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Prediction of protein N-terminal acetylation modification sites based on CNN-BiLSTM-attention model

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computers in Biology and Medicine 2024年 174卷 108330-108330页

作者： Ke, Jinsong Zhao, Jianmei Li, Hongfei Yuan, Lei Dong, Guanghui Wang, Guohua College of Computer and Control Engineering Northeast Forestry University Harbin150040 China College of Life Science Northeast Forestry University Harbin150040 China Department of Hepatobiliary Surgery Quzhou People's Hospital Quzhou324000 China

N-terminal acetylation is one of the most common and important post-translational modifications (PTM) of eukaryotic proteins. PTM plays a crucial role in various cellular processes and disease pathogenesis. Thus, the accurate identification of N-terminal acetylation modifications is important to gain insight into cellular processes and other possible functional mechanisms. Although some algorithmic models have been proposed, most have been developed based on traditional machine learning algorithms and small training datasets. Their practical applications are limited. Nevertheless, deep learning algorithmic models are better at handling high-throughput and complex data. In this study, DeepCBA, a model based on the hybrid framework of convolutional neural network (CNN), bidirectional long short-term memory network (BiLSTM), and attention mechanism deep learning, was constructed to detect the N-terminal acetylation sites. The DeepCBA was built as follows: First, a benchmark dataset was generated by selecting low-redundant protein sequences from the Uniport database and further reducing the redundancy of the protein sequences using the CD-HIT tool. Subsequently, based on the skip-gram model in the word2vec algorithm, tripeptide word vector features were generated on the benchmark dataset. Finally, the CNN, BiLSTM, and attention mechanism were combined, and the tripeptide word vector features were fed into the stacked model for multiple rounds of training. The model performed excellently on independent dataset test, with accuracy and area under the curve of 80.51% and 87.36%, respectively. Altogether, DeepCBA achieved superior performance compared with the baseline model, and significantly outperformed most existing predictors. Additionally, our model can be used to identify disease loci and drug targets. © 2024

关键词： Acetylation

Multi-Unit Floor Plan Recognition and Reconstruction Using Improved Semantic Segmentation of Raster-Wise Floor Plans

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arXiv 2024年

作者： Kratochvila, Lukas de Jong, Gijs Arkesteijn, Monique Bilík, Šimon Zemčík, Tomáš Horak, Karel Rellermeyer, Jan S. Department of Control and Instrumentation Faculty of Electrical Engineering and Communication Brno University of Technology Brno Czech Republic Department of Software Technology Faculty of Electrical Engineering Mathematics and Computer Science TU Delft Delft Netherlands Department of Management in the Built Environment Faculty of Architecture and the Built Environment TU Delft Delft Netherlands Computer Vision and Pattern Recognition Laboratory Department of Computational Engineering Lappeenranta-Lahti University of Technology LUT Lappeenranta Finland Dependable and Scalable Software Systems Institute of Systems Engineering Faculty of Electrical Engineering and Computer Science Leibniz University Hannover Hannover Germany

Digital twins have a major potential to form a significant part of urban management in emergency planning, as they allow more efficient designing of the escape routes, better orientation in exceptional situations, and faster rescue intervention. Nevertheless, creating the twins still remains a largely manual effort, due to a lack of 3D-representations, which are available only in limited amounts for some new buildings. Thus, in this paper we aim to synthesize 3D information from commonly available 2D architectural floor plans. We propose two novel pixel-wise segmentation methods based on the MDA-Unet and MACU-Net architectures with improved skip connections, an attention mechanism, and a training objective together with a reconstruction part of the pipeline, which vectorizes the segmented plans to create a 3D model. The proposed methods are compared with two other state-of-the-art techniques and several benchmark datasets. On the commonly used CubiCasa benchmark dataset, our methods have achieved the mean F1 score of 0.86 over five examined classes, outperforming the other pixel-wise approaches tested. We have also made our code publicly available to support research in the field. © 2024, CC BY.

