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arXiv 2023年

作者： Lekadir, Karim Feragen, Aasa Fofanah, Abdul Joseph Frangi, Alejandro F. Buyx, Alena Emelie, Anais Lara, Andrea Porras, Antonio R. Chan, An-Wen Navarro, Arcadi Glocker, Ben Botwe, Benard O. Khanal, Bishesh Beger, Brigit Wu, Carol C. Cintas, Celia Langlotz, Curtis P. Rueckert, Daniel Mzurikwao, Deogratias Fotiadis, Dimitrios I. Zhussupov, Doszhan Ferrante, Enzo Meijering, Erik Weicken, Eva González, Fabio A. Asselbergs, Folkert W. Prior, Fred Krestin, Gabriel P. Collins, Gary S. Tegenaw, Geletaw S. Kaissis, Georgios Misuraca, Gianluca Tsakou, Gianna Dwivedi, Girish Kondylakis, Haridimos Jayakody, Harsha Woodruf, Henry C. Mayer, Horst Joachim Aerts, Hugo JWL Walsh, Ian Chouvarda, Ioanna Buvat, Irène Tributsch, Isabell Rekik, Islem Duncan, James Kalpathy-Cramer, Jayashree Zahir, Jihad Park, Jinah Mongan, John Gichoya, Judy W. Schnabel, Julia A. Kushibar, Kaisar Riklund, Katrine Mori, Kensaku Marias, Kostas Amugongo, Lameck M. Fromont, Lauren A. Maier-Hein, Lena Alberich, Leonor Cerdá Rittner, Leticia Phiri, Lighton Marrakchi-Kacem, Linda Donoso-Bach, Lluís Martí-Bonmatí, Luis Cardoso, M. Jorge Bobowicz, Maciej Shabani, Mahsa Tsiknakis, Manolis Zuluaga, Maria A. Bielikova, Maria Fritzsche, Marie-Christine Camacho, Marina Linguraru, Marius George Wenzel, Markus De Bruijne, Marleen Tolsgaard, Martin G. Ghassemi, Marzyeh Ashrafuzzaman, Md Goisauf, Melanie Yaqub, Mohammad Abadía, Mónica Cano Mahmoud, Mukhtar M.E. Elattar, Mustafa Rieke, Nicola Papanikolaou, Nikolaos Lazrak, Noussair Díaz, Oliver Salvado, Olivier Pujol, Oriol Sall, Ousmane Guevara, Pamela Gordebeke, Peter Lambin, Philippe Brown, Pieta Abolmaesumi, Purang Dou, Qi Lu, Qinghua Osuala, Richard Nakasi, Rose Zhou, S. Kevin Napel, Sandy Colantonio, Sara Albarqouni, Shadi Joshi, Smriti Carter, Stacy Klein, Stefan Petersen, Steffen E. Aussó, Susanna Awate, Suyash Raviv, Tammy Riklin Cook, Tessa Mutsvangwa, Tinashe E.M. Rogers, Wendy A. Niessen, Wiro J. Puig-Bosch, Xènia Zeng, Yi Mohammed, Yunusa G. Aquino, Yves Saint James Salahuddin, Zohaib Starmans, Martijn P.A. Department de Matemàtiques i Informàtica Universitat de Barcelona Barcelona Spain Barcelona Spain DTU Compute Technical University of Denmark Kgs Lyngby Denmark Department of Mathematics and Computer Science Faculty of Science and Technology Milton Margai Technical University Freetown Sierra Leone Center for Computational Imaging & Simulation Technologies in Biomedicine Schools of Computing and Medicine University of Leeds Leeds United Kingdom Cardiovascular Science and Electronic Engineering Departments KU Leuven Leuven Belgium Institute of History and Ethics in Medicine Technical University of Munich Munich Germany Faculty of Engineering of Systems Informatics and Sciences of Computing Galileo University Guatemala City Guatemala Department of Biostatistics and Informatics Colorado School of Public Health University of Colorado Anschutz Medical Campus AuroraCO United States Department of Medicine Women’s College Research Institute University of Toronto Toronto Canada Universitat Pompeu Fabra BarcelonaBeta Brain Research Center Barcelona Spain Department of Computing Imperial College London London United Kingdom School of Biomedical & Allied Health Sciences University of Ghana Accra Ghana Department of Midwifery & Radiography School of Health & Psychological Sciences City University of London United Kingdom Kathmandu Nepal European Heart Network Brussels Belgium Department of Thoracic Imaging University of Texas MD Anderson Cancer Center Houston United States IBM Research Africa Nairobi Kenya Departments of Radiology Medicine and Biomedical Data Science Stanford University School of Medicine Stanford United States Institute for AI and Informatics in Medicine Klinikum rechts der Isar Technical University Munich Munich Germany Department of Computing Imperial College London London United Kingdom Muhimbili University of Health and Allied Sciences Dar es Salaam Tanzania United Republic of Ioannina Greece Almaty AI Lab Almaty Kazakhstan

