general parameter estimation task and the specific instance considered here are challenging optimization problems, calling for the use of advanced meta-heuristic optimization methods, such as evolutionary or swarm-based methods.ResultsWe apply three global-search meta-heuristic algorithms for numerical optimization, i.e., differential ant-stigmergy algorithm (DASA), particle-swarm optimization (PSO), and differential evolution (DE), as well as a local-search derivative-based algorithm 717 (A717) to the task of estimating parameters in ODEs. We evaluate their performance on the considered representative task along a number of metrics, including the quality of reconstructing the system output and the complete dynamics, as well as the speed of convergence, both on real-experimental data and on artificial pseudo-experimental data with varying amounts of noise. We compare the four optimization methods under a range of observation scenarios, where data of different completeness and accuracy of interpretation are given as input.ConclusionsOverall, the global meta-heuristic methods (DASA, PSO, and DE) clearly and significantly outperform the local derivative-based method (A717). Among the three meta-heuristics, differential evolution (DE) performs best in terms of the objective function, i.e., reconstructing the output, and in terms of convergence. These results hold for both real and artificial data, for all observability scenarios considered, and for all amounts of noise added to the artificial data. In sum, the meta-heuristic methods considered are suitable for estimating the parameters in the ODE model of the dynamics of endocytosis under a range of conditions: With the model and conditions being representative of parameter estimation tasks in ODE models of biochemical systems, our results clearly highlight the promise of bio-inspired meta-heuristic methods for parameter estimation in dynamic system models within system biology.

Project description:Ordinary differential equation (ODE) models are widely used to study biochemical reactions in cellular networks since they effectively describe the temporal evolution of these networks using mass action kinetics. The parameters of these models are rarely known a priori and must instead be estimated by calibration using experimental data. Optimization-based calibration of ODE models on is often challenging, even for low-dimensional problems. Multiple hypotheses have been advanced to explain why biochemical model calibration is challenging, including non-identifiability of model parameters, but there are few comprehensive studies that test these hypotheses, likely because tools for performing such studies are also lacking. Nonetheless, reliable model calibration is essential for uncertainty analysis, model comparison, and biological interpretation. We implemented an established trust-region method as a modular Python framework (fides) to enable systematic comparison of different approaches to ODE model calibration involving a variety of Hessian approximation schemes. We evaluated fides on a recently developed corpus of biologically realistic benchmark problems for which real experimental data are available. Unexpectedly, we observed high variability in optimizer performance among different implementations of the same mathematical instructions (algorithms). Analysis of possible sources of poor optimizer performance identified limitations in the widely used Gauss-Newton, BFGS and SR1 Hessian approximation schemes. We addressed these drawbacks with a novel hybrid Hessian approximation scheme that enhances optimizer performance and outperforms existing hybrid approaches. When applied to the corpus of test models, we found that fides was on average more reliable and efficient than existing methods using a variety of criteria. We expect fides to be broadly useful for ODE constrained optimization problems in biochemical models and to be a foundation for future methods development.

Project description:This study conducts a comparative analysis of the performance of ten novel and well-performing metaheuristic algorithms for parameter estimation of solar photovoltaic models. This optimization problem involves accurately identifying parameters that reflect the complex and nonlinear behaviours of photovoltaic cells affected by changing environmental conditions and material inconsistencies. This estimation is challenging due to computational complexity and the risk of optimization errors, which can hinder reliable performance predictions. The algorithms evaluated include the Crayfish Optimization Algorithm, the Golf Optimization Algorithm, the Coati Optimization Algorithm, the Crested Porcupine Optimizer, the Growth Optimizer, the Artificial Protozoa Optimizer, the Secretary Bird Optimization Algorithm, the Mother Optimization Algorithm, the Election Optimizer Algorithm, and the Technical and Vocational Education and Training-Based Optimizer. These algorithms are applied to solve four well-established photovoltaic models: the single-diode model, the double-diode model, the triple-diode model, and different photovoltaic module models. The study focuses on key performance metrics such as execution time, number of function evaluations, and solution optimality. The results reveal significant differences in the efficiency and accuracy of the algorithms, with some algorithms demonstrating superior performance in specific models. The Friedman test was utilized to rank the performance of the various algorithms, revealing the Growth Optimizer as the top performer across all the considered models. This optimizer achieved a root mean square error of 9.8602187789E-04 for the single-diode model, 9.8248487610E-04 for both the double-diode and triple-diode models and 1.2307306856E-02 for the photovoltaic module model. This consistent success indicates that the Growth Optimizer is a strong contender for future enhancements aimed at further boosting its efficiency and effectiveness. Its current performance suggests significant potential for improvement, making it a promising focus for ongoing development efforts. The findings contribute to the understanding of the applicability and performance of metaheuristic algorithms in renewable energy systems, providing valuable insights for optimizing photovoltaic models.

Dataset Information

Parameter Estimation of Two Spiking Neuron Models With Meta-Heuristic Optimization Algorithms.

Publications

Parameter Estimation of Two Spiking Neuron Models With Meta-Heuristic Optimization Algorithms.

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