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TechRxiv 2021年

作者： Ma, Jie Chai, Qi Huang, Jingyue Liu, Jun You, Yang Zheng, Qinghua National Engineering Lab for Big Data Analytics School of Computer Science and Technology Xi’an Jiaotong University Shaanxi Xi’an710049 China Shaanxi Province Key Laboratory of Satellite and Terrestrial Network Tech. R&D School of Computer Science and Technology Xi’an Jiaotong University Shaanxi Xi’an710049 China The High Performance Computing for Artificial intelligence Lab Department of Computer Science National University of Singapore 117417 Singapore

Textbook Question Answering (TQA) is the task of answering diagram and non-diagram questions given large multimodal contexts consisting of abundant text and diagrams. Deep text understandings and effective learning of diagram semantics are important for this task due to its specificity. In this paper, we propose a Weakly Supervised learning method for TQA (WSTQ), which regards the incompletely accurate results of essential intermediate procedures for this task as supervision to develop Text Matching (TM) and Relation Detection (RD) tasks and then employs the tasks to motivate itself to learn strong text comprehension and excellent diagram semantics respectively. Specifically, we apply the result of text retrieval to build positive as well as negative text pairs. In order to learn deep text understandings, we first pre-train the text understanding module of WSTQ on TM and then fine-tune it on TQA. We build positive as well as negative relation pairs by checking whether there is any overlap between the items/regions detected from diagrams using object detection. The RD task forces our method to learn the relationships between regions, which are crucial to express the diagram semantics. We train WSTQ on RD and TQA simultaneously, i.e., multitask learning, to obtain effective diagram semantics and then improve the TQA performance. Extensive experiments are carried out on CK12-QA and AI2D to verify the effectiveness of WSTQ. Experimental results show that our method achieves significant accuracy improvements of 5.02% and 4.12% on test splits of the above datasets respectively than the current state-of-the-art baseline. We have released our code on https://***/dr-majie/WSTQ. © 2021, CC BY.

关键词： Semantics

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Meta Mask Correction for Nuclei Segmentation in Histopathological Image

Meta Mask Correction for Nuclei Segmentation in Histopatholo...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Jiangbo Shi Chang Jia Zeyu Gao Tieliang Gong Chunbao Wang Chen Li National Engineering Lab for Big Data Analytics Xi’an Jiao tong University Xi’an Shaanxi China School of Computer Science and Technology Xi’an Jiao tong University Xi’an Shaanxi China Shaanxi Province Key Laboratory of Satellite and Terrestrial Network Tech.R&D Xi’an Jiao tong University Xi’an Shaanxi China the First Affiliated Hospital of Xi’an Jiaotong University Xi’an Shaanxi China

ISBN: (纸本)9781665429825

Nuclei segmentation is a fundamental task in digital pathology analysis and can be automated by deep learning-based methods. However, the development of such an automated method requires a large amount of data with precisely annotated masks which is hard to obtain. Training with weakly labeled data is a popular solution for reducing the workload of annotation. In this paper, we propose a novel meta-learning-based nuclei segmentation method which follows the label correction paradigm to leverage data with noisy masks. Specifically, we design a fully conventional meta-model that can correct noisy masks using a small amount of clean meta-data. Then the corrected masks can be used to supervise the training of the segmentation model. Meanwhile, a bi-level optimization method is adopted to alternately update the parameters of the main segmentation model and the meta-model in an end-to-end way. Extensive experimental results on two nuclear segmentation datasets show that our method achieves the state-of-the-art result. It even achieves comparable performance with the model training on supervised data in some noisy settings.

关键词： Training Learning systems Image segmentation Pathology Annotations Biological system modeling Optimization methods

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Structured Information Extraction of Pathology Reports with Attention-based Graph Convolutional Network

Structured Information Extraction of Pathology Reports with ...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Jialun Wu Kaiwen Tang Haichuan Zhang Chunbao Wang Chen Li School of Computer Science and Technology Xi’an Jiaotong University Xi’an Shaanxi China National Engineering Lab for Big Data Analytics Xi’an Jiaotong University Xi’an Shaanxi China Shaanxi Province Key Laboratory of Satellite and Terrestrial Network Tech.R&D Xi’an Jiaotong University Xi’an Shaanxi China School of Computer Science and Technology Qian Xuesen College Xi’an Jiaotong University Xi’an Shaanxi China the First Affiliated Hospital of Xi’an Jiaotong University Xi’an Shaanxi China

