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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Li, Yichong Liu, Xiaojian Cheng, Fan Pan, Xiaoyong Yang, Yang Shanghai Jiao Tong University Department of Computer Science and Engineering Shanghai200240 China Shanghai Jiao Tong University Institute of Image Processing and Pattern Recognition Shanghai200240 China Ministry of Education of China Key Laboratory of System Control and Information Processing Shanghai200240 China Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai200240 China

ISBN: (纸本)9798350386226

RNA-binding proteins (RBPs) are essential for gene expression, and the complex RNA-protein interaction mechanisms require analysis of global RNA information. Therefore, accurate prediction of RBP binding sites on full-length RNA transcripts is crucial for understanding these mechanisms and their roles in diseases. While machine learning methods can predict RBP binding to RNA fragments, extending this to full-length transcripts presents challenges due to sequence length and data imbalance. In this paper, we introduce RBP-Former, a binding site joint prediction model designed specifically for full-length RNA transcripts that can be used for multiple RBPs. This model processes information at both coarse and fine-grained levels to fully exploit sequence data and its interactions with multiple RBPs. We develop multi-level imbalance learning strategies, achieving favorable results on imbalanced data. Our method outperforms existing methods in predicting binding sites on full-length RNA transcripts for multiple RBPs, demonstrating its effectiveness in handling imbalanced label and sample distributions. © 2024 IEEE.

关键词： Binding sites

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Surrogate-Assisted Multiobjective Gene Selection for Cell Classification from Large-Scale Single-Cell RNA Sequencing Data

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IEEE Transactions on Evolutionary Computation 2025年第3期29卷 601-615页

作者： Lin, Jianqing He, Cheng Jiang, Hanjing Huang, Yabing Jin, Yaochu Huazhong University of Science and Technology Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China School of Artificial Intelligence and Automation Wuhan430074 China Huazhong University of Science and Technology State Key Laboratory of Advanced Electromagnetic Technology School of Electrical and Electronic Engineering Wuhan430074 China Renmin Hospital Department of Pathology Wuhan University Wuhan430060 China Westlake University Trustworth and General Artificial Intelligence Laboratory School of Engineering Hangzhou310030 China

Accurate cell classification is crucial but expensive for large-scale single-cell RNA sequencing (scRNA-seq) analysis. Gene selection (GS) emerges as a pivotal technique in identifying gene subsets of scRNA-seq for classification accuracy improvement and gene scale reduction. Nevertheless, the rising scale of scRNA-seq data presents challenges to existing GS methods regarding performance and computational time. Thus, we propose a surrogate-assisted evolutionary algorithm for multiobjective GS to address these deficiencies. An innovative two-phase initialization method is proposed to select sparse solutions to provide preliminary insights into gene contributions. Then, a binary competitive swarm optimizer is proposed for effective global search, where a local search method is embedded to eliminate irrelevant genes for efficiency consideration. Additionally, a surrogate model is adopted to forecast classification accuracy efficiently and substitutes part of the computationally expensive classification process. Experiments are conducted on eight large-scale scRNA-seq datasets with more than 20,000 genes. The effectiveness of the proposed GS method for scRNA-seq cell classification compared with eight state-of-the-art methods is validated. Gene expression analysis results of selected genes further validated the significance of the genes selected by the proposed method in the classification of scRNA-seq data. © 1997-2012 IEEE.

关键词： Gene expression

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Interval Type-2 Fuzzy Hierarchical Adaptive Cruise Following-control for intelligent Vehicles

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IEEE/CAA Journal of Automatica Sinica 2022年第9期9卷 1658-1672页

