检索结果-内蒙古大学图书馆

arXiv 2025年

作者： Zeng, Jinzhe Zhang, Duo Peng, Anyang Zhang, Xiangyu He, Sensen Wang, Yan Liu, Xinzijian Bi, Hangrui Li, Yifan Cai, Chun Zhang, Chengqian Du, Yiming Zhu, Jia-Xin Mo, Pinghui Huang, Zhengtao Zeng, Qiyu Shi, Shaochen Qin, Xuejian Yu, Zhaoxi Luo, Chenxing Ding, Ye Liu, Yun-Pei Shi, Ruosong Wang, Zhenyu Bore, Sigbjørn Løland Chang, Junhan Deng, Zhe Ding, Zhaohan Han, Siyuan Jiang, Wanrun Ke, Guolin Liu, Zhaoqing Lu, Denghui Muraoka, Koki Oliaei, Hananeh Singh, Anurag Kumar Que, Haohui Xu, Weihong Xu, Zhangmancang Zhuang, Yong-Bin Dai, Jiayu Giese, Timothy J. Jia, Weile Xu, Ben York, Darrin M. Zhang, Linfeng Wang, Han School of Artificial Intelligence and Data Science Unversity of Science and Technology of China Hefei China AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing100871 China University of Chinese Academy of Sciences Beijing China Baidu Inc. Beijing China Department of Computer Science University of Toronto TorontoON Canada Department of Chemistry Princeton University PrincetonNJ08540 United States University of Chinese Academy of Sciences Beijing100871 China State Key Laboratory of Physical Chemistry of Solid Surfaces iChEM College of Chemistry and Chemical Engineering Xiamen University Xiamen361005 China College of Integrated Circuits Hunan University Changsha410082 China State Key Laboratory of Advanced Technology for Materials Synthesis and Processing Center for Smart Materials and Device Integration School of Material Science and Engineering Wuhan University of Technology Wuhan430070 China College of Science National University of Defense Technology Changsha410073 China Hunan Key Laboratory of Extreme Matter and Applications National University of Defense Technology Changsha410073 China ByteDance Research Beijing100098 China Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo315201 China College of Materials Science and Opto-Electronic Technology University of Chinese Academy of Sciences Beijing100049 China Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education College of Chemistry Beijing Normal University Beijing100875 China Department of Geosciences Princeton University PrincetonNJ08544 United States Department of Applied Physics and Applied Mathematics Columbia University New YorkNY10027 United States IKKEM Fujian Xiamen361005 China Graduate

In recent years, machine learning potentials (MLPs) have become indispensable tools in physics, chemistry, and materials science, driving the development of software packages for molecular dynamics (MD) simulations and related applications. These packages, typically built on specific machine learning frameworks such as TensorFlow, PyTorch, or JAX, face integration challenges when advanced applications demand communication across different frameworks. The previous TensorFlow-based implementation of DeePMD-kit exemplified these limitations. In this work, we introduce DeePMD-kit version 3, a significant update featuring a multi-backend framework that supports TensorFlow, PyTorch, JAX, and PaddlePaddle backends, and demonstrate the versatility of this architecture through the integration of other MLPs packages and of Differentiable Molecular Force Field. This architecture allows seamless backend switching with minimal modifications, enabling users and developers to integrate DeePMD-kit with other packages using different machine learning frameworks. This innovation facilitates the development of more complex and interoperable workflows, paving the way for broader applications of MLPs in scientific research. Copyright © 2025, The Authors. All rights reserved.

关键词： Molecular dynamics

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Predicting extreme events from data using deep machine learning: when and where

arXiv

引用

arXiv 2022年

作者： Jiang, Junjie Huang, Zi-Gang Grebogi, Celso Lai, Ying-Cheng The Key Laboratory of Biomedical Information Engineering of Ministry of Education Institute of Health and Rehabilitation Science School of Life Science and Technology Research Center for Brain-inspired Intelligence Xi’an Jiaotong University The Key Laboratory of Neuro-informatics & Rehabilitation Engineering of Ministry of Civil Affairs Shaanxi Xi’an China School of Electrical Computer and Energy Engineering Arizona State University TempeAZ85287 United States Institute for Complex Systems and Mathematical Biology School of Natural and Computing Sciences King’s College University of Aberdeen AB24 3UE United Kingdom Department of Physics Arizona State University TempeAZ85287 United States

