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arXiv 2024年

作者： Bunne, Charlotte Roohani, Yusuf Rosen, Yanay Gupta, Ankit Zhang, Xikun Roed, Marcel Alexandrov, Theo AlQuraishi, Mohammed Brennan, Patricia Burkhardt, Daniel B. Califano, Andrea Cool, Jonah Dernburg, Abby F. Ewing, Kirsty Fox, Emily B. Haury, Matthias Herr, Amy E. Horvitz, Eric Hsu, Patrick D. Jain, Viren Johnson, Gregory R. Kalil, Thomas Kelley, David R. Kelley, Shana O. Kreshuk, Anna Mitchison, Tim Otte, Stephani Shendure, Jay Sofroniew, Nicholas J. Theis, Fabian Theodoris, Christina V. Upadhyayula, Srigokul Valer, Marc Wang, Bo Xing, Eric Yeung-Levy, Serena Zitnik, Marinka Karaletsos, Theofanis Regev, Aviv Lundberg, Emma Leskovec, Jure Quake, Stephen R. Department of Computer Science Stanford University StanfordCA United States Genentech South San FranciscoCA United States Chan Zuckerberg Initiative Redwood CityCA United States School of Computer and Communication Sciences School of Life Sciences EPFL Lausanne Switzerland Arc Institute Palo AltoCA United States KTH Royal Institute of Technology Science for Life Laboratory Department of Protein Science Stockholm Sweden Department of Bioengineering Stanford University StanfordCA United States Department of Pharmacology University of California San DiegoCA United States Department of Bioengineering University of California San DiegoCA United States Department of Systems Biology Columbia University New YorkNY United States Cellarity SomervilleMA United States Vagelos College of Physicians and Surgeons Columbia University Irving Medical Center New YorkNY United States Chan Zuckerberg Biohub New YorkNY United States Department of Molecular and Cell Biology University of California Berkeley BerkeleyCA United States Department of Statistics Stanford University StanfordCA United States Chan Zuckerberg Biohub San Francisco CA United States Chan Zuckerberg Institute for Advanced Biological Imaging Redwood CityCA United States Department of Bioengineering University of California BerkeleyCA United States Microsoft Research RedmondWA United States Center for Computational Biology University of California Berkeley BerkeleyCA United States Google Research Mountain ViewCA United States NewLimit San FranciscoCA United States Schmidt city United States Calico Life Sciences LLC San FranciscoCA United States Chan Zuckerberg Biohub Chicago IL United States Northwestern University EvanstonIL United States Cell Biology and Biophysics Unit European Molecular Biology Laboratory Heidelberg Germany Department of Systems Biology Harvard Medical School BostonMA United States Department of Genome Sciences University of Washington SeattleWA Unit

The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells. Here we propose a vision of leveraging advances in AI to construct virtual cells, high-fidelity simulations of cells and cellular systems under different conditions that are directly learned from biological data across measurements and scales. We discuss desired capabilities of such AI Virtual Cells, including generating universal representations of biological entities across scales, and facilitating interpretable in silico experiments to predict and understand their behavior using Virtual Instruments. We further address the challenges, opportunities and requirements to realize this vision including data needs, evaluation strategies, and community standards and engagement to ensure biological accuracy and broad utility. We envision a future where AI Virtual Cells help identify new drug targets, predict cellular responses to perturbations, as well as scale hypothesis exploration. With open science collaborations across the biomedical ecosystem that includes academia, philanthropy, and the biopharma and AI industries, a comprehensive predictive understanding of cell mechanisms and interactions has come into reach. © 2024, CC BY.

关键词： Virtual environments

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CHAOS Challenge - Combined (CT-MR) healthy abdominal organ segmentation

