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Prediction of solar energetic events impacting space weather conditions

Advances in Space Research 2024年

作者： Georgoulis, Manolis K. Yardley, Stephanie L. Guerra, Jordan A. Murray, Sophie A. Ahmadzadeh, Azim Anastasiadis, Anastasios Angryk, Rafal Aydin, Berkay Banerjee, Dipankar Barnes, Graham Bemporad, Alessandro Benvenuto, Federico Bloomfield, D. Shaun Bobra, Monica Campi, Cristina Camporeale, Enrico DeForest, Craig E. Emslie, A. Gordon Falconer, David Feng, Li Gan, Weiqun Green, Lucie M. Guastavino, Sabrina Hapgood, Mike Kempton, Dustin Kitiashvili, Irina Kontogiannis, Ioannis Korsos, Marianna B. Leka, K.D. Massa, Paolo Massone, Anna Maria Nandy, Dibyendu Nindos, Alexander Papaioannou, Athanasios Park, Sung-Hong Patsourakos, Spiros Piana, Michele Rawafi, Nour E. Sadykov, Viacheslav M. Toriumi, Shin Vourlidas, Angelos Wang, Haimin L. Wang, Jason T. Whitman, Kathryn Yan, Yihua Zhukov, Andrei N. Research Center for Astronomy and Applied Mathematics of the Academy of Athens Athens11527 Greece Department of Mathematics Physics and Electrical Engineering Northumbria University Newcastle upon TyneNE1 8ST United Kingdom Department of Meteorology University of Reading ReadingRG6 6ET United Kingdom Paseo Manuel de Lardizabal 4 San Sebastián20018 Spain CIRES University of Colorado BoulderCO80309 United States NOAA Space Weather Prediction Center BoulderCO80305 United States School of Cosmic Physics Dublin Institute for Advanced Studies Dunsink Observatory DublinD15 XR2R Ireland Computer Science Department Georgia State University AtlantaGA30303 United States National Observatory of Athens Penteli15236 Greece Uttarakhand Nainital263001 India NorthWest Research Associates BoulderCO80301 United States INAF Turin Astrophysical Observatory via Osservatorio 20 10025 Pino Torinese Torino Italy MIDA Dipartimento di Matematica Università di Genova via Dodecaneso 35 16146 Genova Italy State of California Office of Data and Innovation 401 I Street Ste 200 SacramentoCA95814 United States Southwest Research Institute BoulderCO80302 United States Department of Physics & Astronomy Western Kentucky University Bowling GreenKY42101 United States Center for Space Plasma and Aeronomic Research University of Alabama in Huntsville HuntsvilleAL35899 United States NASA/Marshall Space Flight Center HuntsvilleAL35812 United States Key Laboratory of Dark Matter and Space Astronomy Purple Mountain Observatory Chinese Academy of Sciences Nanjing210023 China Mullard Space Science Laboratory University College London Holmbury St. MaryRH5 6NT United Kingdom University of Chinese Academy of Sciences Nanjing211135 China Visiting Scientist RAL Space STFC Rutherford Appleton Laboratory Oxfordshire DidcotOX11 0QX United Kingdom NASA Ames Research Center Moffett FieldCA94035 United States An der Sternwarte 16 Potsdam14482 Germany Dipartime

