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Deep optimization design of 2D repetitive control systems with saturating actuators: An adaptive multi-population PSO algorithm. ISA TRANSACTIONS 2023; 140:342-353. [PMID: 37295996 DOI: 10.1016/j.isatra.2023.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/02/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023]
Abstract
This paper presents an optimization design method for a two-dimensional (2D) modified repetitive control system (MRCS) with an anti-windup compensator. Using lifting technology, a 2D hybrid model of the MRCS considering actuator saturation is established to describe the control and learning of the repetitive control. A linear-matrix-inequality (LMI)-based sufficient condition is derived to ensure the stability of the MRCS. Two tuning parameters, the selection of which is critical to the system design, are used in the LMI to adjust the control and learning, and hence the reference-tracking performance. A new cost function, developed through time domain analysis, directly evaluates the control performance of the system without calculating control errors, thus reducing the optimization time. Based on this cost function, an adaptive multi-population particle swarm optimization algorithm is presented to select an optimal pair of tuning parameters in which multiple populations cooperatively search in non-intersecting search intervals. An anti-windup term is added between the low-pass filter and the time delay in the modified repetitive controller to mitigate the undesirable effect of actuator saturation on system performance and stability. Simulations and experiments on the speed control of a rotation control system demonstrate the validity of the approach.
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An improved Fourier Ptychography algorithm for ultrasonic array imaging. Comput Biol Med 2023; 163:107157. [PMID: 37352636 DOI: 10.1016/j.compbiomed.2023.107157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023]
Abstract
Inspired by the optical imaging algorithm, the Fourier Ptychography (FP) algorithm is adopted to improve the resolution of ultrasonic array imaging. In the FP algorithm, the steady-state spectrum is utilized to recover the high-resolution ultrasonic images. Meanwhile, the parameters of FP algorithm are empirical, which can affect the imaging quality of ultrasonic array. Then the particle swarm optimization (PSO) algorithm is used to optimize the parameters of FP algorithm to further improve the imaging quality of ultrasonic array. The tungsten imaging experiments and pig eye imaging experiments are conducted to demonstrate the feasibility and effectiveness of the developed algorithm. In addition, the proposed algorithm and the coherent wave superposition (CWS) algorithm are both based on single plane wave (SPW) algorithms and they are then compared. The results show that the CWS algorithm and FP algorithm have good longitudinal and lateral resolutions, respectively. The particle swarm optimization-based FP (PSOFP) imaging algorithm has both excellent lateral and longitudinal resolutions. The average lateral resolution of PSOFP imaging algorithm is improved by 34.47% compared with CWS imaging algorithm in the tungsten wires experiments, and the lateral boundary structure width of the lens is improved by 49.48% in the pig eye experiments. The proposed algorithm can effectively improve the ultrasonic imaging quality for medical application.
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Application of video image processing in sports action recognition based on particle swarm optimization algorithm. Prev Med 2023:107592. [PMID: 37380132 DOI: 10.1016/j.ypmed.2023.107592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 06/30/2023]
Abstract
The existing sports training methods are mainly aimed at the sports field environment. The traditional sports training is only based on the coaches' visual inspection and combined with their own experience to put forward suggestions, which is relatively inefficient, thus limiting the rise of athletes' sports training level to a certain extent. Based on this background, combining traditional physical education teaching methods with video image processing technology, especially using particle swarm optimization algorithm, can promote the application of human motion recognition technology in physical training. This paper mainly investigates the optimization process of particle swarm optimization algorithm and discusses the development of particle swarm optimization algorithm; Secondly, through video decoding, image noise removal, video enhancement and other methods, complete video image processing and establish the structure of the manikin to achieve the collection of key points of the target, and then collect relevant data with experimental methods The results show that the motion recognition system proposed in this paper can effectively detect the changes of athletes' sampling point path, and can be compared with standard movements, which has a good auxiliary role. With the application of video image processing technology in sports training becoming more and more common, athletes can analyze their training videos in a more intuitive way and find out shortcomings, so as to improve the training effect. This paper studies particle swarm optimization algorithm and applies it to the field of video image processing, which promotes the development of sports action recognition technology based on video processing.
