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Residual block-based multi-label classification and localization network with integral regression for vertebrae labeling

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arXiv 2020年

作者： Qin, Chunli Yao, Demin Zhuang, Han Wang, Hui Shi, Yonghong Song, Zhijian Digital Medical Research Center School of Basic Medical Sciences Fudan University Shanghai Key Laboratory of Medical Imaging Computing Computer Assisted Intervention Shanghai200032 China Medical Research Center and Department of Anatomy Histology and Embryology School of Basic Medical Sciences Fudan University

Accurate identification and localization of the vertebrae in CT scans is a critical and standard preprocessing step for clinical spinal diagnosis and treatment. Existing methods are mainly based on the integration of multiple neural networks, and most of them use the Gaussian heat map to locate the vertebrae's centroid. However, the process of obtaining the vertebrae's centroid coordinates using heat maps is non-differentiable, so it is impossible to train the network to label the vertebrae ***, for end-to-end differential training of vertebra coordinates on CT scans, a robust and accurate automatic vertebral labeling algorithm is proposed in this study. Firstly, a novel residual-based multi-label classification and localization network is developed, which can capture multi-scale features, but also utilize the residual module and skip connection to fuse the multi-level features. Secondly, to solve the problem that the process of finding coordinates is non-differentiable and the spatial structure is not destructible, integral regression module is used in the localization network. It combines the advantages of heat map representation and direct regression coordinates to achieve end-to-end training, and can be compatible with any key point detection methods of medical image based on heat map. Finally, multi-label classification of vertebrae is carried out, which use bidirectional long short term memory (Bi-LSTM) to enhance the learning of long contextual information to improve the classification performance. The proposed method is evaluated on a challenging dataset and the results are significantly better than the state-of-the-art methods (mean localization error Copyright © 2020, The Authors. All rights reserved.

关键词： Classification (of information)

Tumor Detection, Segmentation and Classification Challenge on Automated 3D Breast Ultrasound: The TDSC-ABUS Challenge

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arXiv 2025年

作者： Luo, Gongning Xu, Mingwang Chen, Hongyu Liang, Xinjie Tao, Xing Ni, Dong Jeong, Hyunsu Kim, Chulhong Stock, Raphael Baumgartner, Michael Kirchhoff, Yannick Rokuss, Maximilian Maier-Hein, Klaus Yang, Zhikai Fan, Tianyu Boutry, Nicolas Tereshchenko, Dmitry Moine, Arthur Charmetant, Maximilien Sauer, Jan Du, Hao Bai, Xiang-Hui Raikar, Vipul Pai Montoya-Del-Angel, Ricardo Martí, Robert Luna, Miguel Lee, Dongmin Qayyum, Abdul Mazher, Moona Guo, Qihui Wang, Changyan Awasthi, Navchetan Zhao, Qiaochu Wang, Wei Wang, Kuanquan Wang, Qiucheng Dong, Suyu School of Computer Science and Technology Harbin Institute of Technology Harbin150001 China Department of Mathematics Faculty of Science National University of Singapore Singapore National-Regional Key Technology Engineering Laboratory for Medical Ultrasound School of Biomedical Engineering Shenzhen University Medical School Shenzhen University Shenzhen China Laboratory Shenzhen University Shenzhen China School of Biomedical Engineering and Informatics Nanjing Medical University Nanjing China Pohang Korea Republic of Heidelberg Division of Medical Image Computing Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Germany Heidelberg Germany HIDSS4Health - Helmholtz Information and Data Science School for Health Karlsruhe Heidelberg Germany Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Germany Department of Biomedical Engineering and Health KTH Royal Institute of Technology Stockholm Sweden France FathomX Singapore Saw Swee Hock School of Public Health National University of Singapore Singapore Philips Research University of Girona Spain Department of Robotics and Mechatronics Engineering DGIST Korea Republic of Department of Interdisciplinary Studies of Artificial Intelligence DGIST Korea Republic of National Heart and Lung Institute Faculty of Medicine Imperial College London London United Kingdom Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom Lab School of Communication and Information Engineering Shanghai University Shanghai China Faculty of Science Mathematics and Computer Science Informatics Institute University of Amsterdam Amsterdam1090 GH Netherlands Department of Biomedical Engineering and Physics Amsterdam UMC Amsterdam1081 HV Netherlands Xi’an Jiaotong-Liverpool University China Department of Ultrasound Harbin Medical University Cancer Hospital No. 150 Haping Road Nangang