作者： Hong Mo Yinghui Meng Fei-Yue Wang Dongrui Wu the College of Electric and Information Engineering Changsha University of Science and TechnologyChangsha 410114China the State Key Laboratory of Management and Control for Complex Systems Institute of AutomationChinese Academy of SciencesBeijing 100190 Qingdao Academy of Intelligent Industries Qingda 266109 the Center of China Economic and Social Security University of Chinese Academy of SciencesBeijing 100190China the Ministry of Education Key Laboratory on Image Information Processing and Intelligent Control the School of Artificial Intelligence and AutomationHuazhong University of Science and TechnologyWuhan 430074China

intelligent vehicles can effectively improve traffic congestion and road traffic *** cruise followingcontrol(ACFC)is a vital part of intelligent *** this paper,a new hierarchical vehicle-following control strategy is presented by synthesizing the variable time headway model,type-2 fuzzy control,feedforward+fuzzy proportion integration(PI)feedback(F+FPIF)control,and inverse longitudinal dynamics model of ***,a traditional variable time headway model is improved considering the acceleration of the lead ***,an interval type-2 fuzzy logic controller(IT2 FLC)is designed for the upper structure of the ACFC system to simulate the driver's operating *** reduce the nonlinear influence and improve the tracking accuracy for the desired acceleration,the control strategy of F+FPIF is given for the lower control ***,the lower control method proposed in this paper is compared with the fuzzy PI control and the traditional method(no lower controller for tracking desired acceleration)***,the proportion integration differentiation(PID),linear quadratic regulator(LQR),subsection function control(SFC)and type-1 fuzzy logic control(T1 FLC)are respectively compared with the IT2 FLC in control performance under different ***,the simulation results show the effectiveness of IT2 FLC for the upper structure and F+FPIF control for the lower structure.

关键词： Adaptive cruise following-control(ACFC) feedforward+fuzzy proportion integration(PI)feedback(F+FPIF) type-2 fuzzy control variable time headway

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Remaining Useful Life Prediction for a Multi-stack Solid Oxide Fuel Cell System with Degradation Interactions

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CSEE Journal of Power and Energy Systems 2022年第4期8卷 1207-1214页

作者： Xiaojuan Wu Liangfei Xu Yang Huang Danan Yang Junhao Wang Houjun Wang Xi Li School of Automation Engineering University of Electronic Science and Technology of ChinaChengdu 610054China State Key Lab of Automotive Safety and Energy School of Vehicle and MobilityTsinghua UniversityBeijing 100084China School of Artificial Intelligencei and Automation Key Laboratory of Image Processing and Intelligent Control of Education MinistryHuazhong University of Science and TechnologyWuhan 430074China

Due to the constraints of manufacturing and materials,high-power plants cannot rely on only one solid oxide fuel cell stack.A multi-stack system is a solution for a highpower system,which consists of multiple fuel cell stacks.A short lifetime is one of the main challenges for the fuel cell before largescale commercial applications,and prognostic is an important method to improve the reliability of fuel *** from the traditional prognostic approaches applied to single-stack fuel cell systems,the key problem in multi-stack prediction is how to solve the correlation of multi-stack degradation,which can directly affect the accuracy of *** response to this difficulty,a standard Brownian motion is added to the traditional Wiener process to model the degradation of each stack,and then the probability density function of the remaining useful life(RUL)of each stack is ***,a Copula function is adopted to reflect the dependence between life distributions,so as to obtain the remaining useful life for the whole multi-stack system.1 The simulation results show that compared with the traditional prediction model,the proposed approach has a higher prediction accuracy for multi-stack fuel cell systems.

关键词： Degradation interaction multi-stack remaining useful life(RUL) solid oxide fuel cell(SOFC)

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Structure-free containment control for uncertain underactuated multiple Euler-Lagrange systems

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Science China(Information Sciences) 2023年第11期66卷 150-168页

作者： Housheng SU Yali WU Liren ZHANG Xia CHEN Key Laboratory of Image Processing and Intelligent Control of Education Ministry of China School of Artificial Intelligence and Automation Huazhong University of Science and Technology State Key Laboratory of Advanced Electromagnetic Engineering and Technology School of Electrical and Electronic Engineering Huazhong University of Science and Technology

This article studies the problem of structure-free distributed containment control for uncertain underactuated multiple Euler-Lagrange systems(MELSs) considering disturbances by using a layered approach. First, the second layer is the virtual layer constructed artificially for hierarchical control. We move all virtual nodes to the convex hull formed by leaders in the first layer by implementing containment control algorithms on all virtual nodes. Then, the third layer is the following layer, and we propose an adaptive robust tracking controller to ensure that each follower in the third layer tracks the corresponding virtual node in the second layer. So far, the underactuated MELSs can achieve containment control. Furthermore,through the theoretical derivation, sufficient conditions are obtained to achieve the objective of structure-free containment control. Finally, the effectiveness of the proposed stratified structure-free containment control method is verified by a simulation example.