Aiming to assess the progress and current challenges on the formidable problem of the prediction of solar energetic events since the COSPAR/ International Living With a Star (ILWS) Roadmap paper of Schrijver et al. (2015), we attempt an overview of the current status of global research efforts. By solar energetic events we refer to flares, coronal mass ejections (CMEs), and solar energetic particle (SEP) events. The emphasis, therefore, is on the prediction methods of solar flares and eruptions, as well as their associated SEP manifestations. This work complements the COSPAR International Space Weather Action Teams (ISWAT) review paper on the understanding of solar eruptions by Linton et al. (2023) (hereafter, ISWAT review papers are conventionally referred to as ’Cluster’ papers, given the ISWAT structure). Understanding solar flares and eruptions as instabilities occurring above the nominal background of solar activity is a core solar physics problem. We show that effectively predicting them stands on two pillars: physics and statistics. With statistical methods appearing at an increasing pace over the last 40 years, the last two decades have brought the critical realization that data science needs to be involved, as well, as volumes of diverse ground- and space-based data give rise to a Big data landscape that cannot be handled, let alone processed, with conventional statistics. Dimensionality reduction in immense parameter spaces with the dual aim of both interpreting and forecasting solar energetic events has brought artificial intelligence (AI) methodologies, in variants of machine and deep learning, developed particularly for tackling Big data problems. With interdisciplinarity firmly present, we outline an envisioned framework on which statistical and AI methodologies should be verified in terms of performance and validated against each other. We emphasize that a homogenized and streamlined method validation is another open challenge. The performance of the

关键词： Solar energy

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Simultaneous dimensionality and complexity model selection for spectral graph clustering

arXiv

引用

arXiv 2019年

作者： Yang, Congyuan Priebe, Carey E. Park, Youngser Marchette, David J. Department of Electrical and Computer Engineering Johns Hopkins University Department of Applied Math and Statistics Johns Hopkins University Center for Imaging Science Johns Hopkins University Applied Mathematics and Data Analytics Group Naval Surface Warfare Center Dahlgren Division

Our problem of interest is to cluster vertices of a graph by identifying underlying community structure. Among various vertex clustering approaches, spectral clustering is one of the most popular methods because it is easy to implement while often outperforming more traditional clustering algorithms. However, there are two inherent model selection problems in spectral clustering, namely estimating both the embedding dimension and number of clusters. This paper attempts to address the issue by establishing a novel model selection framework specifically for vertex clustering on graphs under a stochastic block model. The first contribution is a probabilistic model which approximates the distribution of the extended spectral embedding of a graph. The model is constructed based on a theoretical result of asymptotic normality of the informative part of the embedding, and on a simulation result providing a conjecture for the limiting behavior of the redundant part of the embedding. The second contribution is a simultaneous model selection framework. In contrast with the traditional approaches, our model selection procedure estimates embedding dimension and number of clusters simultaneously. Based on our conjectured distributional model, a theorem on the consistency of the estimates of model parameters is stated and proven. The theorem provides statistical support for the validity of our method. Heuristic algorithms via the simultaneous model selection framework for vertex clustering are proposed, with good performance shown in the experiment on synthetic data and on the real application of connectome analysis. Copyright © 2019, The Authors. All rights reserved.

关键词： Embeddings

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SPA-SSD: Exploit Heterogeneity and Parallelism of 3D SLC-TLC Hybrid SSD to Improve Write Performance

SPA-SSD: Exploit Heterogeneity and Parallelism of 3D SLC-TLC...

引用

IEEE International Conference on computer Design: VLSI in computers and Processors, (ICCD)

作者： Wenhui Zhang Qiang Cao Hong Jiang Jie Yao Yuanyuan Dong Puyuan Yang Wuhan National Laboratory for Optoelectronics Key Laboratory of Information Storage System Engineering Research Center of Data Storage Systems and Technology Ministry of Education of China Huazhong University of Science and Technology Wuhan China Department of Computer Science and Engineering University of Texas at Arlington Arlington Texas School of Computer Science and Technology Huazhong University of Science and Technology Wuhan China Alibaba Group. Hangzhou China

