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Author Correction: Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

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Nature methods 2025年第2期22卷 448页

作者： Marieke Vromman Jasper Anckaert Stefania Bortoluzzi Alessia Buratin Chia-Ying Chen Qinjie Chu Trees-Juen Chuang Roozbeh Dehghannasiri Christoph Dieterich Xin Dong Paul Flicek Enrico Gaffo Wanjun Gu Chunjiang He Steve Hoffmann Osagie Izuogu Michael S Jackson Tobias Jakobi Eric C Lai Justine Nuytens Julia Salzman Mauro Santibanez-Koref Peter Stadler Olivier Thas Eveline Vanden Eynde Kimberly Verniers Guoxia Wen Jakub Westholm Li Yang Chu-Yu Ye Nurten Yigit Guo-Hua Yuan Jinyang Zhang Fangqing Zhao Jo Vandesompele Pieter-Jan Volders OncoRNALab Cancer Research Institute Ghent (CRIG) Department of Biomolecular Medicine Ghent University Ghent Belgium. Department of Molecular Medicine University of Padova Padova Italy. Genomics Research Center Academia Sinica Taipei City Taiwan. Institute of Crop Science and Institute of Bioinformatics Zhejiang University Zhejiang China. Department of Biomedical Data Science and of Biochemistry Stanford University Stanford CA USA. Klaus Tschira Institute for Integrative Computational Cardiology Department of Internal Medicine III University Hospital Heidelberg German Center for Cardiovascular Research (DZHK) Heidelberg Germany. School of Basic Medical Science Department of Medical Genetics Wuhan University Wuhan China. EMBL-EBI Hinxton UK. Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine School of Artificial Intelligence and Information Technology Nanjing University of Chinese Medicine Nanjing China. Computational Biology Group Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Jena Germany. Biosciences Institute Faculty of Medical Sciences Newcastle University Newcastle UK. Translational Cardiovascular Research Center University of Arizona - College of Medicine Phoenix Phoenix AZ USA. Sloan Kettering Institute New York NY USA. Bioinformatics Group Department of Computer Science and Interdisciplinary Center for Bioinformatics Universität Leipzig Leipzig Germany. Data Science Institute I-Biostat Hasselt University Hasselt Belgium. State Key Laboratory of Bioelectronics School of Biological Sciences and Medical Engineering Southeast University Nanjing China. Department of Biochemistry and Biophysics National Bioinformatics Infrastructure Sweden Science for Life Laboratory Stockholm University Stockholm Sweden. Center for Molecular Medicine Children's Hospital Fudan University and Shanghai Key Laboratory of Medical Epigenetics International Laboratory of Medical Epigenetics and Metab

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Beyond Low Earth Orbit: Biological research, Artificial Intelligence, and Self-Driving Labs

