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arXiv 2020年

作者： Bao, Guoqing Chen, Huai Liu, Tongliang Gong, Guanzhong Yin, Yong Wang, Lisheng Wang, Xiuying School of Computer Science The University of Sydney J12/1 Cleveland St Darlington SydneyNSW2008 Australia Department of Automation Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai China Department of Radiation Oncology Shandong Cancer Hospital and Institute Shandong First Medical University Shandong Academy of Medical Sciences Jinan250117 China

There is an urgent need for automated methods to assist accurate and effective assessment of COVID-19. Radiology and nucleic acid test (NAT) are complementary COVID-19 diagnosis methods. In this paper, we present an end-to-end multitask learning (MTL) framework (COVID-MTL) that is capable of automated and simultaneous detection (against both radiology and NAT) and severity assessment of COVID-19. COVID-MTL learns different COVID-19 tasks in parallel through our novel random-weighted loss function, which assigns learning weights under Dirichlet distribution to prevent task dominance;our new 3D real-time augmentation algorithm (Shift3D) introduces space variances for 3D CNN components by shifting low-level feature representations of volumetric inputs in three dimensions;thereby, the MTL framework is able to accelerate convergence and improve joint learning performance compared to single-task models. By only using chest CT scans, COVID-MTL was trained on 930 CT scans and tested on separate 399 cases. COVID-MTL achieved AUCs of 0.939 and 0.846, and accuracies of 90.23% and 79.20% for detection of COVID-19 against radiology and NAT, respectively, which outperformed the state-of-the-art models. Meanwhile, COVID-MTL yielded AUC of 0.800 ± 0.020 and 0.813 ± 0.021 (with transfer learning) for classifying control/suspected, mild/regular, and severe/critically-ill cases. To decipher the recognition mechanism, we also identified high-throughput lung features that were significantly related (P © 2020, CC BY.

关键词： Radiology

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Mitosis domain generalization in histopathology images - The MIDOG challenge

arXiv

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arXiv 2022年

作者： Aubreville, Marc Stathonikos, Nikolas Bertram, Christof A. Klopfleisch, Robert ter Hoeve, Natalie Ciompi, Francesco Wilm, Frauke Marzahl, Christian Donovan, Taryn A. Maier, Andreas Breen, Jack Ravikumar, Nishant Chung, Youjin Park, Jinah Nateghi, Ramin Pourakpour, Fattaneh Fick, Rutger H.J. Hadj, Saima Ben Jahanifar, Mostafa Rajpoot, Nasir Dexl, Jakob Wittenberg, Thomas Kondo, Satoshi Lafarge, Maxime W. Koelzer, Viktor H. Liang, Jingtang Wang, Yubo Long, Xi Liu, Jingxin Razavi, Salar Khademi, April Yang, Sen Wang, Xiyue Veta, Mitko Breininger, Katharina Technische Hochschule Ingolstadt Ingolstadt Germany Pathology Department UMC Utrecht Netherlands Institute of Pathology University of Veterinary Medicine Vienna Austria Institute of Veterinary Pathology Freie Universität Berlin Berlin Germany Computational Pathology Group Radboud UMC Nijmegen Netherlands Pattern Recognition Lab Friedrich-Alexander-Universität Erlangen-Nürnberg Germany Department of Anatomic Pathology Schwarzman Animal Medical Center New York United States CISTIB Center for Computational Imaging and Simulation Technologies in Biomedicine School of Computing University of Leeds United Kingdom Korea Advanced Institute of Science and Technology Daejeon Korea Republic of Electrical and Electronics Engineering Department Shiraz University of Technology Shiraz Iran Tehran Iran Tribun Health Paris France Tissue Image Analytics Centre Department of Computer Science University of Warwick United Kingdom Fraunhofer-Institute for Integrated Circuits IIS Erlangen Germany Muroran Institute of Technology Hokkaido Japan Department of Pathology and Molecular Pathology University Hospital University of Zurich Zurich Switzerland School of Life Science and Technology Xidian University Shannxi China Histo Pathology Diagnostic Center Shanghai China Xi'an Jiaotong-Liverpool University Suzhou China Electrical Computer and Biomedical Engineering Ryerson University TorontoON Canada Tencent AI Lab Shenzhen518057 China College of Computer Science Sichuan University Chengdu610065 China Medical Image Analysis Group TU Eindhoven Netherlands Department of Artificial Intelligence in Biomedical Engineering Friedrich-Alexander-Universität Erlangen-Nürnberg Germany