Breast cancer is one of the most common causes of death among women worldwide. Early detection helps in reducing the number of deaths. Automated 3D Breast Ultrasound (ABUS) is a newer approach for breast screening, which has many advantages over handheld mammography such as safety, speed, and higher detection rate of breast cancer. Tumor detection, segmentation, and classification are key components in the analysis of medical images, especially challenging in the context of 3D ABUS due to the significant variability in tumor size and shape, unclear tumor boundaries, and a low signal-to-noise ratio. The lack of publicly accessible, well-labeled ABUS datasets further hinders the advancement of systems for breast tumor analysis. Addressing this gap, we have organized the inaugural Tumor Detection, Segmentation, and Classification Challenge on Automated 3D Breast Ultrasound 2023 (TDSC-ABUS2023). This initiative aims to spearhead research in this field and create a definitive benchmark for tasks associated with 3D ABUS image analysis. In this paper, we summarize the top-performing algorithms from the challenge and provide critical analysis for ABUS image examination. We offer the TDSC-ABUS challenge as an open-access platform at https://***/ to benchmark and inspire future developments in1algorithmic research. © 2025, CC BY.

关键词： image segmentation

Equilibrium and transient thermodynamics: A unified dissipaton–space approach

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arXiv 2020年

作者： Gong, Hong Wang, Yao Zhang, Hou-Dao Qiao, Qin Xu, Rui-Xue Zheng, Xiao Yan, YiJing Department of Chemical Physics University of Science and Technology of China HefeiAnhui230026 China Hefei National Laboratory for Physical Sciences at the Microscale and iChEM Synergetic Innovation Center of Quantum Information and Quantum Physics University of Science and Technology of China Hefei Anhui230026 China Digital Medical Research Center of School of Basic Medical Sciences Fudan University Shanghai200032 China Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention Shanghai200032 China

This work presents a unified dissipaton–equation–of–motion (DEOM) theory and its evaluations on the Helmholtz free energy change due to the isotherm mixing of two isolated subsystems. One is a local impurity and another is a nonlocal Gaussian bath. DEOM constitutes a fundamental theory for such open quantum mixtures. To complete the theory, we construct also the imaginary–time DEOM formalism via an analytical continuation of dissipaton algebra, which would be limited to equilibrium thermodynamics. On the other hand, the real–time DEOM deals with both equilibrium structural and nonequilibrium dynamic properties. Its combination with the thermodynamic integral formalism would be a viable and accurate means to both equilibrium and transient thermodynamics. As illustrations, we report the numerical results on a spin–boson system, with elaborations on the underlying anharmonic features, the thermodynamic entropy versus the von Neumann entropy, and an indication of "solvent–cage" formation. Beside the required asymptotic equilibrium properties, the proposed transient thermodynamics also supports the basic spontaneity criterion. Copyright © 2020, The Authors. All rights reserved.

关键词： Free energy

Bayesian data assimilation for estimating epidemic evolution: A COVID-19 study

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arXiv 2020年

作者： Yang, Xian Wang, Shuo Xing, Yuting Li, Ling Xu, Richard Yi Da Friston, Karl J. Guo, Yike Department of Computer Science Hong Kong Baptist University Hong Kong Special Administrative Region Hong Kong Data Science Institute Imperial College London United Kingdom Digital Medical Research Center School of Basic Medical Sciences Fudan University China Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention China School of Computing University of Kent United Kingdom Faculty of Engineering and Information Technology University of Technology Sydney Australia Institute of Neurology University College London United Kingdom

The evolution of epidemiological parameters, such as instantaneous reproduction number Rt, is important for understanding the transmission dynamics of infectious diseases. Current estimates of time-varying epidemiological parameters often face problems such as lagging observations, averaging inference, and improper quantification of uncertainties. To address these problems, we propose a Bayesian data assimilation framework for time-varying parameter estimation. Specifically, this framework is applied to Rt estimation, resulting in the state-of-the-art 'DARt' system. With DARt, time misalignment caused by lagging observations is tackled by incorporating observation delays into the joint inference of infections and Rt;the drawback of averaging is overcome by instantaneously updating upon new observations and developing a model selection mechanism that captures abrupt changes;the uncertainty is quantified and reduced by employing Bayesian smoothing. We validate the performance of DARt and demonstrate its power in revealing the transmission dynamics of COVID-19. The proposed approach provides a promising solution for accurate and timely estimating transmission dynamics from reported data. Copyright © 2020, The Authors. All rights reserved.

