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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Rui Hu Jiaming Cai Wangjie Zheng Yang Yang Hong-Bin Shen Shanghai Jiao Tong University and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University and Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China Shanghai Jiao Tong University Shanghai China

ISBN: (数字)9781728162157

ISBN: (纸本)9781728162164

Cryo-electron microscopy (cryo-EM) has become a mainstream technology for solving spatial structures of biomacromolecules, while the processing of cryo-EM images is a very challenging task. One of the great challenges is the high noise in the images. A common method is to cluster the images with close projecting angles to get mean images, which are used for 3D reconstruction. However, due to the extremely low signal-to-noise-ratio, common clustering methods often fail to obtain high-quality mean images, leading to poorly reconstructed structures. In this study, we present a new unsupervised learning framework, called NiuEM, to discriminate images captured from different angles and yield cluster-mean images. NiuEM first generates pseudo-labels and then exploits both contrastive loss and cross-entropy loss for training convolutional layers to learn feature representations. Moreover, the pseudo-labels are updated iteratively to enhance the reliability of labels. We assess the performance of NiuEM on four data sets via both visualized and quantitative experiments. Especially, two kinds of metrics are adopted to measure the performance, regarding the clustering quality and the resolution of reconstructed 3D models, respectively. The experimental results show that NiuEM achieves very competitive clustering accuracy in the comparison with the state-of-the-art image clustering methods. Moreover, the cluster mean images yielded by NiuEM lead to better initial 3D models compared with the mainstream reconstruction tools.

关键词： Three-dimensional displays Feature extraction image reconstruction Task analysis Solid modeling Electron microscopy Convolutional neural networks

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FCM-RDpA: TSK fuzzy regression model construction using fuzzy C-means clustering, regularization, droprule, and powerball adabelief

arXiv

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arXiv 2020年

作者： Shi, Zhenhua Wu, Dongrui Guo, Chenfeng Zhao, Changming Cui, Yuqi Wang, Fei-Yue Ministry of Education Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China State Key Laboratory for Management and Control of Complex Systems Institute of Automation Chinese Academy of Sciences Beijing China

To effectively optimize Takagi-Sugeno-Kang (TSK) fuzzy systems for regression problems, a mini-batch gradient descent with regularization, DropRule, and AdaBound (MBGD-RDA) algorithm was recently proposed. This paper further proposes FCM-RDpA, which improves MBGD-RDA by replacing the grid partition approach in rule initialization by fuzzy c-means clustering, and AdaBound by Powerball AdaBelief, which integrates recently proposed Powerball gradient and AdaBelief to further expedite and stabilize parameter optimization. Extensive experiments on 22 regression datasets with various sizes and dimensionalities validated the superiority of FCM-RDpA over MBGD-RDA, especially when the feature dimensionality is higher. We also propose an additional approach, FCM-RDpAx, that further improves FCM-RDpA by using augmented features in both the antecedents and consequents of the rules. Copyright © 2020, The Authors. All rights reserved.

关键词： Gradient methods

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A protocol for structured illumination microscopy with minimal reconstruction artifacts

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Biophysics Reports 2019年第2期5卷 80-90页

作者： Junchao Fan Xiaoshuai Huang Liuju Li Shan Tan Liangyi Chen Key Laboratory of Image Processing and Intelligent Control of Ministry of Education of China School of Automation Huazhong University of Science and Technology State Key Laboratory of Membrane Biology Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular Medicine Peking University