The density of mitotic figures within tumor tissue is known to be highly correlated with tumor proliferation and thus is an important marker in tumor grading. recognition of mitotic figures by pathologists is known to be subject to a strong inter-rater bias, which limits the prognostic value. State-of-the-art deep learning methods can support the expert in this assessment but are known to strongly deteriorate when applied in a different clinical environment than was used for training. One decisive component in the underlying domain shift has been identified as the variability caused by using different whole slide scanners. The goal of the MICCAI MIDOG 2021 challenge has been to propose and evaluate methods that counter this domain shift and derive scanner-agnostic mitosis detection algorithms. The challenge used a training set of 200 cases, split across four scanning systems. As a test set, an additional 100 cases split across four scanning systems, including two previously unseen scanners, were given. The best approaches performed on an expert level, with the winning algorithm yielding an F1 score of 0.748 (CI95: 0.704-0.781). In this paper, we evaluate and compare the approaches that were submitted to the challenge and identify methodological factors contributing to better performance. Copyright © 2022, The Authors. All rights reserved.

关键词： Scanning

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NTIRE 2021 Challenge on image Deblurring

arXiv

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arXiv 2021年

作者： Nah, Seungjun Son, Sanghyun Lee, Suyoung Timofte, Radu Lee, Kyoung Mu Chen, Liangyu Zhang, Jie Lu, Xin Chu, Xiaojie Chen, Chengpeng Xiong, Zhiwei Xu, Ruikang Xiao, Zeyu Huang, Jie Zhang, Yueyi Xi, Si Wei, Jia Bai, Haoran Cheng, Songsheng Wei, Hao Sun, Long Tang, Jinhui Pan, Jinshan Lee, Donghyeon Lee, Chulhee Kim, Taesung Wang, Xiaobing Zhang, Dafeng Pan, Zhihong Lin, Tianwei Wu, Wenhao He, Dongliang Li, Baopu Li, Boyun Xi, Teng Zhang, Gang Liu, Jingtuo Han, Junyu Ding, Errui Tao, Guangpin Chu, Wenqing Cao, Yun Luo, Donghao Tai, Ying Lu, Tong Wang, Chengjie Li, Jilin Huang, Feiyue Chen, Hanting Chen, Shuaijun Guo, Tianyu Wang, Yunhe Zamir, Syed Waqas Arora, Aditya Khan, Salman Hayat, Munawar Khan, Fahad Shahbaz Shao, Ling Zuo, Yushen Ou, Yimin Chai, Yuanjun Shi, Lei Liu, Shuai Lei, Lei Feng, Chaoyu Zeng, Kai Yao, Yuying Liu, Xinran Zhang, Zhizhou Huang, Huacheng Zhang, Yunchen Jiang, Mingchao Zou, Wenbin Miao, Si Kim, Yangwoo Sun, Yuejin Deng, Senyou Ren, Wenqi Cao, Xiaochun Wang, Tao Suin, Maitreya Rajagopalan, A.N. Duong, Vinh Van Nguyen, Thuc Huu Yim, Jonghoon Jeon, Byeungwoo Li, Ru Xie, Junwei Han, Jong-Wook Choi, Jun-Ho Kim, Jun-Hyuk Lee, Jong-Seok Zhang, Jiaxin Peng, Fan Svitov, David Pakulich, Dmitry Kim, Jaeyeob Jeong, Jechang Department of ECE ASRI SNU Korea Republic of Computer Vision Lab ETH Zurich Switzerland University of Science and Technology of China China Megvii China Fudan University China Peking University China Netease Games AI Lab Nanjing University of Science and Technology China Guilin University of Electronic Technology China Samsung Electronics Co. Ltd Sunmoon University Asan Korea Republic of Samsung Research China Beijing China Baidu Research United States Department of Computer Vision Technology Baidu Inc China Fudan University China Megvii China Nanjing University China Tencent Noah's Ark Lab Huawei Technologies Co. Ltd Inception Institute of Artificial Intelligence Tsinghua University Beijing China North China University of Technology China Xiaomi South China University of Technology China Lab of Image Science and Technology Southeast University China China Design Group Co. Ltd China JOYY AI GROUP Fujian Normal University China Shanghai Advanced Research Institute Chinese Academy of Sciences China Institute of Information Engineering Chinese Academy of Sciences China Huawei Noah's Ark Lab Indian Institute of Technology Madras India Department of ECE Sungkyunkwan University Korea Republic of Fuzhou University China Imperial Vision Co. Ltd School of Integrated Technology Yonsei University Korea Republic of Expasoft LLC Institute of Automation and Electrometry The SB RAS Image Communication & Signal Processing Laboratory Hanyang University Korea Republic of