To address the write performance problem suffered by MLC/TLC flash, researchers have proposed hybrid SSD that aims to combine the strengths of SLC flash, used as the write-buffer zone for its superior write performance, and MLC/TLC flash, as the capacity zone for its high storage density. While leveraging SLC as a physical write-buffer zone is proven effective in traditional 2D hybrid SSDs, how to effectively incorporate SLC into a 3D-stacked TLC to form a hybrid SSD has not been studied to the best of our knowledge. Yet this is a timely and important performance issue for 3D-stacked TLC given its one-shot programming scheme that results in much worse write performance than the programming scheme in 2D TLC where pages are associated with different bits of a cell and programmed in sequence separately. We believe that naively adopting the two-physical-zone approach to 3D hybrid SSD will miss a great opportunity for performance optimization because it ignores the inherent four-level parallelism (channel/chip/die/plane) of the flash chip array. To this end, we propose in this paper an SLC and Parallelism Aware hybrid SSD (SPA-SSD) to take full advantages of SLC's superior write performance, the internal multi-level parallelism of SSD, and the high storage density of 3D-stacked TLC flash. Two novel techniques enable SPA-SSD to be highly effective: (1) Type-Parallelism Joint Page Allocation (TPJ-PA), which allocates pages for write transactions according to not only available SLC pages but also parallelism to maximize resource utilization within the hybrid SSD, and (2) Queue-length and Parallelism Constrained data Migration (QPC-DM), which triggers data migration without degrading user write performance by analyzing the device queue length and available flash resources. To evaluate performance of SPA-SSD, a hybrid SSD simulator, called HybridSim, is developed based on MQSim. Experimental results on HybridSim show that TPJ-PA improves write throughput by 60%, while QPC-DM

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SPFLOW: An easy and extensible library for deep probabilistic learning using sum-product networks

arXiv

引用

arXiv 2019年

作者： Molina, Alejandro Vergari, Antonio Stelzner, Karl Peharz, Robert Subramani, Pranav Di Mauro, Nicola Poupart, Pascal Kersting, Kristian Machine Learning Group Computer Science Department TU Darmstadt Germany Probabilistic Learning Group Empirical Inference Department Max-Planck-Institute Germany Machine Learning Group Engineering Dept. University of Cambridge United Kingdom Knowledge Acquisition & Machine Learning Group University of Bari "Aldo Moro" Italy Waterloo AI Institute Vector Institute University of Waterloo CA Canada Centre for Cognitive Science TU Darmstadt Germany

We introduce SPFlow, an open-source Python library providing a simple interface to inference, learning and manipulation routines for deep and tractable probabilistic models called Sum-Product Networks (SPNs). The library allows one to quickly create SPNs both from data and through a domain specific language (DSL). It efficiently implements several probabilistic inference routines like computing marginals, conditionals and (approximate) most probable explanations (MPEs) along with sampling as well as utilities for serializing, plotting and structure statistics on an SPN. Moreover, many of the algorithms proposed in the literature to learn the structure and parameters of SPNs are readily available in SPFlow. Furthermore, SPFlow is extremely extensible and customizable, allowing users to promptly distill new inference and learning routines by injecting custom code into a lightweight functional-oriented API framework. This is achieved in SPFlow by keeping an internal Python representation of the graph structure that also enables practical compilation of an SPN into a TensorFlow graph, C, CUDA or FPGA custom code, significantly speeding-up computations. Copyright © 2019, The Authors. All rights reserved.

关键词： Python

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The need to implement FAIR principles in biomolecular simulations