Background: Despite major advances in artificial intelligence (AI) research for healthcare, the deployment and adoption of AI technologies remain limited in clinical practice. In recent years, concerns have been raised about the clinical, technical, ethical and legal risks associated with healthcare AI. To increase adoption in the real world, it is essential that AI technologies are trusted and accepted by patients, clinicians, health organisations and authorities. This paper describes the FUTURE-AI framework as the first international consensus guideline for trustworthy AI in healthcare. Methods: The FUTURE-AI consortium was founded in 2021 and now comprises 117 interdisciplinary experts from 50 countries representing all continents, including AI scientists, clinical researchers, biomedical ethicists, and social scientists. Over a two-year period, the consortium established guiding principles and best practices for trustworthy and deployable AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. Findings: The FUTURE-AI framework was established based on six guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 30 best practices were defined, addressing technical, clinical, socio-ethical and legal dimensions of trustworthy AI. The recommendations cover the entire lifecycle of healthcare AI, from design, development and validation to regulation, deployment, and monitoring. Interpretation: FUTURE-AI is a structured, risk-informed framework which provides guidance for constructing healthcare AI tools that will be trusted, deployed and adopted in real-world clinical practice. Researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of healthcare AI. Copyright © 2023, The Authors. All rights

关键词： Clinical research

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Certified Quantum Random Numbers from Untrusted Light

引用

Physical Review X 2020年第4期10卷 041048-041048页

作者： David Drahi Nathan Walk Matty J. Hoban Aleksey K. Fedorov Roman Shakhovoy Akky Feimov Yury Kurochkin W. Steven Kolthammer Joshua Nunn Jonathan Barrett Ian A. Walmsley Clarendon Laboratory Department of Physics University of Oxford Oxford OX1 3PU United Kingdom Department of Computer Science University of Oxford Oxford OX1 3QD United Kingdom Dahlem Center for Complex Quantum Systems Freie Universität Berlin 14195 Berlin Germany Department of Computing Goldsmiths University of London London SE14 6NW United Kingdom Russian Quantum Center 100 Novaya Street Skolkovo Moscow 143025 Russia

A remarkable aspect of quantum theory is that certain measurement outcomes are entirely unpredictable to all possible observers. Such quantum events can be harnessed to generate numbers whose randomness is asserted based upon the underlying physical processes. We formally introduce, design, and experimentally demonstrate an ultrafast optical quantum random number generator that uses a totally untrusted photonic source. While considering completely general quantum attacks, we certify and generate in real time random numbers at a rate of 8.05 Gb/s with a composable security parameter of 10−10. Composable security is the most stringent and useful security paradigm because any given protocol remains secure even if arbitrarily combined with other instances of the same, or other, protocols, thereby allowing the generated randomness to be utilized for arbitrary applications in cryptography and beyond. This work achieves the fastest generation of composably secure quantum random numbers ever reported.

关键词： Quantum protocols

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Accurate RNA 3D structure prediction using a language model-based deep learning approach

arXiv

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arXiv 2022年

作者： Shen, Tao Hu, Zhihang Sun, Siqi Liu, Di Wong, Felix Wang, Jiuming Chen, Jiayang Wang, Yixuan Hong, Liang Xiao, Jin Zheng, Liangzhen Krishnamoorthi, Tejas King, Irwin Wang, Sheng Yin, Peng Collins, James J. Li, Yu Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong Zelixir Biotech Shanghai China Research Institute of Intelligent Complex Systems Fudan University Shanghai China Wyss Institute for Biologically Inspired Engineering Harvard University BostonMA United States Department of Systems Biology Harvard Medical School BostonMA United States Institute for Medical Engineering and Science Massachusetts Institute of Technology CambridgeMA United States Broad Institute of MIT and Harvard CambridgeMA United States Synthetic Biology Center Massachusetts Institute of Technology CambridgeMA United States Integrated Biosciences Redwood CityCA United States OneAIM Ltd. Hong Kong Shanghai AI Laboratory Shanghai China The CUHK Shenzhen Research Institute Hi-Tech Park Shenzhen Nanshan China Shenzhen Institute of Advanced Technology Guangdong Shenzhen China School of Molecular Sciences Center for Molecular Design and Biomimetics the Biodesign Institute Arizona State University TempeAZ United States School of Computing and Augmented Intelligence Arizona State University TempeAZ United States

Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design. The structural flexibility of RNA, which leads to scarcity of experimentally determined data, complicates computational prediction efforts. Here, we present RhoFold+, an RNA language model-based deep learning method that accurately predicts 3D structures of single-chain RNAs from sequences. By integrating an RNA language model pre-trained on ∼23.7 million RNA sequences and leveraging techniques to address data scarcity, RhoFold+ offers a fully automated end-to-end pipeline for RNA 3D structure prediction. Retrospective evaluations on RNA-Puzzles and CASP15 natural RNA targets demonstrate RhoFold+’s superiority over existing methods, including human expert groups. Its efficacy and generalizability are further validated through cross-family and cross-type assessments, as well as time-censored benchmarks. Additionally, RhoFold+ predicts RNA secondary structures and inter-helical angles, providing empirically verifiable features that broaden its applicability to RNA structure and function studies. Copyright © 2022, The Authors. All rights reserved.

关键词： Deep learning

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Applications of Game Theory in Vehicular Networks: A Survey

arXiv

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arXiv 2021年

作者： Sun, Zemin Liu, Yanheng Wang, Jian Li, Guofa Anil, Carie Li, Keqiang Guo, Xinyu Sun, Geng Tian, Daxin Cao, Dongpu College of Computer Science and Technology Jilin University Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China Institute of Human Factors and Ergonomics College of Mechatronics and Control Engineering Shenzhen University Guangdong Shenzhen518060 China School of Computer Science and Engineering VIT-AP Andhra Pradesh Amaravati522237 India College of Engineering Nanjing Agricultural University Nanjing210031 China State Key Laboratory of Automotive Safety and Energy Department of Automotive Engineering Tsinghua University Beijing100084 China Beijing Advanced Innovation Center for Big Data and Brain Computing Beijing Key Laboratory for Cooperative Vehicle Infrastructure Systems and Safety Control School of Transportation Science and Engineering Beihang University Beijing100191 China Waterloo Cognitive Autonomous Driving Lab University of Waterloo N2L 3G1 Canada

In the Internet of things (IoT) era, vehicles and other intelligent components in an intelligent transportation system (ITS) are connected, forming vehicular networks (VNs) that provide efficient and safe traffic and ubiquitous access to various applications. However, as the number of nodes in an ITS increases, it is challenging to satisfy a varied and large number of service requests with different quality of service (QoS) and security requirements in highly dynamic VNs. Intelligent nodes in VNs can compete or cooperate for limited network resources to achieve the objective for either an individual or a group. Game theory (GT), a theoretical framework designed for strategic interactions among rational decision makers sharing scarce resources, can be used to model and analyze individual or group behaviors of communicating entities in VNs. This paper primarily surveys the recent developments of GT in solving various challenges of VNs. This survey starts with an introduction to the background of VNs. A review of GT models studied in the VNs is then introduced, including the basic concepts, classifications, and applicable vehicular issues. After discussing the requirements of VNs and the motivation of using GT, a comprehensive literature review on GT applications in dealing with the challenges of current VNs is provided. Furthermore, recent contributions of GT to VNs that are integrated with diverse emerging 5G technologies are surveyed. Finally, the lessons learned are given, and several key research challenges and possible solutions of applying GT in VNs are outlined. Copyright © 2021, The Authors. All rights reserved.

关键词： Quality of service

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Automated detection of corrosion in used nuclear fuel dry storage canisters using residual neural networks

arXiv

引用

arXiv 2020年

作者： Papamarkou, Theodore Guy, Hayley Kroencke, Bryce Miller, Jordan Robinette, Preston Schultz, Daniel Hinkle, Jacob Pullum, Laura Schuman, Catherine Renshaw, Jeremy Chatzidakis, Stylianos Computational Sciences and Engineering Division Oak Ridge National Laboratory Oak RidgeTN United States Department of Mathematics North Carolina State University RaleighNC United States Department of Computer Science University of California DavisCA United States Center for Cognitive Ubiquitous Computing Arizona State University TempeAZ United States Presbyterian College ClintonSC United States Innovative Computing Laboratory University of Tennessee KnoxvilleTN United States Computer Science and Mathematics Division Oak Ridge National Laboratory Oak RidgeTN United States Electric Power Research Institute Palo AltoCA United States Reactor and Nuclear Systems Division Oak Ridge National Laboratory Oak RidgeTN United States