ISBN: (数字)9781728162157

ISBN: (纸本)9781728162164

Electronic medical data contains biochemical, imaging, pathological information during diagnosis and treatment. The pathology report is a kind of highly liberalized unstructured textual data, which is the basis and gold standard of cancer diagnosis and is very important for the prognosis and treatment of patients. The application of information extraction technology to pathological reports can obtain structured data that can be understood and analyzed by computers, helping pathologists make appropriate decisions. In this work, we proposed an attention-based graph convolutional network (GCN) for converting unstructured pathological reports into a structured form suitable for computer analysis to improve the current pathologist's workflow, collected medical data from different platforms, and provided more accurate assistance for diagnosis and treatment. We used pathology reports data from TCGA (The Cancer Genome Atlas) database with fine-grained annotations on 3632 pathology reports including four types of cancers. Our method performs better in our pathology report dataset with higher F1 score than traditional methods and deep learning methods. The results indicate that our method is robust, thus may work with other types of cancer pathology report.

关键词： Pathology Cancer Task analysis Annotations Information retrieval Medical diagnostic imaging data mining

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Meta mask correction for nuclei segmentation in histopathological image

arXiv

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arXiv 2021年

作者： Shi, Jiangbo Jia, Chang Gao, Zeyu Gong, Tieliang Wang, Chunbao Li, Chen National Engineering Lab for Big Data Analytics Xi'an Jiao Tong University Shaanxi Xi'an710049 China School of Computer Science and Technology Xi'an Jiao tong University Shaanxi Xi'an710049 China Shaanxi Province Key Laboratory of Satellite and Terrestrial Network Tech.R&D Xi'an Jiao tong University Shaanxi Xi'an710049 China Department of Pathology The First Affiliated Hospital of Xi'an Jiaotong University Shaanxi Xi'an710061 China

关键词： Deep learning

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An integrated GIS-based multivariate adaptive regression splines-cat swarm optimization for improving the accuracy of wildfire susceptibility mapping

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Geocarto International 2023年第1期38卷

作者： Hai, Tao Theruvil Sayed, Biju Majdi, Ali Zhou, Jincheng Sagban, Rafid Band, Shahab S. Mosavi, Amir School of Computer and Information Qiannan Normal University for Nationalities Guizhou Duyun China Key Laboratory of Complex Systems and Intelligent Optimization of Guizhou Guizhou Duyun China Institute for Big Data Analytics and Artificial Intelligence (IBDAAI) Universiti Teknologi MARA Selangor Shah Alam Malaysia Department of Computer Science Dhofar University Salalah Oman Department of Building and Construction Technologies Engineering Al-Mustaqbal University College Hilla Iraq Department of Computer Technology Engineering Technical Engineering College Al-Ayen University Thi-Qar Iraq Future Technology Research Center National Yunlin University of Science and Technology Yunlin Douliou Taiwan John von Neumann Faculty of Informatics Obuda University Budapest Hungary German Research Center for Artificial Intelligence Oldenburg Germany Institute of the Information Society University of Public Service Budapest Hungary

A hybrid machine learning method is proposed for wildfire susceptibility mapping. For modeling a geographical information system (GIS) database including 11 influencing factors and 262 fire locations from 2013 to 2018 is used for developing an integrated multivariate adaptive regression splines (MARS). The cat swarm optimization (CSO) algorithm tunes the parameters of the MARS in order to generate accurate susceptibility maps. From the Pearson correlation results, it is observed that land use, temperature, and slope angle have strong correlation with the fire severity. The results demonstrate that the prediction capability of the MARS-CSO model outperforms model tree, reduced error pruning tree and MARS. The resulting wildfire risk map using MARS-CSO reveals that 20% of the study areas is categorized in the very low wildfire risk class, whereas 40% is under the very high class of fire hazard. © 2023 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

关键词： artificial intelligence cat swarm optimization geospatial machine learning natural hazard Wildfire susceptibility

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Redefining pandemic preparedness:Multidisciplinary insights from the CERP modelling workshop in infectious diseases,workshop report

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Infectious Disease Modelling 2024年第2期9卷 501-518页