关键词： Cell proliferation

Catalpol ameliorates depressive-like behaviors in CUMS mice via oxidative stress-mediated NLRP3 inflammasome and neuroinflammation

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解剖学杂志 2021年第S1期44卷 125-125页

作者： Wu Haoran Wang Yalim Hu Juntao Department of Anatomy Histology and EmbryologyDepartment of Integrative Medicine and NeurobiologySchool of Basic Medical SciencesInstitutes of Brain ScienceState Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain ScienceShanghai Medical CollegeFudan UniversityKey Laboratory of Medical Imaging Computing and Computer Assisted Intervention of ShanghaiShanghai 200032China

The purpose of the present study was to investigate whether catalpol exhibited neuro-protective effects in chronic unpredictable mild stress(CUMS)mice through oxidative stress-mediated nucleotide-binding oligomerizati... 详细信息

关键词： NLRP3 inflammation protective

A Novel Method for the Absolute Pose Problem with Pairwise Constraints

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arXiv 2019年

作者： Liu, Yinlong Li, Xuechen Wang, Manning Chen, Guang Song, Zhijian Knoll, Alois Technische Universität München Digital Medical Research Center School of Basic Medical Sciences Fudan University Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention Tongji University

Absolute pose estimation is a fundamental problem in computer vision, and it is a typical parameter estimation problem, meaning that efforts to solve it will always suffer from outlier-contaminated data. Conventionally, for a fixed dimensionality d and the number of measurements N, a robust estimation problem cannot be solved faster than O(Nd). Furthermore, it is almost impossible to remove d from the exponent of the runtime of a globally optimal algorithm. However, absolute pose estimation is a geometric parameter estimation problem, and thus has special constraints. In this paper, we consider pairwise constraints and propose a globally optimal algorithm for solving the absolute pose estimation problem. The proposed algorithm has a linear complexity in the number of correspondences at a given outlier ratio. Concretely, we first decouple the rotation and the translation subproblems by utilizing the pairwise constraints, and then we solve the rotation subproblem using the branch-and-bound algorithm. Lastly, we estimate the translation based on the known rotation by using another branch-and-bound algorithm. The advantages of our method are demonstrated via thorough testing on both synthetic and real-world data. Copyright © 2019, The Authors. All rights reserved.

关键词： Branch and bound method

Author Correction: Deep learning radiomics can predict axillary lymph node status in early-stage breast cancer

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Nature communications 2021年第1期12卷 4370页

作者： Xueyi Zheng Zhao Yao Yini Huang Yanyan Yu Yun Wang Yubo Liu Rushuang Mao Fei Li Yang Xiao Yuanyuan Wang Yixin Hu Jinhua Yu Jianhua Zhou Department of Ultrasound Sun Yat-Sen University Cancer Center State Key Laboratory of Oncology in South China Collaborative Innovation Center for Cancer Medicine Guangzhou China. Department of Electronic Engineering Fudan University Shanghai China. Paul C. Lauterbur Research Center for Biomedical Imaging Institute of Biomedical and Health Engineering Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China. The key laboratory of medical imaging computing and computer assisted intervention of Shanghai Shanghai China. Department of Electronic Engineering Fudan University Shanghai China. jhyu@***. The key laboratory of medical imaging computing and computer assisted intervention of Shanghai Shanghai China. jhyu@***. Department of Ultrasound Sun Yat-Sen University Cancer Center State Key Laboratory of Oncology in South China Collaborative Innovation Center for Cancer Medicine Guangzhou China. zhoujh@***.

