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Unifying structure analysis and surrogate-driven function regression for glaucoma oct image screening

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arXiv 2019年

作者： Wang, Xi Chen, Hao Luo, Luyang Ran, An-Ran Chan, Poemen P. Tham, Clement C. Cheung, Carol Y. Heng, Pheng-Ann Department of Computer Science and Engineering Chinese University of Hong Kong Hong Kong Hong Kong Imsight Medical Technology Co. Ltd. Department of Ophthalmology and Visual Sciences Chinese University of Hong Kong Hong Kong Hong Kong Guangdong Provincial Key Laboratory of Computer Vision and Virtual Reality Technology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen

Optical Coherence Tomography (OCT) imaging plays an im-portant role in glaucoma diagnosis in clinical practice. Early detection and timely treatment can prevent glaucoma patients from permanent vision loss. However, only a dearth of automated methods has been de-veloped based on OCT images for glaucoma study. In this paper, we present a novel framework to effectively classify glaucoma OCT images from normal ones. A semi-supervised learning strategy with smoothness assumption is applied for surrogate assignment of missing function re-gression labels. Besides, the proposed multi-task learning network is ca-pable of exploring the structure and function relationship from the OCT image and visual field measurement simultaneously, which contributes to classification performance boosting. Essentially, we are the first to unify the structure analysis and function regression for glaucoma screen-ing. It is also worth noting that we build the largest glaucoma OCT image dataset involving 4877 volumes to develop and evaluate the pro-posed method. Extensive experiments demonstrate that our framework outperforms the baseline methods and two glaucoma experts by a large margin, achieving 93.2%, 93.2% and 97.8% on accuracy, F1 score and AUC, respectively. Copyright © 2019, The Authors. All rights reserved.

关键词： Ophthalmology

IRNet: Instance relation network for overlapping cervical cell segmentation

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arXiv 2019年

作者： Zhou, Yanning Chen, Hao Xu, Jiaqi Dou, Qi Heng, Pheng-Ann Department of Computer Science and Engineering Chinese University of Hong Kong Hong Kong Hong Kong Imsight Medical Technology Co. Ltd. Hong Kong Hong Kong Department of Computing Imperial College London London United Kingdom Guangdong Provincial Key Laboratory of Computer Vision and Virtual Reality Technology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China

Cell instance segmentation in Pap smear image remains challenging due to the wide existence of occlusion among translucent cytoplasm in cell clumps. Conventional methods heavily rely on accurate nuclei detection results and are easily disturbed by miscellaneous objects. In this paper, we propose a novel Instance Relation Network (IRNet) for robust overlapping cell segmentation by exploring instance relation interaction. Specifically, we propose the Instance Relation Module to construct the cell association matrix for transferring information among individual cell-instance features. With the collaboration of different instances, the augmented features gain benefits from contextual information and improve semantic consistency. Meanwhile, we proposed a sparsity constrained Duplicate Removal Module to eliminate the misalignment between classification and localization accuracy for candidates selection. The largest cervical Pap smear (CPS) dataset with more than 8000 cell annotations in Pap smear image was constructed for comprehensive evaluation. Our method outperforms other methods by a large margin, demonstrating the effectiveness of exploring instance relation. Copyright © 2019, The Authors. All rights reserved.

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CAS-YNU multi-modal cross-view human action dataset

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CAS-YNU multi-modal cross-view human action dataset

2018 IEEE International Conference on Information and Automation, ICIA 2018

作者： Zhao, Qingsong Cheng, Jun Tao, Dapeng Ji, Xiaopeng Wang, Lei Guangdong Provincial Key Laboratory of Computer Vision and Virtual Reality Technology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences China Shenzhen College of Advanced Technology University of Chinese Academy of Sciences China Chinese University of Hong Kong Hong Kong School of Information Science and Engineering Yunnan University China

