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Why is the winner the best?

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arXiv 2023年

作者： Eisenmann, M. Reinke, A. Weru, V. Tizabi, M.D. Isensee, F. Adler, T.J. Ali, S. Andrearczyk, V. Aubreville, M. Baid, U. Bakas, S. Balu, N. Bano, S. Bernal, J. Bodenstedt, S. Casella, A. Cheplygina, V. Daum, M. de Bruijne, M. Depeursinge, A. Dorent, R. Egger, J. Ellis, D.G. Engelhardt, S. Ganz, M. Ghatwary, N. Girard, G. Godau, P. Gupta, A. Hansen, L. Harada, K. Heinrich, M. Heller, N. Hering, A. Huaulmé, A. Jannin, P. Kavur, A.E. Kodym, O. Kozubek, M. Li, J. Li, H. Ma, J. Martín-Isla, C. Menze, B. Noble, A. Oreiller, V. Padoy, N. Pati, S. Payette, K. Rädsch, T. Rafael-Patiño, J. Bawa, V. Singh Speidel, S. Sudre, C.H. van Wijnen, K. Wagner, M. Wei, D. Yamlahi, A. Yap, M.H. Yuan, C. Zenk, M. Zia, A. Zimmerer, D. Aydogan, D. Bhattarai, B. Bloch, L. Brüngel, R. Cho, J. Choi, C. Dou, Q. Ezhov, I. Friedrich, C.M. Fuller, C. Gaire, R.R. Galdran, A. Faura, Á. García Grammatikopoulou, M. Hong, S. Jahanifar, M. Jang, I. Kadkhodamohammadi, A. Kang, I. Kofler, F. Kondo, S. Kuijf, H. Li, M. Luu, M. Martinčič, T. Morais, P. Naser, M.A. Oliveira, B. Owen, D. Pang, S. Park, J. Park, S. Plotka, S. Puybareau, E. Rajpoot, N. Ryu, K. Saeed, N. Shephard, A. Shi, P. Štepec, D. Subedi, R. Tochon, G. Torres, H.R. Urien, H. Vilaça, J.L. Wahid, K.A. Wang, H. Wang, J. Wang, L. Wang, X. Wiestler, B. Wodzinski, M. Xia, F. Xie, J. Xiong, Z. Yang, S. Yang, Y. Zhao, Z. Maier-Hein, K. Jäger, P.F. Kopp-Schneider, A. Maier-Hein, L. Heidelberg Germany Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Germany Heidelberg Germany School of Computing Faculty of Engineering and Physical Sciences University of Leeds Leeds United Kingdom Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Sierre Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Lausanne Switzerland Technische Hochschule Ingolstadt Ingolstadt Germany University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington SeattleWA United States Department of Computer Science University College London London United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Biomedical Imaging Group Rotterdam Department of Radiology and Nuclear Medicine Erasmus MC Rotterdam Netherlands Department of Computer Science University of Copenhagen Copenhagen Denmark Sierre Switzerland Harvard Medical School Brigham and Women’s Hospital BostonMA United States School of Biomedical Engineering and Imaging Sciences King’s College London London United Kingdom Essen Germany University of Nebraska Medical Center OmahaNE United States Department of Internal Medicine III Heidelberg University Hospital Heidelberg Germany Neurobiology Research Unit Copenhagen University Hospital Rigshospitalet C

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multicenter study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work. © 2023, CC BY.

关键词： Benchmarking

LMS-Net: A learned Mumford-Shah network for binary few-shot medical image segmentation

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Medical Image Analysis 2025年

作者： Shengdong Zhang Fan Jia Xiang Li Hao Zhang Jun Shi Liyan Ma Shihui Ying Department of Mathematics School of Science Shanghai University Shanghai 200444 China Department of Mathematics and Scientific Computing and Imaging (SCI) Institute University of Utah Salt Lake City 84102 UT USA School of Computer Science and Technology East China Normal University Shanghai 200444 China School of Communication and Information Engineering Shanghai University Shanghai 200444 China School of Computer Engineering and Science Shanghai University Shanghai 200444 China School of Mechatronic Engineering and Automation Shanghai Key Laboratory of Intelligent Manufacturing and Robotics Shanghai University Shanghai 200444 China Shanghai Institute of Applied Mathematics and Mechanics Shanghai 200072 China School of Mechanics and Engineering Science Shanghai University Shanghai 200072 China