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Carbon emissions predicting and decoupling analysis based on the PSO-ELM combined prediction model: evidence from Chongqing Municipality, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-28022-w. [PMID: 37280494 DOI: 10.1007/s11356-023-28022-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/27/2023] [Indexed: 06/08/2023]
Abstract
The "14th Five-Year Plan" period is a crucial phase for China to achieve the goal of carbon peaking and carbon neutrality (referred to as the "double carbon"). Thus, it is very important to analyze the main factors affecting carbon emissions and accurately predict the change of carbon emissions to achieve the goal of double carbon. For the slow data updates and the low accuracy of traditional prediction models about the carbon emissions, the key factors of carbon emissions change selected by gray correlation method and the consumption of coal, oil, and natural gas were input into four single prediction models: gray prediction model GM(1,1), ridge regression, BP neural network, and WOA-BP neural network to obtain the fitted and predicted values of carbon emissions, which serve as input to the particle swarm optimization-extreme learning machine (PSO-ELM) model together. Based on the PSO-ELM combined prediction method above and the scenario prediction indicators constructed according to relevant policy documents of Chongqing Municipality, the carbon emission values of Chongqing Municipality during the 14th Five-Year Plan period are predicted in this paper. The empirical results show that carbon emissions of Chongqing Municipality still maintain an upward trend, but the growth rate slow down compared with 1998 to 2018. In general, the carbon emission and GDP of Chongqing Municipality showed a weak decoupling state during 1998 to 2025. By calculation, the PSO-ELM combined prediction model is superior to the above four single prediction models in carbon emission prediction and has good property by the robust testing. The research results can enrich the combined prediction method about the carbon emissions and provide policy suggestions for Chongqing's low-carbon development during the 14th Five-Year Plan period.
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Modelling and forecasting non-renewable energy consumption and carbon dioxide emissions in China using a PSO algorithm-based fractional non-linear grey Bernoulli model. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:69651-69665. [PMID: 37142841 DOI: 10.1007/s11356-023-27189-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/19/2023] [Indexed: 05/06/2023]
Abstract
In China, the consumption of non-renewable energy increases not only in general economic growth but also in large amounts of carbon dioxide (CO2) emissions which cause disasters and catastrophic damages to the environment. To alleviate environmental pressure, it is neccessary to forecast and model the relationship between energy consumption and CO2 emissions. In this study, a fractional non-linear grey Bernoulli (FANGBM(1,1)) model based on particle swarm optimization is proposed to forecast and model non-renewable energy consumption and CO2 emissions in China. Firstly, based on the FANGBM(1,1) model, non-renewable energy consumption in China is predicted. The comparison results of several competitive models show that the FANGBM(1,1) model has the best predictive performance. Then, the relationship between non-renewable energy consumption and CO2 emissions is modeled. On this basis, China's future CO2 emissions are effectively predicted based on the established model. The forecast results show that the growth trend of China's CO2 emissions will continue to grow to 2035, while the prediction results in different scenarios also show that that the different growth rates of renewable energy share lead to different times to peak CO2 emissions. In the end, relevant suggestions are proposed to support China's dual carbon goals.
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A new uncertain remanufacturing scheduling model with rework risk using hybrid optimization algorithm. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:62744-62761. [PMID: 36944839 DOI: 10.1007/s11356-023-26219-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/26/2023] [Indexed: 05/10/2023]
Abstract
As a resource-conserving and environmentally friendly manufacturing paradigm, remanufacturing with the potential to realize sustainability in production has been extensively investigated. Scheduling plays a significant role in achieving the remanufacturing benefits. However, the remanufacturing process involves intricate uncertainties because it takes end-of-life products with different qualities as workblanks, which increases the risk of rework and complicates remanufacturing scheduling. Though the traditional stochastic optimization methods or fuzzy theory have been employed to address uncertainties in the remanufacturing scheduling problem, they are constrained with the limited historical data which renders it difficult to describe uncertainties accurately and intuitively. Therefore, a new uncertain remanufacturing scheduling model with rework risk is proposed, in which the interval grey numbers are applied to describe the uncertainty clearly and consider the rework risk in remanufacturing process. To solve this model, a hybrid optimization algorithm that combines differential evolution and particle swarm optimization algorithms through an efficient representation scheme is proposed. Besides, this algorithm integrates multiple improvements to maintain the diversity of the population and enhance its performance. Simulation experiments are conducted on 18 sets of instances with different scales, and the results demonstrated that the proposed algorithm obtains a better optimal solution than other baseline algorithms on 17 sets of instances. The main finding of this study is providing a new method for solving uncertain remanufacturing scheduling problem with rework risk practically and effectively.
