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QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - analysis of Ranking Scores and Benchmarking Results

arXiv

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arXiv 2021年

作者： Mehta, Raghav Filos, Angelos Baid, Ujjwal Sako, Chiharu McKinley, Richard Rebsamen, Michael Dätwyler, Katrin Meier, Raphael Radojewski, Piotr Murugesan, Gowtham Krishnan Nalawade, Sahil Ganesh, Chandan Wagner, Ben Yu, Fang F. Fei, Baowei Madhuranthakam, Ananth J. Maldjian, Joseph A. Daza, Laura Gómez, Catalina Arbeláez, Pablo Dai, Chengliang Wang, Shuo Reynaud, Hadrien Mo, Yuanhan Angelini, Elsa Guo, Yike Bai, Wenjia Banerjee, Subhashis Pei, Linmin Murat, A.K. Rosas-González, Sarahi Zemmoura, Ilyess Tauber, Clovis Vu, Minh H. Nyholm, Tufve Löfstedt, Tommy Ballestar, Laura Mora Vilaplana, Veronica McHugh, Hugh Talou, Gonzalo Maso Wang, Alan Patel, Jay Chang, Ken Hoebel, Katharina Gidwani, Mishka Arun, Nishanth Gupta, Sharut Aggarwal, Mehak Singh, Praveer Gerstner, Elizabeth R. Kalpathy-Cramer, Jayashree Boutry, Nicolas Huard, Alexis Vidyaratne, Lasitha Rahman, Md Monibor Iftekharuddin, Khan M. Chazalon, Joseph Puybareau, Elodie Tochon, Guillaume Ma, Jun Cabezas, Mariano Llado, Xavier Oliver, Arnau Valencia, Liliana Valverde, Sergi Amian, Mehdi Soltaninejad, Mohammadreza Myronenko, Andriy Hatamizadeh, Ali Feng, Xue Dou, Quan Tustison, Nicholas Meyer, Craig Shah, Nisarg A. Talbar, Sanjay Weber, Marc-André Mahajan, Abhishek Jakab, Andras Wiest, Roland Fathallah-Shaykh, Hassan M. Nazeri, Arash Milchenko, Mikhail Marcus, Daniel Kotrotsou, Aikaterini Colen, Rivka Freymann, John Kirby, Justin Davatzikos, Christos Menze, Bjoern Bakas, Spyridon Gal, Yarin Arbel, Tal McGill University MontrealQC Canada Group University of Oxford Oxford United Kingdom University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine The University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States University Institute of Diagnostic and Interventional Neuroradiology University of Bern Inselspital Bern University Hospital Bern Switzerland Department of Radiology University of Texas Southwestern Medical Center DallasTX United States Department of Bioengineering University of Texas DallasTX United States Advanced Imaging Research Center University of Texas Southwestern Medical Center DallasTX United States Universidad de los Andes Bogotá Colombia Data Science Institute Imperial College London London United Kingdom NIHR Imperial BRC ITMAT Data Science Group Imperial College London London United Kingdom Department of Brain Sciences Imperial College London London United Kingdom Machine Intelligence Unit Indian Statistical Institute Kolkata India Department of CSE University of Calcutta Kolkata India Department of Information Technology Uppsala University Uppsala Sweden Department of Diagnostic Radiology The University of Pittsburgh Medical Center PittsburghPA United States UMR U1253 iBrain Université de Tours Inserm Tours France Department of Radiation Sciences Umeå University Umeå Sweden Department of Computing Science Umeå University Umeå Sweden Signal Theory and Communications Department Universitat Politècnica de Catalunya Barcelona Tech Barcelona Spain Faculty of Medical and Health Sciences University of Auckland Auckland New Zealand Radiology Department Auckland City Hospital Auckland New Zealand Auckland Bioengineering Institute University of Auckland New Zealand Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at https://***/RagMeh11/QU-BraTS. © 2021, CC BY.