The imaging rate of structured illumination microscopy(SIM) reached 188 Hz recently. As the exposure time decreases, the camera detects fewer virtual photons, while the noise level remains the same. As a result, the signal-to-noise ratio(SNR) decreases sharply. Furthermore, the SNR decreases further because of photobleaching and phototoxicity. This decreased quality of SIM raw data may lead to surprising artifacts with various causes, which may confuse a new user of SIM microscopy. We summarize three significant possible sources of severe artifacts in reconstructed super-resolution(SR)images. Ultrafast motion of a biological sample or an uneven illumination pattern is the most difficult to be identified. The estimated parameter could also be incorrect, leading to artifact of regular ***, reconstruction with the Wiener method generates stochastic artifacts due to the amplification of noise during the deconvolution process. To deal with these problems, we have established a protocol to reconstruct ultrafast SIM raw data obtained in low SNR conditions. First, we checked the quality of the raw data with the image J plugin SIMcheck before reconstruction. Then, a modified parameter estimation method was used to improve the precision of the parameters. Finally, an iterative algorithm was used for SIM reconstruction under low signal-to-noise ratio conditions. This procedure effectively suppressed the artifacts in the super-resolution images reconstructed from raw data of low signal-to-noise ratio.

关键词： Ultrafast SIM Low signal-to-noise ratio Reconstruction

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Mem Brain: An Easy-to-Use Online Webserver for Transmembrane Protein Structure Prediction

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Nano-Micro Letters 2018年第1期10卷 12-19页

作者： Xi Yin Jing Yang Feng Xiao Yang Yang Hong-Bin Shen Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Department of Computer Science Shanghai Jiao Tong University Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering

Membrane proteins are an important kind of proteins embedded in the membranes of cells and play crucial roles in living organisms, such as ion channels,transporters, receptors. Because it is difficult to determinate the membrane protein's structure by wet-lab experiments,accurate and fast amino acid sequence-based computational methods are highly desired. In this paper, we report an online prediction tool called Mem Brain, whose input is the amino acid sequence. Mem Brain consists of specialized modules for predicting transmembrane helices, residue–residue contacts and relative accessible surface area of a-helical membrane proteins. Mem Brain achieves aprediction accuracy of 97.9% of ATMH, 87.1% of AP,3.2 ± 3.0 of N-score, 3.1 ± 2.8 of C-score. Mem BrainContact obtains 62%/64.1% prediction accuracy on training and independent dataset on top L/5 contact prediction,respectively. And Mem Brain-Rasa achieves Pearson correlation coefficient of 0.733 and its mean absolute error of13.593. These prediction results provide valuable hints for revealing the structure and function of membrane *** Brain web server is free for academic use and available at ***/bioinf/Mem Brain/.

关键词： Transmembrane a-helices Structure prediction Machine learning Contact map prediction Relative accessible surface area

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Transfer Learning for EEG-Based Brain-Computer Interfaces: A Review of Progress Made Since 2016

arXiv

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arXiv 2020年

作者： Wu, Dongrui Xu, Yifan Lu, Bao-Liang The Ministry of Education Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China The Center for Brain-Like Computing and Machine Intelligence Department of Computer Science and Engineering Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Brain Science and Technology Research Center Qing Yuan Research Institute Shanghai Jiao Tong University 800 Dong Chuan Road Shanghai200240 China

A brain-computer interface (BCI) enables a user to communicate with a computer directly using brain signals. The most common non-invasive BCI modality, electroencephalogram (EEG), is sensitive to noise/artifact and suffers between-subject/within-subject non-stationarity. Therefore, it is difficult to build a generic pattern recognition model in an EEG-based BCI system that is optimal for different subjects, during different sessions, for different devices and tasks. Usually, a calibration session is needed to collect some training data for a new subject, which is time-consuming and user unfriendly. Transfer learning (TL), which utilizes data or knowledge from similar or relevant subjects/sessions/devices/tasks to facilitate learning for a new subject/session/device/task, is frequently used to reduce the amount of calibration effort. This paper reviews journal publications on TL approaches in EEG-based BCIs in the last few years, i.e., since 2016. Six paradigms and applications - motor imagery, event-related potentials, steady-state visual evoked potentials, affective BCIs, regression problems, and adversarial attacks - are considered. For each paradigm/application, we group the TL approaches into cross-subject/session, cross-device, and cross-task settings and review them separately. Observations and conclusions are made at the end of the paper, which may point to future research directions. Copyright © 2020, The Authors. All rights reserved.