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Dual periodic event-triggered control for multi-agent systems with input saturation. ISA TRANSACTIONS 2023; 136:61-74. [PMID: 36610942 DOI: 10.1016/j.isatra.2022.11.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 11/16/2022] [Accepted: 11/26/2022] [Indexed: 05/16/2023]
Abstract
This paper is concerned with the periodic event-triggered consensus of multi-agent systems subject to input saturation. Due to the nonlinearity caused by the input saturation constraint, the accuracy of the event-triggered mechanism to screen data will be reduced. To deal with this problem, a novel dual periodic event-triggered mechanism is first proposed, in which a saturation-assisted periodic event-trigger and a complemental periodic event-trigger work synergistically to screen data more efficiently under the input saturation constraint. In addition, considering the various disturbances in the environment, a more general mixed H∞ and passive performance is introduced to describe the disturbance attenuation level. Based on the Lyapunov-Krasovskii functional, some less conservative consensus criteria are obtained for the multi-agent systems. In addition, under different input saturation constraints, the relationship between the disturbance attenuation level and the data transmission rate is explored. After that, a particle swarm optimization algorithm is a first attempt to estimate and enlarge the region of asymptotic consensus. Finally, an example is given to verify the effectiveness and superiority of our proposed method.
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Design of improved four-coil structure with high uniformity and effective coverage rate. Heliyon 2023; 9:e15193. [PMID: 37089333 PMCID: PMC10119714 DOI: 10.1016/j.heliyon.2023.e15193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/13/2023] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
Helmholtz coils have extensive applications in biological medicine, aerospace, and other industries depending on the simple structure and miraculous magnetic field characteristics. However, the uniform zone generated by them is not appropriate for scientific experiments with large devices. Due to the limitations of Helmholtz coils in application, a novel design technique is proposed to improve the homogeneity and region of magnetic field. The main approach is to add an auxiliary coil on each side of Helmholtz coils to compensate for the magnetic field that exists farther out from the center point. To analyze the size relationship between the auxiliary coil and the main coil to obtain the best magnetic field distribution, the traditional Maclaurin expansion method and particle swarm optimization (PSO) algorithm are used to research and discuss. The magnetic field distribution and the corresponding effective coverage rate (ECR) of the improved schemes with different structural parameters are calculated under the relative deviations of 0.1%, 0.5% and 1%, respectively. The results obtained by the above optimization methods are verified by the finite element software COMSOL and specific experiments. Both optimization methods manifest that the maximum effective coverage rate can be achieved when the size of the auxiliary coil is consistent with that of the main coil. In addition, we compare the improved four-coil structure proposed in this paper with the existing four-coil square structure under the same volume. The data show that the improved structure has certain advantages in the spatial magnetic field distribution. The corresponding tri-axial coil system is established by adopting the parameters on the single axis, which can achieve a constant magnetic field in arbitrary directions by controlling the magnitude and direction of current on each axis. This provides a theoretical basis for the application of magnetic navigation technology.