ISBN: (纸本)9781538680698

Human action recognition is a hot research topic in computer vision, which has extensive applications including human-computer interaction, robot and surveillance. Some outstanding human action datasets have been published. However, they still have some defects, such as the limited modality types, camera views, complexity of scene and action categories. Furthermore, most of them are devised for a subset of the action recognition, such as single-modal recognition and single-view recognition. In this paper, we propose a multi-modal cross-view human action dataset (named CAS-YNU MCHAD). It consists of five synchronous data modalities, including RGB image, depth maps, human segment maps, skeleton data and inertial data. Our dataset contains 14782 action samples from 50 subjects and 10 actions in two perspectives. Extensive benchmark experiments on this dataset are conducted with the state-of-the-art recognition approaches. Experimental results illustrate that it is challenging on cross-view action recognition. We also provide the baseline for the assessment of existing recognition methods. © 2018 IEEE.

关键词： Human computer interaction

CIA-Net: Robust nuclei instance segmentation with contour-aware information aggregation

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arXiv 2019年

作者： Zhou, Yanning Onder, Omer Fahri Dou, Qi Tsougenis, Efstratios Chen, Hao Heng, Pheng-Ann Department of Computer Science and Engineering Chinese University of Hong Kong Hong Kong Hong Kong Imsight Medical Technology Co. Ltd. Hong Kong Hong Kong Department of Computing Imperial College London London United Kingdom Department of Computer Science and Engineering Chinese University of Hong Kong Guangdong Provincial Key Laboratory of Computer Vision and Virtual Reality Technology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China

Accurate segmenting nuclei instances is a crucial step in computer-aided image analysis to extract rich features for cellular estimation and following diagnosis as well as treatment. While it still remains challenging because the wide existence of nuclei clusters, along with the large morphological variances among different organs make nuclei instance segmentation susceptible to over-/under-segmentation. Additionally, the inevitably subjective annotating and mislabeling prevent the network learning from reliable samples and eventually reduce the generalization capability for robustly segmenting unseen organ nuclei. To address these issues, we propose a novel deep neural network, namely Contour-aware Informative Aggregation Network (CIA-Net) with multilevel information aggregation module between two task-specific decoders. Rather than independent decoders, it leverages the merit of spatial and texture dependencies between nuclei and contour by bi-directionally aggregating task-specific features. Furthermore, we proposed a novel smooth truncated loss that modulates losses to reduce the perturbation from outliers. Consequently, the network can focus on learning from reliable and informative samples, which inherently improves the generalization capability. Experiments on the 2018 MICCAI challenge of Multi-Organ-Nuclei-Segmentation validated the effectiveness of our proposed method, surpassing all the other 35 competitive teams by a significant margin. Copyright © 2019, The Authors. All rights reserved.

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An active learning approach for reducing annotation cost in skin lesion analysis

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arXiv 2019年

作者： Shi, Xueying Dou, Qi Xue, Cheng Qin, Jing Chen, Hao Heng, Pheng-Ann Department of Computer Science and Engineering Chinese University of Hong Kong Hong Kong Department of Computing Imperial College London LondonSW7 2AZ United Kingdom Imsight Medical Technology Co. Ltd. Shenzhen China Centre for Smart Health School of Nursing Hong Kong Polytechnic University Hong Kong Guangdong Provincial Key Laboratory of Computer Vision and Virtual Reality Technology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China

Automated skin lesion analysis is very crucial in clinical practice, as skin cancer is among the most common human malignancy. Existing approaches with deep learning have achieved remarkable performance on this challenging task, however, heavily relying on large-scale labelled datasets. In this paper, we present a novel active learning framework for cost-effective skin lesion analysis. The goal is to effectively select and utilize much fewer labelled samples, while the network can still achieve state-of-the-art performance. Our sample selection criteria complementarily consider both informativeness and representativeness, derived from decoupled aspects of measuring model certainty and covering sample diversity. To make wise use of the selected samples, we further design a simple yet effective strategy to aggregate intra-class images in pixel space, as a new form of data augmentation. We validate our proposed method on data of ISIC 2017 Skin Lesion Classification Challenge for two tasks. Using only up to 50% of samples, our approach can achieve state-of-the-art performances on both tasks, which are comparable or exceeding the accuracies with full-data training, and outperform other well-known active learning methods by a large margin. Copyright © 2019, The Authors. All rights reserved.