Nondestructive evaluation methods play an important role in ensuring component integrity and safety in many industries. Operator fatigue can play a critical role in the reliability of such methods. This is important for inspecting high value assets or assets with a high consequence of failure, such as aerospace and nuclear components. Recent advances in convolution neural networks can support and automate these inspection efforts. This paper proposes using residual neural networks (ResNets) for real-time detection of corrosion, including iron oxide discoloration, pitting and stress corrosion cracking, in dry storage stainless steel canisters housing used nuclear fuel. The proposed approach crops nuclear canister images into smaller tiles, trains a ResNet on these tiles, and classifies images as corroded or intact using the per-image count of tiles predicted as corroded by the ResNet. The results demonstrate that such a deep learning approach allows to detect the locus of corrosion via smaller tiles, and at the same time to infer with high accuracy whether an image comes from a corroded canister. Thereby, the proposed approach holds promise to automate and speed up nuclear fuel canister inspections, to minimize inspection costs, and to partially replace human-conducted onsite inspections, thus reducing radiation doses to personnel. Copyright © 2020, The Authors. All rights reserved.

关键词： Deep learning

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Communication lower bound in convolution accelerators

arXiv

引用

arXiv 2019年

作者： Chen, Xiaoming Han, Yinhe Wang, Yu Center for Intelligent Computing Systems State Key Laboratory of Computer Architecture Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China Department of Electronic Engineering Tsinghua University Beijing China

In current convolutional neural network (CNN) accelerators, communication (i.e., memory access) dominates the energy consumption. This work provides comprehensive analysis and methodologies to minimize the communication for CNN accelerators. For the off-chip communication, we derive the theoretical lower bound for any convolutional layer and propose a dataflow to reach the lower bound. This fundamental problem has never been solved by prior studies. The on-chip communication is minimized based on an elaborate workload and storage mapping *** in addition design a communication-optimal CNN accelerator architecture. Evaluations based on the 65nm technology demonstrate that the proposed architecture nearly reaches the theoretical minimum communication in a threelevel memory hierarchy and it is computation dominant. The gap between the energy efficiency of our accelerator and the theoretical best value is only 37-87%. Copyright © 2019, The Authors. All rights reserved.

关键词： Acceleration

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A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge

arXiv

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arXiv 2024年

作者： de la Rosa, Ezequiel Reyes, Mauricio Liew, Sook-Lei Hutton, Alexandre Wiest, Roland Kaesmacher, Johannes Hanning, Uta Hakim, Arsany Zubal, Richard Valenzuela, Waldo Robben, David Sima, Diana M. Anania, Vincenzo Brys, Arne Meakin, James A. Mickan, Anne Broocks, Gabriel Heitkamp, Christian Gao, Shengbo Liang, Kongming Zhang, Ziji Siddiquee, Md Mahfuzur Rahman Myronenko, Andriy Ashtari, Pooya Van Huffel, Sabine Jeong, Hyun-Su Yoon, Chi-Ho Kim, Chulhong Huo, Jiayu Ourselin, Sebastien Sparks, Rachel Clèrigues, Albert Oliver, Arnau Lladó, Xavier Chalcroft, Liam Pappas, Ioannis Bertels, Jeroen Heylen, Ewout Moreau, Juliette Hatami, Nima Frindel, Carole Qayyum, Abdul Mazher, Moona Puig, Domenec Lin, Shao-Chieh Juan, Chun-Jung Hu, Tianxi Boone, Lyndon Goubran, Maged Liu, Yi-Jui Wegener, Susanne Kofler, Florian Ezhov, Ivan Shit, Suprosanna Hernandez Petzsche, Moritz R. Menze, Bjoern Kirschke, Jan S. Wiestler, Benedikt Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Department of Informatics Technical University Munich Germany Icometrix Leuven Belgium ARTORG Center for Biomedical Research University of Bern Bern Switzerland Department of Radiation Oncology University Hospital Bern University of Bern Switzerland University of Bern Bern Switzerland Chan Division of Occupational Science and Occupational Therapy University of Southern California Los AngelesCA United States Stevens Neuroimaging and Informatics Institute Department of Neurology Keck School of Medicine University of Southern California United States University Institute of Diagnostic and Interventional Neuroradiology Inselspital Bern Switzerland University Institute of Diagnostic and Interventional Neuroradiology University Hospital Bern Inselspital University of Bern Bern Switzerland Department of Diagnostic and Interventional neuroradiology University Medical Center Hamburg-Eppendorf Hamburg Germany Department of Medical Imaging Radboud University Medical Center Institute for Health Sciences Nijmegen Netherlands Deepwise AI Lab Beijing China Beijing University of Posts and Telecommunications Bejing China School of Computing and Augmented Intelligence Arizona State University TempeAZ United States NVIDIA Santa ClaraCA United States STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Pohang Korea Republic of School of Biomedical Engineering & Imaging Sciences King’s College London United Kingdom Institute of Computer Vision and Robotics University of Girona Spain Wellcome Centre for Human Neuroimaging University College London London United Kingdom Laboratory of Neuro Imaging Stevens Institute for Neuroimaging and Informatics Keck School of Medicine University of Southern California Los Angeles United States KU Leuven Leuven Belgium CREATIS Université Lyon1 CNRS UMR5220 INSERM U1206 INSA-Lyon Villeurbanne696