作者： Marta C.Nunes Edward Thommes Holger Fröhlich Antoine Flahault Julien Arino Marc Baguelin Matthew biggerstaff Gaston Bizel-Bizellot Rebecca Borchering Giacomo Cacciapaglia Simon Cauchemez Alex Barbier-Chebbah Carsten Claussen Christine Choirat Monica Cojocaru Catherine Commaille-Chapus Chitin Hon Jude Kong Nicolas Lambert Katharina B.Lauer Thorsten Lehr Cédric Mahe Vincent Marechal Adel Mebarki Seyed Moghadas Rene Niehus Lulla Opatowski Francesco Parino Gery Pruvost Andreas Schuppert Rodolphe Thiébaut Andrea Thomas-Bachli Cecile Viboud Jianhong Wu Pascal Crépey Laurent Coudeville Center of Excellence in Respiratory Pathogens(CERP) Hospices Civils de Lyon(HCL)and Centre International de Recherche en Infectiologie(CIRI)Équipe SantéPubliqueÉpidémiologie etÉcologieÉvolutive des Maladies Infectieuses(PHE3ID)Inserm U1111CNRS UMR5308ENS de LyonUniversitéClaude Bernard Lyon 1LyonFrance South African Medical Research Council Vaccines&Infectious Diseases Analytics Research UnitFaculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa New Products and Innovation(NPI) Sanofi Vaccines(Global)TorontoOntarioCanada Department of Mathematics and Statistics University of GuelphGuelphOntarioCanada Fraunhofer Institute for Algorithms and Scientific Computing(SCAI) Department of BioinformaticsSchloss BirlinghovenSankt AugustinGermany University of Bonn Bonn-Aachen International Center for IT(b-it)BonnGermany Institute of Global Health Faculty of MedicineUniversity of GenevaGenevaSwitzerland and Swiss School of Public HealthZürichSwitzerland Department of Mathematics University of ManitobaWinnipegManitobaCanada MRC Centre for Global Infectious Disease Analysis School of Public HealthImperial College LondonLondonUK Centre for Mathematical Modelling of Infectious Diseases Department of Infectious Disease EpidemiologyLondon School of Hygiene&Tropical MedicineLondonUK National Center for Immunization and Respiratory Diseases(NCIRD) US Centers for Disease Control and Prevention(CDC)AtlantaGAUSA Departement of Computational Biology Departement of Global HealthInstitut PasteurParisFrance Institut de Physique des Deux Infinis de Lyon(IP2I) UMR5822IN2P3/CNRSUniversitéClaude Bernard Lyon 1VilleurbanneFrance Mathematical Modelling of Infectious Diseases Unit Institut PasteurUniversitéParis CitéUMR2000 CNRSParisFrance Decision and Bayesian Computation Institut PasteurUniversitéParis CitéCNRS UMR 3571France Fraunhofer-Institute for Translational Medicine and Pharmacology HamburgGermany Institute of Global Health Faculty of MedicineUniversity of

In July 2023,the Center of Excellence in Respiratory Pathogens organized a two-day workshop on infectious diseases modelling and the lessons learnt from the Covid-19 *** report summarizes the rich discussions that occurred during the *** workshop participants discussed multisource data integration and highlighted the benefits of combining traditional surveillance with more novel data sources like mobility data,social media,and wastewater *** advancements were noted in the development of predictive models,with examples from various countries showcasing the use of machine learning and artificial intelligence in detecting and monitoring disease *** role of open collaboration between various stakeholders in modelling was stressed,advocating for the continuation of such partnerships beyond the pandemic.A major gap identified was the absence of a common international framework for data sharing,which is crucial for global pandemic ***,the workshop underscored the need for robust,adaptable modelling frameworks and the integration of different data sources and collaboration across sectors,as key elements in enhancing future pandemic response and preparedness.

关键词： Modelling Covid-19 Infectious diseases Pandemic preparedness Workshop

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Scientific data Lake for High Luminosity LHC project and other data-intensive particle and astro-particle physics experiments

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Journal of Physics: Conference Series 2020年第1期1690卷

作者： A Alekseev A Kiryanov A Klimentov T Korchuganova V Mitsyn D Oleynik A Smirnov S Smirnov A Zarochentsev Compiler Technology Department Ivannikov Institute for System Programming of the RAS Moscow 109004 Russia Cloud technologies and Big Data analytics laboratory Plekhanov Russian University of Economics Moscow 117997 Russia ATLAS group Universidad Andres Bello Santiago 7550196 Chile Department of computing resources and technologies NRC 'Kurchatov Institute' - PNPI 188300 Gatchina Russia Physics Department Brookhaven National Laboratory Upton NY 11973 USA Laboratory of Information Technologies Joint Institute for Nuclear Research Dubna 141980 Russia Institute of Nuclear Physics and Engineering National Research Nuclear University MEPhI Moscow 115409 Russia Laboratory of Ultra-High Energy Physics Saint Petersburg State University Saint Petersburg 198504 Russia