arXiv

引用

arXiv 2024年

作者： Amaro, R. Åqvist, J. Bahar, I. Battistini, F. Bellaiche, A. Beltran, D. Biggin, P.C. Bonomi, M. Bowman, G.R. Bryce, R. Bussi, G. Carloni, P. Case, D. Cavalli, A. Chang, C.A. Cheatham, T.E. Cheung, M.S. Chipot, C. Chong, L.T. Choudhary, P. Cisneros, G.A. Clementi, C. Collepardo-Guevara, R. Coveney, P. Covino, R. Crawford, T.D. Dal Peraro, M. de Groot, B. Delemotte, L. De Vivo, M. Essex, J. Fraternali, F. Gao, J. Gelpí, J.L. Gervasio, F.L. Gonzalez-Nilo, F.D. Grubmüller, H. Guenza, M.G. Guzman, H.V. Harris, S. Head-Gordon, T. Hernandez, R. Hospital, A. Huang, N. Huang, X. Hummer, G. Iglesias-Fernández, J. Jensen, J.H. Jha, S. Jiao, W. Jorgensen, W.L. Kamerlin, S.C.L. Khalid, S. Laughton, C. Levitt, M. Limongelli, V. Lindahl, E. Lindorff-Larsen, K. Loverde, S. Lundborg, M. Luo, Y.L. Luque, F.J. Lynch, C.I. MacKerell, A. Magistrato, A. Marrink, S.J. Martin, H. McCammon, J.A. Merz, K. Moliner, V. Mulholland, A. Murad, S. Naganathan, A.N. Nangia, S. Noe, F. Noy, A. Oláh, J. O'Mara, M. Ondrechen, M.J. Onuchic, J.N. Onufriev, A. Osuna, S. Palermo, G. Panchenko, A.R. Pantano, S. Parish, C. Parrinello, M. Perez, A. Perez-Acle, T. Perilla, J.R. Pettitt, B.M. Pietropaolo, A. Piquemal, J.-P. Poma, A. Praprotnik, M. Ramos, M.J. Ren, P. Reuter, N. Roitberg, A. Rosta, E. Rovira, C. Roux, B. Röthlisberger, U. Sanbonmatsu, K. Schlick, T. Shaytan, A.K. Simmerling, C. Smith, J.C. Sugita, Y. Świderek, K. Taiji, M. Tao, P. Tikhonova, I.G. Tirado-Rives, J. Tuñón, I. Van Der Kamp, M.W. Van der Spoel, D. Velankar, S. Voth, G.A. Wade, R. Warshel, A. Welborn, V.V. Wetmore, S. Wong, C.F. Yang, L.-W. Zacharias, M. Orozco, M. Department of Molecular Biology University of California San DiegoCA United States Department of Cell and Molecular Biology Uppsala University Uppsala Sweden Laufer Center for Physical and Quantitative Biology Renaissance School of Medicine Stony Brook University Stony BrookNY United States Department of Biochemistry and Cell Biology Renaissance School of Medicine Stony Brook University Stony BrookNY United States Barcelona Spain European Molecular Biology Laboratory European Bioinformatics Institute Hinxton United Kingdom Structural Bioinformatics and Computational Biochemistry Department of Biochemistry University of Oxford Oxford United Kingdom Institut Pasteur Université Paris Cité CNRS UMR 3528 Computational Structural Biology Unit Paris France Department of Biochemistry and Biophysics University of Pennsylvania PhiladelphiaPA United States Division of Pharmacy and Optometry University of Manchester Manchester United Kingdom Scuola Internazionale Superiore di Studi Avanzati-SISSA Trieste Italy Computational Biomedicine Institute of Advanced Simulations IAS-5 Institute for Neuroscience and Medicine INM-9 Forschungszentrum Jülich GmbH Jülich Germany Department of Physics and Universitätsklinikum RWTH Aachen University Aachen Germany Department of Chemistry & Chemical Biology Rutgers University PiscatawayNJ United States Istituto Italiano di Tecnologia Drug Discovery and Development Bologna Italy Lausanne Switzerland Department of Chemistry University of California RiversideCA United States Department of Medicinal Chemistry College of Pharmacy University of Utah Salt Lake CityUT United States Department of Physics University of Washington SeattleWA United States Pacific Northwest National Laboratory RichlandWA United States LIA CNRS-UIUC UMR n°7019 Université de Lorraine Vandœuvre-lès-Nancy France Department of Physics University of Illinois at Urbana-Champaign UrbanaIL United States Department of Biochemistry and Molecular Biol