关键词： Benchmarking

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CrowdWatcher: an open-source platform to catch the eye of the crowd

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Quality and User Experience 2019年第1期4卷 1-17页

作者： Lebreton, Pierre Hupont, Isabelle Hirth, Matthias Mäki, Toni Skodras, Evangelos Schubert, Anton Raake, Alexander Group of Networked Sensing and Control (NeSC) Zhejiang University Hangzhou China Institute of Intelligent Systems and Robotics Sorbonne University Paris France User-Centric Analysis of Multimedia Data Group Technische Universität Ilmenau Ilmenau Germany Department of Computer Science Aalto University Espoo Finland Department of Electrical and Computer Engineering University of Patras Patras Greece Audio Visual Technology Group Technische Universität Ilmenau Ilmenau Germany

This paper presents the open-source eye tracking platform CrowdWatcher. It enables researchers to measure gaze location and user engagement in a crowdsourcing context through traditional RGB webcams. The proposed platform particularly advances the field of Quality of Experience (QoE) research, as it allows the experimenter to collect remotely and with very limited effort novel information from crowds of participants, such as their commitment towards a task, attention and decision-making processes. Two different experiments are described that were conducted to demonstrate the platform’s potential. The first experiment addresses the measurement of participants’ behavior while performing a movie selection task. Results show that the platform provides complementary information to traditional self-reported data by taking gaze analysis into account. This is of particular relevance, since in a crowdsourcing context decision processes and attention are difficult to assess, and there is often limited control over the engagement of the test user with the task. A second experiment is conducted in the scenario of a multimedia QoE test. Prediction accuracy is compared to a professional infrared eye tracker. While CrowdWatcher performs less well than the professional eye tracker, it is still able to collect valuable gaze information in the far more challenging environment of crowdsourcing. As an outlook to further application domains, the usage of the platform to measure user engagement allows participants who do not pay attention to the task to be identified.

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Non-SPF routing algorithm based on ordered semi-group preference algebra

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The Journal of China Universities of Posts and Telecommunications 2017年第6期24卷 14-23页

作者： Zhang Yongtang Fan Bo Department of Computer Science and Technology Guangdong Neusoft Institute Foshan 528225 China Guangdong Key Laboratory of Big Data Analysis and Processing Guangzhou 510006 China

Layer 2 network technology is extending beyond its traditional local area implementation and finding wider acceptance in provider＇s metropolitan area networks and large-scale cloud data center networks. This is mainly due to its plug-and-play capability and native mobility support. Many efforts have been put to increase the bisection bandwidth in layer 2 network, which has been constrained by the spanning tree protocol （STP） that layer 2 network uses for preventing looping. The recent trend is to incorporate layer 3＇s routing approach into layer 2 network so that multiple paths can be used for forwarding traffic between any source-destination （S-D） node pair. Equal cost multipath （ECMP） is one such example. However, ECMP may still be limited in generating multiple paths due to its shortest path （lowest cost） requirement. In this paper, we consider a non-shortest-path routing approach, called equal preference multipath （EPMP） based on ordered semi group theory, which can generate more paths than ECMP. In EPMP routing, all the paths with different traditionally-defined costs, such as hops, bandwidth, etc., can be determined equally now and thus they become equal candidate paths. By the comparative tests with ECMP, EPMP routing not only generates more paths, provides 15% higher bisection bandwidth, but also identifies bottleneck links in a hierarchical network when different traffic patterns are applied EPMP is more flexible in controlling the number and length of multipath generation. Simulation results indicate the effectiveness of the proposed algorithm. It is a good reference for non-blocking running of big datacenter networks.

关键词： non-SPF routing algorithm algebraic routing equal preference multipath datacenter networks

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Operational Research: Methods and Applications