We develop a deep convolutional neural network (DCNN) based framework for model-free prediction of the occurrence of extreme events both in time ("when") and in space ("where") in nonlinear physical systems of spatial dimension two. The measurements or data are a set of two-dimensional snapshots or images. For a desired time horizon of prediction, a proper labeling scheme can be designated to enable successful training of the DCNN and subsequent prediction of extreme events in time. Given that an extreme event has been predicted to occur within the time horizon, a space-based labeling scheme can be applied to predict, within certain resolution, the location at which the event will occur. We use synthetic data from the 2D complex Ginzburg-Landau equation and empirical wind speed data of the North Atlantic ocean to demonstrate and validate our machine-learning based prediction framework. The trade-offs among the prediction horizon, spatial resolution, and accuracy are illustrated, and the detrimental effect of spatially biased occurrence of extreme event on prediction accuracy is discussed. The deep learning framework is viable for predicting extreme events in the real world. © 2022, CC BY.

关键词： Forecasting

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SLC7A11 is an unconventional H⁺ transporter in lysosomes

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Cell 2025年

作者： Zhou, Nan Chen, Jingzhi Hu, Meiqin Wen, Na Cai, Weijie Li, Ping Zhao, Liding Meng, Yaping Zhao, Dongdong Yang, Xiaotong Liu, Siyu Huang, Fangqian Zhao, Cheng Feng, Xinghua Jiang, Zikai Xie, Enjun Pan, Hongxu Cen, Zhidong Chen, Xinhui Luo, Wei Tang, Beisha Min, Junxia Wang, Fudi Yang, Junsheng Xu, Haoxing New Cornerstone Science Laboratory and Liangzhu Laboratory the Second Affiliated Hospital and School of Basic Medical Sciences Zhejiang University Hangzhou China Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals College of Pharmaceutical Sciences Zhejiang University of Technology Hangzhou China Department of Cardiology the First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China The Second Affiliated Hospital & the First Affiliated Hospital Institute of Translational Medicine School of Public Health State Key Laboratory of Experimental Hematology Zhejiang University School of Medicine Hangzhou China Department of Neurology & National Clinical Research Centre for Geriatric Disorders Xiangya Hospital Central South University Hunan Changsha China Department of Neurology the Second Affiliated Hospital Zhejiang University School of Medicine Hangzhou China Institute of Fundamental and Transdisciplinary Research and The State Key Lab of Brain-Machine Intelligence Zhejiang University Hangzhou China Department of Molecular Cellular and Developmental Biology University of Michigan Ann Arbor 48109 MI United States

Lysosomes maintain an acidic pH of 4.5–5.0, optimal for macromolecular degradation. Whereas proton influx is produced by a V-type H+ ATPase, proton efflux is mediated by a fast H+ leak through TMEM175 channels, as we... 详细信息

Lysosomes maintain an acidic pH of 4.5–5.0, optimal for macromolecular degradation. Whereas proton influx is produced by a V-type H⁺ ATPase, proton efflux is mediated by a fast H⁺ leak through TMEM175 channels, as well as an unidentified slow pathway. A candidate screen on an orphan lysosome membrane protein (OLMP) library enabled us to discover that SLC7A11, the protein target of the ferroptosis-inducing compound erastin, mediates a slow lysosomal H⁺ leak through downward flux of cystine and glutamate, two H⁺ equivalents with uniquely large but opposite concentration gradients across lysosomal membranes. SLC7A11 deficiency or inhibition caused lysosomal over-acidification, reduced degradation, accumulation of storage materials, and ferroptosis, as well as facilitated α-synuclein aggregation in neurons. Correction of abnormal lysosomal acidity restored lysosome homeostasis and prevented ferroptosis. These studies have revealed an unconventional H⁺ transport conduit that is integral to lysosomal flux of protonatable metabolites to regulate lysosome function, ferroptosis, and Parkinson's disease (PD) pathology. © 2025 The Author(s)

关键词： acidification cystine ferroptosis lysosome pH optimum

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Class2Simi: A noise reduction perspective on learning with noisy labels

arXiv

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arXiv 2020年

作者： Wu, Songhua Xia, Xiaobo Liu, Tongliang Han, Bo Gong, Mingming Wang, Nannan Liu, Haifeng Niu, Gang Trustworthy Machine Learning Lab School of Computer Science University of Sydney Department of Computer Science Hong Kong Baptist University School of Mathematics and Statistics University of Melbourne ISN State Key Laboratory School of Telecommunications Engineering Xidian University Brain-Inspired Technology Co. Ltd. RIKEN Center for Advanced Intelligence Project