关键词： Euler-Lagrange systems underactuated system containment control adaptive-robust control

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SliceProp: A Slice-Wise Bidirectional Propagation Model for Interactive 3D Medical image Segmentation 1

SliceProp: A Slice-Wise Bidirectional Propagation Model for ...

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1st IEEE International Conference on Medical Artificial Intelligence, MedAI 2023

作者： Xu, Xin Lu, Wenjing Lei, Jiahao Qiu, Peng Shen, Hong-Bin Yang, Yang Shanghai Jiao Tong University Key Lab. of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Department of Computer Science and Engineering Shanghai200240 China Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine Department of Vascular Surgery China Shanghai Jiao Tong University Institute of Image Processing and Pattern Recognition Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China

ISBN: (纸本)9798350358780

Interactive medical image segmentation methods have become increasingly popular in recent years. These methods combine manual labeling and automatic segmentation, reducing the workload of annotation while maintaining high accuracy. However, most current interactive segmentation frameworks are limited to 2D image data, and are not suitable for 3D image data due to the large size and high complexity of 3D data, as well as the challenges posed by information asymmetry and sparse annotation. In this paper, we propose SliceProp, an interactive segmentation framework that implements slice-wise Label Bidirectional Propagation (LBP) for 3D medical image segmentation. SliceProp extends the interactive 2D image segmentation algorithm to 3D image segmentation, and can handle 3D data with large size and high complexity. Moreover, equipped with a Backtracking Feedback Check (BFC) module, SliceProp effectively addresses the issues of information asymmetry and spatial sparse annotation in 3D medical image segmentation. Additionally, we adopt an uncertainty-based criterion to pri-oritize the slices to be refined interactively, which enhances the efficiency of the interaction process by enabling the model to focus on the regions with the most unreliable predictions. SliceProp is evaluated on two datasets and achieves promising results compared to state-of-the-art methods. © 2023 IEEE.

关键词： Medical imaging

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Isoform Function Prediction Based on Heterogeneous Graph Attention Networks

Isoform Function Prediction Based on Heterogeneous Graph Att...

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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Guo, Kuo Li, Yifan Chen, Hao Shen, Hong-Bin Yang, Yang Shanghai Jiao Tong University Key Lab. of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Department of Computer Science and Engineering Shanghai200240 China Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Institute of Image Processing and Pattern Recognition Shanghai200240 China Carnegie Mellon University School of Computer Science Computational Biology Department PittsburghPA15213 United States

ISBN: (纸本)9798350337488

Isoforms refer to different mRNA molecules transcribed from the same gene, which can be translated into proteins with varying structures and functions. Predicting the functions of isoforms is an essential topic in bioinformatics as it can provide valuable insights into the intricate mechanisms of gene regulation and biological processes. Conventionally, gene function labels are standardized in Gene Ontology (GO) terms. However, traditional methods for predicting isoform function are largely limited by the absence of isoform-specific labels, sparse annotations, and the vast number of GO terms. To address these issues, we propose HANIso, a deep learning-based method for isoform function prediction. HANIso leverages a pretrained protein language model to extract features from protein sequences. It also integrates heterogeneous information, such as isoform sequence features, GO annotations, and isoform interaction data, using a Heterogeneous Graph Attention Network (HAN). This allows the model to learn the importance of different sources of information and their semantic relationships through the attention mechanism. Our method can predict function labels at both the gene level and isoform level. We conduct experiments on two species datasets, and the results demonstrate that our method outperforms existing methods on both AUROC and AUPRC. HANIso has the potential to overcome the limitations of traditional methods and provide a more accurate and comprehensive understanding of isoform function. © 2023 IEEE.