关键词： Cost effectiveness

A real-time unsupervised background extraction-based target detection method for hyperspectral imagery

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A real-time unsupervised background extraction-based target ...

作者： Li, Cong Gao, Lianru Wu, Yuanfeng Zhang, Bing Plaza, Javier Plaza, Antonio Key Laboratory of Digital Earth Science Institute of Remote Sensing and Digital Earth Chinese Academy of Sciences Beijing100094 China University of Chinese Academy of Sciences Beijing100049 China The College of Computer Science and Software Engineering Computer Vision Research Institute Shenzhen University Shenzhen518060 China Hyperspectral Computing Laboratory Department of Technology of Computers and Communications Escuela Politecnica de Cáceres University of Extremadura Cáceres Spain

Target detection is an important technique in hyperspectral image analysis. The high dimensionality of hyperspectral data provides the possibility of deeply mining the information hiding in spectra, and many targets that cannot be visualized by inspection can be detected. But this also brings some problems such as unknown background interferences at the same time. In this way, extracting and taking advantage of the background information in the region of interest becomes a task of great significance. In this paper, we present an unsupervised background extraction-based target detection method, which is called UBETD for short. The proposed UBETD takes advantage of the method of endmember extraction in hyperspectral unmixing, another important technique that can extract representative material signatures from the images. These endmembers represent most of the image information, so they can be reasonably seen as the combination of targets and background signatures. Since the background information is known, algorithm like target-constrained interference-minimized filter could then be introduced to detect the targets while inhibiting the interferences. To meet the rapidly rising demand of real-time processing capabilities, the proposed algorithm is further simplified in computation and implemented on a FPGA board. Experiments with synthetic and real hyperspectral images have been conducted comparing with constrained energy minimization, adaptive coherence/cosine estimator and adaptive matched filter to evaluate the detection and computational performance of our proposed method. The results indicate that UBETD and its hardware implementation RT-UBETD can achieve better performance and are particularly prominent in inhibiting interferences in the background. On the other hand, the hardware implementation of RT-UBETD can complete the target detection processing in far less time than the data acquisition time of hyperspectral sensor like HyMap, which confirms strict real-ti

关键词： Field programmable gate arrays (FPGA)

Variable population memetic search: A case study on the critical node problem

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arXiv 2019年

作者： Zhou, Yangming Hao, Jin-Kao Fu, Zhang-Hua Wang, Zhe Lai, Xiangjing School of Information Science and Engineering East China University of Science and Technology 130 Meilong Road Shanghai200237 China Key Laboratory of Advanced Control and Optimization for Chemical Processes Ministry of Education Department of Computer Science LERIA Université d'Angers 2 Boulevard Lavoisier Angers49045 France Institut Universitaire de France 1 rue Descartes Paris75231 France Robotics Laboratory for Logistics Service Institute of Robotics and Intelligent Manufacturing Chinese University of Hong Kong Shenzhen Institute of Artificial Intelligence and Robotics for Society Shenzhen518172 China Institute of Advanced Technology Nanjing University of Posts and Telecommunications Nanjing210023 China