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Research on fault location algorithm of TPSS based on PSOA. PeerJ Comput Sci 2023; 9:e1213. [PMID: 37346653 PMCID: PMC10280258 DOI: 10.7717/peerj-cs.1213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/21/2022] [Indexed: 06/23/2023]
Abstract
It is extremely important to research traction power supply system (TPSS) protection technology in order to ensure the safe operation of urban rail transit. A TPSS includes rails, return cables, rail potential limiting devices, one-way conducting devices, drainage cabinets, ballast beds, and tunnel structural reinforcements. In urban rail transit, on the basis of the dynamic characteristics of the TPSS, a fault location algorithm based on particle swarm optimization algorithm (PSOA) is developed. An evaluation of multi-point monitoring data is proposed based on fuzzy processing of the average value of polarization potential forward deviation and multi-attribute decision-making. Monitoring points and standard comparison threshold values are determined by the distribution law of stray currents. In conjunction with the actual project, the model is trained using field measured data. Based on the results, TPSSOA is able to achieve optimal discharge current control, reduce network losses and improve power quality. Moreover, the reconstruction results demonstrate the high usability of the proposed method, which will provide guidance to design the TPSS in the future.
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Design and Application of Vague Set Theory and Adaptive Grid Particle Swarm Optimization Algorithm in Resource Scheduling Optimization. JOURNAL OF GRID COMPUTING 2023; 21:24. [PMID: 37089625 PMCID: PMC10103021 DOI: 10.1007/s10723-023-09660-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Abstract
The purpose of resource scheduling is to deal with all kinds of unexpected events that may occur in life, such as fire, traffic jam, earthquake and other emergencies, and the scheduling algorithm is one of the key factors affecting the intelligent scheduling system. In the traditional resource scheduling system, because of the slow decision-making, it is difficult to meet the needs of the actual situation, especially in the face of emergencies, the traditional resource scheduling methods have great disadvantages. In order to solve the above problems, this paper takes emergency resource scheduling, a prominent scheduling problem, as an example. Based on Vague set theory and adaptive grid particle swarm optimization algorithm, a multi-objective emergency resource scheduling model is constructed under different conditions. This model can not only integrate the advantages of Vague set theory in dealing with uncertain problems, but also retain the advantages of adaptive grid particle swarm optimization that can solve multi-objective optimization problems and can quickly converge. The research results show that compared with the traditional resource scheduling optimization algorithm, the emergency resource scheduling model has higher resolution accuracy, more reasonable resource allocation, higher efficiency and faster speed in dealing with emergency events than the traditional resource scheduling model. Compared with the conventional fuzzy theory emergency resource scheduling model, its handling speed has increased by more than 3.82 times.
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A particle swarm optimization algorithm based on an improved deb criterion for constrained optimization problems. PeerJ Comput Sci 2022; 8:e1178. [PMID: 37346308 PMCID: PMC10280275 DOI: 10.7717/peerj-cs.1178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 11/14/2022] [Indexed: 06/23/2023]
Abstract
To solve the nonlinear constrained optimization problem, a particle swarm optimization algorithm based on the improved Deb criterion (CPSO) is proposed. Based on the Deb criterion, the algorithm retains the information of 'excellent' infeasible solutions. The algorithm uses this information to escape from the local best solution and quickly converge to the global best solution. Additionally, to further improve the global search ability of the algorithm, the DE strategy is used to optimize the personal best position of the particle, which speeds up the convergence speed of the algorithm. The performance of our method was tested on 24 benchmark problems from IEEE CEC2006 and three real-world constraint optimization problems from CEC2020. The simulation results show that the CPSO algorithm is effective.
