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arXiv 2022年

作者： Callahan, Tiffany J. Stefanski, Adrianne L. Wyrwa, Jordan M. Zeng, Chenjie Ostropolets, Anna Banda, Juan M. Baumgartner, William A. Boyce, Richard D. Casiraghi, Elena Coleman, Ben D. Collins, Janine H. Deakyne-Davies, Sara J. Feinstein, James A. Haendel, Melissa A. Lin, Asiyah Y. Martin, Blake Matentzoglu, Nicolas A. Meeker, Daniella Reese, Justin Sinclair, Jessica Taneja, Sanya B. Trinkley, Katy E. Vasilevsky, Nicole A. Williams, Andrew Zhang, Xingman A. Denny, Joshua C. Robinson, Peter N. Ryan, Patrick Hripcsak, George Bennett, Tellen D. Hunter, Lawrence E. Kahn, Michael G. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States National Human Genome Research Institute National Institutes of Health BethesdaMD20892 United States Department of Computer Science Georgia State University AtlantaGA30303 United States Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15260 United States Computer Science Università degli Studi di Milano Milan20122 Italy Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States The Jackson Laboratory for Genomic Medicine FarmingtonCT06032 United States Department of Haematology University of Cambridge Cambridge United Kingdom Department of Research Informatics & Data Science Analytics Resource Center Children’s Hospital Colorado AuroraCO80045 United States University of Colorado Anschutz School of Medicine AuroraCO80045 United States Center for Health AI University of Colorado Anschutz Medical Campus AuroraCO80045 United States Departments of Biomedical Informatics and Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Semanticly Athens Greece Yale School of Medicine New HavenCT06510 United States HealthLinc ValparaisoIN46383 United States Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Family Medicine University of Colorado Anschutz School of Medicine AuroraCO80045 United States Translational and Integrative Sciences Lab University of Colorado Anschutz Medical Campus AuroraCO80045 United States Tufts Institute for Clinical Research and Health Policy Studies Tufts University Bos

Background: Common data models solve many challenges of standardizing electronic health record (EHR) data, but are unable to semantically integrate all the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. Objective: We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Results: Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68-99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. Conclusions: By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping. © 2022, CC BY.

关键词： Ontology

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11th German Conference on Chemoinformatics (GCC 2015) Abstracts

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JOURNAL OF CHEMINFORMATICS 2016年第SUPPL 1期8卷 1-27页

作者： [Anonymous] GDCh-CIC Division Associated Board Member Beilstein-Institut zur Förderung der Chemischen Wissenschaften Trakehner Str. 7-9 60487 Frankfurt Germany. ufechner@beilstein-institut.de. Division Medicinal Chemistry Amsterdam Institute for Molecules Medicines and Systems (AIMMS) VU University Amsterdam The Netherlands. Centre for Bioinformatics Uni Hamburg Bundesstr. 43 20146 Hamburg Germany. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. stefan.guessregen@***. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. GlaxoSmithKline Stevenage SG1 2NY UK. nicola.j.richmond@***. Discngine Paris 75011 France. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. marwin.segler@wwu.de. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. Bundeskriminalamt Wiesbaden Central Analytics II 65173 Wiesbaden Germany. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. shea@chem.ucsb.edu. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. Chemistry Department Ludwig-Maximilians-Universität München Butenandtstr. 7 81377 Munich Germany. Inorganic Chemistry and Center for Nanointegration University of Duisburg-Essen Essen Germany. CAM-D Technologies Essen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. achim.zielesny@w-hs.de. Leiden University Leiden Netherlands. j.fraaije@chem.leidenuniv.nl. Culgi BV Berlin Germany. Physikalische Chemie III TU Dortmund 44227 Dortmund Germany. stefan.kast@tu-dortmund.de. Centre for Molecular Informatics Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW United Kingdom. kcb27@cam.ac.uk. Centre for Molecular Informatics Department of Chemistry

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PennyLane: Automatic differentiation of hybrid quantum-classical computations