关键词： Semantic Segmentation

Performance evaluation of electrostatic precipitator transformer by considering power quality

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e-Prime - Advances in Electrical engineering, Electronics and Energy 2024年 10卷

作者： Khakroei, Mohammad Mostafaei, Mohsen Rajeooni, Ashkan Mirzaei MAPNA Electric & Control Engineering & Manufacturing Company (MECO) Alborz Iran Department of Electrical Engineering and Computer Science York University Toronto Canada MAPNA Generator Engineering and Manufacturing Company (PARS) Alborz Iran

Electrostatic precipitators (ESPs) are industrial emission control units. The ESPs are designed to trap and remove dust particles from the exhaust gas stream by using the force of an electric field, which is produced by a high-voltage power supply. One of the main problems of these power supplies is the presence of non-linear elements that adversely affect the power quality of the system. In this paper, a transformer/rectifier (T/R) set is modeled as a high-voltage power supply for an ESP, and the distribution of electromagnetic forces on the set is analyzed using the Finite Element Method (FEM). Additionally, the current waveform and Total Harmonic Distortion (THD) of the T/R set are modified by designing and utilizing a passive filter for the system. First, the working principle and operation of the T/R set are modeled. Then, the electromagnetic design of the T/R set is evaluated by the finite element method and the transient analysis of the flux densities, and associated radial and axial components of electromagnetic forces distribution on the T/R set. Afterward, a wire-plate ESP configuration is modeled and analyzed based on the Electric potential and Electric field. Finally, the design method of the passive filter is explained, and it is shown that the utilization of the designed passive filter has significantly reduced the THD of the T/R set. © 2024 The Authors

关键词： Electrostatic precipitator (ESP) Finite element method (FEM) Transformer/Rectifier (T/R) set

computer Vision-control-Based CNN-PID for Mobile Robot

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computers, Materials & Continua 2021年第7期68卷 1065-1079页

作者： Rihem Farkh Mohammad Tabrez Quasim Khaled Al jaloud Saad Alhuwaimel Shams Tabrez Siddiqui College of Engineering Muzahimiyah BranchKing Saud UniversityP.O.Box 2454Riyadh11451Saudi Arabia College of Computing and Information Technology University of BishaBisha67714Saudi Arabia King Abdulaziz City for Science and Technology Saudi Arabia Department of Computer Science College of Computer Science and Information TechnologyJazan UniversityJazanSaudi Arabia Department of Electrical Engineering Laboratory for AnalysisConception and Control of SystemsLR-11-ES20National Engineering School of TunisTunis El Manar UniversityTunisTunisia

With the development of artificial intelligence technology,various sectors of industry have *** them,the autonomous vehicle industry has developed considerably,and research on self-driving control systems using artificial intelligence has been extensively *** on the use of image-based deep learning to monitor autonomous driving systems have recently been *** this paper,we propose an advanced control for a serving robot.A serving robot acts as an autonomous line-follower vehicle that can detect and follow the line drawn on the floor and move in specified *** robot should be able to follow the trajectory with speed *** controllers were used simultaneously to achieve *** neural networks(CNNs)are used for target tracking and trajectory prediction,and a proportional-integral-derivative controller is designed for automatic steering and speed *** study makes use of a Raspberry PI,which is responsible for controlling the robot car and performing inference using CNN,based on its current image input.

关键词： Autonomous car pid control deep learning convolutional neural network differential drive system raspberry pi

Extracting Stress-Related EEG Patterns from Pre-Sleep EEG for Forecasting Slow-Wave Sleep Deficiency

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IEEE Transactions on Neural Systems and Rehabilitation engineering 2024年 32卷 1817-1827页

作者： Su, Cheng-Hua Ko, Li-Wei Jung, Tzyy-Ping Onton, Julie Tzou, Shey-Cherng Juang, Jia-Chi Hsu, Chung-Yao Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu300 Taiwan Institute of Electrical and Control Engineering National Yang Ming Chiao Tung University Hsinchu300 Taiwan Kaohsiung Medical University Drug Development and Value Creation Research Center Department of Biomedical Science and Environmental Biology Kaohsiung807 Taiwan University of California San Diego Swartz Center for Computational Neuroscience La Jolla CA92093 United States National Yang Ming Chiao Tung University Department of Computer Science Hsinchu300 Taiwan University of California San Diego Institute for Neural Computation La Jolla CA92093 United States National Yang Ming Chiao Tung University Department of Biological Science and Technology Hsinchu300 Taiwan Kaohsiung Medical University Hospital Sleep Disorders Center Department of Neurology Kaohsiung807 Taiwan Kaohsiung Medical University College of Medicine Department of Neurology Kaohsiung807 Taiwan