arXiv

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arXiv 2023年

作者： Petropoulos, Fotios Laporte, Gilbert Aktas, Emel Alumur, Sibel A. Archetti, Claudia Ayhan, Hayriye Battarra, Maria Bennell, Julia A. Bourjolly, Jean-Marie Boylan, John E. Breton, Michèle Canca, David Charlin, Laurent Chen, Bo Cicek, Cihan Tugrul Cox, Louis Anthony Currie, Christine S.M. Demeulemeester, Erik Ding, Li Disney, Stephen M. Ehrgott, Matthias Eppler, Martin J. Erdogan, Güneş Fortz, Bernard Franco, L. Alberto Frische, Jens Greco, Salvatore Gregory, Amanda J. Hämäläinen, Raimo P. Herroelen, Willy Hewitt, Mike Holmström, Jan Hooker, John N. Işık, Tugçe Johnes, Jill Kara, Bahar Y. Karsu, Özlem Kent, Katherine Köhler, Charlotte Kunc, Martin Kuo, Yong-Hong Letchford, Adam N. Leung, Janny Li, Dong Li, Haitao Lienert, Judit Ljubić, Ivana Lodi, Andrea Lozano, Sebastián Lurkin, Virginie Martello, Silvano McHale, Ian G. Midgley, Gerald Morecroft, John D.W. Mutha, Akshay Oguz, Ceyda Petrovic, Sanja Pferschy, Ulrich Psaraftis, Harilaos N. Rose, Sam Saarinen, Lauri Salhi, Said Song, Jing-Sheng Sotiros, Dimitrios Stecke, Kathryn E. Strauss, Arne K. Tarhan, Istenç Thielen, Clemens Toth, Paolo Van Woensel, Tom Vanden Berghe, Greet Vasilakis, Christos Vaze, Vikrant Vigo, Daniele Virtanen, Kai Wang, Xun Weron, Rafal White, Leroy Yearworth, Mike Yıldırım, E. Alper Zaccour, Georges Zhao, Xuying School of Management University of Bath Bath United Kingdom Makridakis Open Forecasting Center University of Nicosia Nicosia Cyprus Department of Decision Sciences HEC Montréal Montreal Canada Molde University College Molde Norway Cranfield School of Management Cranfield University Cranfield United Kingdom Department of Management Sciences University of Waterloo Waterloo Canada ESSEC Business School in Paris Department of Information Systems Decision Sciences and Statistics Cergy France H. Milton Stewart School of Industrial and Systems Engineering Georgia Institute of Technology Atlanta United States Centre for Decision Research Leeds University Business School University of Leeds Leeds United Kingdom Université du Québec à Montréal Montreal Canada Centre for Marketing Analytics and Forecasting Lancaster University Management School Lancaster University Lancaster United Kingdom School of Engineering Department of Industrial Engineering and Management Science I University of Seville Seville Spain Mila-Quebec AI Institute Montreal Canada Warwick Business School University of Warwick Coventry United Kingdom Department of Industrial Engineering Atilim University Ankara Turkey Department of Business Analytics University of Colorado School of Business Denver United States Cox Associates Denver United States Mathematical Sciences University of Southampton Southampton United Kingdom Faculty of Economics and Business Research Center for Operations Management KU Leuven Leuven Belgium Durham University Business School Durham University Durham United Kingdom Center for Simulation Analytics and Modelling University of Exeter Business School Exeter United Kingdom Department of Management Science Lancaster University Management School Lancaster University Lancaster United Kingdom University of St. Gallen St. Gallen Switzerland HEC - Management School of the University of Liège Liège Belgium Département d'Informatique Université Libre de Bruxelles Bruss

Throughout its history, Operational Research has evolved to include a variety of methods, models and algorithms that have been applied to a diverse and wide range of contexts. This encyclopedic article consists of two main sections: methods and applications. The first aims to summarise the up-to-date knowledge and provide an overview of the state-of-the-art methods and key developments in the various subdomains of the field. The second offers a wide-ranging list of areas where Operational Research has been applied. The article is meant to be read in a nonlinear fashion. It should be used as a point of reference or first-port-of-call for a diverse pool of readers: academics, researchers, students, and practitioners. The entries within the methods and applications sections are presented in alphabetical order. The authors dedicate this paper to the 2023 Turkey/Syria earthquake victims. We sincerely hope that advances in OR will play a role towards minimising the pain and suffering caused by this and future catastrophes. © 2023, CC BY.