arXiv

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arXiv 2018年

作者： Bergholm, Ville Izaac, Josh Schuld, Maria Gogolin, Christian Ahmed, Shahnawaz Ajith, Vishnu Alam, M. Sohaib Alonso-Linaje, Guillermo AkashNarayanan, B. Asadi, Ali Arrazola, Juan Miguel Azad, Utkarsh Banning, Sam Blank, Carsten Bromley, Thomas R. Cordier, Benjamin A. Ceroni, Jack Delgado, Alain Matteo, Olivia Di Dusko, Amintor Garg, Tanya Guala, Diego Hayes, Anthony Hill, Ryan Ijaz, Aroosa Isacsson, Theodor Ittah, David Jahangiri, Soran Jain, Prateek Jiang, Edward Khandelwal, Ankit Kottmann, Korbinian Lang, Robert A. Lee, Christina Loke, Thomas Lowe, Angus McKiernan, Keri Meyer, Johannes Jakob Montañez-Barrera, J.A. Moyard, Romain Niu, Zeyue O’Riordan, Lee James Oud, Steven Panigrahi, Ashish Park, Chae-Yeun Polatajko, Daniel Quesada, Nicolás Roberts, Chase Sá, Nahum Schoch, Isidor Shi, Borun Shu, Shuli Sim, Sukin Singh, Arshpreet Strandberg, Ingrid Soni, Jay Száva, Antal Thabet, Slimane Vargas-Hernández, Rodrigo A. Vincent, Trevor Vitucci, Nicola Weber, Maurice Wierichs, David Wiersema, Roeland Willmann, Moritz Wong, Vincent Zhang, Shaoming Killoran, Nathan Xanadu 777 Bay Street Toronto Canada Wallenberg Centre for Quantum Technology Department of Microtechnology and Nanoscience Chalmers University of Technology Gothenburg412 96 Sweden Indian Institute of Information Technology Kottayam India NASA Ames Research Center Moffett FieldCA94035 United States Mountain ViewCA94043 United States data cybernetics Martin-Kolmsperger-Str 26 Landsberg86899 Germany Department of Medical Informatics and Clinical Epidemiology Oregon Health and Science University PortlandOR97202 United States Dept. of Electrical and Computer Engineering The University of British Columbia VancouverBCV6T 1Z4 Canada Department of Physics Indian Institute of Technology Roorkee Uttarakhand Roorkee India qBraid 5235 South Harper Court ChicagoIL60615 United States Factal Analytics Level 2 Chimes Building Plot 61 Sector - 44 Haryana Gurgaon122003 India Centre for High Energy Physics Indian Institute of Science Karnataka Bengaluru560012 India ICFO - Institut de Ciencies Fotoniques The Barcelona Institute of Science and Technology Av. Carl Friedrich Gauss 3 Castelldefels Barcelona08860 Spain Chemical Physics Theory Group Department of Chemistry University of Toronto Canada DUG Technology 76 Kings Park Rd West PerthWA6005 Australia Rigetti Computing 2919 Seventh Street BerkeleyCA94710 United States Dahlem Center for Complex Quantum Systems Freie Universität Berlin Berlin14195 Germany Institute for Advanced Simulation Jülich Supercomputing Centre Forschungszentrum Jülich Jülich52425 Germany University of Amsterdam Netherlands School of Physical Sciences National Institute of Science Education and Research HBNI Odisha Jatni752 050 India Cervest United Kingdom Centro Brasileiro de Pesquisas Físicas Rua Dr. Xavier Sigaud 150 Rio de Janeiro22290-180 Brazil Zurich8092 Switzerland Neo4j UK Ltd United Kingdom Zapata Computing Inc. United States ITC Infotech Bangalore India Department of Microtechnology and Nanoscienc

PennyLane is a Python 3 software framework for differentiable programming of quantum computers. The library provides a unified architecture for near-term quantum computing devices, supporting both qubit and continuous-variable paradigms. PennyLane’s core feature is the ability to compute gradients of variational quantum circuits in a way that is compatible with classical techniques such as backpropagation. PennyLane thus extends the automatic differentiation algorithms common in optimization and machine learning to include quantum and hybrid computations. A plugin system makes the framework compatible with any gate-based quantum simulator or hardware. We provide plugins for hardware providers including the Xanadu Cloud, Amazon Braket, and IBM Quantum, allowing PennyLane optimizations to be run on publicly accessible quantum devices. On the classical front, PennyLane interfaces with accelerated machine learning libraries such as TensorFlow, PyTorch, JAX, and Autograd. PennyLane can be used for the optimization of variational quantum eigensolvers, quantum approximate optimization, quantum machine learning models, and many other applications. Copyright © 2018, The Authors. All rights reserved.