The communities that embraced data archiving efforts decades ago are now, in the era of data-driven biology, those gaining the most from the AI revolution. The structural biology community was a pioneer in this regard by establishing the Protein data Bank (PDB) in 1971 and making data accessible using the FAIR (Findable, Accessible, Interoperable and Reusable) principles even before these were articulated [1, 2]. The genomics/bioinformatics community has followed the example, establishing many widely used databases [3, 4]. By contrast, molecular simulation has been anchored in usage paradigms dating back to the seventies, when molecular dynamics (MD) simulation was first applied to study biomacromolecules [5]. At that time, MD was used by theoretical physicists and chemists in "proof of concept" simulations. Still, fifty years later, MD has evolved into a cornerstone molecular biology technique that can provide accurate quantitative analysis and property prediction. MD is now employed by tens of thousands of researchers worldwide, accounting for roughly 15% of global supercomputer usage. Unfortunately, these rich and costly data are not systematically maintained, and when further analyses are required, simulations have to be rerun-an unacceptable situation from scientific, environmental and sustainability standpoints. In this letter, we argue for a collaborative endeavor to archive MD simulation data and describe ongoing efforts to establish cost-effective and sustainable data archiving strategies. © 2024, CC BY-NC-SA.

关键词： Biotic

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Deep learning for detection and segmentation of artefact and disease instances in gastrointestinal endoscopy

arXiv

引用

arXiv 2020年

作者： Ali, Sharib Dmitrieva, Mariia Ghatwary, Noha Bano, Sophia Polat, Gorkem Temizel, Alptekin Krenzer, Adrian Hekalo, Amar Guo, Yun Bo Matuszewski, Bogdan Gridach, Mourad Voiculescu, Irina Yoganand, Vishnusai Chavan, Arnav Raj, Aryan Nguyen, Nhan T. Tran, Dat Q. Huynh, Le Duy Boutry, Nicolas Rezvy, Shahadate Chen, Haijian Choi, Yoon Ho Subramanian, Anand Balasubramanian, Velmurugan Gao, Xiaohong W. Hu, Hongyu Liao, Yusheng Stoyanov, Danail Daul, Christian Realdon, Stefano Cannizzaro, Renato Lamarque, Dominique Tran-Nguyen, Terry Bailey, Adam Braden, Barbara East, James Rittscher, Jens Institute of Biomedical Engineering and Big Data Institute Old Road Campus University of Oxford Oxford United Kingdom Translational Gastroenterology Unit Experimental Medicine Div. John Radcliffe Hospital University of Oxford Oxford United Kingdom Oxford NIHR Biomedical Research Centre Oxford United Kingdom Université de Versailles St-Quentin en Yvelines Hôpital Ambroise Paré France Instituto Onclologico Veneto IOV-IRCCS Padova Italy CRO Centro Riferimento Oncologico IRCCS Aviano Italy Computer Engineering Department Arab Academy for Science and Technology Alexandria Egypt Department of Computer Science University College London London United Kingdom CRAN UMR 7039 University of Lorraine CNRS Nancy France Graduate School of Informatics Middle East Technical University Ankara Turkey Department of Artificial Intelligence and Knowledge Systems University of Würzburg Germany School of Engineering University of Central Lancashire United Kingdom Department of Computer Science University of Oxford United Kingdom Mimyk Medical Simulations Pvt Ltd Indian Institute of Science Bengaluru India Dhanbad India Hanoi Viet Nam Le Kremlin-BicêtreF-94270 France School of Science and Technology Middlesex University London United Kingdom Department of Computer Science School of Informatics Xiamen University China Sungkyunkwan University Seoul Korea Republic of Claritrics India Pvt Ltd Chennai India School of Medical Science and Technology Indian Institute of Technology KharagpurWest Bengal India Shanghai Jiaotong University Shanghai China Ibn Zohr University Computer Science HIT Agadir Morocco