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Research on exercise fatigue estimation method of Pilates rehabilitation based on ECG and sEMG feature fusion. BMC Med Inform Decis Mak 2022; 22:67. [PMID: 35303877 PMCID: PMC8932330 DOI: 10.1186/s12911-022-01808-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/11/2022] [Indexed: 11/15/2022] Open
Abstract
Purpose Surface electromyography (sEMG) is vulnerable to environmental interference, low recognition rate and poor stability. Electrocardiogram (ECG) signals with rich information were introduced into sEMG to improve the recognition rate of fatigue assessment in the process of rehabilitation. Methods Twenty subjects performed 150 min of Pilates rehabilitation exercise. Twenty subjects performed 150 min of Pilates rehabilitation exercise. ECG and sEMG signals were collected at the same time. Aftering necessary preprocessing, the classification model of improved particle swarm optimization support vector machine base on sEMG and ECG data fusion was established to identify three different fatigue states (Relaxed, Transition, Tired). The model effects of different classification algorithms (BPNN, KNN, LDA) and different fused data types were compared. Results IPSO-SVM had obvious advantages in the classification effect of sEMG and ECG signals, the average recognition rate was 87.83%. The recognition rates of sEMG and ECG fusion feature classification models were 94.25%, 92.25%, 94.25%. The recognition accuracy and model performance was significantly improved. Conclusion The sEMG and ECG signal after feature fusion form a complementary mechanism. At the same time, IPOS-SVM can accurately detect the fatigue state in the process of Pilates rehabilitation. On the same model, the recognition effect of fusion of sEMG and ECG(Relaxed: 98.75%, Transition:92.25%, Tired:94.25%) is better than that of only using sEMG signal or ECGsignal. This study establishes technical support for establishing relevant man–machine devices and improving the safety of Pilates rehabilitation.
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Parameter identification of Hammerstein-Wiener nonlinear systems with unknown time delay based on the linear variable weight particle swarm optimization. ISA TRANSACTIONS 2022; 120:89-98. [PMID: 33814264 DOI: 10.1016/j.isatra.2021.03.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
This paper deals with the parameter estimation of Hammerstein-Wiener (H-W) nonlinear systems which have unknown time delay. The linear variable weight particle swarm method is formulated for such time delay systems. This algorithm transforms the nonlinear system identification issue into a function optimization issue in the parameter space, then utilizes the parallel searching ability of the particle swarm optimization and the iterative identification technique to realize the simultaneous estimation of all parameters and the unknown time delay. Finally, parameters in the linear submodule, nonlinear submodule and the time delay are separated from the optimum parameter. Moreover, two illustrative examples are exhibited to evaluate the effectiveness of the proposed method. The simulation results demonstrate that the derived method has fast convergence speed and high estimation accuracy for estimating H-W systems with unknown time delay, and it is applied to the identification of the bed temperature systems.
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Prediction of per capita water consumption for 31 regions in China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:29253-29264. [PMID: 33555473 DOI: 10.1007/s11356-021-12368-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Considering the shortage of per capita water resources in China, the paper established a fractional order accumulated grey prediction model (FGM(1,1)) to predict per capita water consumption of 31 regions (provinces, municipalities, and autonomous regions) in China from 2019 to 2024. The results show that per capita water consumption varies greatly across the different regions. Among them, per capita water consumption of nine regions (i.e., Beijing, Tianjin, Inner Mongolia, Jiangsu, Henan, Hubei, Guizhou, Yunnan, and Shaanxi) shows an increasing trend, whereas per capita water consumption in other 22 regions shows a downward trend. The predictive results can provide a basis for water resource management in China.
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Expeditious COVID-19 similarity measure tool based on consolidated SCA algorithm with mutation and opposition operators. Appl Soft Comput 2021; 104:107197. [PMID: 33642960 PMCID: PMC7895693 DOI: 10.1016/j.asoc.2021.107197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 11/21/2022]
Abstract
COVID-19 is a global pandemic that aroused the interest of scientists to prevent it and design a drug for it. Nowadays, presenting intelligent biological data analysis tools at a low cost is important to analyze the biological structure of COVID-19. The global alignment algorithm is one of the important bioinformatics tools that measure the most accurate similarity between a pair of biological sequences. The huge time consumption of the standard global alignment algorithm is its main limitation especially for sequences with huge lengths. This work proposed a fast global alignment tool (G-Aligner) based on meta-heuristic algorithms that estimate similarity measurements near the exact ones at a reasonable time with low cost. The huge length of sequences leads G-Aligner based on standard Sine–Cosine optimization algorithm (SCA) to trap in local minima. Therefore, an improved version of SCA was presented in this work that is based on integration with PSO. Besides, mutation and opposition operators are applied to enhance the exploration capability and avoiding trapping in local minima. The performance of the improved SCA algorithm (SP-MO) was evaluated on a set of IEEE CEC functions. Besides, G-Aligner based on the SP-MO algorithm was tested to measure the similarity of real biological sequence. It was used also to measure the similarity of the COVID-19 virus with the other 13 viruses to validate its performance. The tests concluded that the SP-MO algorithm has superiority over the relevant studies in the literature and produce the highest average similarity measurements 75% of the exact one.