Motion blur is a common photography artifact in dynamic environments that typically comes jointly with the other types of degradation. This paper reviews the NTIRE 2021 Challenge on image Deblurring. In this challenge report, we describe the challenge specifics and the evaluation results from the 2 competition tracks with the proposed solutions. While both the tracks aim to recover a high-quality clean image from a blurry image, different artifacts are jointly involved. In track 1, the blurry images are in a low resolution while track 2 images are compressed in JPEG format. In each competition, there were 338 and 238 registered participants and in the final testing phase, 18 and 17 teams competed. The winning methods demonstrate the state-of-the-art performance on the image deblurring task with the jointly combined artifacts. © 2021, CC BY-NC-ND.

关键词： image enhancement

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Tasks integrated networks: Joint detection and retrieval for image search

arXiv

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arXiv 2020年

作者： Zhang, Lei He, Zhenwei Yang, Yi Wang, Liang Gao, Xinbo School of Microelectronics and Communication Engineering Chongqing University Chongqing400044 China Center for Artificial Intelligence University of Technology Sydney Australia National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Sciences Beijing100190 China Chongqing Key Laboratory of Image Cognition Chongqing University of Posts and Telecommunications Chongqing400065 China

The traditional object (person) retrieval (re-identification) task aims to learn a discriminative feature representation with intra-similarity and inter-dissimilarity, which supposes that the objects in an image are manually or automatically pre-cropped exactly. However, in many real-world searching scenarios (e.g., video surveillance), the objects (e.g., persons, vehicles, etc.) are seldom accurately detected or annotated. Therefore, object-level retrieval becomes intractable without bounding-box annotation, which leads to a new but challenging topic, i.e. image-level search with multi-task integration of joint detection and retrieval. In this paper, to address the image search issue, we first introduce an end-to-end Integrated Net (I-Net), which has three merits: 1) A Siamese architecture and an on-line pairing strategy for similar and dissimilar objects in the given images are designed. Benefited by the Siamese structure, I-Net learns the shared feature representation, because, on which, both object detection and classification tasks are handled. 2) A novel on-line pairing (OLP) loss is introduced with a dynamic feature dictionary, which alleviates the multi-task training stagnation problem, by automatically generating a number of negative pairs to restrict the positives. 3) A hard example priority (HEP) based softmax loss is proposed to improve the robustness of classification task by selecting hard categories. The shared feature representation of I-Net may restrict the task-specific flexibility and learning capability between detection and retrieval tasks. Therefore, with the philosophy of divide and conquer, we further propose an improved I-Net, called DC-I-Net, which makes two new contributions: 1) two modules are tailored to handle different tasks separately in the integrated framework, such that the task specification is guaranteed. 2) A class-center guided HEP loss (C2HEP) by exploiting the stored class centers is proposed, such that the intra-similarity a

关键词： Object recognition

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Learning tubule-sensitive CNNs for pulmonary airway and artery-vein segmentation in CT

arXiv

引用

arXiv 2020年

作者： Qin, Yulei Zheng, Hao Gu, Yun Huang, Xiaolin Yang, Jie Wang, Lihui Yao, Feng Zhu, Yue-Min Yang, Guang-Zhong Institute of Image Processing and Pattern Recognition Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province School of Computer Science and Technology Guizhou University Guiyang China Department of Thoracic Surgery Shanghai Chest Hospital Shanghai Jiao Tong University Shanghai China Université de Lyon INSA Lyon CREATIS CNRS INSERM UMR 5220 VilleurbanneU1206 France Institute of Medical Robotics School of Biomedical Engineering Shanghai Jiao Tong University Shanghai China

