Enhanced segment particle swarm optimization for large-scale kinetic parameter estimation of escherichia coli network model

The development of a large-scale metabolic model of Escherichia coli (E. coli) is very crucial to identify the potential solution of industrially viable productions. However, the large-scale kinetic parameters estimation using optimization algorithms is still not applied to the main metabolic pathway of the E. coli model, and they’re a lack of accuracy result been reported for current parameters estimation using this approach. Thus, this research aimed to estimate large-scale kinetic parameters of the main metabolic pathway of the E. coli model. In this regard, a Local Sensitivity Analysis, Segment Particle Swarm Optimization (Se-PSO) algorithm, and the Enhanced Segment Particle Swarm Optimization (ESe-PSO) algorithm was adapted and proposed to estimate the parameters. Initially, PSO algorithm was adapted to find the globally optimal result based on unorganized particle movement in the search space toward the optimal solution. This development then introduces the Se-PSO algorithm in which the particles are segmented to find a local optimal solution at the beginning and later sought by the PSO algorithm. Additionally, the study proposed an Enhance Se-PSO algorithm to improve the linear value of inertia weigh

A Comparison of Particle Swarm optimization and Global African Buffalo Optimization

The performance of Particle Swarm Optimization (PSO) brings attention to the field of algorithms when deals with different optimization problems. Due to her simple implementation, small consumption, and very effective in finding a solution in many problems, (PSO) becomes well known to the field of algorithms. In addition, the late proposed algorithms mostly are compared to the well-known algorithm such as PSO. Thus, the Global African Buffalo Optimization (GABO) was proposed lately and yet not been compared to the old well-known algorithms in terms of accuracy and time consumption. However, in this paper, a comparison between Particle Swarm Optimization (PSO) and Global African Buffalo Optimization (GABO) algorithms was performed. Five different nonlinear equations with their upper and lower boundaries values were selected as the test optimization functions problem in addition to PSO was applied to real case study. The experimental results illustrated the differences in the performances of both algorithms toward the optimum solution. At the end of the experiments, the PSO algorithm quickly convergence towards the optimum solution using a few particles and iterations rather than GABO. However, the experimental result showed that PSO achieved good results in all the test cases within a short time. In many cases, PSO and GABO are promising optimization methods

Review : Machine and deep learning methods in Malaysia for COVID-19

The global pandemic of the coronavirus disease COVID-19 has impacted a variety of operations. This dilemma is also attributable to the lockdown measures taken by the afflicted nations. The entire or partial shutdown enacted by nations across the globe affected the majority of hospitals and clinics until the pandemic was contained. The judgements made by the authorities of each impacted nation vary based on a number of variables, including the nation's severity of reported cases, the availability of vaccines, beds in intensive care unit (ICU), staff number, patient number, and medicines. Consequently, this work offers a thorough analysis of the most recent machine learning (ML) and deep learning (DL) approaches for COVID-19 that can assist the medical field in offering quick and exact COVID-19 diagnosis in Malaysia. This research aims to review the machine learning and deep learning methods that were used to help diagnose COVID-19 in Malaysia

Estimation of small-scale kinetic parameters of escherichia coli (E. coli) model by enhanced segment particle swarm optimization algorithm ese-pso

The ability to create “structured models” of biological simulations is becoming more and more commonplace. Although computer simulations can be used to estimate the model, they are restricted by the lack of experimentally available parameter values, which must be approximated. In this study, an Enhanced Segment Particle Swarm Optimization (ESe-PSO) algorithm that can estimate the values of small-scale kinetic parameters is described and applied to E. coli’s main metabolic network as a model system. The glycolysis, phosphotransferase system, pentose phosphate, the TCA cycle, gluconeogenesis, glyoxylate pathways, and acetate formation pathways of Escherichia coli are represented by the Differential Algebraic Equations (DAE) system for the metabolic network. However, this algorithm uses segments to organize particle movements and the dynamic inertia weight ((Formula presented.)) to increase the algorithm’s exploration and exploitation potential. As an alternative to the state-of-the-art algorithm, this adjustment improves estimation accuracy. The numerical findings indicate a good agreement between the observed and predicted data. In this regard, the result of the ESe-PSO algorithm achieved superior accuracy compared with the Segment Particle Swarm Optimization (Se-PSO), Particle Swarm Optimization (PSO), Genetic Algorithm (GA), and Differential Evolution (DE) algorithms. As a result of this innovative approach, it was concluded that small-scale and even entire cell kinetic model parameters can be developed