关键词： Decision making

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Toward Complete Transformation of Sodium Polysulfides by Regulating the Second-Shell Coordinating Environment of Atomically Dispersed Fe

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Angewandte Chemie 2023年第26期135卷

作者： Ruilin Bai Qiaosong Lin Xinyu Li Fangxin Ling Huijuan Wang Sha Tan Lingxiang Hu Mingze Ma Prof. Xiaojun Wu Yu Shao Xianhong Rui Prof. Enyuan Hu Dr. Yu Yao Prof. Yan Yu Hefei National Research Center for Physical Sciences at the Microscale Department of Materials Science and Engineering CAS Key Laboratory of Materials for Energy Conversion University of Science and Technology of China Hefei Anhui 230026 China Contribution: Conceptualization (lead) Writing - original draft (lead) State Key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 Liaoning China University of Chinese Academy of Sciences Beijing 100049 China Contribution: Data curation (lead) Contribution: Formal analysis (equal) Contribution: Investigation (lead) Experimental Center of Engineering and Material Science University of Science and Technology of China Hefei 230026 China Contribution: Methodology (equal) Chemistry Division Brookhaven National Laboratory Upton NY USA Contribution: Resources (equal) Department of Electrical Engineering and Computer Science Institut Polytechnique de Paris 91120 Palaiseau Île-de-France France Contribution: Software (equal) Contribution: Data curation (equal) Jiujiang DeFu Technology Co. Ltd. Jiujiang Jiangxi 332000 (P. R. China School of Materials and Energy Guangdong University of Technology Guangzhou 510006 China Contribution: Validation (lead) Contribution: Methodology (lead) Contribution: Writing - review & editing (lead) National Synchrotron Radiation Laboratory Hefei Anhui 230026 China Contribution: Project administration (lead) Writing - review & editing (lead)

Room temperature sodium-sulfur (RT Na-S) batteries are highly competitive as potential energy storage devices. Nevertheless, their actually achieved reversible capacities are far below the theoretical value due to incomplete transformation of polysulfides. Herein, atomically dispersed Fe-N/S active center by regulating the second-shell coordinating environment of Fe single atom is proposed. The Fe−N 4 S 2 coordination structure with enhanced local electronic concentration around the Fermi level is revealed via synchrotron radiation X-ray absorption spectroscopy (XAS) and theoretical calculations, which can not only significantly promote the transformation kinetics of polysulfides, but induce uniform Na deposition for dendrite-free Na anode. As a result, the obtained S cathode delivers a high initial reversible capacity of 1590 mAh g −1 , nearly the theoretical value. This work opens up a new avenue to facilitate the complete transformation of polysulfides for RT Na-S batteries.

关键词： Catalysis Coordinating Environment Fe Single Atom RT Na-S Batteries Transformation Kinetics

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The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI

arXiv

引用

arXiv 2023年

作者： Moawad, Ahmed W. Janas, Anastasia Baid, Ujjwal Ramakrishnan, Divya Saluja, Rachit Ashraf, Nader Jekel, Leon Amiruddin, Raisa Adewole, Maruf Albrecht, Jake Anazodo, Udunna Aneja, Sanjay Anwar, Syed Muhammad Bergquist, Timothy Calabrese, Evan Chiang, Veronica Chung, Verena Conte, Gian Marco Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Iglesias, Juan Eugenio Jiang, Zhifan Johanson, Elaine Kazerooni, Anahita Fathi Kofler, Florian Krantchev, Kiril LaBella, Dominic Van Leemput, Koen Li, Hongwei Bran Linguraru, Marius George Link, Katherine E. Liu, Xinyang Maleki, Nazanin Meier, Zeke Menze, Bjoern H. Moy, Harrison Osenberg, Klara Piraud, Marie Reitman, Zachary Shinohara, Russel Takeshi Tahon, Nourel hoda Nada, Ayman Velichko, Yuri S. Wang, Chunhao Wiestler, Benedikt Wiggins, Walter Shafique, Umber Willms, Klara Avesta, Arman Bousabarah, Khaled Chakrabarty, Satrajit Gennaro, Nicolo Holler, Wolfgang Kaur, Manpreet LaMontagne, Pamela Lin, MingDe Lost, Jan Marcus, Daniel S. Maresca, Ryan Merkaj, Sarah Nada, Ayaman Pedersen, Gabriel Cassinelli von Reppert, Marc Sotiras, Aristeidis Teytelboym, Oleg Tillmans, Niklas Westerhoff, Malte Youssef, Ayda Godfrey, Devon Floyd, Scott Rauschecker, Andreas Villanueva-Meyer, Javier Pflüger, Irada Cho, Jaeyoung Bendszus, Martin Brugnara, Gianluca Cramer, Justin Perez-Carillo, Gloria Guzman J. Johnson, Derek R. Kam, Anthony Kwan, Benjamin Yin Ming Lai, Lillian Lall, Neil U. Memon, Fatima Patro, Satya Narayana Petrovic, Bojan So, Tiffany Y. Thompson, Gerard Wu, Lei Schrickel, E. Brooke Bansal, Anu Barkhof, Frederik Besada, Cristina Chu, Sammy Druzgal, Jason Dusoi, Alexandru Farage, Luciano Feltrin, Fabricio Fong, Amy Fung, Steve H. Gray, R. Ian Ikuta, Ichiro Iv, Michael Postma, Alida A. Mahajan, Amit Joyner, David Krumpelman, Chase Letourneau-Guillon, Laurent Lincoln, Christie M. Maros, Mate E. Miller, Elka Morón, Fanny Nimchinsky, Esther A. Ozsarlak, Ozkan Patel, Uresh Rohatgi, Saurabh Saha, Atin Sayah, Anousheh Schwartz, Eric D. Shih, Robert Shiroishi, Mark Trinity health Mid Atlantic Hosiptals DarbyPA United States Department of Radiology and Biomedical Imaging Yale School of Medicine New HavenCT United States Division of Computational Pathology Department of Pathology and Laboratory Medicine School of Medicine Indiana University IndianapolisIN United States Department of Electical and Computer Engineering Cornell University Cornell Tech New YorkNY United States Department of Radiology Weill Cornell Medicine New YorkNY United States ImagineQuant Children’s Hospital of Philadelphia PhiladelphiaPA United States College of Medicine Alfaisal University Riyadh Saudi Arabia DKFZ Division of Translational Neurooncology The WTZ German Cancer Consortium DKTK Partner Site University Hospital Essen Essen Germany Medical Artificial Intelligence Lab Crestview Radiology Lagos Nigeria Sage Bionetworks SeattleWA United States Montreal Neurological Institute McGill University Montreal Canada lab Crestview Radiology Lagos Nigeria Department of Therapeutic Radiology Yale School of Medicine New HavenCT United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Department of Radiology Mayo Clinic RochesterMN United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Neurosurgery Yale School of Medicine New HavenCT United States Center for Global Health Perelman School of Medicine University of Pennsylvania PA United States Department of Informatics Technical University Munich Germany Children’s Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Children’s National Hospital WashingtonDC United States PrecisionFDA U.S. Food and Drug Administration S

The translation of AI-generated brain metastases (BM) segmentation into clinical practice relies heavily on diverse, high-quality annotated medical imaging datasets. The BraTS-METS 2023 challenge has gained momentum for testing and benchmarking algorithms using rigorously annotated internationally compiled real-world datasets. This study presents the results of the segmentation challenge and characterizes the challenging cases that impacted the performance of the winning algorithms. Untreated brain metastases on standard anatomic MRI sequences (T1, T2, FLAIR, T1PG) from eight contributed international datasets were annotated in stepwise method: published UNET algorithms, student, neuroradiologist, final approver neuroradiologist. Segmentations were ranked based on lesion-wise Dice and Hausdorff distance (HD95) scores. False positives (FP) and false negatives (FN) were rigorously penalized, receiving a score of 0 for Dice and a fixed penalty of 374 for HD95. The mean scores for the teams were calculated. Eight datasets comprising 1303 studies were annotated, with 402 studies (3076 lesions) released on Synapse as publicly available datasets to challenge competitors. Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing. Segmentation accuracy was measured as rank across subjects, with the winning team achieving a LesionWise mean score of 7.9. The Dice score for the winning team was 0.65 ± 0.25. Common errors among the leading teams included false negatives for small lesions and misregistration of masks in space. The Dice scores and lesion detection rates of all algorithms diminished with decreasing tumor size, particularly for tumors smaller than 100 mm3. In conclusion, algorithms for BM segmentation require further refinement to balance high sensitivity in lesion detection with the minimization of false positives and negatives. The BraTS-METS 2023 challenge successfully curated well-annotated, diverse d

