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NiuEM: A Nested-iterative Unsupervised Learning Model for Single-particle Cryo-EM image processing

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NiuEM: A Nested-iterative Unsupervised Learning Model for Si...

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

One-shot distributed algorithm for generalized eigenvalue problem

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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

Random features for kernel approximation: A survey on algorithms, theory, and beyond

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arXiv 2020年

作者： Liu, Fanghui Huang, Xiaolin Chen, Yudong Suykens, Johan A.K. KU Leuven LeuvenB-3001 Belgium Institute of Image Processing and Pattern Recognition Institute of Medical Robotics Shanghai Jiao Tong University Shanghai200240 China School of Operations Research and Information Engineering Cornell University IthacaNY14850 United States

The class of random features is one of the most popular techniques to speed up kernel methods in large-scale problems. Related works have been recognized by the NeurIPS Test-of-Time award in 2017 and the ICML Best Paper Finalist in 2019. The body of work on random features has grown rapidly, and hence it is desirable to have a comprehensive overview on this topic explaining the connections among various algorithms and theoretical results. In this survey, we systematically review the work on random features from the past ten years. First, the motivations, characteristics and contributions of representative random features based algorithms are summarized according to their sampling schemes, learning procedures, variance reduction properties and how they exploit training data. Second, we review theoretical results that center around the following key question: how many random features are needed to ensure a high approximation quality or no loss in the empirical/expected risks of the learned estimator. Third, we provide a comprehensive evaluation of popular random features based algorithms on several large-scale benchmark datasets and discuss their approximation quality and prediction performance for classification. Last, we discuss the relationship between random features and modern over-parameterized deep neural networks (DNNs), including the use of high dimensional random features in the analysis of DNNs as well as the gaps between current theoretical and empirical results. This survey may serve as a gentle introduction to this topic, and as a users' guide for practitioners interested in applying the representative algorithms and understanding theoretical results under various technical assumptions. We hope that this survey will facilitate discussion on the open problems in this topic, and more importantly, shed light on future research directions. Copyright © 2020, The Authors. All rights reserved.

关键词： Surveys

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

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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

An Ensemble Model for Error Modeling with Pseudoinverse Learning Algorithm

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

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

DAmageNet: A universal adversarial dataset

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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

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

Web Page Classification Algorithm Based on Semi-Supervised Support Vector Machine 2

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Web Page Classification Algorithm Based on Semi-Supervised S...

2nd IEEE Advanced Information Management, Communicates, Electronic and Automation Control Conference, IMCEC 2018

作者： Huang, Wenqing You, Hui Zhejiang Sci-Tech University Institute of Computer Vision Image Processing and Pattern Recognition Acceptable School of Information Hangzhou China

ISBN: (纸本)9781538618035

Most web page classification algorithms are learning algorithms under the single-instance single-label framework. Multi-Instance Multi-Label learning is a new machine learning framework. MIMLSVM+ algorithm, using degenerate strategy to transform multiple instances into single instances, and then decomposing multiple labels into a series of two types of classification problems, that is, building an SVM for each label. Because the MIMLSVM+ algorithm degrades the multi-label problem into a series of two types of classification problems, the processing of each label will lose the contact information between the labels independently. Therefore, multi-tasking technology is introduced to make use of the multi-tasking learning framework based on nuclear to validate the MIMLSVM+ expand, get E-MIMLSVM+ algorithm. The paper improves E-MIMLSVM+ algorithm by using the semi-supervised learning method. Experimental results show that the proposed method can achieve higher classification accuracy. © 2018 IEEE.

关键词： Learning algorithms

Analysis of Least Squares Regularized Regression in Reproducing Kernel Kreın Spaces

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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