The Endoscopy computer Vision Challenge (EndoCV) is a crowd-sourcing initiative to address eminent problems in developing reliable computer aided detection and diagnosis endoscopy systems and suggest a pathway for clinical translation of technologies. Whilst endoscopy is a widely used diagnostic and treatment tool for hollow-organs, there are several core challenges often faced by endoscopists, mainly: 1) presence of multi-class artefacts that hinder their visual interpretation, and 2) difficulty in identifying subtle precancerous precursors and cancer abnormalities. Artefacts often affect the robustness of deep learning methods applied to the gastrointestinal tract organs as they can be confused with tissue of interest. EndoCV2020 challenges are designed to address research questions in these remits. In this paper, we present a summary of methods developed by the top 17 teams and provide an objective comparison of state-of-the-art methods and methods designed by the participants for two sub-challenges: i) artefact detection and segmentation (EAD2020), and ii) disease detection and segmentation (EDD2020). Multi-center, multi-organ, multi-class, and multi-modal clinical endoscopy datasets were compiled for both EAD2020 and EDD2020 sub-challenges. The out-of-sample generalization ability of detection algorithms was also evaluated. Whilst most teams focused on accuracy improvements, only a few methods hold credibility for clinical usability. The best performing teams provided solutions to tackle class imbalance, and variabilities in size, origin, modality and occurrences by exploring data augmentation, data fusion, and optimal class thresholding techniques. © 2020, CC BY-NC-SA.

关键词： Endoscopy

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Automatic knowledge Graph Construction: A Report on the 2019 ICDM/ICBK Contest

Automatic Knowledge Graph Construction: A Report on the 2019...

引用

IEEE International Conference on data Mining (ICDM)

作者： Xindong Wu Jia Wu Xiaoyi Fu Jiachen Li Peng Zhou Xu Jiang Mininglamp Academy of Sciences Mininglamp Technology Beijing China Key Laboratory of Knowledge Engineering with Big Data (Hefei Univ. of Technology) Ministry of Education Hefei China Department of Computing Macquarie University Sydney Australia School of Computer Science and Technology Anhui University Hefei China

Automatic knowledge graph construction seeks to build a knowledge graph from unstructured text in a specific domain or cross multiple domains, without human intervention. IEEE ICDM 2019 and ICBK 2019 invited teams from both degree-granting institutions and industrial labs to compete in the 2019 knowledge Graph Contest by automatically constructing knowledge graphs in at least two different domains. This article reports the outcomes of the Contest. The participants were expected to build a model to extract knowledge represented as triplets from text data and develop a web application to visualize the triplets. Awards were given to five teams. Their models and key techniques used to construct knowledge graphs are summarized.

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Biomedical image analysis competitions: The state of current participation practice

