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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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Abnormal resting-state EEG power and impaired inhibition control in young smokers

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Neuroscience Letters 2021年第0期761卷 136120-136120页

作者： Dong, Fang Li, Xiaojian Zhang, Yunmiao Jia, Shaodi Zhang, Shidi Xue, Ting Ren, Yan Lv, Xiaoqi Yuan, Kai Yu, Dahua Inner Mongolia Key Laboratory of Pattern Recognition and Intelligent Image Processing School of Information Engineering Inner Mongolia University of Science and Technology Baotou 014010 Inner Mongolia China College of Information Engineering Inner Mongolia University of Technology Hohhot 010051 Inner Mongolia China School of Life Science and Technology Xidian University Xi'an 710071 Shaanxi China

Exposure to nicotine during adolescence may cause neurophysiological changes and increase the risks of developing nicotine dependence;it can even lead to lifelong smoking. The intake of nicotine may also lead to abnormal patterns of oscillatory brain activity and inhibition control deficits. However, little is known about the specific relationship between oscillatory brain activity during the resting state and inhibition control capacity in young smokers. In the present study, we acquired resting-state electroencephalography (EEG) data from thirty-four young smokers and 39 age-matched non-smoking controls. Inhibition control performance was measured by a Go/NoGo task. Compared with non-smoking controls, we detected reduced low-frequency delta band activity in the frontal, central and posterior cortices of young smokers. Furthermore, young smokers committed more errors in response to infrequent NoGo trials. Notably, we demonstrated that delta absolute power in the frontal region was negatively correlated with NoGo errors and that alpha power in the central region was positively correlated with NoGo errors in non-smoking controls but not in young smokers. These findings may suggest that these inhibitory control processes were associated with alterations in oscillatory brain activity during the resting state. Our findings suggest that alterations of power spectra in delta bands may act as a useful biomarker of inhibitory control performance and provide a scientific basis for the diagnosis and treatment of nicotine addiction in adolescents. © 2021 Elsevier B.V.

关键词： Brain oscillations Electroencephalography (EEG) Inhibition control Resting state Young smokers

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One-shot distributed algorithm for generalized eigenvalue problem

arXiv

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arXiv 2020年

作者： Lyu, Kexin He, Fan Huang, Xiaolin Yang, Jie Chen, Liming Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University MOE Key Laboratory of System Control and Information Processing 800 Dongchuan Road Shanghai200240 China Institute of Medical Robotics Shanghai Jiao Tong University 800 Dongchuan Road Shanghai200240 China Ecole Centrale de Lyon France

Nowadays, more and more datasets are stored in a distributed way for the sake of memory storage or data privacy. The generalized eigenvalue problem (GEP) plays a vital role in a large family of high-dimensional statistical models. However, the existing distributed method for eigenvalue decomposition cannot be applied in GEP for the divergence of the empirical covariance matrix. Here we propose a general distributed GEP framework with one-shot communication for GEP. If the symmetric data covariance has repeated eigenvalues, e.g., in canonical component analysis, we further modify the method for better convergence. The theoretical analysis on approximation error is conducted and the relation to the divergence of the data covariance, the eigenvalues of the empirical data covariance, and the number of local servers is analyzed. Numerical experiments also show the effectiveness of the proposed algorithms. Copyright © 2020, The Authors. All rights reserved.

关键词： Eigenvalues and eigenfunctions

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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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An Ensemble Model for Error Modeling with Pseudoinverse Learning Algorithm

An Ensemble Model for Error Modeling with Pseudoinverse Lear...

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IEEE International Conference on Systems, Man and Cybernetics

作者： Sibo Feng Xiaodan Deng Ping Guo Bo Zhao Qian Yin Hongfeng Wang Image Processing and Pattern Recognition Laboratory Beijing Normal University Beijing China School of Information Management Dezhou University Shandong China

In Bayesian theory, the maximum posterior estimator uses prior information to estimate the noise in the machine learning model by adding the regularization term. The regularization terms L 1 and L 2 correspond to Laplacian prior and Guassian prior, respectively. In existing deep learning models, in order to use the gradient descent optimization algorithm and achieve good results, most models take L 2 regularization as the regularization term of the network model to fit the complex Guassian noise. However in practice, the Laplace noise and the Guassian noise are both considered as data noise. For multi-layer perceptrons, the difficulty caused by adding L 1 and L 2 into the optimization function of the network is solved by proposing an ensemble model for error modeling through adopting the divide and conquer strategy. First, several base learners are trained to fit different noise distributions of data, then the final results can be obtained by taking the results of each base leaner as new data to train a meta leaner, and get the final results. Among them, coordinate regression method is used to solve L 1 loss, while the pseudo-inverse learning algorithm is employed to solve L 2 loss. Both methods are nongradient optimization algorithms. The comparison results of the model on several data sets show that the proposed ensemble model achieves better performance.