Sleep is vital to our daily activity. Lack of proper sleep can impair functionality and overall health. While stress is known for its detrimental impact on sleep quality, the precise effect of pre-sleep stress on subsequent sleep structure remains unknown. This study introduced a novel approach to study the pre-sleep stress effect on sleep structure, specifically slow-wave sleep (SWS) deficiency. To achieve this, we selected forehead resting EEG immediately before and upon sleep onset to extract stress-related neurological markers through power spectra and entropy analysis. These markers include beta/delta correlation, alpha asymmetry, fuzzy entropy (FuzzEn) and spectral entropy (SpEn). Fifteen subjects were included in this study. Our results showed that subjects lacking SWS often exhibited signs of stress in EEG, such as an increased beta/delta correlation, higher alpha asymmetry, and increased FuzzEn in frontal EEG. Conversely, individuals with ample SWS displayed a weak beta/delta correlation and reduced FuzzEn. Finally, we employed several supervised learning models and found that the selected neurological markers can predict subsequent SWS deficiency. Our investigation demonstrated that the classifiers could effectively predict varying levels of slow-wave sleep (SWS) from pre-sleep EEG segments, achieving a mean balanced accuracy surpassing 0.75. The SMOTE-Tomek resampling method could improve the performance to 0.77. This study suggests that stress-related neurological markers derived from pre-sleep EEG can effectively predict SWS deficiency. Such information can be integrated with existing sleep-improving techniques to provide a personalized sleep forecasting and improvement solution. © 2001-2011 IEEE.

关键词： Entropy

control of Nonlinear Systems Under Multiple Time-Varying Output Constraints: A Single Funnel Approach

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arXiv 2023年

作者： Mehdifar, Farhad Lindemann, Lars Bechlioulis, Charalampos P. Dimarogonas, Dimos V. The Division of Decision and Control Systems KTH Royal Institute of Technology Stockholm Sweden Thomas Lord Department of Computer Science University of Southern California Los AngelesCA United States The Division of Systems and Control The Department of Electrical and Computer Engineering University of Patras Patra Greece

This paper proposes a novel control framework for handling (potentially coupled) multiple time-varying output constraints for uncertain nonlinear systems. First, it is shown that the satisfaction of multiple output constraints boils down to ensuring the positiveness of a scalar variable (the signed distance from the time-varying output-constrained set’s boundary). Next, a single funnel constraint is designed properly, whose satisfaction ensures convergence to and invariance of the time-varying output-constrained set. Then a robust and low-complexity funnel-based feedback controller is designed employing the prescribed performance control method. Finally, a simulation example clarifies and verifies the proposed approach. Copyright © 2023, The Authors. All rights reserved.

关键词： Time varying control systems

State Derivative Normalization for Continuous-Time Deep Neural Networks

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arXiv 2024年

作者： Weigand, Jonas Beintema, Gerben I. Ulmen, Jonas Görges, Daniel Tóth, Roland Schoukens, Maarten Ruskowski, Martin Chair of Machine Tools and Control Systems RPTU Kaiserslautern The German Research Center for Artificial Intelligence Kaiserslautern Germany Group The Department of Electrical Engineering Eindhoven University of Technology Netherlands The Systems and Control Laboratory The Institute for Computer Science and Control Budapest Hungary Institute for Electromobility RPTU Kaiserslautern Germany

The importance of proper data normalization for deep neural networks is well known. However, in continuous-time state-space model estimation, it has been observed that improper normalization of either the hidden state or hidden state derivative of the model estimate, or even of the time interval can lead to numerical and optimization challenges with deep learning based methods. This results in a reduced model quality. In this contribution, we show that these three normalization tasks are inherently coupled. Due to the existence of this coupling, we propose a solution to all three normalization challenges by introducing a normalization constant at the state derivative level. We show that the appropriate choice of the normalization constant is related to the dynamics of the to-be-identified system and we derive multiple methods of obtaining an effective normalization constant. We compare and discuss all the normalization strategies on a benchmark problem based on experimental data from a cascaded tanks system and compare our results with other methods of the identification literature. © 2024, CC BY-SA.