关键词： Image segmentation

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Allen: A High-Level Trigger on GPUs for LHCb

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Computing and Software for Big science 2020年第1期4卷 1-11页

作者： Aaij, R. Albrecht, J. Belous, M. Billoir, P. Boettcher, T. Brea Rodríguez, A. vom Bruch, D. Cámpora Pérez, D.H. Casais Vidal, A. Craik, D.C. Fernandez Declara, P. Funke, L. Gligorov, V.V. Jashal, B. Kazeev, N. Martínez Santos, D. Pisani, F. Pliushchenko, D. Popov, S. Quagliani, R. Rangel, M. Reiss, F. Sánchez Mayordomo, C. Schwemmer, R. Sokoloff, M. Stevens, H. Ustyuzhanin, A. Vilasís Cardona, X. Williams, M. Nikhef National Institute for Subatomic Physics Amsterdam Netherlands Fakultät Physik Technische Universität Dortmund Dortmund Germany National Research University Higher School of Economics Moscow Russian Federation Yandex School of Data Analysis Moscow Russian Federation LPNHE Sorbonne Université Paris Diderot Sorbonne Paris Cité CNRS/IN2P3 Paris France Massachusetts Institute of Technology Cambridge United States Instituto Galego de Física de Altas Enerxías (IGFAE) Universidade de Santiago de Compostela Santiago de Compostela Spain Faculty of Science and Engineering Maastricht University Maastricht Netherlands European Organization for Nuclear Research (CERN) Geneva Switzerland Department of Computer Science and Engineering University Carlos III of Madrid Madrid Spain Instituto de Física Corpuscular Centro Mixto Universidad de Valencia CSIC Valencia Spain INFN Sezione di Bologna Bologna Italy Università di Bologna Bologna Italy National Research University Higher School of Economics Saint Petersburg Russian Federation National University of Science and Technology MISIS Moscow Russian Federation Instituto de Física Universidade Federal do Rio de Janeiro (UFRJ) Rio de Janeiro Brazil University of Cincinnati Cincinnati OH United States DS4DS la Salle Universitat Ramon Llull Barcelona Spain

We describe a fully GPU-based implementation of the first level trigger for the upgrade of the LHCb detector, due to start data taking in 2021. We demonstrate that our implementation, named Allen, can process the 40 Tbit/s data rate of the upgraded LHCb detector and perform a wide variety of pattern recognition tasks. These include finding the trajectories of charged particles, finding proton–proton collision points, identifying particles as hadrons or muons, and finding the displaced decay vertices of long-lived particles. We further demonstrate that Allen can be implemented in around 500 scientific or consumer GPU cards, that it is not I/O bound, and can be operated at the full LHC collision rate of 30 MHz. Allen is the first complete high-throughput GPU trigger proposed for a HEP experiment. © 2020, The Author(s).

关键词： GPU LHCb Real-time data selection Trigger

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The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)