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CirRNAPL: A web server for the identification of circRNA based on extreme learning machine. Comput Struct Biotechnol J 2020; 18:834-842. [PMID: 32308930 PMCID: PMC7153170 DOI: 10.1016/j.csbj.2020.03.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 03/29/2020] [Accepted: 03/29/2020] [Indexed: 12/27/2022] Open
Abstract
Circular RNA (circRNA) plays an important role in the development of diseases, and it provides a novel idea for drug development. Accurate identification of circRNAs is important for a deeper understanding of their functions. In this study, we developed a new classifier, CirRNAPL, which extracts the features of nucleic acid composition and structure of the circRNA sequence and optimizes the extreme learning machine based on the particle swarm optimization algorithm. We compared CirRNAPL with existing methods, including blast, on three datasets and found CirRNAPL significantly improved the identification accuracy for the three datasets, with accuracies of 0.815, 0.802, and 0.782, respectively. Additionally, we performed sequence alignment on 564 sequences of the independent detection set of the third data set and analyzed the expression level of circRNAs. Results showed the expression level of the sequence is positively correlated with the abundance. A user-friendly CirRNAPL web server is freely available at http://server.malab.cn/CirRNAPL/.
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Key Words
- ACC, Accuracy
- CNN, Convolutional Neural Networks
- Circular RNA
- DAC, Dinucleotide-based auto-covariance
- DACC, Dinucleotide-based auto-cross-covariance
- DCC, Dinucleotide-based cross-covariance
- ELM, extreme learning machine
- Expression level
- Extreme learning machine
- GAC, Geary autocorrelation
- Identification
- MAC, Moran autocorrelation
- MCC, Matthews Correlation Coefficient
- MRMD, Maximum-Relevance-Maximum-Distance
- NMBAC, Normalized Moreau–Broto autocorrelation
- PC-PseDNC-General, General parallel correlation pseudo-dinucleotide composition
- PCGs, protein coding genes
- PSO, particle swarm optimization algorithm
- Particle swarm optimization algorithm
- PseDPC, Pseudo-distance structure status pair composition
- PseSSC, Pseudo-structure status composition
- RBF, radial basis function
- RF, random forest
- SC-PseDNC-General, General series correlation pseudo-dinucleotide composition
- SE, Sensitivity
- SP, Specifity
- SVM, support vector machine
- Triplet, Local structure-sequence triplet element
- circRNA, circular RNA
- lncRNAs, long non-coding RNAs
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PSO-CFDP: A Particle Swarm Optimization-Based Automatic Density Peaks Clustering Method for Cancer Subtyping. Hum Hered 2019; 84:9-20. [PMID: 31412348 DOI: 10.1159/000501481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 06/13/2019] [Indexed: 12/27/2022] Open
Abstract
Cancer subtyping is of great importance for the prediction, diagnosis, and precise treatment of cancer patients. Many clustering methods have been proposed for cancer subtyping. In 2014, a clustering algorithm named Clustering by Fast Search and Find of Density Peaks (CFDP) was proposed and published in Science, which has been applied to cancer subtyping and achieved attractive results. However, CFDP requires to set two key parameters (cluster centers and cutoff distance) manually, while their optimal values are difficult to be determined. To overcome this limitation, an automatic clustering method named PSO-CFDP is proposed in this paper, in which cluster centers and cutoff distance are automatically determined by running an improved particle swarm optimization (PSO) algorithm multiple times. Experiments using PSO-CFDP, as well as LR-CFDP, STClu, CH-CCFDAC, and CFDP, were performed on four benchmark data-sets and two real cancer gene expression datasets. The results show that PSO-CFDP can determine cluster centers and cutoff distance automatically within controllable time/cost and, therefore, improve the accuracy of cancer subtyping.
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