Population-based memetic algorithms have been successfully applied to solve many difficult combinatorial problems. Often, a population of fixed size was used in such algorithms to record some best solutions sampled during the search. However, given the particular features of the problem instance under consideration, a population of variable size would be more suitable to ensure the best search performance possible. In this work, we propose variable population memetic search (VPMS), where a strategic population sizing mechanism is used to dynamically adjust the population size during the memetic search process. Our VPMS approach starts its search from a small population of only two solutions to focus on exploitation, and then adapts the population size according to the search status to continuously influence the balancing between exploitation and exploration. We illustrate an application of the VPMS approach to solve the challenging critical node problem (CNP). We show that the VPMS algorithm integrating a variable population, an effective local optimization procedure (called diversified late acceptance search) and a backbone-based crossover operator performs very well compared to state-of-the-art CNP algorithms. The algorithm is able to discover new upper bounds for 13 instances out of the 42 popular benchmark instances, while matching 23 previous best-known upper bounds. Copyright © 2019, The Authors. All rights reserved.

关键词： Population statistics

The medical segmentation decathlon

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arXiv 2021年

作者： Antonelli, Michela Reinke, Annika Bakas, Spyridon Farahani, keyvan Kopp-Schneider, Annette Landman, Bennett A. Litjens, Geert Menze, Bjoern Ronneberger, Olaf Summers, Ronald M. van Ginneken, Bram Bilello, Michel Bilic, Patrick Christ, Patrick F. Do, Richard K.G. Gollub, Marc J. Heckers, Stephan H. Huisman, Henkjan Jarnagin, William R. McHugo, Maureen K. Napel, Sandy Golia Pernicka, Jennifer S. Rhode, Kawal Tobon-Gomez, Catalina Vorontsov, Eugene Hulsmon, Hankan Meakin, James A. Ourselin, Sebastien Wiesenfarth, Manuel Arbeláez, Pablo Bae, Byeonguk Chen, Sihong Daza, Laura Feng, Jianjiang He, Baochun Isensee, Fabian Ji, Yuanfeng Jia, Fucang Kim, Namkug Kim, Ildoo Merhof, Dorit Pai, Akshay Park, Beomhee Perslev, Mathias Rezaiifar, Ramin Rippel, Oliver Sarasua, Ignacio Shen, Wei Son, Jaemin Wachinger, Christian Wang, Liansheng Wang, Yan Xia, Yingda Xu, Daguang Xu, Zhanwei Zheng, Yefeng Simpson, Amber L. Maier-Hein, Lena Cardoso, M. Jorge School of Biomedical Engineering & Imaging Sciences King’s College London London United Kingdom Heidelberg Germany Heidelberg Germany Faculty of Mathematics and Computer Science University of Heidelberg Heidelberg Germany University of Pennsylvania PhiladelphiaPA United States BethesdaMD United States Heidelberg Germany Electrical Engineering and Computer Science Vanderbilt University NashvilleTN United States Radboud University Medical Center Radboud Institute for Health Sciences Nijmegen Netherlands Quantitative Biomedicine University of Zurich Zurich Switzerland DeepMind London United Kingdom School of Computing Department of Biomedical and Molecular Sciences Queen’s University KingstonON Canada Department of Surgery Memorial Sloan Kettering Cancer Center New YorkNY United States BethesdaMD United States Department of Informatics Technische Universität München Germany Department of Radiology Memorial Sloan Kettering Cancer Center New YorkNY United States Department of Psychiatry & Behavioral Sciences Vanderbilt University Medical Center NashvilleTN United States Department of Radiology Stanford University StanfordCA United States Department of Computer Science and Software Engineering École Polytechnique de Montréal Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Medical Faculty University of Heidelberg Heidelberg Germany VUNO Inc. Seoul Korea Republic of Universidad de los Andes Colombia Department of Automation Tsinghua University Beijing China Heidelberg Germany Department of Computer Science Xiamen University Xiamen361005 China Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China Kakao Brain Korea Republic of Institute of Imaging & Computer Vision RWTH Aachen University Aachen Germany Cere