arXiv

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arXiv 2020年

作者： Kavur, A. Emre Gezer, N. Sinem Barış, Mustafa Conze, Pierre-Henri Groza, Vladimir Pham, Duc Duy Chatterjee, Soumick Ernst, Philipp Özkan, Savaş Baydar, Bora Lachinov, Dmitry Han, Shuo Pauli, Josef Isensee, Fabian Perkonigg, Matthias Sathish, Rachana Rajan, Ronnie Aslan, Sinem Sheet, Debdoot Dovletov, Gurbandurdy Speck, Oliver Nürnberger, Andreas Maier-Hein, Klaus H. Akar, Gözde Bozdagı Ünal, Gözde Dicle, Oguz Selver, M. Alper Graduate School of Natural and Applied Sciences Dokuz Eylul University Izmir Turkey Department of Radiology Faculty Of Medicine Dokuz Eylul University Izmir Turkey Dept. of Ophthalmology and Optometry Medical Uni. of Vienna Austria Intelligent Systems Faculty of Engineering University of Duisburg-Essen Germany Division of Medical Image Computing German Cancer Research Center Heidelberg Germany CIR Lab Dept of Biomedical Imaging and Image-guided Therapy Medical Uni. of Vienna Austria IMT Atlantique LaTIM UMR 1101 Brest France Department of Electrical and Electronics Engineering Middle East Technical University Ankara Turkey Department of Electrical Engineering Indian Institute of Technology Kharagpur India School of Medical Science and Technology Indian Institute of Technology Kharagpur India Ca’ Foscari University of Venice ECLT DAIS Venice Italy Ege University International Computer Institute Izmir Turkey Johns Hopkins University Baltimore United States Data and Knowledge Engineering Group Otto von Guericke University Magdeburg Germany Magnetic Resonance Otto von Guericke University Magdeburg Germany Median Technologies Valbonne France Department of Computer Engineering Istanbul Technical University Istanbul Turkey Department of Electrical and Electronics Engineering Dokuz Eylul University Izmir Turkey

—Segmentation of abdominal organs has been a comprehensive, yet unresolved, research field for many years. In the last decade, intensive developments in deep learning (DL) have introduced new state-of-the-art segmentation systems. Despite outperforming the overall accuracy of existing systems, the effects of DL model properties and parameters on the performance is hard to interpret. This makes comparative analysis a necessary tool to achieve explainable studies and systems. Moreover, the performance of DL for emerging learning approaches such as cross-modality and multi-modal tasks have been rarely discussed. In order to expand the knowledge in these topics, CHAOS – Combined (CT-MR) Healthy Abdominal Organ Segmentation challenge has been organized in the IEEE International Symposium on Biomedical Imaging (ISBI), 2019, in Venice, Italy. Despite a large number of the previous abdomen related challenges, the majority of which are focused on tumor/lesion detection and/or classification with a single modality, CHAOS providesboth abdominal CT and MR data from healthy subjects. Five different and complementary tasks have been designed to analyze the capabilities of the current approaches from multiple perspectives. The results are investigated thoroughly, compared with manual annotations and interactive methods. The outcomes are reported in detail to reflect the latest advancements in the field. CHAOS challenge and data will be available online to provide a continuous benchmark resource for segmentation. Copyright © 2020, The Authors. All rights reserved.

关键词： Medical imaging

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An AI-based approach to detect cognitive impairment from digital voice recordings of neuropsychological assessments

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Alzheimer's & Dementia 2022年第S7期18卷

作者： Samad Amini Boran Hao Lifu Zhang Mengting Song Aman Gupta Cody Karjadi Vijaya B. Kolachalama Rhoda Au Ioannis Paschalidis Division of Systems Engineering Boston University Boston MA USA Department of Electrical & Computer Engineering Boston University Boston MA USA The Framingham Heart Study Boston University School of Medicine Boston MA USA Hariri Institute for Computing and Computational Science & Engineering Boston University Boston MA USA Boston University School of Medicine Boston MA USA Faculty of Computing & Data Sciences Boston University Boston MA USA The Framingham Heart Study Boston University School of Medicine Boston University School of Public Health Boston MA USA Department of Biomedical Engineering Boston University Boston MA USA

Background Reliable cognitive impairment screening tools that are easy to administer and minimally time consuming are greatly needed. Given the high sensitivity of neuropsychological (NP) exams in detection of cognitive decline, we seek to develop an automated screening tool to detect dementia and mild cognitive impairment (MCI) based on digital voice recordings of NP assessments. This could enable wide-spread screening for dementia and accelerate preventative efforts. Method We used natural language processing methods to create a screening tool that identifies different stages of dementia based on automated transcription of digital voice recordings. The transcribed sentences were classified into 8 main sub-tests including memory assessment, naming and language skill, verbal fluency, general questions, etc. Using the idea of transfer learning, we encoded the participants' sentences into quantitative data. This data and the participants’ demographic variables such as age, sex, Apoe gene, and education were employed to train and test three binary classification tasks, (I) Normal cognition versus Dementia, (II) Normal/MCI versus Dementia, and (III) Normal versus MCI. Result We evaluated the performance of the classification tasks using the digital voice recordings of NP assessments, collected from the Framingham Heart Study, containing 410 cognitively intact subjects, 387 MCI, and 287 subjects with dementia. The average Area Under the Curve (AUC) on the held-out test data reached 92.6%, 88.0%, and 74.4% for differentiating Normal from Dementia, Normal or MCI from Dementia, and Normal from MCI, respectively. Looking at the importance of the sub-tests in differentiating MCI from Normal, we note that general questions can be more useful for assessment of MCI, whereas verbal fluency would not be as useful in this task. Conclusion The proposed approach offers a fully automated identification of MCI and dementia based on a recorded NP test, providing an opportunity to develo