arXiv

引用

arXiv 2021年

作者： Sanders, Lauren M. Yang, Jason H. Scott, Ryan T. Qutub, Amina Ann Martin, Hector Garcia Berrios, Daniel C. Hastings, Jaden J.A. Rask, Jon Mackintosh, Graham Hoarfrost, Adrienne L. Chalk, Stuart Kalantari, John Khezeli, Kia Antonsen, Erik L. Babdor, Joel Barker, Richard Baranzini, Sergio E. Beheshti, Afshin Delgado-Aparicio, Guillermo M. Glicksberg, Benjamin S. Greene, Casey S. Haendel, Melissa Hamid, Arif A. Heller, Philip Jamieson, Daniel Jarvis, Katelyn J. Komarova, Svetlana V. Komorowski, Matthieu Kothiyal, Prachi Mahabal, Ashish Manor, Uri Mason, Christopher E. Matar, Mona Mias, George I. Miller, Jack Myers, Jerry G. Nelson, Charlotte Oribello, Jonathan Park, Seung-Min Parsons-Wingerter, Patricia Prabhu, R.K. Reynolds, Robert J. Saravia-Butler, Amanda Saria, Suchi Sawyer, Aenor Singh, Nitin Kumar Soboczenski, Frank Snyder, Michael Soman, Karthik Theriot, Corey A. van Valen, David Venkateswaran, Kasthuri Warren, Liz Worthey, Liz Zitnik, Marinka Costes, Sylvain V. Blue Marble Space Institute of Science Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States Center for Emerging and Re-Emerging Pathogens Department of Microbiology Biochemistry and Molecular Genetics Rutgers New Jersey Medical School NewarkNJ07103 United States KBR Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States AI MATRIX Consortium Department of Biomedical Engineering University of Texas San Antonio and UT Health Sciences San AntonioTX78249 United States Biological Systems and Engineering Division Lawrence Berkeley National Lab. BerkeleyCA94608 United States DOE Agile BioFoundry EmeryvilleCA94608 United States Joint BioEnergy Institute EmeryvilleCA94608 United States Department of Physiology and Biophysics Weill Cornell Medicine New YorkNY10065 United States Office of the Center Director NASA Ames Research Center Moffett Field CA94035 United States Bay Area Environmental Research Institute NASA Ames Research Center Moffett Field CA94035 United States Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States Department of Chemistry University of North Florida JacksonvilleFL32224 United States Center for Individualized Medicine Department of Surgery Department of Quantitative Health Sciences Mayo Clinic RochesterMN55905 United States Department of Emergency Medicine Center for Space Medicine Baylor College of Medicine HoustonTX77030 United States Department of Microbiology and Immunology Department of Otolaryngology Head and Neck Surgery University of California San Francisco San FranciscoCA94143 United States The Gilroy AstroBiology Research Group The University of Wisconsin - Madison MadisonWI53706 United States Weill Institute for Neurosciences Department of Neurology University of California San Francisco San FranciscoCA94158 United States Data Science Analytics Georgia Institute of Technology Lima15024

Space biology research aims to understand fundamental effects of spaceflight on organisms, develop foundational knowledge to support deep space exploration, and ultimately bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals, and humans for sustained multi-planetary life. To advance these aims, the field leverages experiments, platforms, data, and model organisms from both spaceborne and ground-analog studies. As research is extended beyond low Earth orbit, experiments and platforms must be maximally autonomous, light, agile, and intelligent to expedite knowledge discovery. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration on artificial intelligence, machine learning, and modeling applications which offer key solutions toward these space biology challenges. In the next decade, the synthesis of artificial intelligence into the field of space biology will deepen the biological understanding of spaceflight effects, facilitate predictive modeling and analytics, support maximally autonomous and reproducible experiments, and efficiently manage spaceborne data and metadata, all with the goal to enable life to thrive in deep space. © 2021, CC BY.

关键词： Predictive analytics

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Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health