The next phase of LHC Operations – High Luminosity LHC (HL-LHC), which is aimed at ten-fold increase in the luminosity of proton-proton collisions at the energy of 14 TeV, is expected to start operation in 2027-2028 and will deliver an unprecedented scientific data volume of multi-exabyte scale. This amount of data has to be stored and the corresponding storage system should ensure fast and reliable data delivery for processing by scientific groups distributed all over the world. The present LHC computing and data processing model will not be able to provide the required infrastructure growth even taking into account the expected hardware technology evolution. To address this challenge the new state-of-the-art computing infrastructure technologies are now being developed and are presented here. The possibilities of application of the HL-LHC distributed data handling technique for other particle and astro-particle physics experiments dealing with large-scale data volumes like DUNE, LSST, Belle-II, JUNO, SKAO etc. are also discussed.

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Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition

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database : the journal of biological databases and curation 2023年第2023期2023卷 baac108页

作者： Davy Weissenbacher Karen O'Connor Siddharth Rawal Yu Zhang Richard Tzong-Han Tsai Timothy Miller Dongfang Xu Carol Anderson Bo Liu Qing Han Jinfeng Zhang Igor Kulev Berkay Köprü Raul Rodriguez-Esteban Elif Ozkirimli Ammer Ayach Roland Roller Stephen Piccolo Peijin Han V G Vinod Vydiswaran Ramya Tekumalla Juan M Banda Parsa Bagherzadeh Sabine Bergler João F Silva Tiago Almeida Paloma Martinez Renzo Rivera-Zavala Chen-Kai Wang Hong-Jie Dai Luis Alberto Robles Hernandez Graciela Gonzalez-Hernandez Department of Computational Biomedicine Cedars-Sinai Medical Center Los Angeles CA USA. DBEI The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Computer Science and Information Engineering National Central University No. 300 Zhongda Rd Zhongli District Taoyuan 320 Taiwan. IoX Center National Taiwan University Da'an District Section 4 Roosevelt Rd No. 1 Barry Lam Hall Taipei 106 Taiwan. Research Center for Humanities and Social Sciences Academia Sinica No. 128 Section 2 Academia Rd Nangang District Taipei 115 Taiwan. Computational Health Informatics Program Boston Children's Hospital Boston MA USA. Department of Pediatrics Harvard Medical School Boston MA USA. NVIDIA Santa Clara CA USA. Department of Statistics Florida State University Tallahassee FL USA. Data and Analytics Chapter F. Hoffmann-La Roche Ltd Switzerland. Pharmaceutical Research and Early Development Roche Innovation Center Basel Switzerland. Speech and Language Technology Lab DFKI Berlin Germany. Department of Biology Brigham Young University Provo UT USA. Department of Computational Medicine and Bioinformatics Medical School University of Michigan Ann Arbor MI USA. Department of Learning Health Sciences Medical School University of Michigan Ann Arbor MI USA. School of Information University of Michigan Ann Arbor MI USA. Department of Computer Science Georgia State University Atlanta GA USA. CLaC Labs Concordia University Montreal Canada. DETI Institute of Electronics and Informatics Engineering of Aveiro University of Aveiro Portugal. Department of Computation University of A Coruña Spain. Computer Science and Engineering Department Universidad Carlos III de Madrid Madrid Spain. Big Data Laboratory Chunghwa Telecom Laboratories Taoyuan Taiwan. Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Electrical Engineering College of Electrical Engineering and Computer Sci

This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user's publicly available tweets (the user's 'timeline'). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user's timeline that mention specific health-related concepts such as medications requires addressing extreme imbalance. Task 3 called for detecting tweets in a user's timeline that mentions a medication name and, for each detected mention, extracting its span. The organizers made available a corpus consisting of 182 049 tweets publicly posted by 212 Twitter users with all medication mentions manually annotated. The corpus exhibits the natural distribution of positive tweets, with only 442 tweets (0.2%) mentioning a medication. This task was an opportunity for participants to evaluate methods that are robust to class imbalance beyond the simple lexical match. A total of 65 teams registered, and 16 teams submitted a system run. This study summarizes the corpus created by the organizers and the approaches taken by the participating teams for this challenge. The corpus is freely available at https://***/tasks/biocreative-vii/track-3/. The methods and the results of the competing systems are analyzed with a focus on the approaches taken for learning from class-imbalanced data.