关键词： Brain computer interface

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BoostTree and BoostForest for Ensemble Learning

arXiv

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arXiv 2020年

作者： Zhao, Changming Wu, Dongrui Huang, Jian Yuan, Ye Zhang, Hai-Tao Peng, Ruimin Shi, Zhenhua Key Laboratory of the Ministry of Education for Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China Shenzhen Huazhong University of Science and Technology Research Institute Shenzhen China The Autonomous Intelligence Unmanned Systems Engineering Research Center of Ministry of Education of China The State Key Lab of Digital Manufacturing Equipment and Technology Wuhan China

Bootstrap aggregating (Bagging) and boosting are two popular ensemble learning approaches, which combine multiple base learners to generate a composite model for more accurate and more reliable performance. They have been widely used in biology, engineering, healthcare, etc. This paper proposes BoostForest, which is an ensemble learning approach using BoostTree as base learners and can be used for both classification and regression. BoostTree constructs a tree model by gradient boosting. It increases the randomness (diversity) by drawing the cut-points randomly at node splitting. BoostForest further increases the randomness by bootstrapping the training data in constructing different BoostTrees. BoostForest generally outperformed four classical ensemble learning approaches (Random Forest, Extra-Trees, XGBoost and LightGBM) on 35 classification and regression datasets. Remarkably, BoostForest tunes its parameters by simply sampling them randomly from a parameter pool, which can be easily specified, and its ensemble learning framework can also be used to combine many other base learners. Copyright © 2020, The Authors. All rights reserved.

关键词： Classification (of information)

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Residential virtual power plant with photovoltaic output forecasting and demand response

Residential virtual power plant with photovoltaic output for...

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作者： Cui, Shichang Wang, Yan-Wu Lin, Xiangning Xiao, Jiang-Wen School of Automation Huazhong University of Science and Technology Wuhan China Key Laboratory of Image Processing and Intelligent Control Ministry of Education Huazhong University of Science and Technology Wuhan China Hubei Provincial Collaborative Innovation Center for New Energy Microgrid China Three Gorges University Yichang China State Key Laboratory of Advanced Electromagnetic Engineering and Technology Huazhong University of Science and Technology Wuhan China

Decreasing conventional power supply is promoting the development of the distributed renewable energy sources, such as solar power and wind power. Recently rooftop photovoltaic has been widely applied, and accordingly efficient energy management is getting increasingly important for fully use of renewable energy and the peak shaving of the main grid. This paper investigates the residential energy management as a small-scale virtual power plant (VPP) connected to the main grid includes distributed energy resources, energy storages and residential loads. The self-organizing map (SOM) and the radical basis function (RBF) networks are adopted to classify the weather types and predict hourly photovoltaic output precisely. In a time-of-use electricity market, price-based demand response is applied to adjust the demand. The residential VPP has two goals: maximum profit by selling surplus power to grid and minimum power purchased from grid. The two goals are integrated as an optimization object by introducing a weight parameter. The algorithm combining receding horizon optimization and linear programming is proposed to solve the optimization problem in residential VPP. Numerical simulation tests can help to find the most suitable value of the weight parameter. Different scenarios are simulated and discussed to demonstrate the performance of the VPP and the proposed algorithm. © 2019 Chinese Automatic control Society and John Wiley & Sons Australia, Ltd

关键词： Energy management

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A protocol for structured illumination microscopy with minimal reconstruction artifacts

引用

生物物理学报 2019年第2期5卷 80-90页

作者： Junchao Fan Xiaoshuai Huang Liuju Li Shan Tan Liangyi Chen Key Laboratory of Image Processing and Intelligent Control of Ministry of Education of China School of Automation Huazhong University of Science and Technology Wuhan 430074 China State Key Laboratory of Membrane Biology Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular Medicine Peking University Beijing 100084 China

