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Drug discovery and development constitute a laborious and costly undertaking. The success of a drug hinges not only good efficacy but also acceptable absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties. Overall, up to 50% of drug development failures have been contributed from undesirable ADMET profiles. As a multiple parameter objective, the optimization of the ADMET properties is extremely challenging owing to the vast chemical space and limited human expert knowledge. In this study, a freely available platform called Chemical Molecular Optimization, Representation and Translation (ChemMORT) is developed for the optimization of multiple ADMET endpoints without the loss of potency (https://cadd.nscc-tj.cn/deploy/chemmort/). ChemMORT contains three modules: Simplified Molecular Input Line Entry System (SMILES) Encoder, Descriptor Decoder and Molecular Optimizer. The SMILES Encoder can generate the molecular representation with a 512-dimensional vector, and the Descriptor Decoder is able to translate the above representation to the corresponding molecular structure with high accuracy. Based on reversible molecular representation and particle swarm optimization strategy, the Molecular Optimizer can be used to effectively optimize undesirable ADMET properties without the loss of bioactivity, which essentially accomplishes the design of inverse QSAR. The constrained multi-objective optimization of the poly (ADP-ribose) polymerase-1 inhibitor is provided as the case to explore the utility of ChemMORT.
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Aprendizado Profundo , Humanos , Desenvolvimento de Medicamentos , Descoberta de Drogas , Inibidores de Poli(ADP-Ribose) PolimerasesRESUMO
BACKGROUND: Drug design is a challenging and important task that requires the generation of novel and effective molecules that can bind to specific protein targets. Artificial intelligence algorithms have recently showed promising potential to expedite the drug design process. However, existing methods adopt multi-objective approaches which limits the number of objectives. RESULTS: In this paper, we expand this thread of research from the many-objective perspective, by proposing a novel framework that integrates a latent Transformer-based model for molecular generation, with a drug design system that incorporates absorption, distribution, metabolism, excretion, and toxicity prediction, molecular docking, and many-objective metaheuristics. We compared the performance of two latent Transformer models (ReLSO and FragNet) on a molecular generation task and show that ReLSO outperforms FragNet in terms of reconstruction and latent space organization. We then explored six different many-objective metaheuristics based on evolutionary algorithms and particle swarm optimization on a drug design task involving potential drug candidates to human lysophosphatidic acid receptor 1, a cancer-related protein target. CONCLUSION: We show that multi-objective evolutionary algorithm based on dominance and decomposition performs the best in terms of finding molecules that satisfy many objectives, such as high binding affinity and low toxicity, and high drug-likeness. Our framework demonstrates the potential of combining Transformers and many-objective computational intelligence for drug design.
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Algoritmos , Desenho de Fármacos , Humanos , Simulação de Acoplamento Molecular , Receptores de Ácidos Lisofosfatídicos/metabolismo , Receptores de Ácidos Lisofosfatídicos/química , Inteligência ArtificialRESUMO
In order to predict the anti-trypanosome effect of carbazole-derived compounds by quantitative structure-activity relationship, five models were established by the linear method, random forest, radial basis kernel function support vector machine, linear combination mix-kernel function support vector machine, and nonlinear combination mix-kernel function support vector machine (NLMIX-SVM). The heuristic method and optimized CatBoost were used to select two different key descriptor sets for building linear and nonlinear models, respectively. Hyperparameters in all nonlinear models were optimized by comprehensive learning particle swarm optimization with low complexity and fast convergence. Furthermore, the models' robustness and reliability underwent rigorous assessment using fivefold and leave-one-out cross-validation, y-randomization, and statistics including concordance correlation coefficient (CCC), [Formula: see text] , [Formula: see text] , and [Formula: see text] . Among all the models, the NLMIX-SVM model, which was established by support vector regression using a nonlinear combination of radial basis kernel function, sigmoid kernel function, and linear kernel function as a new kernel function, demonstrated excellent learning and generalization abilities as well as robustness: [Formula: see text] = 0.9581, mean square error (MSE) = 0.0199 for the training set and [Formula: see text] = 0.9528, MSE = 0.0174 for the test set. [Formula: see text] , [Formula: see text] , CCC, [Formula: see text] , [Formula: see text], and [Formula: see text] are 0.9539, 0.8908, 0.9752, 0.9529, 0.9528, and 0.9633, respectively. The NLMIX-SVM method proved to be a promising way in quantitative structure-activity relationship research. In addition, molecular docking experiments were conducted to analyze the properties of new derivatives, and a new potential candidate drug molecule was ultimately found. In summary, this study will provide help for the design and screening of novel anti-trypanosome drugs.
