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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

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

Towards a unified quadrature framework for large-scale kernel machines

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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 Shanghai Jiao Tong University Shanghai200240 China Institute of Medical Robotics Shanghai Jiao Tong University Shanghai200240 China School of Operations Research and Information Engineering Cornell University IthacaNY14850 United States

In this paper, we develop a quadrature framework for large-scale kernel machines via a numerical integration representation. Considering that the integration domain and measure of typical kernels, e.g., Gaussian kernels, arc-cosine kernels, are fully symmetric, we leverage deterministic fully symmetric interpolatory rules to efficiently compute quadrature nodes and associated weights for kernel approximation. The developed interpolatory rules are able to reduce the number of needed nodes while retaining a high approximation accuracy. Further, we randomize the above deterministic rules by the classical Monte-Carlo sampling and control variates techniques with two merits: 1) The proposed stochastic rules make the dimension of the feature mapping flexibly varying, such that we can control the discrepancy between the original and approximate kernels by tuning the dimnension. 2) Our stochastic rules have nice statistical properties of unbiasedness and variance reduction with fast convergence rate. In addition, we elucidate the relationship between our deterministic/stochastic interpolatory rules and current quadrature rules for kernel approximation, including the sparse grids quadrature and stochastic spherical-radial rules, thereby unifying these methods under our framework. Experimental results on several benchmark datasets show that our methods compare favorably with other representative kernel approximation based methods. Copyright © 2020, The Authors. All rights reserved.

关键词： Stochastic systems

The effect of data augmentation on classification of atrial fibrillation in short single-lead ecg signals using deep neural networks

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arXiv 2020年

作者： Hatamian, Faezeh Nejati Ravikumar, Nishant Vesal, Sulaiman Kemeth, Felix P. Struck, Matthias Maier, Andreas Department of Image Processing and Medical Technology Fraunhofer Institute for Integrated Circuits IIS Erlangen Germany Pattern Recognition Lab Department of Computer Science Friedrich-Alexander University Erlangen-Nrnberg Erlangen Germany School of Computing LICAMM Leeds Institute of Cardiovascular and Metabolic Medicine School of Medicine University of Leeds United Kingdom

Cardiovascular diseases are the most common cause of mortality worldwide. Detection of atrial fibrillation (AF) in the asymptomatic stage can help prevent strokes. It also improves clinical decision making through the delivery of suitable treatment such as, anticoagulant therapy, in a timely manner. The clinical significance of such early detection of AF in electrocardiogram (ECG) signals has inspired numerous studies in recent years, of which many aim to solve this task by leveraging machine learning algorithms. ECG datasets containing AF samples, however, usually suffer from severe class imbalance, which if unaccounted for, affects the performance of classification algorithms. Data augmentation is a popular solution to tackle this problem. In this study, we investigate the impact of various data augmentation algorithms, e.g., oversampling, Gaussian Mixture Models (GMMs) and Generative Adversarial Networks (GANs), on solving the class imbalance problem. These algorithms are quantitatively and qualitatively evaluated, compared and discussed in detail. The results show that deep learning-based AF signal classification methods benefit more from data augmentation using GANs and GMMs, than oversampling. Furthermore, the GAN results in circa 3% better AF classification accuracy in average while performing comparably to the GMM in terms of f1-score. Copyright © 2020, The Authors. All rights reserved.

关键词： Diseases

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

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Research Square

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

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

Current Progress and Challenges in Large-scale 3D Mitochondria Instance Segmentation