关键词： Machine learning

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

arXiv

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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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P10.25.A ATR INHIBITION IN EXPERIMENTAL GLIOMA: DISCOVERY AND VALIDATION OF MOLECULAR TARGETS FOR FUNCTIONALLY-INSTRUCTED COMBINATION THERAPIES

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Neuro-Oncology 2023年第SUPPLEMENT_2期25卷 ii68–ii68页

作者： Walter, B Hirsch, S Kuhlburger, L Stahl, A Schnabel, L Haeusser, L A Tsiami, F Ploeger, S Aghaallaei, N Dick, A M Skokowa, J Schmees, C Templin, M Schenke-Layland, K Tatagiba, M Nahnsen, S Merk, D Tabatabai, G Hertie Institute for Clinical Brain Research Tübingen Germany Quantitative Biology Center Eberhard Karls University Tübingen Tübingen Germany Biomedical Data Science Department of Computer Science Eberhard Karls University Tübingen Tübingen Germany NMI Natural and Medical Sciences Institute at the University of Tübingen Reutlingen Germany German Consortium for Translational Cancer Research (DKTK) Partner site Tübingen Tübingen Germany Division of Translational Oncology Department of Internal Medicine II University Hospital Tübingen Tübingen Germany Institute of Biomedical Engineering Dept. for Medical Technologies and regenerative Medicine Eberhard Karls University Tübingen Tübingen Germany Center for Neuro-Oncology Comprehensive Cancer Center Tübingen-Stuttgart Eberhard Karls University Tübingen Tübingen Germany

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

arXiv

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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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Learning from learning machines: A new generation of AI technology to meet the needs of science

arXiv

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arXiv 2021年

作者： Pion-Tonachini, Luca Bouchard, Kristofer Martin, Hector Garcia Peisert, Sean Holtz, W. Bradley Aswani, Anil Dwivedi, Dipankar Wainwright, Haruko Pilania, Ghanshyam Nachman, Benjamin Marrone, Babetta L. Falco, Nicola Prabhat Arnold, Daniel Wolf-Yadlin, Alejandro Powers, Sarah Climer, Sharlee Jackson, Quinn Carlson, Ty Sohn, Michael Zwart, Petrus Kumar, Neeraj Justice, Amy Tomlin, Claire Jacobson, Daniel Micklem, Gos Gkoutos, Georgios V. Bickel, Peter J. Cazier, Jean-Baptiste Müller, Juliane Webb-Robertson, Bobbie-Jo Stevens, Rick Anderson, Mark Kreutz-Delgado, Ken Mahoney, Michael W. Brown, James B. Pattern Computer Inc. Friday HarborWA98250 United States Biosciences Area Lawrence Berkeley National Lab BerkeleyCA94803 United States Computational Research Division Lawrence Berkeley National Lab BerkeleyCA94720 United States Helen Wils Neuroscience Institute Redwood Center for Theoretical Neuroscience Uc Berkeley BerkeleyCA94720 United States Doe Agile BioFoundry Lawrence Berkeley National Laboratory BerkeleyCA94803 United States Joint BioEnergy Institute Lawrence Berkeley National Laboratory BerkeleyCA94803 United States Bcam Basque Center for Applied Mathematics Bilbao48009 Spain Computer Science University of California Davis DavisCA95616 United States Cenic La MiradaCA90638 United States Health Informatics University of California Davis School of Medicine SacramentoCA95817 United States Berkeley Institute for Data Science University of California Berkeley BerkeleyCA94720 United States Industrial Engineering and Operations Research University of California Berkeley BerkeleyCA94720 United States Environmental & Earth Sciences Area Lawrence Berkeley National Laboratory BerkeleyCA94803 United States Nuclear Engineering University of California Berkeley BerkeleyCA94720 United States Materials Science and Technology Division Los Alamos National Laboratory Los AlamosNM87545 United States Physics Division Lawrence Berkeley National Lab BerkeleyCA94720 United States Bioscience Division Los Alamos National Laboratory Los AlamosNM87545 United States Earth and Environmental Sciences Area Lawrence Berkeley National Lab BerkeleyCA94803 United States Energy Technologies Area Lawrence Berkeley National Lab BerkeleyCA94803 United States Computing and Computational Sciences Oak Ridge National Laboratory Oak RidgeTN37831 United States Industrial & Systems Engineering The University of Tennessee KnoxvilleTN37996 United States Department of Computer Science University of Missouri-Saint Louis St. LouisMO63121 United

We outline emerging opportunities and challenges to enhance the utility of AI for scientific discovery. The distinct goals of AI for industry versus the goals of AI for science create tension between identifying patterns in data versus discovering patterns in the world from data. If we address the fundamental challenges associated with "bridging the gap" between domain-driven scientific models and data-driven AI learning machines, then we expect that these AI models can transform hypothesis generation, scientific discovery, and the scientific process itself. © 2021, CC BY.