关键词： Ordinary differential equations

Reduced Network Cumulative Constraint Violation for Distributed Bandit Convex Optimization under Slater’s Condition

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arXiv 2024年

作者： Zhang, Kunpeng Yi, Xinlei Ding, Jinliang Cao, Ming Johansson, Karl H. Yang, Tao State Key Laboratory of Synthetical Automation for Process Industries Northeastern University Shenyang110819 China Department of Control Science and Engineering College of Electronics and Information Engineering Tongji University Shanghai201800 China Engineering and Technology Institute Groningen Faculty of Science and Engineering University of Groningen GroningenAG 9747 Netherlands Division of Decision and Control Systems School of Electrical Engineering and Computer Science KTH Royal Institute of Technology Sweden Digital Futures Stockholm10044 Sweden

This paper studies the distributed bandit convex optimization problem with time-varying inequality constraints, where the goal is to minimize network regret and cumulative constraint violation. To calculate network cumulative constraint violation, existing distributed bandit online algorithms solving this problem directly use the clipped constraint function to replace its original constraint function. However, the use of the clipping operation renders Slater’s condition (i.e, there exists a point that strictly satisfies the inequality constraints at all iterations) ineffective to achieve reduced network cumulative constraint violation. To tackle this challenge, we propose a new distributed bandit online primal–dual algorithm. If local loss functions are convex, we show that the proposed algorithm establishes an O(T max{c,1−c})network regret bound and an O(T 1−c/2) network cumulative constraint violation bound, where T is the total number of iterations and c ∈ (0, 1) is a user-defined trade-off parameter. When Slater’s condition holds, the network cumulative constraint violation bound is reduced to O(T 1−c). In addition, if local loss functions are strongly convex, for the case where strongly convex parameters are unknown, the network regret bound is reduced to O(T1−c), and the network cumulative constraint violation bound is O(T1−c/2) and O(T1−c) without and with Slater’s condition, respectively. For the case where strongly convex parameters are known, the network regret bound is further reduced to O)(log(T)), and the network cumulative constraint violation bound is reduced to O(log(T)T) and O(log(T)) without and with Slater’s condition, respectively. To the best of our knowledge, this paper is among the first to establish reduced (network) cumulative constraint violation bounds for (distributed) bandit convex optimization with time-varying constraints under Slater’s condition. Finally, a numerical example is provided to verify the theoretical results. Copyright © 2

关键词： Convex optimization

Designing a Trajectory control System for Wheelchairs with a Combination of Automatic and Manual Steering Methods

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Periodica Polytechnica Transportation engineering 2024年第4期52卷 412-422页

作者： Vu, Van Tan Nguyen, Quang Thinh Nakagawa, Chihiro Nguyen, Trung Nguyen Le, Thanh Long Nguyen, Van Vinh Hoang, Thi Lan Anh Do, Trong Tu Mihály, András Gáspár, Péter Department of Automotive Mechanical Engineering Faculty of Mechanical Engineering University of Transport and Communications Building A6 no. 3 Cau Giay Street Lang Thuong Ward Dong Da District Hanoi100000 Viet Nam Japan Technology Solution Joint Stock Company 9 Dau Ma Street Section 2 Thi Cau Ward Bac Ninh Bac Ninh222000 Viet Nam School of Engineering Osaka Metropolitan University 1-1 Gakuen-cho Nakaku Sakai Osaka599-8531 Japan Emergency abdominal surgery Department Viet Duc University Hospital no. 40 Trang Thi Street Hanoi100000 Viet Nam Mechanical and Power Engineering Faculty Electric Power University no. 235 Hoang Quoc Viet Street Co Nhue Ward Bac Tu Liem District Hanoi100000 Viet Nam Systems and Control Laboratory Institute for Computer Science and Control Hungarian Research Network Kende u. 13-17 Budapest1111 Hungary

A wheelchair is a specialized form of Personal Mobility Vehicle (PMV) designed to help people with disabilities move safely to their desired locations. Unlike conventional PMVs, wheelchairs for people with disabilities are challenging to manually control in environments with heavy traffic. This study focuses on designing and feasibility testing of control systems for PMVs to meet safety and efficiency standards, even in complex environments. First, a control structure model for PMVs is proposed. This is followed by the application of a combination of First In First Out (FIFO) and Dijkstra traffic control methods to determine effective trajectories for PMVs. The proposed control system is then tested on the campus of the University of Transport and Communications. Simulation results show that when comparing the travel time of 10 PMVs, the order execution time for each PMV remains stable (within 10%) for up to 20 PMVs. However, when the number of PMVs increases to 25, 30, 35, and 40 vehicles, the order execution time increases by 35%, 55%, 103%, and 119%, respectively. These results demonstrate that the system can control a large number of PMVs, ensuring safety, flexibility, and efficiency. © 2024 Budapest University of Technology and Economics. All rights reserved.

关键词： Travel time