arXiv

引用

arXiv 2021年

作者： Scott, Ryan T. Antonsen, Erik L. Sanders, Lauren M. Hastings, Jaden J.A. Park, Seung-Min Mackintosh, Graham Reynolds, Robert J. Hoarfrost, Adrienne L. Sawyer, Aenor Greene, Casey S. Glicksberg, Benjamin S. Theriot, Corey A. Berrios, Daniel C. Miller, Jack Babdor, Joel Barker, Richard Baranzini, Sergio E. Beheshti, Afshin Chalk, Stuart Delgado-Aparicio, Guillermo M. Haendel, Melissa Hamid, Arif A. Heller, Philip Jamieson, Daniel Jarvis, Katelyn J. Kalantari, John Khezeli, Kia Komarova, Svetlana V. Komorowski, Matthieu Kothiyal, Prachi Mahabal, Ashish Manor, Uri Martin, Hector Garcia Mason, Christopher E. Matar, Mona Mias, George I. Myers, Jerry G. Nelson, Charlotte Oribello, Jonathan Parsons-Wingerter, Patricia Prabhu, R.K. Qutub, Amina Ann Rask, Jon Saravia-Butler, Amanda Saria, Suchi Singh, Nitin Kumar Soboczenski, Frank Snyder, Michael Soman, Karthik van Valen, David Venkateswaran, Kasthuri Warren, Liz Worthey, Liz Yang, Jason H. Zitnik, Marinka Costes, Sylvain V. KBR Space Biosciences Division NASA Ames Research Center Moffett FieldCA94035 United States Department of Emergency Medicine Center for Space Medicine Baylor College of Medicine HoustonTX77030 United States Blue Marble Space Institute of Science Space Biosciences Division NASA Ames Research Center Moffett FieldCA94035 United States Department of Physiology and Biophysics Weill Cornell Medicine New YorkNY10065 United States Department of Urology Department of Radiology Stanford University School of Medicine StanfordCA94305 United States Bay Area Environmental Research Institute NASA Ames Research Center Moffett FieldCA94035 United States Mortality Research & Consulting Inc. HoustonTX77058 United States Space Biosciences Division NASA Ames Research Center Moffett FieldCA94035 United States UC Space Health Department of Orthopaedic Surgery University of California San Francisco San FranciscoCA94143 United States Center for Health AI Department of Biochemistry and Molecular Genetics University of Colorado School of Medicine Anschutz Medical Campus AuroraCO80045 United States Hasso Plattner Institute for Digital Health at Mount Sinai Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New YorkNY10065 United States Department of Preventive Medicine and Community Health UTMB GalvestonTX77551 United States Human Health and Performance Directorate NASA Johnson Space Center HoustonTX77058 United States Department of Microbiology and Immunology Department of Otolaryngology Head and Neck Surgery University of California San Francisco San FranciscoCA94143 United States The Gilroy AstroBiology Research Group The University of Wisconsin Madison MadisonWI53706 United States Weill Institute for Neurosciences Department of Neurology University of California San Francisco San FranciscoCA94158 United States Department of Chemistry University of North Florida JacksonvilleFL32224 United States Data Scienc

Human space exploration beyond low Earth orbit will involve missions of significant distance and duration. To effectively mitigate myriad space health hazards, paradigm shifts in data and space health systems are necessary to enable Earth-independence, rather than Earth-reliance. Promising developments in the fields of artificial intelligence and machine learning for biology and health can address these needs. We propose an appropriately autonomous and intelligent Precision Space Health system that will monitor, aggregate, and assess biomedical statuses;analyze and predict personalized adverse health outcomes;adapt and respond to newly accumulated data;and provide preventive, actionable, and timely insights to individual deep space crew members and iterative decision support to their crew medical officer. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration, on future applications of artificial intelligence in space biology and health. In the next decade, biomonitoring technology, biomarker science, spacecraft hardware, intelligent software, and streamlined data management must mature and be woven together into a Precision Space Health system to enable humanity to thrive in deep space. © 2021, CC BY.

关键词： Earth (planet)

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MedShapeNet - A Large-Scale dataset of 3D Medical Shapes for computer Vision