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Carbazóis , Relação Quantitativa Estrutura-Atividade , Máquina de Vetores de Suporte , Carbazóis/farmacologia , Tripanossomicidas/farmacologiaRESUMO
We have developed a global optimization program named PGA based on particle swarm optimization algorithm coupled with genetic operators for the structures of atomic clusters. The effectiveness and efficiency of the PGA program can be demonstrated by efficiently obtaining the tetrahedral Au20 and double-ring tubular B20, and identifying the ground state ZrSi 17 - 20 - $$ {\mathrm{ZrSi}}_{17\hbox{--} 20}^{-} $$ clusters through the comparison between the simulated and the experimental photoelectron spectra (PESs). Then, the PGA was applied to search for the global minimum structures of Mg n - $$ {\mathrm{Mg}}_n^{-} $$ (n = 3-30) clusters, new structures have been found for sizes n = 6, 7, 12, 14, and medium-sized 21-30 were first determined. The high consistency between the simulated spectra and the experimental ones once again demonstrates the efficiency of the PGA program. Based on the ground-state structures of these Mg n - $$ {\mathrm{Mg}}_n^{-} $$ (n = 3-30) clusters, their structural evolution and electronic properties were subsequently explored. The performance on Au20, B20, ZrSi 17 - 20 - $$ {\mathrm{ZrSi}}_{17\hbox{--} 20}^{-} $$ , and Mg n - $$ {\mathrm{Mg}}_n^{-} $$ (n = 3-30) clusters indicates the promising potential of the PGA program for exploring the global minima of other clusters. The code is available for free upon request.
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In the development of targeted drugs, anticancer peptides (ACPs) have attracted great attention because of their high selectivity, low toxicity and minimal non-specificity. In this work, we report a framework of ACPs generation, which combines Wasserstein autoencoder (WAE) generative model and Particle Swarm Optimization (PSO) forward search algorithm guided by attribute predictive model to generate ACPs with desired properties. It is well known that generative models based on Variational AutoEncoder (VAE) and Generative Adversarial Networks (GAN) are difficult to be used for de novo design due to the problems of posterior collapse and difficult convergence of training. Our WAE-based generative model trains more successfully (lower perplexity and reconstruction loss) than both VAE and GAN-based generative models, and the semantic connections in the latent space of WAE accelerate the process of forward controlled generation of PSO, while VAE fails to capture this feature. Finally, we validated our pipeline on breast cancer targets (HIF-1) and lung cancer targets (VEGR, ErbB2), respectively. By peptide-protein docking, we found candidate compounds with the same binding sites as the peptides carried in the crystal structure but with higher binding affinity and novel structures, which may be potent antagonists that interfere with these target-mediated signaling.
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Neoplasias da Mama , Algoritmos , Neoplasias da Mama/tratamento farmacológico , Feminino , Humanos , Pulmão , Peptídeos , ProteínasRESUMO
Biomass waste-derived engineered biochar for CO2 capture presents a viable route for climate change mitigation and sustainable waste management. However, optimally synthesizing them for enhanced performance is time- and labor-intensive. To address these issues, we devise an active learning strategy to guide and expedite their synthesis with improved CO2 adsorption capacities. Our framework learns from experimental data and recommends optimal synthesis parameters, aiming to maximize the narrow micropore volume of engineered biochar, which exhibits a linear correlation with its CO2 adsorption capacity. We experimentally validate the active learning predictions, and these data are iteratively leveraged for subsequent model training and revalidation, thereby establishing a closed loop. Over three active learning cycles, we synthesized 16 property-specific engineered biochar samples such that the CO2 uptake nearly doubled by the final round. We demonstrate a data-driven workflow to accelerate the development of high-performance engineered biochar with enhanced CO2 uptake and broader applications as a functional material.