arXiv

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arXiv 2023年

作者： Kazerooni, Anahita Fathi Khalili, Nastaran Liu, Xinyang Haldar, Debanjan Jiang, Zhifan Anwar, Syed Muhammed Albrecht, Jake Adewole, Maruf Anazodo, Udunna Anderson, Hannah Bagheri, Sina Baid, Ujjwal Bergquist, Timothy Borja, Austin J. Calabrese, Evan Chung, Verena Conte, Gian-Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Haldar, Shuvanjan Iglesias, Juan Eugenio Janas, Anastasia Johansen, Elaine Jones, Blaise V. Kofler, Florian LaBella, Dominic Lai, Hollie Anne Van Leemput, Koen Li, Hongwei Bran Maleki, Nazanin McAllister, Aaron S. Meier, Zeke Menze, Bjoern Moawad, Ahmed W. Nandolia, Khanak K. Pavaine, Julija Piraud, Marie Poussaint, Tina Prabhu, Sanjay P. Reitman, Zachary Rodriguez, Andres Rudie, Jeffrey D. Sanchez-Montano, Mariana Shaikh, Ibraheem Salman Shah, Lubdha M. Sheth, Nakul Shinohara, Russel Taki Tu, Wenxin Viswanathan, Karthik Wang, Chunhao Ware, Jeffrey B. Wiestler, Benedikt Wiggins, Walter Zapaishchykova, Anna Aboian, Mariam Bornhorst, Miriam de Blank, Peter Deutsch, Michelle Fouladi, Maryam Hoffman, Lindsey Kann, Benjamin Lazow, Margot Mikael, Leonie Nabavizadeh, Ali Packer, Roger Resnick, Adam Rood, Brian Vossough, Arastoo Bakas, Spyridon Linguraru, Marius George Children’s Hospital of Philadelphia PhiladelphiaPA United States Department of Neurosurgery University of Pennsylvania PhiladelphiaPA United States University of Pennsylvania PhiladelphiaPA United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Department of Neurosurgery Thomas Jefferson University Hospital PA United States Sage Bionetworks United States Lab Crestview Radiology Lagos Nigeria McGill University MontrealQC Canada Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Neurosurgery The University of Southern California CA United States Department of Radiology Duke University Medical Center United States Mayo Clinic MN United States Center for Global Health Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Informatics Technical University Munich Germany TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States Biomedical Engineering Rutgers University New BrunswickNJ United States Athinoula A Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Yale University New HavenCT United States PrecisionFDA U.S. Food and Drug Administration Silver SpringMD United States Cincinnati Children’s Hospital Medical Center United States Helmholtz AI Helmholtz Munich Germany Department of Radiation Oncology Duke University Medical Center United States Department of Radiology Children’s Health Orange County CA United States Department of Applied Mathematics and Computer Science Technical University of Denmark Denmark Department of Radiol

Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children. The five-year survival rate for high-grade gliomas in children is less than 20%. Due to their rarity, the diagnosis of these entities is often delayed, their treatment is mainly based on historic treatment concepts, and clinical trials require multi-institutional collaborations. The MICCAI Brain Tumor Segmentation (BraTS) Challenge is a landmark community benchmark event with a successful history of 12 years of resource creation for the segmentation and analysis of adult glioma. Here we present the CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs 2023 challenge, which represents the first BraTS challenge focused on pediatric brain tumors with data acquired across multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. The BraTS-PEDs 2023 challenge focuses on benchmarking the development of volumentric segmentation algorithms for pediatric brain glioma through standardized quantitative performance evaluation metrics utilized across the BraTS 2023 cluster of challenges. Models gaining knowledge from the BraTS-PEDs multi-parametric structural MRI (mpMRI) training data will be evaluated on separate validation and unseen test mpMRI dataof high-grade pediatric glioma. The CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs 2023 challenge brings together clinicians and AI/imaging scientists to lead to faster development of automated segmentation techniques that could benefit clinical trials, and ultimately the care of children with brain tumors. © 2023, CC BY.

关键词： Tumors

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Influential groups for seeding and sustaining nonlinear contagion in heterogeneous hypergraphs

arXiv

引用

arXiv 2021年

作者： St-Onge, Guillaume Iacopini, Iacopo Latora, Vito Barrat, Alain Petri, Giovanni Allard, Antoine Hébert-Dufresne, Laurent Département de Physique de Génie Physique et d’Optique Université Laval QuébecQCG1V 0A6 Canada Centre Interdisciplinaire en Modélisation Mathématique Université Laval QuébecQCG1V 0A6 Canada Department of Network and Data Science Central European University Vienna1100 Austria Aix Marseille Univ Université de Toulon CNRS CPT Marseille France Centre for Advanced Spatial Analysis University College London LondonW1T 4TJ United Kingdom School of Mathematical Sciences Queen Mary University of London Mile End Road LondonE1 4NS United Kingdom Dipartimento di Fisica ed Astronomia Università di Catania INFN CataniaI-95123 Italy Complexity Science Hub Josefstädter Strasse 39 ViennaA 1080 Austria Tokyo Institute of Technology Tokyo Japan Mathematics and Complex Systems Research Area ISI Foundation Turin Italy ISI Global Science Foundation New York United States Vermont Complex Systems Center University of Vermont BurlingtonVT05401 United States Department of Computer Science University of Vermont BurlingtonVT05401 United States