Few-shot semantic segmentation (FSS) methods have shown great promise in handling data-scarce scenarios, particularly in medical image segmentation tasks. However, most existing FSS architectures lack sufficient interpretability and fail to fully incorporate the underlying physical structures of semantic regions. To address these issues, in this paper, we propose a novel deep unfolding network, called the Learned Mumford-Shah Network (LMS-Net), for the FSS task. Specifically, motivated by the effectiveness of pixel-to-prototype comparison in prototypical FSS methods and the capability of deep priors to model complex spatial structures, we leverage our learned Mumford-Shah model (LMS model) as a mathematical foundation to integrate these insights into a unified framework. By reformulating the LMS model into prototype update and mask update tasks, we propose an alternating optimization algorithm to solve it efficiently. Further, the iterative steps of this algorithm are unfolded into corresponding network modules, resulting in LMS-Net with clear interpretability. Comprehensive experiments on three publicly available medical segmentation datasets verify the effectiveness of our method, demonstrating superior accuracy and robustness in handling complex structures and adapting to challenging segmentation scenarios. These results highlight the potential of LMS-Net to advance FSS in medical imaging applications. Our code will be available at: https://***/SDZhang01/LMSNet .

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Efficient exascale discretizations: High-order finite element methods

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arXiv 2021年

作者： Kolev, Tzanio Fischer, Paul Min, Misun Dongarra, Jack Brown, Jed Dobrev, Veselin Warburton, Tim Tomov, Stanimire Shephard, Mark S. Abdelfattah, Ahmad Barra, Valeria Beams, Natalie Camier, Jean-Sylvain Chalmers, Noel Dudouit, Yohann Karakus, Ali Karlin, Ian Kerkemeier, Stefan Lan, Yu-Hsiang Medina, David Merzari, Elia Obabko, Aleksandr Pazner, Will Rathnayake, Thilina Smith, Cameron W. Spies, Lukas Swirydowicz, Kasia Thompson, Jeremy Tomboulides, Ananias Tomov, Vladimir Center for Applied Scientific Computing Lawrence Livermore National Laboratory LivermoreCA94550 United States Mathematics and Computer Science Argonne National Laboratory LemontIL60439 United States Department of Computer Science University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Mechanical Science and Engineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States Innovative Computing Laboratory University of Tennessee KnoxvilleTN37996 United States Department of Computer Science University of Colorado BoulderCO80309 United States Scientific Computation Research Center Rensselaer Polytechnic Institute TroyNY12180 United States Department of Mathematics Virginia Tech BlacksburgVA24061 United States AMD Research AustinTX78735 United States Mechanical Engineering Department Middle East Technical University Ankara06800 Turkey Occalytics LLC WeehawkenNJ07086 United States Department of Nuclear Engineering Penn StatePA16802 United States Pacific Northwest National Laboratory WA99352 United States

Efficient exploitation of exascale architectures requires rethinking of the numerical algorithms used in many large-scale applications. These architectures favor algorithms that expose ultra fine-grain parallelism and maximize the ratio of floating point operations to energy intensive data movement. One of the few viable approaches to achieve high efficiency in the area of PDE discretizations on unstructured grids is to use matrix-free/partially-assembled high-order finite element methods, since these methods can increase the accuracy and/or lower the computational time due to reduced data motion. In this paper we provide an overview of the research and development activities in the Center for Efficient Exascale Discretizations (CEED), a co-design center in the Exascale computing Project that is focused on the development of next-generation discretization software and algorithms to enable a wide range of finite element applications to run efficiently on future hardware. CEED is a research partnership involving more than 30 computational scientists from two US national labs and five universities, including members of the Nek5000, MFEM, MAGMA and PETSc projects. We discuss the CEED co-design activities based on targeted benchmarks, miniapps and discretization libraries and our work on performance optimizations for large-scale GPU architectures. We also provide a broad overview of research and development activities in areas such as unstructured adaptive mesh refinement algorithms, matrix-free linear solvers, high-order data visualization, and list examples of collaborations with several ECP and external applications. Copyright © 2021, The Authors. All rights reserved.

关键词： Data visualization

DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning Potentials

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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

Correction: Sign language mobile apps: a systematic review of current app evaluation progress and solution framework

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Evolving Systems 2024年第5期15卷 1989-1989页

作者： David, Dianes Alamoodi, A. H. Albahri, O. S. Garfan, Salem Albahri, A. S. Zaidan, B. B. Chen, Juliana Faculty of Computing and Meta-Technology (FKMT) Universiti Pendidikan Sultan Idris (UPSI) Perak Malaysia MEU Research Unit Middle East University Amman Jordan Applied Science Research Center Applied Science Private University Amman Jordan Department of Computer Science and Information Technology La Trobe University Melbourne Australia Computer Techniques Engineering Department Mazaya University College Nasiriyah Iraq Iraqi Commission for Computers and Informatics (ICCI) Baghdad Iraq Technical College Imam Ja’afar Al-Sadiq University Baghdad Iraq Future Technology Research Center National Yunlin University of Science and Technology Douliou Taiwan ROC Discipline of Nutrition and Dietetics Susan Wakil School of Nursing and Midwifery Faculty of Medicine and Health The University of Sydney Camperdown Australia Charles Perkins Centre The University of Sydney Camperdown Australia