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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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The Past, Present, and Future of the Brain Imaging data Structure (BIDS)

arXiv

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arXiv 2023年

作者： Poldrack, Russell A. Markiewicz, Christopher J. Appelhoff, Stefan Ashar, Yoni K. Auer, Tibor Baillet, Sylvain Bansal, Shashank Beltrachini, Leandro Bénar, Christian G. Bertazzoli, Giacomo Bhogawar, Suyash Blair, Ross W. Bortoletto, Marta Boudreau, Mathieu Brooks, Teon L. Calhoun, Vince D. Castelli, Filippo Maria Clement, Patricia Cohen, Alexander L. Cohen-Adad, Julien D'Ambrosio, Sasha de Hollander, Gilles de la Iglesia-Vayá, María de la Vega, Alejandro Delorme, Arnaud Devinsky, Orrin Draschkow, Dejan Duff, Eugene Paul DuPre, Elizabeth Earl, Eric Esteban, Oscar Feingold, Franklin W. Flandin, Guillaume Galassi, Anthony Gallitto, Giuseppe Ganz, Melanie Gau, Rémi Gholam, James Ghosh, Satrajit S. Giacomel, Alessio Gillman, Ashley G. Gleeson, Padraig Gramfort, Alexandre Guay, Samuel Guidali, Giacomo Halchenko, Yaroslav O. Handwerker, Daniel A. Hardcastle, Nell Herholz, Peer Hermes, Dora Honey, Christopher J. Innis, Robert B. Ioanas, Horea-Ioan Jahn, Andrew Karakuzu, Agah Keator, David B. Kiar, Gregory Kincses, Balint Laird, Angela R. Lau, Jonathan C. Lazari, Alberto Legarreta, Jon Haitz Li, Adam Li, Xiangrui Love, Bradley C. Lu, Hanzhang Maumet, Camille Mazzamuto, Giacomo Meisler, Steven L. Mikkelsen, Mark Mutsaerts, Henk Nichols, Thomas E. Nikolaidis, Aki Nilsonne, Gustav Niso, Guiomar Norgaard, Martin Okell, Thomas W. Oostenveld, Robert Ort, Eduard Park, Patrick J. Pawlik, Mateusz Pernet, Cyril R. Pestilli, Franco Petr, Jan Phillips, Christophe Poline, Jean-Baptiste Pollonini, Luca Raamana, Pradeep Reddy Ritter, Petra Rizzo, Gaia Robbins, Kay A. Rockhill, Alexander P. Rogers, Christine Rokem, Ariel Rorden, Chris Routier, Alexandre Saborit-Torres, Jose Manuel Salo, Taylor Schirner, Michael Smith, Robert E. Spisak, Tamas Sprenger, Julia Swann, Nicole C. Szinte, Martin Takerkart, Sylvain Thirion, Bertrand Thomas, Adam G. Torabian, Sajjad Varoquaux, Gael Voytek, Bradley Welzel, Julius Wilson, Martin Yarkoni, Tal Gorgolewski, Krzysztof J. Department of Psychology Stanford University StanfordCA United States Max Planck Institute for Human Development Berlin Germany University of Colorado Anschutz Medical Campus AuroraCO United States School of Psychology University of Surrey Guildford United Kingdom McConnell Brain Imaging Centre Montréal Neurological Institute McGill University Montréal Canada Department of Bioengineering University of California San Diego La Jolla CA United States School of Physics Astronomy Cardiff University Wales United Kingdom Institut de Neurosciences des Systèmes Marseille France Neurophysiology Lab IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia Italy Center for Mind/Brain Sciences - CIMeC University of Trento TN Rovereto Italy Brigham and Women’s Hospital BostonMA United States Massachusetts General Hospital BostonMA United States Harvard Medical School BostonMA United States Rackspace Technology San AntonioTX United States NeuroPoly Lab Polytechnique Montréal MontréalQC Canada Georgia State Georgia Tech Emory AtlantaGA United States University of Florence Sesto Fiorentino Italy Bioretics srl Cesena Italy Department of Medical Imaging Ghent University Hospital Ghent Belgium Department of Diagnostic Sciences Ghent University Ghent Belgium Department of Neurology Boston Children's Hospital BostonMA United States Dipartimento di Scienze della Salute dell'Università degli Studi di Milano Milan Italy Department of Clinical and Experimental Epilepsy University College London United Kingdom Zurich Center for Neuroeconomics Department of Economics University of Zurich Zurich Switzerland UMIB-FISABIO Valencia Spain The University of Texas at Austin AustinTX United States SCCN University of California San Diego La Jolla CA United States Department of Neurology NYU Langone Medical Center New YorkNY United States Department of Experimental Psychology University of Oxford Oxford United Kingdom UK Dementia Research Ins

The Brain Imaging data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS. © 2023, CC BY.

关键词： data structures

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