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Dióxido de Carbono , Aprendizagem Baseada em Problemas , Carvão Vegetal , AdsorçãoRESUMO
The recent wireless communication systems require high gain, lightweight, low profile, and simple antenna structures to ensure high efficiency and reliability. The existing microstrip patch antenna (MPA) design approaches attain low gain and high return loss. To solve this issue, the geometric dimensions of the antenna should be optimized. The improved Particle Swarm Optimization (PSO) algorithm which is the combination of PSO and simulated annealing (SA) approach (PSO-SA) is employed in this paper to optimize the width and length of the inset-fed rectangular microstrip patch antennas for Ku-band and C-band applications. The inputs to the proposed algorithm such as substrate height, dielectric constant, and resonant frequency and outputs are optimized for width and height. The return loss and gain of the antenna are considered for the fitness function. To calculate the fitness value, the Feedforward Neural Network (FNN) is employed in the PSO-SA approach. The design and optimization of the proposed MPA are implemented in MATLAB software. The performance of the optimally designed antenna with the proposed approach is evaluated in terms of the radiation pattern, return loss, Voltage Standing Wave Ratio (VSWR), gain, computation time, directivity, and convergence speed.
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Accurate detection of pollutant levels in water bodies using fusion algorithms combined with spectral data has become a critical issue for water conservation. However, the number of samples is too small and the model is unstable, which often leads to poor prediction and fails to achieve the measurement goal well. To address these challenges, this paper proposes a practical and effective method to precisely predict the concentrations of nitrite pollution in aquatic environments. The proposed method consists of three steps. Firstly, the dimension of the spectral data is reduced using Kernel Principal Component Analysis (KPCA), followed by sample augmentation using Generative Adversarial Network (GAN) to reduce calculation cost and increase the diversity and scale of the data. Secondly, several improvement strategies, including multi-cluster competitive and adaptive parameter updating, are introduced to enhance the capability of the Particle Swarm Optimization (PSO) algorithm. The improved PSO algorithm is then applied to optimize the initialization weights and biases of the Back Propagation neural network, thereby improving the model fitting and training performance. Finally, the developed prediction model is employed to predict the test set samples. The result suggests that the R2, RMSE, and MAE values are 0.976290, 0.008626, and 0.006617, which outperform the state-of-the-art and provided a promising model for the prediction of nitrite concentration in water.
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Nitritos , Água , Redes Neurais de Computação , Algoritmos , Análise de Componente PrincipalRESUMO
The burgeoning demand for durable and eco-friendly road infrastructure necessitates the exploration of innovative materials and methodologies. This study investigates the potential of Graphene Oxide (GO), a nano-material known for its exceptional dispersibility and mechanical reinforcement capabilities, to enhance the sustainability and durability of concrete pavements. Leveraging the synergy between advanced artificial intelligence techniques-Artificial Neural Networks (ANN), Genetic Algorithms (GA), and Particle Swarm Optimization (PSO)-it is aimed to delve into the intricate effects of Nano-GO on concrete's mechanical properties. The empirical analysis, underpinned by a comparative evaluation of ANN-GA and ANN-PSO models, reveals that the ANN-GA model excels with a minimal forecast error of 2.73%, underscoring its efficacy in capturing the nuanced interactions between GO and cementitious materials. An optimal concentration is identified through meticulous experimentation across varied Nano-GO dosages that amplify concrete's compressive, flexural, and tensile strengths without compromising workability. This optimal dosage enhances the initial strength significantly, and positions GO as a cornerstone for next-generation premium-grade pavement concretes. The findings advocate for the further exploration and eventual integration of GO in road construction projects, aiming to bolster ecological sustainability and propel the adoption of a circular economy in infrastructure development.
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Quantum key distribution (QKD) is a secure communication method that enables two parties to securely exchange a secret key. The secure key rate is a crucial metric for assessing the efficiency and practical viability of a QKD system. There are several approaches that are utilized in practice to calculate the secure key rate. In this manuscript, QKD and error rate optimization based on optimized multi-head self-attention and gated-dilated convolutional neural network (QKD-ERO-MSGCNN) is proposed. Initially, the input signals are gathered from 6G wireless networks which face obstacles to channel. For extending maximum transmission distances and improving secret key rates, the signals are fed to the variable velocity strategy particle swarm optimization algorithm, then the signals are fed to MSGCNN for analysing the quantum bit error rate reduction. The MSGCNN is optimized by intensified sand cat swarm optimization. The performance of the QKD-ERO-MSGCNN approach attains 15.57%, 23.89%, and 31.75% higher accuracy when analysed with existing techniques, like device-independent QKD utilizing random quantum states, practical continuous-variable QKD and feasible optimization parameters, entanglement and teleportation in QKD for secure wireless systems, and QKD for large scale networks methods, respectively.