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Preface

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Lecture Notes in Computer science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2001年 2037卷 V-VI页

作者： Boers, Egbert J. W. Cagnoni, Stefano Gottlieb, Jens Hart, Emma Lanzi, Pier Luca Raidl, Günther R. Smith, Robert E. Tijink, Harald Leiden Institute of Advanced Computer Science Leiden University Niels Bohrweg 1 Leiden Netherlands Dept. of Computer Engineering University of Parma Parco Area delle Scienze 181/a Parma Italy SAP AG Neurottstrasse 16 Walldorf Germany Napier University School of Computing 219 Colinton Road Edinburgh United Kingdom Polytechnic of Milan Piazza Leonardo da Vinci 32 Milan Italy Algorithms and Data Structur es Group Institute of Computer Graphics Vienna University of Technology Favoritenstrasse 9-11/186 Vienna Austria The Intelligent Computer Systems Centre The University of The West of England Coldharbour Lane Frenchay Bristol United Kingdom Data and Knowledge Systems Department National Aerospace Laboratory NLR P.O. Box 153 Emmeloord Netherlands

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Preface

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Lecture Notes in Computer science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2000年 1803卷 6-6页

作者： Cagnoni, Stefano Poli, Riccardo Li, Yun Smith, George Corne, David Oates, Martin Hart, Emma Lanzi, Pier Luca Boers, Egbert J. W. Paechter, Ben Fogarty, Terence C. University of Parma Department of Computer Engineering Parco delle Scienze 181/a Parma Italy The University of Birmingham School of Computer Science Edgbaston Birmingham United Kingdom University of Glasgow Electronics and Electrical Engineering Rankine Building Glasgow United Kingdom University of East Anglia Department of Information Systems Norwich United Kingdom University of Reading P.O. Box 225 Whiteknights Reading United Kingdom BT Labs at Adastral Park Dept. Complex Systems Laboratory Martlesham Heath Suffolk United Kingdom University of Edinburgh Division of Informatics 80 South Bridge Edinburgh United Kingdom Milan Polytechnic Department of Electronics and Informatics Piazza Leonard0 da Vinci 32 Milan Italy National Aerospace Laboratory NLR Data and Knowledge Systems Dept I.C.T. Division Anthony Fokkerweg 2 Amsterdam Netherlands Napier University School of Computing 219 Colinton Road Edinburgh United Kingdom South Bank University School of Computing Information Systems and Mathematics 103 Borough Road London United Kingdom

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Keep Your Friends Close and Your Colleagues Nearby: The Hidden Ties That Improve STEM Education

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Change 2019年第1期51卷 42页

作者： Mestre, Jose P. Herman, Geoffrey L. Tomkin, Jonathan H. West, Matthew Jose P. Mestre (mestre@illinois.edu). A theoretical nuclear physicist by training Mestre’s research focuses on the learning of physics contributing in areas such as the acquisition and use of knowledge by experts and novices transfer of learning problem solving and instructional design. He has offered Congressional testimony on The Science of Learning has published numerous articles and books and is a Fellow of the American Physical Society.http://***/0000-0003-2110-1954 Geoffrey L. Herman (glherman@illinois.edu). Herman has a Ph.D. in Electrical and Computer Engineering and is a Teaching Assistant Professor in Computer Science and a Research Assistant Professor in the Department of Curriculum & Instruction at the University of Illinois. His research focuses on how students learn engineering and computing concepts and studying processes for creating systemic instructional change in college settings. Previously he was a postdoctoral researcher in Engineering Education at Purdue University.http://***/0000-0002-9501-2295 Jonathan H. Tomkin (tomkin@illinois.edu). Tomkin is a mathematically based geoscientist with two research focus areas: first he uses models and large data sets to determine how climates glaciers tectonics and landscapes interact. Second he explores how new technological and organizational approaches can improve STEM education. He produced the first geoscience MOOC is the editor of an open-source textbook and has published widely in both geoscience and STEM education. Matthew West (mwest@illinois.edu). Matthew West is an Associate Professor of Mechanical Science and Engineering at the University of Illinois with research interests in scientific computing that include time integration of deterministic and stochastic systems distributed computation and particle methods for simulation and estimation. In education he researches computer-based assessment and the development of innovative teaching cultures. Professor West is a University of Illinois Distinguished Teacher-Scholar and Colleg

A science department on the campus of the University of Illinois has received numerous national awards for excellence in undergraduate teaching. The secret to their success? For nearly two decades, they have collaboratively used evidence-based instructional practices (EBIP) in their introductory level courses. Despite these successes and efforts to spread their EBIP, no other departments followed this department's lead. Then, suddenly six years ago, many instructors from other departments began adopting EBIP in their classrooms. This article asks what was the catalyst for this change? Why had previous attempts at institutional change failed? The authors answer these questions by analyzing their efforts to transform the teaching practices in large-enrollment science and engineering introductory courses on their campus.