Learning with noisy labels has attracted a lot of attention in recent years, where the mainstream approaches are in pointwise manners. Meanwhile, pairwise manners have shown great potential in supervised metric learning and unsupervised contrastive learning. Thus, a natural question is raised: does learning in a pairwise manner mitigate label noise? To give an affirmative answer, in this paper, we propose a framework called Class2Simi: it transforms data points with noisy class labels to data pairs with noisy similarity labels, where a similarity label denotes whether a pair shares the class label or not. Through this transformation, the reduction of the noise rate is theoretically guaranteed, and hence it is in principle easier to handle noisy similarity labels. Amazingly, DNNs that predict the clean class labels can be trained from noisy data pairs if they are first pretrained from noisy data points. Class2Simi is computationally efficient because not only this transformation is on-the-fly in mini-batches, but also it just changes loss computation on top of model prediction into a pairwise manner. Its effectiveness is verified by extensive experiments. Copyright © 2020, The Authors. All rights reserved.

关键词： Noise abatement

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Optimizing network resource allocation with graph pointer neural network in large-scale AI systems

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Digital Communications and Networks 2024年

作者： Peiying Zhang Yilin Li Athanasios V. Vasilakos Konstantin Igorevich Kostromitin Jianyong Zhang Mohsen Guizani Qingdao Institute of Software College of Computer Science and Technology China University of Petroleum (East China) Qingdao 266580 China State Key Laboratory of Integrated Services Networks Xidian University Xi'an 710071 China Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center (National Supercomputer Center in Jinan) Qilu University of Technology (Shandong Academy of Sciences) Jinan 250013 China Department of Networks and Communications College of Computer Science and Information Technology Imam Abdulrahman Bin Faisal University P.O. Box 1982 Dammam 31441 Saudi Arabia Department of Physics of Nanoscale Systems South Ural State University Chelyabinsk 454080 the Russian Federation Institute of Lightwave Technology Beijing Jiaotong University Beijing 100044 China Key Lab of All Optical Network and Advanced Telecommunication of EMC Institute of Lightwave Technology Beijing Jiaotong University Beijing 100044 China Machine Learning Department Mohamed Bin Zayed University of Artificial Intelligence (MBZUAI) Abu Dhabi 999041 United Arab Emirates

For increasingly complex communication demands of large-scale AI communication systems, the Space-Air-Ground Integrated Network (SAGIN) better caters to demands but also raises concerns about resource scarcity and diversity. This paper innovatively combines Graph Pointer Neural Networks (GPNN) and Reinforcement Learning (RL) to enhance resource allocation efficiency. The method leverages the advantages of GPNN in handling graph data and RL in optimizing decisions in dynamic environments. It also targets the optimization goal of maximizing resource allocation while minimizing deployment latency. This paper begins by modeling SAGIN and elucidating the SAGIN logical architecture based on Software-defined Networking (SDN). Subsequently, it introduces an SFC deployment algorithm aimed at joint optimization of resource allocation and latency. The algorithm leverages GPNN and RL to deploy virtual nodes and links, with the goal of optimizing resource allocation and deployment latency. Experiment findings conclusively demonstrate that the efficacy of proposed algorithm in effectively weighing limited heterogeneous resources and minimum mapping delay. Notably, when compared to three other SFC mapping algorithms MLRL, NFVdeep, and RL, the proposed algorithm consistently outperforms them, with an average improvement of 10.17% in long-term average reward/cost, 11.21% in link resource utilization ratio, 15.34% in node resource utilization ratio, and 16.38% in acceptance ratio.

关键词： Space-air-ground integrated network Topological structure Reinforcement learning Service function chain Graph pointer neural network

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Multi-stage Speaker Extraction with Utterance and Frame-Level Reference Signals

arXiv

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arXiv 2020年

作者： Ge, Meng Xu, Chenglin Wang, Longbiao Chng, Eng Siong Dang, Jianwu Li, Haizhou Tianjin Key Laboratory of Cognitive Computing and Application College of Intelligence and Computing Tianjin University Tianjin China School of Computer Science and Engineering Nanyang Technological University Singapore Japan Advanced Institute of Science and Technology Ishikawa Japan Department of Electrical and Computer Engineering National University of Singapore Singapore Machine Listening Lab University of Bremen Germany