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Algoritmos , Redes Neurais de Computação , Tecnologia sem Fio , Segurança Computacional , HumanosRESUMO
Poria Cum Radix Pini is a rare medicinal fungus that contains several potential therapeutic ingredients. On this basis, a particle swarm mathematical model was used to optimize the extraction process of total triterpenes from P. Cum Radix Pini, and xanthine oxidase inhibitors were screened using affinity ultrafiltration mass spectrometry. Meanwhile, the accuracy of the ultrafiltration assay was verified by molecular docking experiments and molecular dynamics analysis, and the mechanism of action of the active compounds for the treatment of gout was analyzed by enzymatic reaction kinetics and network pharmacology. A high-speed countercurrent chromatography method combined with the consecutive injection and the economical two-phase solvent system preparation using functional activity coefficient of universal quasichemical model (UNIFAC) mathematical model was developed for increasing the yield of target compound. In addition, dehydropachymic acid and pachymic acid were used as competitive inhibitors, and 3-O-acetyl-16alpha-hydroxydehydrotrametenolic acid and dehydrotrametenolic acid were used as mixed inhibitors. Then, activity-oriented separation and purification were performed by high-speed countercurrent chromatography combined with semi-preparative high-performance liquid chromatography and the purity of the four compounds isolated was higher than 90%. It will help to provide more opportunities to discover and develop new potential therapeutic remedies from health care food resources.
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Gota , Poria , Poria/química , Xantina Oxidase , Simulação de Acoplamento Molecular , Cromatografia Líquida de Alta Pressão/métodos , Inibidores Enzimáticos/farmacologia , Distribuição Contracorrente , Gota/tratamento farmacológicoRESUMO
Pan-sharpening is an image fusion approach that combines the spectral information in multispectral (MS) images with the spatial properties of PAN (Panchromatic) images. This vital technique is used in categorization, detection, and other remote sensing applications. In the first step, the article focuses on increasing the finer spatial details in the MS image with PAN images using two levels of fusion without causing spectral deterioration. The suggested fusion method efficiently utilizes image transformation techniques and spatial domain image fusion methods. The luminance component of MS images typically contains spatial features that are not as detailed as the PAN images. A multiscale transform is applied to the intensity/luminance component and PAN image to introduce features into the intensity component. In the first level of processing, coefficients obtained from the non-subsampled contourlet transform are subjected to particle swarm optimization weighted block-based fusion. The second level of fusion is carried out using the concept of spatial frequency to reduce spectral distortion. Numerous reference and non-reference parameters are used to evaluate the sharpened image's quality. In the next step, the article focuses on designing an evaluation metric for analysing spectral distortion based on the Bhattacharyya coefficient and distance. The Bhattacharyya coefficient and distance are calculated for each segmented region to assess the sharpened images' quality. Spectral degradation analysis using proposed techniques can also be useful for analysing materials in the segmented regions. The research findings demonstrate that the spatial features of fused images obtained from the proposed technique increased with the least spectral degradation.
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This paper presents the design and the non-linearity optimization of a new vertical non-contact angle sensor based on the electromagnetic induction principle. The proposed sensor consists of a stator part (with one solenoidal excitation coil and three sinusoidal receiver coils) and a rotor part (with six rectangular metal sheets). The receiver coil was designed based on the differential principle, which eliminates the effect of the excitation coil on the induced voltage of the receiver coil, and essentially decouples the excitation field from the eddy current field. Moreover, the induced voltages in the three receiver coils are three-phase sinusoidal signals with a phase difference of 10°, which are linearized by CLARK transformation. To minimize the sensor non-linearity, the Plackett-Burman technique was used, which identified the stator radius and the rotor blade thickness as the key factors affecting the sensor linearity. Then, the particle swarm algorithm with decreasing inertia weights was utilized to optimize the sensor linearity. A sensor prototype was made and tested in the laboratory, where the experimental results showed that the sensor non-linearity was only 0.648% and 0.645% in the clockwise and counterclockwise directions, respectively. Notably, the non-linearity of the sensor was less than -0.696% at different speeds.