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES’22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. By assessing them against a hidden test set, we identified strengths, weaknesses, and potential biases. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model combines the individual algorithms’ strengths and achieved superior ischemic lesion detection and segmentation accuracy (median Dice score: 0.82, median lesion-wise F1 score: 0.86) on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers like lesion types and affected vascular territories. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm’s segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model’s generalizability (median Dice score: 0.82, median lesion-wise F1 score: 0.86). The algorithm’s outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)rad

关键词： Diagnosis

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A meta-inspired termite queen algorithm for global optimization and engineering design problems

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Engineering Applications of Artificial Intelligence 2022年 111卷

作者： Peng Chen Shihua Zhou Qiang Zhang Nikola Kasabov Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian 116622 China School of Computer Science and Technology Dalian University of Technology Dalian 116024 China Knowledge Engineering and Discovery Research Institute Auckland University of Technology Auckland 1010 New Zealand Intelligent Systems Research Center Ulster University Londonderry BT52 1SA UK

This paper proposes a novel bio-inspired termite queen algorithm (TQA) to solve optimization problems by simulating the division of labor in termite populations under a queen’s rule. TQA is benchmarked on a set of 23 functions to test its performance at solving global optimization problems, and applied to six real-world engineering design problems to verify its reliability and effectiveness. Comparative simulation studies with other algorithms are conducted, from whose results it is observed that TQA satisfactorily solves global optimization problems and engineering design problems.

关键词： Termite queen algorithm Benchmarked functions Loss minimization Metaheuristic technique Engineering design problems

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Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations

arXiv

引用

arXiv 2022年

作者： Chen, Qingyu Allot, Alexis Leaman, Robert Islamaj, Rezarta Du, Jingcheng Fang, Li Wang, Kai Xu, Shuo Zhang, Yuefu Bagherzadeh, Parsa Bergler, Sabine Bhatnagar, Aakash Bhavsar, Nidhir Chang, Yung-Chun Lin, Sheng-Jie Tang, Wentai Zhang, Hongtong Tavchioski, Ilija Pollak, Senja Tian, Shubo Zhang, Jinfeng Otmakhova, Yulia Yepes, Antonio Jimeno Dong, Hang Wu, Honghan Dufour, Richard Labrak, Yanis Chatterjee, Niladri Tandon, Kushagri Laleye, Fréjus A.A. Rakotoson, Loïc Chersoni, Emmanuele Gu, Jinghang Friedrich, Annemarie Pujari, Subhash Chandra Chizhikova, Mariia Sivadasan, Naveen Saipradeep, V.G. Lu, Zhiyong National Center for Biotechnology Information National Library of Medicine National Institutes of Health MD United States School of Biomedical Informatics UT Health Texas United States Raymond G. Perelman Center for Cellular and Molecular Therapeutics Children's Hospital of Philadelphia Philadelphia United States Department of Pathology Laboratory Medicine University of Pennsylvania Perelman School of Medicine Philadelphia United States College of Economics and Management Beijing University of Technology Beijing China CLaC Labs Concordia University Montreal Canada Navrachana University Vadodara India Graduate Institute of Data Science Taipei Medical University Taipei Taiwan College of Computer Science and Technology Dalian University of Technology Dalian China Computer and Information Science University of Ljubljana Ljubljana Slovenia Jožef Stefan Institute Ljubljana Slovenia Department of Statistics Florida State University Tallahassee United States School of Computing and Information Systems University of Melbourne Melbourne Australia School of Computing Technologies RMIT University Melbourne Australia Centre for Medical Informatics Usher Institute University of Edinburgh Edinburgh United Kingdom Institute of Health Informatics University College London London United Kingdom LS2N Nantes University Nantes France LIA Avignon University Avignon France Department of Mathematics Indian Institute of Technology Delhi New Delhi India Opscidia Paris France Department of Chinese and Bilingual Studies The Hong Kong Polytechnic University Hong Kong Heidelberg University Heidelberg Germany Bosch Center for Artificial Intelligence Renningen Germany Universidad de Jaén Jaén Spain TCS Research Life Sciences Hyderabad India