The imaging rate of structured illumination microscopy (SIM) reached 188 Hz *** the exposure time decreases,the camera detects fewer virtual photons,while the noise level remains the *** a result,the signal-to-noise ratio (SNR) decreases ***,the SNR decreases further because of photobleaching and *** decreased quality of SIM raw data may lead to surprising artifacts with various causes,which may confuse a new user of SIM *** summarize three significant possible sources of severe artifacts in reconstructed super-resolution (SR) *** motion of a biological sample or an uneven illumination pattern is the most difficult to be *** estimated parameter could also be incorrect,leading to artifact of regular ***,reconstruction with the Wiener method generates stochastic artifacts due to the amplification of noise during the deconvolution *** deal with these problems,we have established a protocol to reconstruct ultrafast SIM raw data obtained in low SNR ***,we checked the quality of the raw data with the imageJ plugin SIMcheck before ***,a modified parameter estimation method was used to improve the precision of the ***,an iterative algorithm was used for SIM reconstruction under low signal-to-noise ratio *** procedure effectively suppressed the artifacts in the super-resolution images reconstructed from raw data of low signal-to-noise ratio.

关键词： Ultrafast SIM Low signal-to-noise ratio Reconstruction

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$H_{\infty}$ consensus control of fractional-order multi-agent systems over the directed graph

$H_{\infty}$ consensus control of fractional-order multi-age...

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Chinese control Conference (CCC)

作者： Lin Chen Wen-Sen Wang Hao Wu Yan Lei Jiang-Wen Xiao Key Laboratory of Image Processing and Intelligent Control Ministry of Education State grid shanxi electric power research institute

In this paper, the H ∞ consensus of fractional-order multi-agent systems with directed communication graph is investigated. It's the first time to introduce the H ∞ control to investigate the consensus problem of the fractional-order multi-agent systems. In view of Mittag-Leffler stability theory and fractional Lyapunov directed method, a sufficient condition is presented to guarantee all the agents reach consensus with the desired H ∞ performance. Finally, the results are verified by several numerical simulations.

关键词： Multi-agent systems control systems Laplace equations Eigenvalues and eigenfunctions Power system stability Stability analysis Graph theory

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Integration of nonlinear disturbance observer within proxy-based sliding mode control for pneumatic muscle actuators

arXiv

引用

arXiv 2019年

作者： Cao, Yu Huang, Jian Wu, Dongrui Zhang, Mengshi Xiong, Caihua Li, Zhijun Key Laboratory for Image Processing and Intelligent Control of Education Ministry of China School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China School of Mechanical Science Engineering State Key Laboratory of Digital Manufacturing Equipment and Technology Huazhong University of Science and Technology Wuhan430074 China College of Automation Science and Engineering South China University of Technology Guangzhou510641 China

This paper presents an integration of nonlinear disturbance observer within proxy-based sliding mode control (IDO-PSMC) approach for Pneumatic Muscle Actuators (PMAs). Due to the nonlinearities, uncertainties, hysteresis, and timevarying characteristics of the PMA, the model parameters are difficult to be identified accurately, which results in unmeasurable uncertainties and disturbances of the system. To solve this problem, a novel design of proxy-based sliding mode controller (PSMC) combined with a nonlinear disturbance observer (DO) is used for the tracking control of the PMA. Our approach combines both the merits of the PSMC and the DO so that it is effective in both reducing the "chattering" phenomeno n and improving the system robustness. A constrained Firefly Algorithm is used to search for the optimal control parameters. Based on the Lyapunov theorem, the states of the PMA are shown to be globally uniformly ultimately bounded. Extensive experiments were conducted to verify the superior performance of our approach, in multiple tracking scenarios. Copyright © 2019, The Authors. All rights reserved.

关键词： Sliding mode control

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