A practical guide to machine learning interatomic potentials – Status and future

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arXiv 2025年

作者： Jacobs, Ryan Morgan, Dane Attarian, Siamak Meng, Jun Shen, Chen Wu, Zhenghao Xie, Clare Yijia Yang, Julia H. Artrith, Nongnuch Blaiszik, Ben Ceder, Gerbrand Choudhary, Kamal Csanyi, Gabor Cubuk, Ekin Dogus Deng, Bowen Drautz, Ralf Fu, Xiang Godwin, Jonathan Honavar, Vasant Isayev, Olexandr Johansson, Anders Kozinsky, Boris Martiniani, Stefano Ong, Shyue Ping Poltavsky, Igor Schmidt, K.J. Takamoto, So Thompson, Aidan Westermayr, Julia Wood, Brandon M. Department of Materials Science and Engineering University of Wisconsin-Madison MadisonWI55705 United States Harvard University Center for the Environment Harvard University CambridgeMA02138 United States John A. Paulson School of Engineering and Applied Sciences Harvard University CambridgeMA02138 United States Materials Chemistry and Catalysis Debye Institute for Nanomaterials Science Utrecht University Utrecht3584 CG Netherlands Globus University of Chicago ChicagoIL United States Data Science and Learning Division Argonne National Laboratory LemontIL United States Department of Materials Science and Engineering University of California BerkeleyCA94720 United States Materials Sciences Division Lawrence Berkeley National Laboratory CA94720 United States Material Measurement Laboratory National Institute of Standards and Technology GaithersburgMD20899 United States Department of Engineering University of Cambridge CambridgeCB2 1PZ United Kingdom Google DeepMind Mountain ViewCA United States Ruhr-Universität Bochum Bochum44780 Germany Meta United States Orbital Materials London United Kingdom Department of Computer Science and Engineering The Pennsylvania State University University ParkPA United States College of Information Sciences and Technology The Pennsylvania State University University ParkPA United States Artificial Intelligence Research Laboratory The Pennsylvania State University University ParkPA United States Center for Artificial Intelligence Foundations and Scientific Applications The Pennsylvania State University University ParkPA United States Department of Chemistry Mellon College of Science Carnegie Mellon University PittsburghPA15213 United States Computational Biology Department School of Computer Science Carnegie Mellon University PittsburghPA15213 United States Courant Institute of Mathematical Sciences New York University New YorkNY10003 United States Center for Soft Matter Research Department of P

The rapid development and large body of literature on machine learning interatomic potentials (MLIPs) can make it difficult to know how to proceed for researchers who are not experts but wish to use these tools. The spirit of this review is to help such researchers by serving as a practical, accessible guide to the state-of-the-art in MLIPs. This review paper covers a broad range of topics related to MLIPs, including (i) central aspects of how and why MLIPs are enablers of many exciting advancements in molecular modeling, (ii) the main underpinnings of different types of MLIPs, including their basic structure and formalism, (iii) the potentially transformative impact of universal MLIPs for both organic and inorganic systems, including an overview of the most recent advances, capabilities, downsides, and potential applications of this nascent class of MLIPs, (iv) a practical guide for estimating and understanding the execution speed of MLIPs, including guidance for users based on hardware availability, type of MLIP used, and prospective simulation size and time, (v) a manual for what MLIP a user should choose for a given application by considering hardware resources, speed requirements, energy and force accuracy requirements, as well as guidance for choosing pre-trained potentials or fitting a new potential from scratch, (vi) discussion around MLIP infrastructure, including sources of training data, pre-trained potentials, and hardware resources for training, (vii) summary of some key limitations of present MLIPs and current approaches to mitigate such limitations, including methods of including long-range interactions, handling magnetic systems, and treatment of excited states, and finally (viii) we finish with some more speculative thoughts on what the future holds for the development and application of MLIPs over the next 3-10+ years. © 2025, CC BY.