Speaker extraction requires a sample speech from the target speaker as the reference. However, enrolling a speaker with a long speech is not practical. We propose a speaker extraction technique, that performs in multiple stages to take full advantage of short reference speech sample. The extracted speech in early stages is used as the reference speech for late stages. For the first time, we use frame-level sequential speech embedding as the reference for target speaker. This is a departure from the traditional utterance-based speaker embedding reference. In addition, a signal fusion scheme is proposed to combine the decoded signals in multiple scales with automatically learned weights. Experiments on WSJ0-2mix and its noisy versions (WHAM! and WHAMR!) show that SpEx++ consistently outperforms other state-of-the-art baselines. Copyright © 2020, The Authors. All rights reserved.

关键词： Embeddings

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BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

引用

Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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DPA-2: a large atomic model as a multi-task learner

arXiv

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arXiv 2023年

作者： Zhang, Duo Liu, Xinzijian Zhang, Xiangyu Zhang, Chengqian Cai, Chun Bi, Hangrui Du, Yiming Qin, Xuejian Peng, Anyang Huang, Jiameng Li, Bowen Shan, Yifan Zeng, Jinzhe Zhang, Yuzhi Liu, Siyuan Li, Yifan Chang, Junhan Wang, Xinyan Zhou, Shuo Liu, Jianchuan Luo, Xiaoshan Wang, Zhenyu Jiang, Wanrun Wu, Jing Yang, Yudi Yang, Jiyuan Yang, Manyi Gong, Fu-Qiang Zhang, Linshuang Shi, Mengchao Dai, Fu-Zhi York, Darrin M. Liu, Shi Zhu, Tong Zhong, Zhicheng Lv, Jian Cheng, Jun Jia, Weile Chen, Mohan Ke, Guolin Weinan, E. Zhang, Linfeng Wang, Han AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing100871 China University of Chinese Academy of Sciences Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo315201 China CAS Key Laboratory of Magnetic Materials and Devices Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology Chinese Academy of Sciences Ningbo315201 China School of Electronics Engineering and Computer Science Peking University Beijing100871 China Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai200062 China Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States Department of Chemistry Princeton University PrincetonNJ08540 United States College of Chemistry and Molecular Engineering Peking University Beijing100871 China Yuanpei College Peking University Beijing100871 China School of Electrical Engineering and Electronic Information Xihua University Chengdu610039 China State Key Laboratory of Superhard Materials College of Physics Jilin University Changchun130012 China Key Laboratory of Material Simulation Methods & Software of Ministry of Education College of Physics Jilin University Changchun130012 China International Center of Future Science Jilin University Changchun130012 China Key Laboratory for Quantum Materials of Zhejiang Province Department of Physics School of Science Westlake University Zhejiang Hangzhou310030 China Atomistic Simulations Italia

The rapid advancements in artificial intelligence (AI) are catalyzing transformative changes in atomic modeling, simulation, and design. AI-driven potential energy models have demonstrated the capability to conduct large-scale, long-duration simulations with the accuracy of ab initio electronic structure methods. However, the model generation process remains a bottleneck for large-scale applications. We propose a shift towards a model-centric ecosystem, wherein a large atomic model (LAM), pre-trained across multiple disciplines, can be efficiently fine-tuned and distilled for various downstream tasks, thereby establishing a new framework for molecular modeling. In this study, we introduce the DPA-2 architecture as a prototype for LAMs. Pre-trained on a diverse array of chemical and materials systems using a multi-task approach, DPA-2 demonstrates superior generalization capabilities across multiple downstream tasks compared to the traditional single-task pre-training and fine-tuning methodologies. Our approach sets the stage for the development and broad application of LAMs in molecular and materials simulation research. Copyright © 2023, The Authors. All rights reserved.

关键词： Multi-task learning

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QUBIQ: Uncertainty Quantification for Biomedical Image Segmentation Challenge