关键词： STEM Education Evidence Based Practice Teaching Methods Undergraduate Study College Faculty Educational Change Communities of Practice Mentors School CultureIllinois

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

arXiv

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arXiv 2024年

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

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

关键词： Diagnosis

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The chemical evolution of the solar neighbourhood for planet-hosting stars

arXiv

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arXiv 2023年

作者： Pignatari, Marco Trueman, Thomas C.L. Womack, Kate A. Gibson, Brad K. Côté, Benoit Turrini, Diego Sneden, Christopher Mojzsis, Stephen J. Stancliffe, Richard J. Fong, Paul Lawson, Thomas V. Keegans, James D. Pilkington, Kate Passy, Jean-Claude Beers, Timothy C. Lugaro, Maria ELKH Konkoly Thege M. út 15–17 BudapestH-1121 Hungary CSFK MTA Centre of Excellence Konkoly Thege Miklós út 15-17. BudapestH-1121 Hungary E. A. Milne Centre for Astrophysics Department of Physics and Mathematics University of Hull HU6 7RX United Kingdom INAF - Turin Astrophysical Observatory Via Osservatorio 20 Pino Torinese10025 Italy INAF - Institute of Space Astrophysics and Planetology Via Fosso del Cavaliere 100 Rome00133 Italy ICSC National Research Centre for High Performance Computing Big Data and Quantum Computing Via Magnanelli 2 Casalecchio di Reno40033 Italy Department of Astronomy and McDonald Observatory The University of Texas AustinTX78712 United States NuGrid Collaboration Joint Institute for Nuclear Astrophysics Center for the Evolution of the Elements United States Department of Physics and Astronomy University of Victoria VictoriaBCV8P 5C2 Canada Pázmány Péter sétány 1/c BudapestH-1117 Hungary H.H. Wills Physics Laboratory University of Bristol Tyndall Avenue BristolBS8 1TL United Kingdom Centre of Excellence for Data Science Artificial Intelligence and Modelling University of Hull HU6 7RX United Kingdom Astrophysics Group Lennard-Jones Laboratories Keele University KeeleST5 5BG United Kingdom School of Physical Sciences The Open University Milton KeynesMK7 6AA United Kingdom Max Planck Institute for Intelligent Systems Tübingen Germany Department of Physics and Astronomy University of Notre Dame Notre DameIN46556 United States ELTE Eötvös Loránd University Institute of Physics Pázmány Péter sétány 1/A Budapest1117 Hungary School of Physics and Astronomy Monash University VIC3800 Australia

Theoretical physical-chemical models for the formation of planetary systems depend on data quality for the Sun’s composition, that of stars in the solar neighbourhood, and of the estimated "pristine" compositions for stellar systems. The effective scatter and the observational uncertainties of elements within a few hundred parsecs from the Sun, even for the most abundant metals like carbon, oxygen and silicon, are still controversial. Here we analyse the stellar production and the chemical evolution of key elements that underpin the formation of rocky (C, O, Mg, Si) and gas/ice giant planets (C, N, O, S). We calculate 198 galactic chemical evolution (GCE) models of the solar neighbourhood to analyse the impact of different sets of stellar yields, of the upper mass limit for massive stars contributing to GCE (Mup) and of supernovae from massive-star progenitors which do not eject the bulk of the iron-peak elements (faint supernovae). Even considering the GCE variation produced via different sets of stellar yields, the observed dispersion of elements reported for stars in the Milky Way disk is not reproduced. Among others, the observed range of super-solar [Mg/Si] ratios, sub-solar [S/N], and the dispersion of up to 0.5 dex for [S/Si] challenge our models. The impact of varying Mup depends on the adopted supernova yields. Thus, observations do not provide a constraint on the Mup parametrization. When including the impact of faint supernova models in GCE calculations, elemental ratios vary by up to 0.1-0.2 dex in the Milky Way disk;this modification better reproduces observations. Copyright © 2023, The Authors. All rights reserved.

关键词： Dispersions

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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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BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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