arXiv

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arXiv 2023年

作者： Li, Jianning Zhou, Zongwei Yang, Jiancheng Pepe, Antonio Gsaxner, Christina Luijten, Gijs Qu, Chongyu Zhang, Tiezheng Chen, Xiaoxi Li, Wenxuan Wodzinski, Marek Friedrich, Paul Xie, Kangxian Jin, Yuan Ambigapathy, Narmada Nasca, Enrico Solak, Naida Melito, Gian Marco Vu, Viet Duc Memon, Afaque R. Schlachta, Christopher De Ribaupierre, Sandrine Patel, Rajnikant Eagleson, Roy Chen, Xiaojun Mächler, Heinrich Kirschke, Jan Stefan de la Rosa, Ezequiel Christ, Patrick Ferdinand Li, Hongwei Bran Ellis, David G. Aizenberg, Michele R. Gatidis, Sergios Küstner, Thomas Shusharina, Nadya Heller, Nicholas Andrearczyk, Vincent Depeursinge, Adrien Hatt, Mathieu Sekuboyina, Anjany Löffler, Maximilian Liebl, Hans Dorent, Reuben Vercauteren, Tom Shapey, Jonathan Kujawa, Aaron Cornelissen, Stefan Langenhuizen, Patrick Ben-Hamadou, Achraf Rekik, Ahmed Pujades, Sergi Boyer, Edmond Bolelli, Federico Grana, Costantino Lumetti, Luca Salehi, Hamidreza Ma, Jun Zhang, Yao Gharleghi, Ramtin Beier, Susann Sowmya, Arcot Garza-Villarreal, Eduardo A. Balducci, Thania Angeles-Valdez, Diego Souza, Roberto Rittner, Leticia Frayne, Richard Ji, Yuanfeng Ferrari, Vincenzo Chatterjee, Soumick Dubost, Florian Schreiber, Stefanie Mattern, Hendrik Speck, Oliver Haehn, Daniel John, Christoph Nürnberger, Andreas Pedrosa, João Ferreira, Carlos Aresta, Guilherme Cunha, António Campilho, Aurélio Suter, Yannick Garcia, Jose Lalande, Alain Vandenbossche, Vicky Van Oevelen, Aline Duquesne, Kate Mekhzoum, Hamza Vandemeulebroucke, Jef Audenaert, Emmanuel Krebs, Claudia van Leeuwen, Timo Vereecke, Evie Heidemeyer, Hauke Röhrig, Rainer Hölzle, Frank Badeli, Vahid Krieger, Kathrin Gunzer, Matthias Chen, Jianxu van Meegdenburg, Timo Dada, Amin Balzer, Miriam Fragemann, Jana Jonske, Frederic Rempe, Moritz Malorodov, Stanislav Bahnsen, Fin H. Seibold, Constantin Jaus, Alexander Marinov, Zdravko Jaeger, Paul F. Stiefelhagen, Rainer Santos, Ana Sofia Lindo, Mariana Ferreira, André Alves, Victor Kamp, Michael Abourayya, Amr Nensa, Felix Hörst, Fabian Brehmer, Alexander Hein Girardetstraße 2 Essen45131 Germany Graz University of Technology Inffeldgasse 16c Graz8010 Austria Graz Austria The Department of Computer Science Johns Hopkins University Malone Hall 3400 N Charles St BaltimoreMD21218 United States Rte Cantonale Lausanne1015 Switzerland The Department of Measurement and Electronics AGH University of Science and Technology Krakow Poland Sierre Switzerland Department of Biomedical Engineering University of Basel Hegenheimermattweg Allschwil167C CH-4123 Switzerland The Boston College 140 Commonwealth Ave Chestnut HillMA02467 United States University Hospital B7-200 339 Windermere Road LondonN6A 5A5 Canada The Department of Radiology Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai200240 China The Research Center for Connected Healthcare Big Data ZhejiangLab Zhejiang Hangzhou311121 China The Faculty of Statistics Technical University Dortmund August-Schmidt-Straße 1 Dortmund44227 Germany The Institute of Mechanics Graz University of Technology Kopernikusgasse 24/IV Graz8010 Austria The Institute of Biomedical Manufacturing and Life Quality Engineering State Key Laboratory of Mechanical System and Vibration School of Mechanical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai200240 China The Department of Cardiac Surgery Medical University Graz Auenbruggerplatz 29 Graz8036 Austria The Department of Diagnostic and Interventional Radiology University Hospital Giessen Justus-Liebig-University Giessen Klinikstraße 33 Giessen35392 Germany The Department of Mechanical Engineering Mehran University of Engineering and Technology Jamshoro Sindh76062 Pakistan The Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China The Geschäftsführender Oberarzt Abteilung für Interventionelle und Diagnostische Neuroradiologie Universitätsklinikum der Technischen Universität München Ismaningerstr. 22 München81675 Germany icometrix Kolonel Be

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 datasets with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://***/ and https://***/Jianningli/*** Codes 68T01 © 2023, CC BY.