arXiv

引用

arXiv 2024年

作者： Li, Hongwei Bran Navarro, Fernando Ezhov, Ivan Bayat, Amirhossein Das, Dhritiman Kofler, Florian Shit, Suprosanna Waldmannstetter, Diana Paetzold, Johannes C. Hu, Xiaobin Wiestler, Benedikt Zimmer, Lucas Amiranashvili, Tamaz Prabhakar, Chinmay Berger, Christoph Weidner, Jonas Alonso-Basanta, Michelle Rashid, Arif Baid, Ujjwal Adel, Wesam Alis, Deniz Baheti, Bhakti Bai, Yingbin Bhat, Ishaan Cetindag, Sabri Can Chen, Wenting Cheng, Li Dutande, Prasad Dular, Lara Elattar, Mustafa A. Feng, Ming Gao, Shengbo Huisman, Henkjan Hu, Weifeng Innani, Shubham Ji, Wei Karimi, Davood Kuijf, Hugo J. Kwak, Jin Tae Le, Hoang Long Li, Xiang Lin, Huiyan Liu, Tongliang Ma, Jun Ma, Kai Ma, Ting Oksuz, Ilkay Holland, Robbie Oliveira, Arlindo L. Pal, Jimut Bahan Pei, Xuan Qiao, Maoying Saha, Anindo Selvan, Raghavendra Shen, Linlin Silva, Joao Lourenco Spiclin, Ziga Talbar, Sanjay Wang, Dadong Wang, Wei Wang, Xiong Wang, Yin Xi, Ruiling Xu, Kele Yang, Yanwu Yergin, Mert Yu, Shuang Zeng, Lingxi Zhang, YingLin Zhao, Jiachen Zheng, Yefeng Zukovec, Martin Do, Richard Becker, Anton Simpson, Amber Konukoglu, Ender Jakab, Andras Bakas, Spyridon Joskowicz, Leo Menze, Bjoern Department of Informatics Technical University of Munich Germany Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School United States Department of Quantitative Biomedicine University of Zurich Switzerland University Children’s Hospital Zurich University of Zurich Switzerland Department of Radioncology and Radiation Theraphy Klinikum rechts der Isar Technical University of Munich Germany Department of Information Technology and Electrical Engineering ETH-Zurich Switzerland Department of Radiology Memorial Sloan Kettering Cancer Center New York City United States Department of Biomedical and Molecular Sciences Queen’s University Canada TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany McGovern Institute Massachusetts Institute of Technology United States Institute for Diagnostic and Interventional Radiology Unveristy Zurich Hospital Switzerland BioMedIA Imperial College London United Kingdom Department of Radiation Oncology University of Pennsylvania PA United States University of Pennsylvania PA United States Department of Radiation Oncology Winship Cancer Institute of Emory University Georgia United States Nile University Cairo Egypt Department of Medical Sciences Acibadem University Istanbul Turkey Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Trustworthy Machine Learning Lab University of Sydney Australia Image Sciences Institute University Medical Center Utrecht Netherlands Computer Engineering Department Istanbul Technical University Istanbul Turkey School of Computer Science Shenzhen University Shenzhen China University of Alberta United States University of Ljubljana Faculty of Electrical Engineering Ljubljana Slovenia Tongji University Shanghai China OPPO Research Institute Shanghai China School of Biological and Medical Engineering Beihang University Beijing China Harvard Medical School Boston

Uncertainty in medical image segmentation tasks, especially inter-rater variability, arising from differences in interpretations and annotations by various experts, presents a significant challenge in achieving consistent and reliable image segmentation. This variability not only reflects the inherent complexity and subjective nature of medical image interpretation but also directly impacts the development and evaluation of automated segmentation algorithms. Accurately modeling and quantifying this variability is essential for enhancing the robustness and clinical applicability of these algorithms. We report the set-up and summarize the benchmark results of the Quantification of Uncertainties in Biomedical Image Quantification Challenge (QUBIQ), which was organized in conjunction with International Conferences on Medical Image Computing and computer-Assisted Intervention (MICCAI) 2020 and 2021. The challenge focuses on the uncertainty quantification of medical image segmentation which considers the omnipresence of inter-rater variability in imaging datasets. The large collection of images with multi-rater annotations features various modalities such as MRI and CT;various organs such as the brain, prostate, kidney, and pancreas;and different image dimensions 2D-vs-3D. A total of 24 teams submitted different solutions to the problem, combining various baseline models, Bayesian neural networks, and ensemble model techniques. The obtained results indicate the importance of the ensemble models, as well as the need for further research to develop efficient 3D methods for uncertainty quantification methods in 3D segmentation tasks. © 2024, CC BY-NC-ND.