arXiv

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arXiv 2022年

作者： Eisenmann, Matthias Reinke, Annika Weru, Vivienn Tizabi, Minu Dietlinde Isensee, Fabian Adler, Tim J. Godau, Patrick Cheplygina, Veronika Kozubek, Michal Maier-Hein, Klaus Jäger, Paul F. Kopp-Schneider, Annette Maier-Hein, Lena Ali, Sharib Gupta, Anubha Kybic, Jan Noble, Alison de Solórzano, Carlos Ortiz Pachade, Samiksha Petitjean, Caroline Sage, Daniel Wei, Donglai Wilden, Elizabeth Alapatt, Deepak Andrearczyk, Vincent Baid, Ujjwal Bakas, Spyridon Balu, Niranjan Bano, Sophia Bawa, Vivek Singh Bernal, Jorge Bodenstedt, Sebastian Casella, Alessandro Choi, Jinwook Commowick, Olivier Daum, Marie Depeursinge, Adrien Dorent, Reuben Egger, Jan Eichhorn, Hannah Engelhardt, Sandy Ganz, Melanie Girard, Gabriel Hansen, Lasse Heinrich, Mattias Heller, Nicholas Hering, Alessa Huaulmé, Arnaud Kim, Hyunjeong Li, Hongwei Bran Landman, Bennett Li, Jianning Ma, Jun Martel, Anne Martín-Isla, Carlos Menze, Bjoern Nwoye, Chinedu Innocent Oreiller, Valentin Padoy, Nicolas Pati, Sarthak Payette, Kelly Sudre, Carole van Wijnen, Kimberlin Vardazaryan, Armine Vercauteren, Tom Wagner, Martin Wang, Chuanbo Yap, Moi Hoon Yu, Zeyun Yuan, Chun Zenk, Maximilian Zia, Aneeq Zimmerer, David Bao, Rina Choi, Chanyeol Cohen, Andrew Dzyubachyk, Oleh Galdran, Adrian Gan, Tianyuan Guo, Tianqi Gupta, Pradyumna Haithami, Mahmood Ho, Edward Jang, Ikbeom Li, Zhili Luo, Zhengbo Lux, Filip Makrogiannis, Sokratis Müller, Dominik Oh, Young-Tack Pang, Subeen Pape, Constantin Polat, Gorkem Reed, Charlotte Rosalie Ryu, Kanghyun Scherr, Tim Thambawita, Vajira Wang, Haoyu Wang, Xinliang Xu, Kele Yeh, Hung Yeo, Doyeob Yuan, Yixuan Zeng, Yan Zhao, Xin Abbing, Julian Adam, Jannes Adluru, Nagesh Agethen, Niklas Ahmed, Salman Al Khalil, Yasmina Alenyà, Mireia Alhoniemi, Esa An, Chengyang Arega, Tewodros Weldebirhan Avisdris, Netanell Aydogan, Dogu Baran Bai, Yingbin Calisto, Maria Baldeon Basaran, Berke Doga Beetz, Marcel Bian, Hao Blansit, Kevin Bloch, Louise Bohnsack, Robert Bosticardo, Sara Breen, Jack Brudfors, Mikael Brüngel, Raphael Cabezas, Mariano Cacciola, Alb Heidelberg Division of Intelligent Medical Systems Germany Heidelberg HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Biostatistics Germany Heidelberg Division of Medical Image Computing Germany Heidelberg HI Applied Vision Lab Germany IT University of Copenhagen Copenhagen Denmark Centre for Biomedical Image Analysis Masaryk University Brno Czech Republic Heidelberg Interactive Machine Learning Group Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg DKFZ University Hospital Heidelberg Germany School of Computing University of Leeds Leeds United Kingdom SBILab Department of ECE IIIT-Delhi India Faculty of Electrical Engineering Czech Technical University Prague Czech Republic Institute of Biomedical Engineering University of Oxford United Kingdom Center for Applied Medical Research Pamplona Spain Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Université de Rouen Normandie France Lausanne Switzerland School of Engineering and Applied Science Harvard University United States ICube University of Strasbourg CNRS France Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Techno-Pôle 3 Sierre3960 Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Rue du Bugnon 46 LausanneCH-1011 Switzerland University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington United States Wellcome EPSRC Centre for Interventional and Surgical Sciences University College London London United Kingdom Visual Artificial Intelligence Lab Oxford Brookes University Oxford United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Spain Dresden Fetscherstraße 74 PF 64 Dresden01307 Germany

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps. © 2022, CC BY.

关键词： Benchmarking

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OncoReg: Medical Image Registration for Oncological Challenges

arXiv

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arXiv 2025年

作者： Heyer, Wiebke Elser, Yannic Berkel, Lennart Song, Xinrui Xu, Xuanang Yan, Pingkun Jia, Xi Duan, Jinming Li, Zi Mok, Tony C.W. Li, BoWen Staackmann, Christian Großbröhmer, Christoph Hansen, Lasse Hering, Alessa Sieren, Malte M. Heinrich, Mattias P. Institute of Medical Informatics University of Lübeck Lübeck Germany Institute of Radiology and Nuclear Medicine University Hospital Schleswig-Holstein Lübeck Germany Department of Biomedical Engineering Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute TroyNY United States School of Computer Science University of Birmingham Birmingham United Kingdom Division of Informatics Imaging and Data Sciences University of Manchester United Kingdom DAMO Academy Alibaba Group Hangzhou China Hangzhou Shengshi Technology Co. Ltd Hangzhou China Department of Radiation Oncology University Hospital Schleswig-Holstein Lübeck Germany EchoScout GmbH Lübeck Germany Radboud University Medical Center Nijmegen Netherlands Institute of Radiology and Nuclear Medicine Institute of Interventional Radiology University Hospital Schleswig-Holstein Lübeck Germany