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TechRxiv

TechRxiv 2023年

作者： Franco-Barranco, Daniel Lin, Zudi Jang, Won-Dong Wang, Xueying Shen, Qijia Yin, Wenjie Fan, Yutian Li, Mingxing Chen, Chang Xiong, Zhiwei Xin, Rui Liu, Hao Chen, Huai Li, Zhili Zhao, Jie Chen, Xuejin Pape, Constantin Conrad, Ryan De Folter, Jozefus Nightingale, Luke Jones, Martin L. Liu, Yanling Ziaei, Dorsa Huschauer, Stephan Arganda-Carreras, Ignacio Pfister, Hanspeter Wei, Donglai The Department of Computer Science and Artificial Intelligence University of the Basque Country Donostia-San Sebastian Spain San Sebastian Spain Ikerbasque Basque Foundation for Science Bilbao Spain Biofisika Institute CSIC UPV/EHU Bilbao Spain Harvard University All-ston MA United States The Department of Molecular and Cellular Biology Harvard University CambridgeMA United States The Wellcome Centre for Integrative Neuroimaging FMRIB Nuffield Department of Clinical Neurosciences University of Oxford Oxford United Kingdom University of Science and Technology of China Anhui China The Institute of Image Processing and Pattern Recognition Department of Automation Shanghai Jiao Tong University Shanghai China The National Engineering Laboratory for Brain-inspired Intelligence Technology and Application University of Science and Technology of China Anhui China The Georg-August University Goettingen Germany The Center for Molecular Microscopy Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda United States The Cancer Research Technology Program Frederick National Laboratory for Cancer Research Frederick United States The Francis Crick Institute London United Kingdom The Advanced Biomedical Computational Science Group Frederick National Laboratory for Cancer Research FrederickMD United States The Computer Science Department Boston College Chestnut Hill MA United States

In this paper, we present the results of the MitoEM challenge on mitochondria 3D instance segmentation from electron microscopy images, organized in conjunction with the IEEE-ISBI 2021 conference. Our benchmark dataset consists of two large-scale 3D volumes, one from human and one from rat cortex tissue, which are 3,600 times larger than previously used datasets. At the time of paper submission, 257 participants had registered for the challenge, 14 teams had submitted their results, and six teams participated in the challenge workshop. Here, we present eight top-performing approaches from the challenge participants, along with our own baseline strategies. Posterior to the challenge, annotation errors in the ground truth were corrected without altering the final ranking. Additionally, we present a retrospective evaluation of the scoring system which revealed that (1) the challenge metric was permissive with the false positive predictions and (2) the size-based grouping of instances did not correctly categorize mitochondria of interest. Thus, we propose a new scoring system that better reflects the correctness of the segmentation results. Although several of the top methods are compared favorably to our own baselines, substantial errors remain unsolved for mitochondria with challenging morphologies. Thus, the challenge remains open for submission and automatic evaluation, with all volumes available for download. © 2023, CC BY.

关键词： Electron microscopy

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

Unsupervised Local Discrimination for Medical images

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arXiv 2021年

作者： Chen, Huai Wang, Renzhen Wang, Xiuying Li, Jieyu Fang, Qu Li, Hui Bai, Jianhao Peng, Qing Meng, Deyu Wang, Lisheng Institute of Image Processing and Pattern Recognition Department of Automation Shanghai Jiao Tong University Shanghai200240 China School of Mathematics and Statistics Ministry of Education Key Lab of Intelligent Networks and Network Security Xi’an Jiaotong University Xi’an710049 China The School of Computer Science The University of Sydney SydneyNSW2006 Australia Department of Ophthalmology Shanghai Tenth People’s Hospital Tongji University Shanghai200240 China The Cooperative Medianet Innovation Center Shanghai Jiao Tong University Shanghai200240 China The Changchun GeneScience Pharmaceutical Co. LTD China

Contrastive learning, which aims to capture general representation from unlabeled images to initialize the medical analysis models, has been proven effective in alleviating the high demand for expensive annotations. Current methods mainly focus on instance-wise comparisons to learn the global discriminative features, however, pretermitting the local details to distinguish tiny anatomical structures, lesions, and tissues. To address this challenge, in this paper, we propose a general unsupervised representation learning framework, named local discrimination (LD), to learn local discriminative features for medical images by closely embedding semantically similar pixels and identifying regions of similar structures across different images. Specifically, this model is equipped with an embedding module for pixel-wise embedding and a clustering module for generating segmentation. And these two modules are unified through optimizing our novel region discrimination loss function in a mutually beneficial mechanism, which enables our model to reflect structure information as well as measure pixel-wise and region-wise similarity. Furthermore, based on LD, we propose a center-sensitive one-shot landmark localization algorithm and a shape-guided cross-modality segmentation model to foster the generalizability of our model. When transferred to downstream tasks, the learned representation by our method shows a better generalization, outperforming representation from 18 state-of-the-art (SOTA) methods and winning 9 out of all 12 downstream tasks. Especially for the challenging lesion segmentation tasks, the proposed method achieves significantly better performances. The source codes are publicly available at https://***/HuaiChen-1994/LDLearning. Copyright © 2021, The Authors. All rights reserved.

关键词： Embeddings