关键词： Digital storage

Correction to: Deep CNN-based autonomous system for safety measures in logistics transportation

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Soft computing 2021年第18期25卷 12371-12371页

作者： Rouari, Abdelkarim Moussaoui, Abdelouahab Chahir, Youssef Rauf, Hafiz Tayyab Kadry, Seifedine Computer Science Department Faculty of Sciences Ferhat Abbas University Setif Setif Algeria Computer Science Department University of Caen Caen France Department of Computer Science Faculty of Engineering & Informatics University of Bradford Bradford UK Faculty of applied computing and technology Noroff University College Kristiansand Norway

RETRACTED ARTICLE: SmartPharma: Blockchain Enabled Internet of Things for Smart Pharmaceutical Traceability System

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IETE Journal of Research 2023年第11期69卷 XLIV-LVII页

作者： M. Kavitha Margret E. Golden Julie Y. Harold Robinson D. Vijayanandh S. Vimal Seifidine Kadry Ahmed M. El-Sherbeeny Mohammed A. El-Meligy 1 Department of Computer Science and Engineering Sri Krishna College of Technology Coimbatore India 2 Department of Computer Science and Engineering Anna University Regional Campus Tirunelveli India 3 School of Information Technology and Engineering Vellore Institute of Technology Vellore India 4 Department of Electrical and Electronics Engineering Hindustan College of Engineering and Technology Coimbatore India 5 Department of Artificial Intelligence and Data Science Ramco Institute of Technology Rajapalayam Tamilnadu India 6 Faculty of Applied Computing and Technology Noroff University College Kristiansand Norway 7 Industrial Engineering Department College of Engineering King Saud University Riyadh11421 Saudi Arabia

We, the Editor, Institution and Publisher of the journal IETE Journal of Research, have retracted the following article, which is part of the Special Issue titled “Federated Learning for Blockchain Systems and Industrial Internet of Things”:M. Kavitha Margret, E. Golden Julie, Y. Harold Robinson, D. Vijayanandh, S. Vimal, Seifidine Kadry, Ahmed M. El-Sherbeeny & Mohammed A. El-Meligy (2021) SmartPharma: Blockchain Enabled Internet of Things for Smart Pharmaceutical Traceability System, IETE Journal of Research, DOI: 10.1080/03772063.2021.1994041Following publication, concerns were raised about the peer review and decision-making processes for this special *** an investigation by the Taylor & Francis Publishing Ethics & Integrity team, in full cooperation with the Editor-in-Chief and the Institution, it was confirmed that the articles included in this special issue were not reviewed appropriately, in line with the Journal's peer review standards and *** the stringency of the peer review process is core to the integrity of the publication process, the Editor and Publisher have decided to retract all of the articles within the above-named Special *** journal has not confirmed if the authors were aware of this compromised peer review *** journal is committed to correcting the scientific record and will fully cooperate with any institutional investigations into this matter. The authors have been informed of this *** have been informed in our decision-making by our editorial policies and the COPE *** retracted articles will remain online to maintain the scholarly record, but they will be digitally watermarked on each page as ‘Retracted’.

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GPU algorithms for efficient exascale discretizations

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arXiv 2021年

作者： Abdelfattah, Ahmad Barra, Valeria Beams, Natalie Bleile, Ryan Brown, Jed Camier, Jean-Sylvain Carson, Robert Chalmers, Noel Dobrev, Veselin Dudouit, Yohann Fischer, Paul Karakus, Ali Kerkemeier, Stefan Kolev, Tzanio Lan, Yu-Hsiang Merzari, Elia Min, Misun Phillips, Malachi Rathnayake, Thilina Rieben, Robert Stitt, Thomas Tomboulides, Ananias Tomov, Stanimire Tomov, Vladimir Vargas, Arturo Warburton, Tim Weiss, Kenneth Center for Applied Scientific Computing Lawrence Livermore National Laboratory LivermoreCA94550 United States Mathematics and Computer Science Argonne National Laboratory LemontIL60439 United States Department of Computer Science University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Mechanical Science and Engineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States Innovative Computing Laboratory University of Tennessee KnoxvilleTN37996 United States Department of Computer Science University of Colorado BoulderCO80309 United States Department of Mathematics Virginia Tech BlacksburgVA24061 United States AMD Research Advanced Micro Devices Inc. AustinTX78735 United States Weapons and Complex Integration Lawrence Livermore National Laboratory LivermoreCA94550 United States Computational Engineering Division Lawrence Livermore National Laboratory LivermoreCA94550 United States Department of Nuclear Engineering Penn State PA16802 United States Department of Mechanical Engineering Aristotle University of Thessaloniki 54124 Greece Mechanical Engineering Department Middle East Technical University Ankara06800 Turkey

In this paper we describe the research and development activities in the Center for Efficient Exascale Dis-cretization within the US Exascale computing Project, targeting state-of-the-art high-order finite-element algorithms for high-order applications on GPU-accelerated platforms. We discuss the GPU developments in several components of the CEED software stack, including the libCEED, MAGMA, MFEM, libParanumal, and Nek projects. We report performance and capability improvements in several CEED-enabled applications on both NVIDIA and AMD GPU systems. © 2021, CC BY-NC-ND.

关键词： Finite element method