关键词： Image segmentation

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The state-of-the-art in Cardiac MRI Reconstruction: Results of the CMRxRecon Challenge in MICCAI 2023

arXiv

引用

arXiv 2024年

作者： Lyu, Jun Qin, Chen Wang, Shuo Wang, Fanwen Li, Yan Wang, Zi Guo, Kunyuan Ouyang, Cheng Tänzer, Michael Liu, Meng Sun, Longyu Sun, Mengting Li, Qin Shi, Zhang Hua, Sha Li, Hao Chen, Zhensen Zhang, Zhenlin Xin, Bingyu Metaxas, Dimitris N. Yiasemis, George Teuwen, Jonas Zhang, Liping Chen, Weitian Pang, Yanwei Liu, Xiaohan Razumov, Artem Dylov, Dmitry V. Dou, Quan Yan, Kang Xue, Yuyang Du, Yuning Dietlmeier, Julia Garcia-Cabrera, Carles Hemidi, Ziad Al-Haj Vogt, Nora Xu, Ziqiang Zhang, Yajing Chu, Ying-Hua Chen, Weibo Bai, Wenjia Zhuang, Xiahai Qin, Jing Wu, Lianmin Yang, Guang Qu, Xiaobo Wang, He Wang, Chengyan Psychiatry Neuroimaging Laboratory Brigham and Women’s Hospital Harvard Medical School 399 Revolution Drive BostonMA02215 United States Department of Electrical and Electronic Engineering & I-X Imperial College London United Kingdom Digital Medical Research Center School of Basic Medical Sciences Fudan University Shanghai China Department of Bioengineering & I-X Imperial College London LondonW12 7SL United Kingdom Cardiovascular Magnetic Resonance Unit Royal Brompton Hospital Guy’s and St Thomas’ NHS Foundation Trust LondonSW3 6NP United Kingdom Department of Radiology Ruijin Hospital Shanghai Jiao Tong University School of Medicine Shanghai China Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance National Institute for Data Science in Health and Medicine Institute of Artificial Intelligence Xiamen University Xiamen361102 China Department of Computing Department of Brain Sciences Imperial College London LondonSW7 2AZ United Kingdom Human Phenome Institute Fudan University 825 Zhangheng Road Pudong New District Shanghai201203 China Department of Radiology Zhongshan Hospital Fudan University Shanghai China Department of Cardiovascular Medicine Ruijin Hospital Lu Wan Branch Shanghai Jiao Tong University School of Medicine Shanghai China Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai200433 China Department of Computer Science Rutgers University PiscatawayNJ08854 United States AI for Oncology Netherlands Cancer Institute Plesmanlaan 121 Amsterdam1066 CX Netherlands Department of Imaging and Interventional Radiology The Chinese University of Hong Kong Hong Kong TJK-BIIT Lab School of Electrical and Information Engineering Tianjin University Tianjin300072 China Skolkovo Institute Of Science And Technology Center for Artificial Intelligence Technology 30/1 Bolshoy blvd. Moscow121205 Russia Department of Biomedical Engineering University of Virginia

Cardiac magnetic resonance imaging (MRI) provides detailed and quantitative evaluation of the heart’s structure, function, and tissue characteristics with high-resolution spatial-temporal imaging. However, its slow imaging speed and motion artifacts are notable limitations. Undersampling reconstruction, especially data-driven algorithms, has emerged as a promising solution to accelerate scans and enhance imaging performance using highly under-sampled data. Nevertheless, the scarcity of publicly available cardiac k-space datasets and evaluation platform hinder the development of data-driven reconstruction algorithms. To address this issue, we organized the Cardiac MRI Reconstruction Challenge (CMRxRecon) in 2023, in collaboration with the 26th International Conference on Medical Image Computing and computer-Assisted Intervention (MICCAI). CMRxRecon presented an extensive k-space dataset comprising cine and mapping raw data, accompanied by detailed annotations of cardiac anatomical structures. With overwhelming participation, the challenge attracted more than 285 teams and over 600 participants. Among them, 22 teams successfully submitted Docker containers for the testing phase, with 7 teams submitted for both cine and mapping tasks. All teams use deep learning based approaches, indicating that deep learning has predominately become a promising solution for the problem. The first-place winner of both tasks utilizes the E2E-VarNet architecture as backbones. In contrast, U-Net is still the most popular backbone for both multi-coil and single-coil reconstructions. This paper provides a comprehensive overview of the challenge design, presents a summary of the submitted results, reviews the employed methods, and offers an in-depth discussion that aims to inspire future advancements in cardiac MRI reconstruction models. The summary emphasizes the effective strategies observed in Cardiac MRI reconstruction, including backbone architecture, loss function, pre-processing techn

关键词： Mapping

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