Learning data-adaptive non-parametric kernels

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The Journal of Machine Learning Research

The Journal of Machine Learning Research 2020年第1期21卷 8590-8628页

作者： Fanghui Liu Xiaolin Huang Chen Gong Jie Yang Li Li Department of Electrical Engineering ESAT-STADIUS KU Leuven Belgium Institute of Image Processing and Pattern Recognition Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China PCA Lab Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information of Ministry of Education School of Computer Science and Engineering Nanjing University of Science and Technology China and Department of Computing Hong Kong Polytechnic University Hong Kong SAR China Department of Automation BNRist Tsinghua University China

In this paper, we propose a data-adaptive non-parametric kernel learning framework in margin based kernel methods. In model formulation, given an initial kernel matrix, a data-adaptive matrix with two constraints is imposed in an entry-wise scheme. Learning this data-adaptive matrix in a formulation-free strategy enlarges the margin between classes and thus improves the model flexibility. The introduced two constraints are imposed either exactly (on small data sets) or approximately (on large data sets) in our model, which provides a controllable trade-off between model flexibility and complexity with theoretical demonstration. In algorithm optimization, the objective function of our learning framework is proven to be gradient-Lipschitz continuous. Thereby, kernel and classifier/regressor learning can be efficiently optimized in a unified framework via Nesterov's acceleration. For the scalability issue, we study a decomposition-based approach to our model in the large sample case. The effectiveness of this approximation is illustrated by both empirical studies and theoretical guarantees. Experimental results on various classification and regression benchmark data sets demonstrate that our non-parametric kernel learning framework achieves good performance when compared with other representative kernel learning based algorithms.

关键词： support vector machines non-parametric kernel learning gradient-Lipschitz continuous

REFUGE2 CHALLENGE: A TREASURE TROVE FOR MULTI-DIMENSION ANALYSIS AND EVALUATION IN GLAUCOMA SCREENING

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arXiv 2022年

作者： Fang, Huihui Li, Fei Wu, Junde Fu, Huazhu Sun, Xu Son, Jaemin Yu, Shuang Zhang, Menglu Yuan, Chenglang Bian, Cheng Lei, Baiying Zhao, Benjian Xu, Xinxing Li, Shaohua Fumero, Francisco Sigut, José Almubarak, Haidar Bazi, Yakoub Guo, Yuanhao Zhou, Yating Baid, Ujjwal Innani, Shubham Guo, Tianjiao Yang, Jie Orlando, José Ignacio Bogunović, Hrvoje Zhang, Xiulan Xu, Yanwu The REFUGE2 Challenge Australia State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat-Sen University Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science Guangzhou China Intelligent Healthcare Unit Baidu Inc. Beijing China The Institute of High Performance Computing Agency for Science Technology and Research Singapore Yatiris Group PLADEMA Institute CONICET UNICEN Tandil Argentina Christian Doppler Lab for Artificial Intelligence in Retina Department of Ophthalmology and Optometry Medical University of Vienna Vienna Austria VUNO Inc Seoul Korea Republic of Tencent HealthCare Tencent Shenzhen China Computer Vision Institute College of Computer Science and Software Engineering of Shenzhen University Shenzhen China School of Biomedical Engineering Health Science Center Shenzhen University China Xiaohe Healthcare ByteDance Guangdong Guangzhou510000 China School of Biomedical Engineering Shenzhen University China College of Computer Science & Software Engineering Shenzhen University China Department of Computer Science and Systems Engineering Universidad de La Laguna Spain Saudi Electronic University Saudi Arabia King Saud University Saudi Arabia Institute of Automation Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China SGGS Institute of Engineering and Technology India Institute of Medical Robotics Shanghai Jiao Tong University China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University China

With the rapid development of artificial intelligence (AI) in medical image processing, deep learning in color fundus photography (CFP) analysis is also evolving. Although there are some open-source, labeled datasets of CFPs in the ophthalmology community, large-scale datasets for screening only have labels of disease categories, and datasets with annotations of fundus structures are usually small in size. In addition, labeling standards are not uniform across datasets, and there is no clear information on the acquisition device. Here we release a multi-annotation, multi-quality, and multi-device color fundus image dataset for glaucoma analysis on an original challenge-Retinal Fundus Glaucoma Challenge 2nd Edition (REFUGE2). The REFUGE2 dataset contains 2000 color fundus images with annotations of glaucoma classification, optic disc/cup segmentation, as well as fovea localization. Meanwhile, the REFUGE2 challenge sets three sub-tasks of automatic glaucoma diagnosis and fundus structure analysis and provides an online evaluation framework. Based on the characteristics of multi-device and multi-quality data, some methods with strong generalizations are provided in the challenge to make the predictions more robust. This shows that REFUGE2 brings attention to the characteristics of real-world multi-domain data, bridging the gap between scientific research and clinical application. © 2022, CC BY-NC-ND.

关键词： Color