关键词： Training Optimization Data models Neural networks Computational modeling Matrix decomposition Estimation

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Relationship between pulmonary nodule malignancy and surrounding pleurae, airways and vessels: a quantitative study using the public LIDC-IDRI dataset

arXiv

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arXiv 2021年

作者： Qin, Yulei Gu, Yun Zhang, Hanxiao Yang, Jie Wang, Lihui Wang, Zhexin Yao, Feng Zhu, Yue-Min Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai200240 China Institute of Medical Robotics Shanghai Jiao Tong University Shanghai200240 China CREATIS INSA Lyon CNRS UMR 5220 INSERM U1206 Université de Lyon Villeurbanne69621 France Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province School of Computer Science and Technology Guizhou University Guiyang550025 China Department of Thoracic Surgery Shanghai Chest Hospital Shanghai Jiao Tong University Shanghai200025 China

Objectives: To investigate whether the pleurae, airways and vessels surrounding a nodule on non-contrast computed tomography (CT) can discriminate benign and malignant pulmonary nodules. Materials and Methods: The LIDC-IDRI dataset, one of the largest publicly available CT database, was exploited for study. A total of 1556 nodules from 694 patients were involved in statistical analysis, where nodules with average scorings 3 were respectively denoted as benign and malignant. Besides, 339 nodules from 113 patients with diagnosis ground-truth were independently evaluated. Computer algorithms were developed to segment pulmonary structures and quantify the distances to pleural surface, airways and vessels, as well as the counting number and normalized volume of airways and vessels near a nodule. Odds ratio (OR) and Chi-square (χ2) testing were performed to assess the correlation between features of surrounding structures and nodule malignancy. A non-parametric receiver operating characteristic (ROC) analysis was conducted in logistic regression to evaluate discrimination ability of each structure. Results: For the benign and malignant groups, the average distances from nodules to pleural surface, airways and vessels are respectively (6.56, 5.19), (37.08, 26.43) and (1.42, 1.07) mm. The correlation between nodules and the counting number of airways and vessels that contact or project towards nodules are respectively (OR=22.96, χ2=105.04) and (OR=7.06, χ2=290.11). The correlation between nodules and the volume of airways and vessels are (OR=9.19, χ2=159.02) and (OR=2.29, χ2=55.89). The areas-under-curves (AUCs) for pleurae, airways and vessels are respectively 0.5202, 0.6943 and 0.6529. Conclusion: Our results show that malignant nodules are often surrounded by more pulmonary structures compared with benign ones, suggesting that features of these structures could be viewed as lung cancer biomarkers. © 2021, CC BY.

关键词： Computerized tomography

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DAmageNet: A universal adversarial dataset

arXiv

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arXiv 2019年

作者： Chen, Sizhe Huang, Xiaolin He, Zhengbao Sun, Chengjin Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University MOE Key Laboratory of System Control and Information Processing 800 Dongchuan Road Shanghai200240 China

It is now well known that deep neural networks (DNNs) are vulnerable to adversarial attack. Adversarial samples are similar to the clean ones, but are able to cheat the attacked DNN to produce incorrect predictions in high confidence. But most of the existing adversarial attacks have high success rate only when the information of the attacked DNN is well-known or could be estimated by massive queries. A promising way is to generate adversarial samples with high transferability. By this way, we generate 96020 transferable adversarial samples from original ones in imageNet. The average difference, measured by root means squared deviation, is only around 3.8 on average. However, the adversarial samples are misclassified by various models with an error rate up to 90%. Since the images are generated independently with the attacked DNNs, this is essentially zero-query adversarial attack. We call the dataset DAmageNet, which is the first universal adversarial dataset that beats many models trained in imageNet. By finding the drawbacks, DAmageNet could serve as a benchmark to study and improve robustness of DNNs. DAmageNet could be downloaded in http://***/Show/56/122 Copyright © 2019, The Authors. All rights reserved.

关键词： Deep neural networks

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Cross-receptive Focused Inference Network for Lightweight image Super-Resolution

arXiv

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arXiv 2022年

作者： Li, Wenjie Li, Juncheng Gao, Guangwei Deng, Weihong Zhou, Jiantao Yang, Jian Qi, Guo-Jun The Intelligent Visual Information Perception Laboratory Institute of Advanced Technology Nanjing University of Posts and Telecommunications Nanjing210046 China The Provincial Key Laboratory for Computer Information Processing Technology Soochow University Suzhou215006 China The School of Communication and Information Engineering Shanghai University Shanghai200444 China Jiangsu Key Laboratory of Image and Video Understanding for Social Safety Nanjing University of Science and Technology Nanjing210094 China The Pattern Recognition and Intelligent System Laboratory School of Artificial Intelligence Beijing University of Posts and Telecommunications Beijing100876 China The State Key Laboratory of Internet of Things for Smart City Department of Computer and Information Science Faculty of Science and Technology University of Macau 999078 China The School of Computer Science and Technology Nanjing University of Science and Technology Nanjing210094 China The Research Center for Industries of the Future The School of Engineering Westlake University Hangzhou310024 China OPPO Research SeattleWA98101 United States

