Application of genetic algorithm‐kernel partial least square as a novel non‐linear feature selection method: partitioning of drug molecules

Noorizadeh, Hadi; Sobhanardakani, Soheil; Ahmadi, Taher; Mortazavi, S. S.; Noorizadeh, Mehrab

doi:10.1002/dta.275

Cited by 6 publications

(6 citation statements)

References 43 publications

(61 reference statements)

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“…Especially, the compounds with halogen structures on the benzene ring had the highest activity, while 5a – 5n , compounds with an aromatic ring structure, had the lower activity. According to the existing literature, we speculated that rosin-based amide derivatives would have larger molecular space structure due to the introduction of an aromatic ring, which may result in the weakening of the penetration ability of drug molecules to membranes or tissues and the absorption and transmission of drugs in fungi. , All of these factors can block the binding of the drugs to the receptors and in turn affect the antifungal effect of compounds …”

Section: Resultsmentioning

confidence: 99%

Antifungal Application of Rosin Derivatives from Renewable Pine Resin in Crop Protection

Pan

Jiang

et al. 2020

J. Agric. Food Chem.

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In the current work, we synthesized two series of dehydroabietyl amide derivatives from natural product rosin and evaluated their antifungal effects on Valsa mali, Phytophthora capsici, Botrytis cinerea, Sclerotinia sclerotiorum, and Fusarium oxysporum. In vitro and in vivo antifungal activities results indicated that rosin-based amide compounds containing thiophene heterocycles had better inhibitory effects on B. cinerea. In particular, compound 5b (5-fluoro-2-thiophene dehydroabietyl amide) exhibited the excellent antifungal properties against B. cinerea with an EC 50 of 0.490 mg/L, which was lower compared to the positive control penthiopyrad (0.562 mg/L). Physiological and biochemical studies showed that the primary action mechanism of compound 5b on B. cinerea changes mycelial morphology, increases cell membrane permeability, and inhibits the TCA pathway in respiratory metabolism. Furthermore, QSAR and SAR studies revealed that charge distribution of rosin-based amides derivatives have a key role in the antifungal activity through the hydrogen bonding, conjugation, and electrostatic interaction between the compounds and the receptors of the target. To sum up, this study contributes to the development of rosin-based antifungal agents with a novel structure and preferable biological activity.

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Section: Resultsmentioning

confidence: 99%

Antifungal Application of Rosin Derivatives from Renewable Pine Resin in Crop Protection

Pan

Jiang

et al. 2020

J. Agric. Food Chem.

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“…For the implementation of a GA, it is necessary to previously define its parameters such as crossing probability p c , mutation probability p m [38], population size p and number of generations g [32]. The completion criterion can be determined by the number of generations (iterations) g or the convergence of results [39].…”

Section: Genetic Algorithmsmentioning

confidence: 99%

KPLS Optimization With Nature-Inspired Metaheuristic Algorithms

Mello-Román

Hernández

2020

IEEE Access

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Kernel partial least squares regression (KPLS) is a technique used in several scientific areas because of its high predictive ability. This paper proposes a methodology to simultaneously estimate both the parameters of the kernel function and the number of components of the KPLS regression to maximize its predictive ability. A metaheuristic optimization problem was proposed taking the cumulative cross-validation coefficient as an objective function to be maximized. It was solved using nature-inspired metaheuristic algorithms: the genetic algorithm, particle swarm optimization, grey wolf optimization and the firefly algorithm. To validate the results and have a reference measure of the efficiency of the natureinspired metaheuristic algorithms, derivative-free optimization algorithms were also applied: Hooke-Jeeves and Nelder-Mead. The metaheuristic algorithms estimated optimal values of both of the kernel function parameters and the number of components in the KPLS regression. INDEX TERMS Partial least squares regression, kernel-based method, cross-validation method, and nature-inspired metaheuristic algorithms.

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“…Quantitative structure–retention relationship (QSRR) techniques based on different molecular descriptors have been successfully used to model organic chemicals properties 16. A number of reports, deals with QSRR calculation of several compounds have been published in the literature 17–19…”

Section: Introductionmentioning

confidence: 99%

QSRR using evolved artificial neural network for 52 common pharmaceuticals and drugs of abuse in hair from UPLC–TOF‐MS

Noorizadeh

Farmany

Narimani

et al. 2011

Drug Testing and Analysis

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A quantitative structure-retention relationship (QSRR) study based on an artificial neural network (ANN) was carried out for the prediction of the ultra-performance liquid chromatography-Time-of-Flight mass spectrometry (UPLC-TOF-MS) retention time (RT) of a set of 52 pharmaceuticals and drugs of abuse in hair. The genetic algorithm was used as a variable selection tool. A partial least squares (PLS) method was used to select the best descriptors which were used as input neurons in neural network model. For choosing the best predictive model from among comparable models, square correlation coefficient R(2) for the whole set calculated based on leave-group-out predicted values of the training set and model-derived predicted values for the test set compounds is suggested to be a good criterion. Finally, to improve the results, structure-retention relationships were followed by a non-linear approach using artificial neural networks and consequently better results were obtained. This also demonstrates the advantages of ANN.

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Application of genetic algorithm‐kernel partial least square as a novel non‐linear feature selection method: partitioning of drug molecules

Cited by 6 publications

References 43 publications

Antifungal Application of Rosin Derivatives from Renewable Pine Resin in Crop Protection

Antifungal Application of Rosin Derivatives from Renewable Pine Resin in Crop Protection

KPLS Optimization With Nature-Inspired Metaheuristic Algorithms

QSRR using evolved artificial neural network for 52 common pharmaceuticals and drugs of abuse in hair from UPLC–TOF‐MS

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