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Recent advancements in sensor technologies, coupled with signal processing and machine learning, have enabled real-time traffic control systems to effectively adapt to changing traffic conditions. Cameras, as sensors, offer a cost-effective means to determine the number, location, type, and speed of vehicles, aiding decision-making at traffic intersections. However, the effective use of cameras for traffic surveillance requires proper calibration. This paper proposes a new optimization-based method for camera calibration. In this approach, initial calibration parameters are established using the Direct Linear Transformation (DLT) method. Then, optimization algorithms are applied to further refine the calibration parameters for the correction of nonlinear lens distortions. A significant enhancement in the optimization process is achieved through the integration of the Genetic Algorithm (GA) and Particle Swarm Optimization (PSO) into a combined Integrated GA and PSO (IGAPSO) technique. The effectiveness of this method is demonstrated through the calibration of eleven roadside cameras at three different intersections. The experimental results show that when compared to the baseline DLT method, the vehicle localization error is reduced by 22.30% with GA, 22.31% with PSO, and 25.51% with IGAPSO.
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The finite element numerical simulation results of deep pit deformation are greatly influenced by soil layer parameters, which are crucial in determining the accuracy of deformation prediction results. This study employs the orthogonal experimental design to determine the combinations of various soil layer parameters in deep pits. Displacement values at specific measurement points were calculated using PLAXIS 3D under these varying parameter combinations to generate training samples. The nonlinear mapping ability of the Back Propagation (BP) neural network and Particle Swarm Optimization (PSO) were used for sample global optimization. Combining these with actual onsite measurements, we inversely calculate soil layer parameter values to update the input parameters for PLAXIS 3D. This allows us to conduct dynamic deformation prediction studies throughout the entire excavation process of deep pits. The results indicate that the use of the PSO-BP neural network for inverting soil layer parameters effectively enhances the convergence speed of the BP neural network model and avoids the issue of easily falling into local optimal solutions. The use of PLAXIS 3D to simulate the excavation process of the pit accurately reflects the dynamic changes in the displacement of the retaining structure, and the numerical simulation results show good agreement with the measured values. By updating the model parameters in real-time and calculating the pile displacement under different working conditions, the absolute errors between the measured and simulated values of pile top vertical displacement and pile body maximum horizontal displacement can be effectively reduced. This suggests that inverting soil layer parameters using measured values from working conditions is a feasible method for dynamically predicting the excavation process of the pit. The research results have some reference value for the selection of soil layer parameters in similar areas.
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Photovoltaic (PV) panels are one of the popular green energy resources and PV panel parameter estimations are one of the popular research topics in PV panel technology. The PV panel parameters could be used for PV panel health monitoring and fault diagnosis. Recently, a PV panel parameters estimation method based in neural network and numerical current predictor methods has been developed. However, in order to further improve the estimation accuracies, a new approach of PV panel parameter estimation is proposed in this paper. The output current and voltage dynamic responses of a PV panel are measured, and the time series of the I-V vectors will be used as input to an artificial neural network (ANN)-based PV model parameter range classifier (MPRC). The MPRC is trained using an I-V dataset with large variations in PV model parameters. The results of MPRC are used to preset the initial particles' population for a particle swarm optimization (PSO) algorithm. The PSO algorithm is used to estimate the PV panel parameters and the results could be used for PV panel health monitoring and the derivation of maximum power point tracking (MMPT). Simulations results based on an experimental I-V dataset and an I-V dataset generated by simulation show that the proposed algorithms can achieve up to 3.5% accuracy and the speed of convergence was significantly improved as compared to a purely PSO approach.