Several biological and social contagion phenomena, such as superspreading events or social reinforcement, are the results of multi-body interactions, for which hypergraphs offer a natural mathematical description. In this paper, we develop a novel mathematical framework based on approximate master equations to study contagions on random hypergraphs with a heterogeneous structure, both in terms of group size (hyperedge cardinality) and of membership of nodes to groups (hyperdegree). The characterization of the inner dynamics of groups provides an accurate description of the contagion process, without losing the analytical tractability. Using a contagion model where multi-body interactions are mapped onto a nonlinear infection rate, our two main results show how large groups are influential, in the sense that they drive both the early spread of a contagion and its endemic state (i.e., its stationary state). First, we provide a detailed characterization of the phase transition, which can be continuous or discontinuous with a bistable regime, and derive analytical expressions for the critical and tricritical points. We find that large values of the third moment of the membership distribution suppress the emergence of a discontinuous phase transition. Furthermore, the combination of heterogeneous group sizes and nonlinear contagion facilitates the onset of a mesoscopic localization phase, where contagion is sustained only by the largest groups, thereby inhibiting bistability as well. Second, we formulate the problem of optimal seeding for hypergraph contagion, and we compare two strategies: tuning the allocation of seeds according to either individual node or group properties. We find that, when the contagion is sufficiently nonlinear, groups are more effective seeds of contagion than individual nodes. Copyright © 2021, The Authors. All rights reserved.

关键词： Graph theory

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Cover Image, Volume 8, Issue 2

引用

WIREs Water 2021年第2期8卷

作者： Giri Kattel Jessica Reeves Andrew Western Wenjing Zhang Wei Jing Suzanne McGowan Lan Cuo Peter Scales Kim Dowling Qiang He Lei Wang Samantha Capon Zenghui Pan Jiansheng Cui Lulu Zhang Luo Xiao Chun Liu Ke Zhang Chuanyu Gao Zaifeng Tian Yongding Liu Department of Infrastructure Engineering The University of Melbourne Melbourne Australia College of Environmental Science and Technology Hebei University of Science and Technology Shijiazhuang China Department of Hydraulic Engineering Tsinghua University Beijing China Faculty of Health and Life Sciences Federation University Australia Ballarat Australia Contribution: Conceptualization Data curation Formal analysis Funding acquisition Investigation Methodology Resources Supervision Validation Visualization Writing - original draft Writing - review & editing Contribution: Investigation Methodology Writing - review & editing School of Geography The University of Melbourne Melbourne Australia Contribution: Investigation Methodology Visualization Department of Geography Nottingham University Nottingham UK Institute of Tibetan Plateau Research Chinese Academy of Sciences Beijing China Department of Chemical Engineering The University of Melbourne Melbourne Australia School of Science Engineering and Information Technology Federation University Ballarat Australia Department of Geology University of Johannesburg South Africa Contribution: Investigation Writing - review & editing Department of Civil and Environmental Engineering The University of Tennessee Knoxville Tennessee USA Contribution: Investigation Validation Writing - review & editing Australian Rivers Institute Griffith University Brisbane Australia Hebei Institute of Water Science Shijiazhuang China Contribution: Investigation Validation Contribution: Funding acquisition Resources Contribution: Investigation Contribution: Funding acquisition Investigation Nanjing Institute of Geography and Limnology Chinese Academy of Sciences Nanjing China The Northeast Institute of Geography and Agroecology Chinese Academy of Sciences Changchun China Hebei Environmental Science Institute Shijiazhuang China Institute of Hydrobiology Chinese Academy of Sciences Wuhan China

The cover image is based on the Focus Article Healthy waterways and ecologically sustainable cities in Beijing-Tianjin-Hebei urban agglomeration (northern China): Challenges and future directions by Giri Kattel et al....

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