The COVID-19 pandemic has been severely impacting global society since December 2019. The related findings such as vaccine and drug development have been reported in biomedical literature - at a rate of about 10,000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200,000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g., Diagnosis and Treatment) to the articles in LitCovid. The annotated topics have been widely used for navigating the COVID literature, rapidly locating articles of interest, and other downstream studies. However, annotating the topics has been the bottleneck of manual curation. Despite the continuing advances in biomedical text mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset - consisting of over 30,000 articles with manually reviewed topics - was created for training and testing. It is one of the largest multi-label classification datasets in biomedical scientific literature. Nineteen teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181, and 0.9394 for macro F1-score, micro F1-score, and instance-based F1-score, respectively. Notably, these scores are substantially higher (e.g., 12%, higher for macro F1-score) than the corresponding scores of the state-of-art multi-label classification method. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is pub

关键词： COVID-19

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FAIR for AI: An interdisciplinary and international community building perspective

arXiv

引用

arXiv 2022年

作者： Huerta, E.A. Blaiszik, Ben Brinson, L. Catherine Bouchard, Kristofer E. Diaz, Daniel Doglioni, Caterina Duarte, Javier M. Emani, Murali Foster, Ian Fox, Geoffrey Harris, Philip Heinrich, Lukas Jha, Shantenu Katz, Daniel S. Kindratenko, Volodymyr Kirkpatrick, Christine R. Lassila-Perini, Kati Madduri, Ravi K. Neubauer, Mark S. Psomopoulos, Fotis E. Roy, Avik Rübel, Oliver Zhao, Zhizhen Zhu, Ruike Data Science and Learning Division Argonne National Laboratory LemontIL60439 United States Department of Computer Science University of Chicago ChicagoIL60637 United States Globus University of Chicago ChicagoIL60637 United States Department of Mechanical Engineering and Materials Science Duke University DurhamNC27708 United States Scientific Data Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Biological Systems & Engineering Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Helen Wills Neuroscience Institute University of California Berkeley BerkeleyCA94720 United States Department of Physics University of California La Jolla San DiegoCA92093 United States Lund University Department of Physics Box 118 Lund221 00 Sweden School of Physics & Astronomy The University of Manchester ManchesterM13 9PL United Kingdom Leadership Computing Facility Argonne National Laboratory LemontIL60439 United States Biocomplexity Institute Department of Computer Science University of Virginia CharlottesvilleVA22904 United States Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Technical University Munich Arcisstraße 21 München80333 Germany Computational Science Initiative Brookhaven National Laboratory UptonNY11973 United States Electrical and Computer Engineering Rutgers The State University of New Jersey PiscatawayNJ08854 United States National Center for Supercomputing Applications University of Illinois Urbana-Champaign UrbanaIL61801 United States Department of Computer Science University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Electrical & Computer Engineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States School of Information Sciences University of Illinois at Urbana-Champaign UrbanaIL61801 United States San Diego Supercomputer Center University of California La Jolla San DiegoCA

A foundational set of findable, accessible, interoperable, and reusable (FAIR) principles were proposed in 2016 as prerequisites for proper data management and stewardship, with the goal of enabling the reusability of scholarly data. The principles were also meant to apply to other digital assets, at a high level, and over time, the FAIR guiding principles have been reinterpreted or extended to include the software, tools, algorithms, and workflows that produce data. FAIR principles are now being adapted in the context of AI models and datasets. Here, we present the perspectives, vision, and experiences of researchers from different countries, disciplines, and backgrounds who are leading the definition and adoption of FAIR principles in their communities of practice, and discuss outcomes that may result from pursuing and incentivizing FAIR AI research. The material for this report builds on the FAIR for AI Workshop held at Argonne National laboratory on June 7, 2022. Copyright © 2022, The Authors. All rights reserved.

关键词： Information management

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