In modern cancer research, the vast volume of medical data generated is often underutilised due to challenges related to patient privacy. The OncoReg Challenge addresses this issue by enabling researchers to develop and validate image registration methods through a two-phase framework that ensures patient privacy while fostering the development of more generalisable AI models. Phase one involves working with a publicly available dataset, while phase two focuses on training models on a private dataset within secure hospital networks. OncoReg builds upon the foundation established by the Learn2Reg Challenge by incorporating the registration of interventional cone-beam computed tomography (CBCT) with standard planning fan-beam CT (FBCT) images in radiotherapy. Accurate image registration is crucial in oncology, particularly for dynamic treatment adjustments in image-guided radiotherapy, where precise alignment is necessary to minimise radiation exposure to healthy tissues while effectively targeting tumours. This work details the methodology and data behind the OncoReg Challenge and provides a comprehensive analysis of the competition entries and results. Findings reveal that feature extraction plays a pivotal role in this registration task. A new method emerging from this challenge demonstrated its versatility, while established approaches continue to perform comparably to newer techniques. Both deep learning and classical approaches still play significant roles in image registration, with the combination of methods—particularly in feature extraction—proving most effective. © 2025, CC BY.

关键词： Deep learning

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A Sparse Model-inspired Deep Thresholding Network for Exponential Signal Reconstruction—Application in Fast Biological Spectroscopy

arXiv

引用

arXiv 2020年

作者： Wang, Zi Guo, Di Tu, Zhangren Huang, Yihui Zhou, Yirong Wang, Jian Feng, Liubin Lin, Donghai You, Yongfu Agback, Tatiana Orekhov, Vladislav Qu, Xiaobo Department of Electronic Science Biomedical Intelligent Cloud R&D Center Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance National Institute for Data Science in Health and Medicine Xiamen University China School of Computer and Information Engineering Xiamen University of Technology Xiamen China College of Chemistry and Chemical Engineering Key Laboratory for Chemical Biology of Fujian Province High-field NMR Center Xiamen University Xiamen China China Mobile Group Xiamen China Biomedical Intelligent Cloud R&D Center Xiamen University Xiamen China Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden Department of Chemistry and Molecular Biology University of Gothenburg Gothenburg Sweden

The non-uniform sampling is a powerful approach to enable fast acquisition but requires sophisticated reconstruction algorithms. Faithful reconstruction from partial sampled exponentials is highly expected in general signal processing and many applications. Deep learning has shown astonishing potential in this field but many existing problems, such as lack of robustness and explainability, greatly limit its applications. In this work, by combining merits of the sparse model-based optimization method and data-driven deep learning, we propose a deep learning architecture for spectra reconstruction from undersampled data, called MoDern. It follows the iterative reconstruction in solving a sparse model to build the neural network and we elaborately design a learnable soft-thresholding to adaptively eliminate the spectrum artifacts introduced by undersampling. Extensive results on both synthetic and biological data show that MoDern enables more robust, high-fidelity, and ultra-fast reconstruction than the state-of-the-art methods. Remarkably, MoDern has a small number of network parameters and is trained on solely synthetic data while generalizing well to biological data in various scenarios. Furthermore, we extend it to an open-access and easy-to-use cloud computing platform (XCloud-MoDern), contributing a promising strategy for further development of biological applications. Copyright © 2020, The Authors. All rights reserved.

关键词： Signal reconstruction

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