International challenges have become the de facto standard for comparative assessment of image analysis algorithms given a specific task. Segmentation is so far the most widely investigated medical image processing task, but the various segmentation challenges have typically been organized in isolation, such that algorithm development was driven by the need to tackle a single specific clinical problem. We hypothesized that a method capable of performing well on multiple tasks will generalize well to a previously unseen task and potentially outperform a custom-designed solution. To investigate the hypothesis, we organized the Medical Segmentation Decathlon (MSD)—a biomedical image analysis challenge, in which algorithms compete in a multitude of both tasks and modalities. The underlying data set was designed to explore the axis of difficulties typically encountered when dealing with medical images, such as small data sets, unbalanced labels, multi-site data and small objects. The MSD challenge confirmed that algorithms with a consistent good performance on a set of tasks preserved their good average performance on a different set of previously unseen tasks. Moreover, by monitoring the MSD winner for two years, we found that this algorithm continued generalizing well to a wide range of other clinical problems, further confirming our hypothesis. Three main conclusions can be drawn from this study: (1) state-of-the-art image segmentation algorithms are mature, accurate, and generalize well when retrained on unseen tasks;(2) consistent algorithmic performance across multiple tasks is a strong surrogate of algorithmic generalizability;(3) the training of accurate AI segmentation models is now commoditized to non AI *** Codes 68T07. © 2021, CC BY-NC-SA.

关键词： Image segmentation

Author Correction: Development and clinical deployment of a smartphone-based visual field deep learning system for glaucoma detection

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NPJ digital medicine 2022年第1期5卷 38页

作者： Fei Li Diping Song Han Chen Jian Xiong Xingyi Li Hua Zhong Guangxian Tang Sujie Fan Dennis S C Lam Weihua Pan Yajuan Zheng Ying Li Guoxiang Qu Junjun He Zhe Wang Ling Jin Rouxi Zhou Yunhe Song Yi Sun Weijing Cheng Chunman Yang Yazhi Fan Yingjie Li Hengli Zhang Ye Yuan Yang Xu Yunfan Xiong Lingfei Jin Aiguo Lv Lingzhi Niu Yuhong Liu Shaoli Li Jiani Zhang Linda M Zangwill Alejandro F Frangi Tin Aung Ching-Yu Cheng Yu Qiao Xiulan Zhang Daniel S W Ting State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat-Sen University Guangzhou People's Republic of China. ShenZhen Key Lab of Computer Vision and Pattern Recognition Shenzhen Institutes of Advanced Technology The Chinese Academy of Sciences Shenzhen People's Republic of China. University of Chinese Academy of Sciences Beijing People's Republic of China. Department of Ophthalmology The First Affiliated Hospital of Kunming Medical University Kunming People's Republic of China. The First Hospital of Shijiazhuang City Shijiazhuang People's Republic of China. gxtykyy@***. Handan City Eye Hospital Handan People's Republic of China. C-MER (Shenzhen) Dennis Lam Eye Hospital International Eye Research Institute of The Chinese University of Hong Kong (Shenzhen) Shenzhen People's Republic of China. The Eye Hospital WMU at Hangzhou Hangzhou People's Republic of China. Department of Ophthalmology The Second Hospital of Jilin University Changchun People's Republic of China. SenseTime Group Limited Hong Kong People's Republic of China. Department of Ophthalmology The Second Affiliated Hospital of Guizhou Medical University Kaili People's Republic of China. Department of Ophthalmology The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an People's Republic of China. Department of Ophthalmology The Third Affiliated Hospital of Nanchang University Nanchang People's Republic of China. The First Hospital of Shijiazhuang City Shijiazhuang People's Republic of China. Hamilton Glaucoma Center Shiley Eye Institute Viterbi Family Department of Ophthalmology UC San Diego La Jolla CA United States. CISTIB Center for Computational Imaging and Simulation Technologies in Biomedicine Schools of Computing and Medicine University of Leeds Leeds UK. Singapore Eye Research Institute and Singapore National Eye Centre Singapore Singapore. ShenZhen Key Lab of Computer Vision and Pattern Recognition Shenzhen Institutes of Advanced Technology The Chinese Academy of Sci