Recently, Transformer-based methods have shown impressive performance in single image super-resolution (SISR) tasks due to the ability of global feature extraction. However, the capabilities of Transformers that need to incorporate contextual information to extract features dynamically are neglected. To address this issue, we propose a lightweight Cross-receptive Focused Inference Network (CFIN) that consists of a cascade of CT Blocks mixed with CNN and Transformer. Specifically, in the CT block, we first propose a CNN-based Cross-Scale Information Aggregation Module (CIAM) to enable the model to better focus on potentially helpful information to improve the efficiency of the Transformer phase. Then, we design a novel Cross-receptive Field Guided Transformer (CFGT) to enable the selection of contextual information required for reconstruction by using a modulated convolutional kernel that understands the current semantic information and exploits the information interaction within different self-attention. Extensive experiments have shown that our proposed CFIN can effectively reconstruct images using contextual information, and it can strike a good balance between computational cost and model performance as an efficient model. Source codes will be available at https://***/IVIPLab/CFIN. Copyright © 2022, The Authors. All rights reserved.

关键词： Semantics

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Analysis of Least Squares Regularized Regression in Reproducing Kernel Kreın Spaces

arXiv

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arXiv 2020年

作者： Liu, Fanghui Shi, Lei Huang, Xiaolin Yang, Jie Suykens, Johan A.K. Department of Electrical Engineering [ESAT-STADIUS KU Leuven LeuvenB-3001 Belgium Institute of Image Processing and Pattern Recognition Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China Shanghai Key Laboratory for Contemporary Applied Mathematics School of Mathematical Sciences Fudan University Shanghai China

In this paper, we study the asymptotical properties of least squares regularized regression with indefinite kernels in reproducing kernel Kreın spaces (RKKS). The classical approximation analysis cannot be directly applied to study its asymptotical behavior under the framework of learning theory as this problem is in essence non-convex and outputs stationary points. By introducing a bounded hyper-sphere constraint to such non-convex regularized risk minimization problem, we theoretically demonstrate that this problem has a globally optimal solution with a closed form on the sphere, which makes our approximation analysis feasible in RKKS. Accordingly, we modify traditional error decomposition techniques, prove convergence results for the introduced hypothesis error based on matrix perturbation theory, and derive learning rates of such regularized regression problem in RKKS. Under some conditions, the derived learning rates in RKKS are the same as that in reproducing kernel Hilbert spaces (RKHS), which is actually the first work on approximation analysis of regularized learning algorithms in RKKS. Copyright © 2020, The Authors. All rights reserved.

关键词： Learning algorithms

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EEG-Based Brain-Computer Interfaces Are Vulnerable to Backdoor Attacks

Research Square

引用

Research Square 2021年

作者： Meng, Lubin Huang, Jian Zeng, Zhigang Jiang, Xue Yu, Shan Jung, Tzyy-Ping Lin, Chin-Teng Chavarriaga, Ricardo Wu, Dongrui 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 Brainnetome Center and National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Sciences Beijing China La Jolla CA United States Center for Advanced Neurological Engineering Institute of Engineering in Medicine UCSD La Jolla CA United States Centre of Artificial Intelligence Faculty of Engineering and Information Technology University of Technology Sydney Australia ZHAW DataLab Zürich University of Applied Sciences Winterthur8401 Switzerland

Research and development of electroencephalogram (EEG) based brain-computer interfaces (BCIs) have advanced rapidly, partly due to the wide adoption of sophisticated machine learning approaches for decoding the EEG signals. However, recent studies have shown that machine learning algorithms are vulnerable to adversarial attacks, e.g., the attacker can add tiny adversarial perturbations to a test sample to fool the model, or poison the training data to insert a secret backdoor. Previous research has shown that adversarial attacks are also possible for EEG-based BCIs. However, only adversarial perturbations have been considered, and the approaches are theoretically sound but very difficult to implement in practice. This article proposes to use narrow period pulse for poisoning attack of EEG-based BCIs, which is more feasible in practice and has never been considered before. One can create dangerous backdoors in the machine learning model by injecting poisoning samples into the training set. Test samples with the backdoor key will then be classified into the target class specified by the attacker. What most distinguishes our approach from previous ones is that the backdoor key does not need to be synchronized with the EEG trials, making it very easy to implement. The effectiveness and robustness of the backdoor attack approach is demonstrated, highlighting a critical security concern for EEG-based BCIs. © 2021, CC BY.

关键词： Electroencephalography

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