关键词： Large dataset

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Dual encoding for zero-example video retrieval

arXiv

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arXiv 2018年

作者： Dong, Jianfeng Li, Xirong Xu, Chaoxi Ji, Shouling He, Yuan Yang, Gang Wang, Xun College of Computer and Information Engineering Zhejiang Gongshang University Key Lab of Data Engineering and Knowledge Engineering Renmin University of China AI & Media Computing Lab School of Information Renmin University of China College of Computer Science Zhejiang University Alibaba-Zhejiang University Joint Research Institute of Frontier Technologies Alibaba Group

This paper attacks the challenging problem of zero-example video retrieval. In such a retrieval paradigm, an end user searches for unlabeled videos by ad-hoc queries described in natural language text with no visual example provided. Given videos as sequences of frames and queries as sequences of words, an effective sequence-to-sequence cross-modal matching is required. The majority of existing methods are concept based, extracting relevant concepts from queries and videos and accordingly establishing associations between the two modalities. In contrast, this paper takes a concept-free approach, proposing a dual deep encoding network that encodes videos and queries into powerful dense representations of their own. Dual encoding is conceptually simple, practically effective and end-to-end. As experiments on three benchmarks, i.e. MSR-VTT, TRECVID 2016 and 2017 Ad-hoc Video Search show, the proposed solution establishes a new state-of-the-art for zero-example video retrieval. Copyright © 2018, The Authors. All rights reserved.

关键词： Signal encoding

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Prediction of solar energetic events impacting space weather conditions

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Advances in Space research 2024年

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

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

关键词： Solar energy

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From FAIR to CURE: Guidelines for Computational Models of Biological Systems

arXiv

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arXiv 2025年

作者： Sauro, Herbert M. Agmon, Eran Blinov, Michael L. Gennari, John H. Hellerstein, Joe Heydarabadipour, Adel Hunter, Peter Jardine, Bartholomew E. May, Elebeoba Nickerson, David P. Smith, Lucian P. Bader, Gary D. Bergmann, Frank Boyle, Patrick M. Dräger, Andreas Faeder, James R. Feng, Song Freire, Juliana Fröhlich, Fabian Glazier, James A. Gorochowski, Thomas E. Helikar, Tomas Hoops, Stefan Imoukhuede, Princess Keating, Sarah M. Konig, Matthias Laubenbacher, Reinhard Loew, Leslie M. Lopez, Carlos F. Lytton, William W. McCulloch, Andrew Mendes, Pedro Myers, Chris J. Myers, Jerry G. Mulugeta, Lealem Niarakis, Anna van Niekerk, David D. Olivier, Brett G. Patrie, Alexander A. Quardokus, Ellen M. Radde, Nicole Rohwer, Johann M. Sahle, Sven Schaff, James C. Sego, T.J. Shin, Janis Snoep, Jacky L. Vadigepalli, Rajanikanth Wiley, H. Steve Waltemath, Dagmar Moraru, Ion Department of Bioengineering University of Washington SeattleWA98195-5061 United States Intelligent Systems Engineering and Biocomplexity Institute Indiana University Street BloomingtonIN47408 United States Center for Cardiovascular Biology University of Washington SeattleWA98195-5061 United States eScience Institute University of Washington SeattleWA98195-5061 United States Institute for Stem Cell and Regenerative Medicine University of Washington SeattleWA98195-5061 United States School of Biological Sciences University of Bristol 24 Tyndall Avenue BristolBS8 1TQ United Kingdom Departments of Physiology & Pharmacology Neurology Downstate Health Science University BrooklynNY11203 United States Department of Neurology Kings County Hospital BrooklynNY11203 United States NASA-John H. Glenn Research Center MS 110-3 21000 Brookpark Road ClevelandOH44135 United States Center for Cell Analysis and Modeling UConn Health 263 Farmington Avenue FarmingtonCT06030-6406 United States Amsterdam Institute for Life and Environment Vrije Universiteit Amsterdam De Boelelaan 1108 Amsterdam1081 HZ Netherlands Department of Pathology and Genomic Medicine Thomas Jefferson University 1020 Locust St PhiladelphiaPA19107 United States Biological Sciences Division Pacific Northwest National Laboratory 902 Battelle Blvd RichlandWA99354 United States Auckland Bioengineering Institute University of Auckland Auckland1010 New Zealand Center of Integrative Biology University of Toulouse III-Paul Sabatier 165 Rue Marianne Grunberg-Manago Toulouse31400 France Lifeware Group Inria Building Alan Turing 1 Rue Honoré d’Estienne d’Orves Palaiseau91120 France Multiscale Modeling Group Altos Labs Redwood CityCA94065 United States partner site Tübingen Tübingen Germany Ottfried-Müller-Str. 37 Tübingen72076 Germany 06120 Germany Department of Computer Science Center for Data Science New York University New YorkNY11201 United States Department of Bi

Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data and models are key to progress. For this reason, and recognizing that such models are a very special type of "data", we argue that computational models, especially mechanistic models prevalent in medicine, physiology and systems biology, deserve a complementary set of guidelines. We propose the CURE principles, emphasizing that models should be Credible, Understandable, Reproducible, and Extensible. We delve into each principle, discussing verification, validation, and uncertainty quantification for model credibility;the clarity of model descriptions and annotations for understandability;adherence to standards and open science practices for reproducibility;and the use of open standards and modular code for extensibility and reuse. We outline recommended and baseline requirements for each aspect of CURE, aiming to enhance the impact and trustworthiness of computational models, particularly in biomedical applications where credibility is paramount. Our perspective underscores the need for a more disciplined approach to modeling, aligning with emerging trends such as Digital Twins and emphasizing the importance of data and modeling standards for interoperability and reuse. Finally, we emphasize that given the non-trivial effort required to implement the guidelines, the community moves to automate as many of the guidelines as possible. © 2025, CC BY.

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Augmentation of wastewater-based epidemiology with machine learning to support global health surveillance

Nature Water

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Nature Water 2025年 1-11页

作者： Eva Aßmann Christopher Irrgang Hugues Richard Martin Hölzer Timo Greiner Alexander Ullrich Matthew Wade Shelesh Agrawal Susanne Lackner Fabian Amman Sindy Böttcher Markus Landthaler Emanuel Wyler Serghei Mangul Viorel Munteanu Fotis Psomopoulos Maureen Smith Maria Trofimova Max von Kleist Centre for Artificial Intelligence in Public Health Research (ZKI-PH) Robert Koch Institute Berlin Germany Genome Competence Center (MF1) Robert Koch Institute Berlin Germany Department of Infectious Disease Epidemiology Robert Koch Institute Berlin Germany Chief Data Officer Group UK Health Security Agency London UK Chair of Water and Environmental Biotechnology Institute IWAR Department of Civil and Environmental Engineering Sciences Technical University of Darmstadt Darmstadt Germany CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria Institute for Hygiene and Applied Immunology Medical University of Vienna Vienna Austria Gastroenteritis and Hepatitis Pathogens and Enteroviruses (FG15) Robert Koch Institute Berlin Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Germany Institute for Biology Humboldt-Universität zu Berlin Berlin Germany Titus Family Department of Clinical Pharmacy USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences University of Southern California Los Angeles CA USA Department of Biological and Morphofunctional Sciences College of Medicine and Biological Sciences Stefan cel Mare University of Suceava Suceava Romania Department of Computers Informatics and Microelectronics Technical University of Moldova Chisinau Moldova Institute of Applied Biosciences Center for Research and Technology Hellas Thessaloniki Greece Systems Medicine of Infectious Disease (P5) Robert Koch Institute Berlin Germany Department of Mathematics and Computer Science Freie Universität Berlin Berlin Germany

Wastewater-based epidemiology (WBE) has proven to be a valuable tool for monitoring the evolution and spread of global health threats, from pathogens to antimicrobial resistances. Throughout the COVID-19 pandemic, multiple wastewater surveillance programmes have advanced statistical and machine learning methods for detecting pathogens from wastewater sequencing data and correlating measured targets with the represented population to infer meaningful conclusions for public health. Integrating contextual data can account for measurement uncertainties across the WBE workflow that affect the reliability of analyses. However, the broader availability and harmonization of data are major obstacles to method development. Here we review the benefits and limitations of wastewater-related data streams, highlighting the potential of machine learning to leverage these streams for normalization and other WBE applications. We emphasize the relevance of developing global frameworks for integrating WBE with other health surveillance systems and discuss next steps to address current and foreseeable challenges for robust and interpretable machine learning-enhanced WBE.

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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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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

引用

NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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