Training convolutional neural networks (CNNs) for segmentation of pulmonary airway, artery, and vein is challenging due to sparse supervisory signals caused by the severe class imbalance between tubular targets and background. We present a CNNs-based method for accurate airway and artery-vein segmentation in non-contrast computed tomography. It enjoys superior sensitivity to tenuous peripheral bronchioles, arterioles, and venules. The method first uses a feature recalibration module to make the best use of features learned from the neural networks. Spatial information of features is properly integrated to retain relative priority of activated regions, which benefits the subsequent channel-wise recalibration. Then, attention distillation module is introduced to reinforce representation learning of tubular objects. Fine-grained details in high-resolution attention maps are passing down from one layer to its previous layer recursively to enrich context. Anatomy prior of lung context map and distance transform map is designed and incorporated for better artery-vein differentiation capacity. Extensive experiments demonstrated considerable performance gains brought by these components. Compared with state-of-the-art methods, our method extracted much more branches while maintaining competitive overall segmentation performance. Codes and models are available at http://***/News/56. © 2020, CC BY.

关键词： Computerized tomography

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The Effect of Data Augmentation on Classification of Atrial Fibrillation in Short Single-Lead ECG Signals Using Deep Neural Networks

The Effect of Data Augmentation on Classification of Atrial ...

引用

IEEE International Conference on Acoustics, Speech and Signal processing

作者： Faezeh Nejati Hatamian Nishant Ravikumar Sulaiman Vesal Felix P. Kemeth Matthias Struck Andreas Maier Department of Image Processing and Medical Technology Fraunhofer Institute for Integrated Circuits IIS Erlangen Germany Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB) School of Computing LICAMM Leeds Institute of Cardiovascular and Metabolic Medicine School of Medicine University of Leeds United Kingdom Pattern Recognition Lab Friedrich-Alexander University Erlangen-Nürnberg Erlangen Germany

ISBN: (数字)9781509066315

ISBN: (纸本)9781509066322

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.

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Alleviating class-wise gradient imbalance for pulmonary airway segmentation

arXiv

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arXiv 2020年

作者： Zheng, Hao Qin, Yulei Gu, Yun Xie, Fangfang Yang, Jie Sun, Jiayuan Yang, Guang-Zhong Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong Univeristy Shanghai China School of Biomedical Engineering Shanghai Jiao Tong Univeristy Shanghai China Department of Respiratory and Critical Care Medicine Department of Respiratory Endoscopy Shanghai Chest Hospital Shanghai Engineering Research Center of Respiratory Endoscopy Shanghai China

— Automated airway segmentation is a prerequisite for pre-operative diagnosis and intra-operative navigation for pulmonary intervention. Due to the small size and scattered spatial distribution of peripheral bronchi, this is hampered by a severe class imbalance between foreground and background regions, which makes it challenging for CNN-based methods to parse distal small airways. In this paper, we demonstrate that this problem is arisen by gradient erosion and dilation of the neighborhood voxels. During back-propagation, if the ratio of the foreground gradient to background gradient is small while the class imbalance is local, the foreground gradients can be eroded by their neighborhoods. This process cumulatively increases the noise information included in the gradient flow from top layers to the bottom ones, limiting the learning of small structures in CNNs. To alleviate this problem, we use group supervision and the corresponding WingsNet to provide complementary gradient flows to enhance the training of shallow layers. To further address the intra-class imbalance between large and small airways, we design a General Union loss function that obviates the impact of airway size by distance-based weights and adaptively tunes the gradient ratio based on the learning process. Extensive experiments on public datasets demonstrate that the proposed method can predict the airway structures with higher accuracy and better morphological completeness than the baselines. Copyright © 2020, The Authors. All rights reserved.

关键词： Erosion

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Prediction of σ54 promoters in prokaryotes based on SVM–Adaboost

Prediction of σ54 promoters in prokaryotes based on SVM–Ad...