关键词： alternative splicing gene ontology heterogeneous graph attention network isoform function prediction protein language model

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RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs

RBP-Former: Joint Prediction of RNA-protein Binding Sites on...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Yichong Li Xiaojian Liu Fan Cheng Xiaoyong Pan Yang Yang Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai China Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai China

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

关键词： Proteins Protein engineering Accuracy RNA Machine learning Predictive models Data models Gene expression Bioinformatics Diseases

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Generation Maintenance Scheduling for Power Systems Considering the Risk Quantification of Hybrid Uncertainty

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IEEE Transactions on Power Systems 2025年

作者： Yang, Xiao Zhao, Yong Li, Yuanzheng Huang, Cheng Ding, Qiang Key Laboratory of Image Information Processing and Intelligent Control of Ministry of Education of China Huazhong University of Science and Technology School of Artificial Intelligence and Automation Wuhan430074 China Power Science Research Institute of State Grid Jiangsu Electric Power Company China China Electric Power Research Institute Company China

The accurate quantification of risk caused by uncertainty forms a crucial foundation for formulating the generation maintenance scheduling (GMS) of power systems. However, the probability distribution functions (PDFs) of uncertain variables such as wind power and load are challenging to model accurately or are unknown, which makes it difficult to measure their economic risk and formulate appropriate GMS for power systems. To address this issue, we consider hybrid uncertainty from wind power and load, and propose a novel interval-probabilistic worst conditional value-at-risk (IP-WCVaR)-based generation maintenance scheduling method. Firstly, a novel IP-WCVaR method is proposed to measure the risk of the interval and probabilistic hybrid uncertainty, and the analytical mathematical model of the IP-WCVaR is derived through typical scenarios of probability correction. On this basis, the positive and negative spinning reserve models are established using the IP-WCVaR and then integrated into the GMS model, which enhances the resilience of the power system. Finally, the new risk-averse GMS model is formulated as the lower and upper boundary optimal models, which are transformed into tractable mixed integer linear programming problems based on the interval extreme value theory. The effectiveness and superiority of the proposed IP-WCVaR method are verified on the modified IEEE 24-bus and IEEE 118-bus power systems. © 1969-2012 IEEE.

关键词： Mixed-integer linear programming

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Optimizing Binary Sequence Excitation Signals for Rapid Impedance Spectrum Measurement in Proton Exchange Membrane Fuel Cells

Optimizing Binary Sequence Excitation Signals for Rapid Impe...

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第43届中国控制会议

作者： Jingzhi Lei Chuang Sheng Jingjing Wang Liansong Yu Xi Li School of Artificial Intelligence and Automation Key Laboratory of Image Processing and Intelligent Control of Education MinistryHuazhong University of Science and Technology State Grid Electric Power Research Institute Wuhan Nanrui Limited Liability Company Shenzhen Huazhong University of Science and Technology Research Institute

ISBN: (数字)9789887581581

ISBN: (纸本)9798350366907

With the increasing demand for efficient and reliable renewable energy sources,Proton Exchange Membrane Fuel Cells(PEMFCs) have emerged as a promising *** experiments demonstrate that Electrochemical Impedance Spectroscopy(EIS) effectively differentiates various states of *** broadband signals as testing excitations significantly reduces EIS measurement time,facilitating real-time monitoring of PEMFCs' health under dynamic *** signal design requires maintaining adequate amplitude across frequency components for noise resistance while minimizing signal peak value to reduce operational *** paper introduces an EIS simulation environment,leveraging PEMFCs' impedance and electrochemical noise *** focuses on optimizing the excitation signal's amplitude-frequency distribution using discrete interval binary *** results indicate that our method achieves minimal perturbation amplitude while preserving measurement accuracy in amplitude-frequency signal design.

关键词： Proton exchange membrane fuel cell Electrochemical impedance spectroscopy Electrochemical noise Excitation signal optimization

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