Kinetic paramaters identification for large-scle metabolic model of escherichia coli

One of the biggest challenging in metabolic engineering is to design an accurate model of large-scale of metabolic network in metabolic engineering field; which require an appropriate sensitivity analysis and optimization techniques. This research focusing on identifying the optimize values of large-scale kinetic parameters of E. coli model. The model under study consist of five metabolic pathways which are Glycolysis, Pentose Phosphate, TCA cycle, Gluconegenesis and Glycoxylate; which contain 194 kinetic parameters to be optimize. This model also includes PTS system in addition to Acetate formation, 23 metabolites, 28 enzymatic reactions and 10 co-factors. The experimental data were run in 0.1 and 0.2 dilution rates at continuous culture on steady-state condition. The One-At-A-Time Sensitivity Measure and Particle Swarm Optimization (PSO) techniques was applied to the model under study in order to identify the optimum values of the kinetics. The result stated from the One-At-A-Time Sensitivity Measure shows that there are 7 kinetics affecting highly in the model response under 0.1 dilution rate, while in 0.2 there are 8 kinetics affecting highly in the model response also. The result stated from PSO shows that, this technique can minimize the errors of our simulation result by % as compare to (Ishii et al., 2007) and % as compare to (Hoque et al., 2005). Based on the results found by the techniques, these tichniques can be applied to correct the model response through large-scale kinetic parameters

An Enhanced Segment Particle Swarm Optimization Algorithm for Kinetic Parameters Estimation of the Main Metabolic Model of Escherichia Coli

Building a biologic model that describes the behavior of a cell in biologic systems is aimed at understanding the physiology of the cell, predicting the production of enzymes and metabolites, and providing a suitable data that is valid for bio-products. In addition, building a kinetic model requires the estimation of the kinetic parameters, but kinetic parameters estimation in kinetic modeling is a difficult task due to the nonlinearity of the model. As a result, kinetic parameters are mostly reported or estimated from different laboratories in different conditions and time consumption. Hence, based on the aforementioned problems, the optimization algorithm methods played an important role in addressing these problems. In this study, an Enhanced Segment Particle Swarm Optimization algorithm (ESe-PSO) was proposed for kinetic parameters estimation. This method was proposed to increase the exploration and the exploitation of the Segment Particle Swarm Optimization algorithm (Se-PSO). The main metabolic model of E. coli was used as a benchmark which contained 172 kinetic parameters distributed in five pathways. Seven kinetic parameters were well estimated based on the distance minimization between the simulation and the experimental results. The results revealed that the proposed method had the ability to deal with kinetic parameters estimation in terms of time consumption and distance minimization

Estimation of Small-Scale Kinetic Parameters of <i>Escherichia coli</i> (<i>E. coli</i>) Model by Enhanced Segment Particle Swarm Optimization Algorithm ESe-PSO

The ability to create “structured models” of biological simulations is becoming more and more commonplace. Although computer simulations can be used to estimate the model, they are restricted by the lack of experimentally available parameter values, which must be approximated. In this study, an Enhanced Segment Particle Swarm Optimization (ESe-PSO) algorithm that can estimate the values of small-scale kinetic parameters is described and applied to E. coli’s main metabolic network as a model system. The glycolysis, phosphotransferase system, pentose phosphate, the TCA cycle, gluconeogenesis, glyoxylate pathways, and acetate formation pathways of Escherichia coli are represented by the Differential Algebraic Equations (DAE) system for the metabolic network. However, this algorithm uses segments to organize particle movements and the dynamic inertia weight (ω) to increase the algorithm’s exploration and exploitation potential. As an alternative to the state-of-the-art algorithm, this adjustment improves estimation accuracy. The numerical findings indicate a good agreement between the observed and predicted data. In this regard, the result of the ESe-PSO algorithm achieved superior accuracy compared with the Segment Particle Swarm Optimization (Se-PSO), Particle Swarm Optimization (PSO), Genetic Algorithm (GA), and Differential Evolution (DE) algorithms. As a result of this innovative approach, it was concluded that small-scale and even entire cell kinetic model parameters can be developed