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The identification of slag inclusion defects in welds is of the utmost importance in guaranteeing the integrity, safety, and prolonged service life of welded structures. Most research focuses on different kinds of weld defects, but branch research on categories of slag inclusion material is limited and critical for safeguarding the quality of engineering and the well-being of personnel. To address this issue, we design a simulated method using ultrasonic testing to identify the inclusion of material categories in austenitic stainless steel. It is based on a simulated experiment in a water environment, and six categories of cubic specimens, including four metallic and two non-metallic materials, are selected to simulate the slag materials of the inclusion defects. Variational mode decomposition optimized by particle swarm optimization is employed for ultrasonic signals denoising. Moreover, the phase spectrum of the denoised signal is utilized to extract the phase characteristic of the echo signal from the water-slag specimen interface. The experimental results show that our method has the characteristics of appropriate decomposition and good denoising performance. Compared with famous signal denoising algorithms, the proposed method extracted the lowest number of intrinsic mode functions from the echo signal with the highest signal-to-noise ratio and lowest normalized cross-correlation among all of the comparative algorithms in signal denoising of weld slag inclusion defects. Finally, the phase spectrum can ascertain whether the slag inclusion is a thicker or thinner medium compared with the weld base material based on the half-wave loss existing or not in the echo signal phase.
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Frequency encoding chipless Radio Frequency Identification (RFID) tags have been frequently using the radar cross section (RCS) parameter to determine the resonant frequencies corresponding to the encoded information. Recent advancements in chipless RFID design have focused on the generation of multiple frequencies without considering the frequency position and signal amplitude. This article proposes a novel method for chipless RFID tag design, in which the RCS response can be located at an exact position, corresponding to the desired encoding signal spectrum. To achieve this, the empirical Taguchi method (TM), in combination with particle swarm optimization (PSO), is used to automatically search for optimal design parameters for chipless RFID tags with a fast response time, to comply with the frequency encoding requirements in the presence of the mutual coupling effect. The proposed design method is validated using I-slotted chipless tag structures that are fabricated and measured with different sets of resonant frequencies.
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In the field of rice processing and cultivation, it is crucial to adopt efficient, rapid and user-friendly techniques to detect the flavor values of various rice varieties. The conventional methods for flavor value assessment mainly rely on chemical analysis and technical evaluation, which not only deplete the rice resources but also incur significant time and labor costs. In this study, hyperspectral imaging technology was utilized in combination with an improved Particle Swarm Optimization Support Vector Machine (PSO-SVM) algorithm, i.e., the Grid Iterative Search Particle Swarm Optimization Support Vector Machine (GISPSO-SVM) algorithm, introducing a new non-destructive technique to determine the flavor value of rice. The method captures the hyperspectral feature data of different rice varieties through image acquisition, preprocessing and feature extraction, and then uses these features to train a model using an optimized machine learning algorithm. The results show that the introduction of GIS algorithms in a PSO-optimized SVM is very effective and can improve the parameter finding ability. In terms of flavor value prediction accuracy, the Principal Component Analysis (PCA) combined with the GISPSO-SVM algorithm achieved 96% accuracy, which was higher than the 93% of the Competitive Adaptive Weighted Sampling (CARS) algorithm. And the introduction of the GIS algorithm in different feature selection can improve the accuracy to different degrees. This novel approach helps to evaluate the flavor values of new rice varieties non-destructively and provides a new perspective for future rice flavor value detection methods.
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Positioning, coverage, and connectivity play important roles in next-generation wireless network applications. The coverage in a wireless sensor network (WSN) is a measure of how effectively a region of interest (ROI) is monitored and targets are detected by the sensor nodes. The random deployment of sensor nodes results in poor coverage in WSNs. Additionally, battery depletion at the sensor nodes creates coverage holes in the ROI and affects network coverage. To enhance the coverage, determining the optimal position of the sensor nodes in the ROI is essential. The objective of this study is to define the optimal locations of sensor nodes prior to their deployment in the given network terrain and to increase the coverage area using the proposed version of an enhanced particle swarm optimization (EPSO) algorithm for different frequency bands. The EPSO algorithm avoids the deployment of sensor nodes in close proximity to each other and ensures that every target is covered by at least one sensor node. It applies a probabilistic coverage model based on the Euclidean distances to detect the coverage holes in the initial deployment of sensor nodes and guarantees a higher coverage probability. Delaunay triangulation (DT) helps to enhance the coverage of a given network terrain in the presence of targets. The combination of EPSO and DT is applied to cover the holes and optimize the position of the remaining sensor nodes in the WSN. The fitness function of the EPSO algorithm yielded converged results with the average number of iterations of 78, 82, and 80 at 3.6 GHz, 26 GHz, and 38 GHz frequency bands, respectively. The results of the sensor deployment and coverage showed that the required coverage conditions were met with a communication radius of 4 m compared with 6-120 m with the existing works.