关键词： Learning systems

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Resting-state dynamic functional network connectivity predicts cognition in 37,784 participants of UK Biobank

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Alzheimer's & Dementia 2023年第S3期19卷

作者： Mohammad S.E. Sendi Elaheh Zendehrouh Robyn L Miller David H Salat Vince D Calhoun School of Electrical and Computer Engineering (ECE) at the Georgia Institute of Technology Atlanta GA USA Tri-Institutional Georgia State University/Georgia Institute of Technology/Emory University Center for Translational Research in Neuroimaging and Data Science Atlanta GA USA Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia Tech Atlanta GA USA Georgia State University Atlanta GA USA Neuroimaging Research for Veterans Center VA Boston Healthcare System Jamaica Plain MA USA Massachusetts General Hospital Charlestown MA USA Harvard Medical School Boston MA USA Athinoula A. Martinos Center for Biomedical Imaging Charlestown MA USA

Background Age-related cognitive decline after 65 is a well-known phenomenon, but little is known about how brain functional changes are related to cognitive decline. To this end, previous studies explored the link between functional network connectivity (FNC) estimated from resting-state functional MRI (rs-fMRI) and cognitive scores in healthy adults. FNC is often assumed to be static over time. However, this assumption runs contrary to the dynamic nature of brain FNC, and dynamic FNC (dFNC) has been recently introduced to overcome this limitation. The current study investigated the relationship between dFNC estimated from 36,263 individuals from UK Biobank and cognition. Method We used the resting-state fMRI (duration: 5min) data of 37,784 (20,157 females) adults’ brains, demographic information (age:64.06± 7.51), and cognitive scores from the UK Biobank in which the cognitive scores include fluid intelligence (FI), reaction time (RT), and pairs matching (Pairs). We adapted group independent component analysis to extract 53 data-driven components for the whole brain using a fully automated approach (Fig.1: Step1). Next, we used the sliding window and Pearson correlation to estimate the dFNC among 53 components (Fig.1: Step2). We used k-means clustering to put dFNCs of all individuals into three separated states and calculated individual state vectors (Fig.1: Step3). Then, we estimated 32 dFNC features based on three estimated states and state vectors (Fig.1: Step4). Finally, we trained a two-fold cross-validation support vector regression to predict the cognitive scores (Fig.1: Step5). Result The estimated dFNC feature predicted FI score with high accuracy (the correlation between measure and predicted score is R = 0.043, p = 6.6e −17 , Fig.2A), mean time to correctly identify match in RT task (R = 0.065, p = 1.9 −34 , Fig.2B), and time to complete Pairs task (R = 0.049, p = 1.3e −20 , Fig.2C). Conclusion Here we explored the link between dFNC features and cogniti

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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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Brain state instability as a biomarker of Alzheimer’s disease progression: A dynamic functional network connectivity study

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Alzheimer's & Dementia 2021年第S1期17卷

作者： Mohammad S.E. Sendi Elaheh Zendehrouh Robyn L Miller Elizabeth C. Mormino David H Salat Vince D Calhoun School of Electrical and Computer Engineering (ECE) at the Georgia Institute of Technology Atlanta GA USA Tri-Institutional Georgia State University/Georgia Institute of Technology/Emory University Center for Translational Research in Neuroimaging and Data Science Atlanta GA USA Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia Tech Atlanta GA USA Georgia State University Atlanta GA USA Stanford University School of Medicine Palo Alto CA USA Neuroimaging Research for Veterans Center VA Boston Healthcare System Boston MA USA Massachusetts General Hospital Charlestown MA USA Harvard Medical School Boston MA USA

Background Finding a biomarker predicting the Alzheimer’s disease (AD) progression from a healthy stage to mild cognitive impairment (MCI), mild dementia (MD) and further to AD is an essential step toward early medical intervention. In recent years, dynamic functional network connectivity (dFNC) from resting state-fMRI, which estimates brain states during the scan, revealed excellent knowledge about AD progression's underlying mechanism. The current study explored whether the AD brain produces similar and stable dFNC states across different scanning sessions and introduced dFNC state (or brain) instability as a potential biomarker of AD progression. Method The data from the longitudinal Open Access Series of Imaging Studies (OASIS)-3 cohort were used in this study. The dataset contains two rs-fMRI sessions on the same day of 1048 healthy controls or HC (clinical dementia rating sum of boxes or CDR-SOB=0, age= 70.80± 8.57), 193 MCI (4.5=0.2). We used Group-independent component analysis to extract independent components of the whole-brain for each subject. Next, we applied the sliding window with Pearson correlation to estimate dFNC of each individual in each session. Subsequently, k-means clustering (k=3, L1-norm as a distance metric, and 1000 iterations) separately was applied to put the dFNCs of each group and session in three distinct states. Pearson correlation between the cluster (state) centroid was used to assess the similarity of state across two sessions. Result We found that HC and MCI groups generate similar dFNC states in both sessions in which The correlation between inter-session “matched” states for HCs and MCIs was more than 0.99 (p<0.0001). But, MD patients did not generate similar brain states across two sessions. This points to a degradation in the stabi

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