引用

Chinese Automation Congress (CAC)

作者： Yongxian Fan Qingqi Zhu Chengwei Lv Xianyong Pan School of Computer and Information Security Guilin University of Electronic Technology Guilin Guangxi Key Laboratory of System Control and Information Processing Ministry of Education of China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai China

σ 54 promoters are responsible for transcriptional carbon and nitrogen in prokaryotes. However, it is costly and difficult by experimental identification of them, especially in the postgenomic era with avalanche of sequencing data. Thus, it is imperative to develop efficiently and rapidly computational algorithms to identify the σ 54 promoters. In this study, a novel predictor named SVM-Adaboost was developed to predict σ 54 promoters from sequences alone, it used the Adaboost algorithm as the core, and support vector machine (SVM) as weak base predictors. SVM-Adaboost integrated SVM predictors to construct a more powerful and robust ensemble predictor. In SVM-Adaboost, we used pseudo k-tuple nucleotide composition method to encode DNA sequences, and then a feature selection method was used to further select the discriminate features for subsequent classification. We strictly evaluate the SVM-Adaboost on a constructed gold-standard σ 54 promoter dataset using ten-fold cross validation 100 times, and achieved an average accuracy of 96.06%.

关键词： DNA Support vector machines Feature extraction Training Prediction algorithms Benchmark testing Computational modeling

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S2PAD: Secure self-certified public auditing for data integrity in cloud storage and its extension

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International Journal of Information and Communication technology 2018年第1-2期12卷 113-130页

作者： Zhang, Jianhong Zhao, Xubing Zhen, Weina College of Sciences North China University of Technology Beijing100144 China ISN Key State Lab Xidian University Xi’an Shaanxi710071 China Institute of Image Process and Pattern Recognize North China University of Technology Beijing100144 China

Cloud storage is an important service of cloud computing, it can offer services for data owners in a pay-as-you-go fashion. In cloud storage, after data files are outsourced, data owner no longer has physical controls over the storage. To protect the outsourced data in cloud storage against corruptions, several public auditing schemes for data integrity checking were proposed to achieve data integrity checking. The existing auditing schemes make the auditor execute high computation to check data integrity. It might become a burden for a lot of data owner. To solve the above problem, we propose a novel public auditing scheme with public verifiability and constant communication cost based on self-certified signature scheme in this paper. Thorough analysis shows that our proposed scheme is secure and efficient. The security of our scheme is based on the fixed inversion (FI) problem of the bilinear map and the inversion of hash function. Finally, based on the above protocol, we extend it into multi-user setting. Copyright © 2018 Inderscience Enterprises Ltd.

关键词： Cloud storage

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Sparse generalized canonical correlation analysis: Distributed alternating iteration based approach

arXiv

引用

arXiv 2020年

作者： Cai, Jia Lv, Kexin Huo, Junyi Huang, Xiaolin Yang, Jie School of Statistics and Mathematics Guangdong University of Finance & Economics Big Data and Educational Statistics Application Laboratory 21 Chisha Road Guangzhou Guangdong510320 China 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 School of Electronics and Computer Science University of Southampton University Road SouthamptonSO17 1BJ United Kingdom

Sparse canonical correlation analysis (CCA) is a useful statistical tool to detect latent information with sparse structures. However, sparse CCA works only for two datasets, i.e., there are only two views or two distinct objects. To overcome this limitation, in this paper, we propose a sparse generalized canonical correlation analysis (GCCA), which could detect the latent relations of multiview data with sparse structures. Moreover, the introduced sparsity could be considered as Laplace prior on the canonical variates. Specifically, we convert the GCCA into a linear system of equations and impose 1 minimization penalty for sparsity pursuit. This results in a nonconvex problem on Stiefel manifold, which is difficult to solve. Motivated by Boyd’s consensus problem, an algorithm based on distributed alternating iteration approach is developed and theoretical consistency analysis is investigated elaborately under mild conditions. Experiments on several synthetic and real world datasets demonstrate the effectiveness of the proposed algorithm. Copyright © 2020, The Authors. All rights reserved.

关键词： Statistical mechanics

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