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Research Square 2021年

作者： Kuchroo, Manik Huang, Jessie Wong, Patrick Grenier, Jean-Christophe Shung, Dennis Tong, Alexander Lucas, Carolina Klein, Jon Burkhardt, Daniel B. Gigante, Scott Godavarthi, Abhinav Rieck, Bastian Israelow, Benjamin Simonov, Michael Mao, Tianyang Oh, Ji Eun Silva, Julio Takahashi, Takehiro Odio, Camila D. Casanovas-Massana, Arnau Fournier, John Farhadian, Shelli Dela Cruz, Charles S. Ko, Albert I. Hirn, Matthew J. Wilson, F. Perry Hussin, Julie Wolf, Guy Iwasaki, Akiko Krishnaswamy, Smita Department of Neuroscience Yale University New HavenCT United States Department of Computer Science Yale University New HavenCT United States Department of Immunobiology Yale University New HavenCT United States Montreal Heart Institute MontréalQC Canada Department of Medicine Yale University New HavenCT United States Department of Genetics Yale University New HavenCT United States Computational Biology Bioinformatics Program Yale University New HavenCT United States Department of Applied Mathematics Yale University New HavenCT United States Department of Biosystems Science and Engineering ETH Zurich Switzerland Department of Epidemiology of Microbial Diseases Yale School of Public Health New HavenCT United States Department of Medicine Section of Infectious Diseases Yale University School of Medicine New HavenCT United States Department of Medicine Section of Pulmonary and Critical Care Medicine Yale University School of Medicine New HavenCT United States Department of Computational Mathematics Science and Engineering Michigan State University East LansingMI United States Department of Mathematics Michigan State University East LansingMI United States Clinical and Translational Research Accelerator Department of Medicine Yale University New HavenCT United States Faculty of Medicine Université de Montréal Québec Canada Mila – Quebec AI institute MontréalQC Canada Department of Mathematics and Statistics Université de Montréal MontréalQC Canada Howard Hughes Medical Institute Chevy ChaseMD United States

The biomedical community is producing increasingly high dimensional datasets, integrated from hundreds of patient samples, which current computational techniques struggle to explore. To uncover biological meaning from these complex datasets, we present an approach called Multiscale PHATE, which learns abstracted biological features from data that can be directly predictive of disease. Built on a coarse graining process called diffusion condensation, Multiscale PHATE learns a data topology that can be analyzed at coarse levels for high level summarizations of data, as well as at fine levels for detailed representations on subsets. We apply Multiscale PHATE to study the immune response to COVID-19 in 54 million cells from 168 hospitalized patients. Through our analysis of patient samples, we identify CD16hiCD66blo neutrophil and IFNγ+GranzymeB+ Th17 cell responses enriched in patients who die. Furthermore, we show that population groupings Multiscale PHATE discovers can be directly fed into a classifier to predict disease outcome. We also use Multiscale PHATE-derived features to construct two different manifolds of patients, one from abstracted flow cytometry features and another directly on patient clinical features, both associating immune subsets and clinical markers with outcome. © 2021, CC BY.

关键词： Coronavirus

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Exponential acceleration of macroscopic quantum tunneling in a Floquet Ising model

arXiv

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arXiv 2023年

作者： Grattan, George Barton, Brandon A. Feeney, Sean Mossi, Gianni Patnaik, Pratik Sagal, Jacob C. Carr, Lincoln D. Oganesyan, Vadim Kapit, Eliot Quantum Engineering Program Colorado School of Mines 1523 Illinois St CO Golden80401 United States Department of Computer Science Colorado School of Mines 1500 Illinois St CO Golden80401 United States Department of Applied Mathematics and Statistics Colorado School of Mines 1500 Illinois St CO Golden80401 United States Department of Physics Colorado School of Mines 1523 Illinois St CO Golden80401 United States KBR Inc. 601 Jefferson St. HoustonTX77002 United States NASA Ames Research Center Moffett FieldCA94035 United States Department of Physics and Astronomy College of Staten Island CUNY Staten IslandNY10314 United States Physics program and Initiative for the Theoretical Sciences The Graduate Center CUNY New YorkNY10016 United States Center for Computational Quantum Physics Flatiron Institute 162 5th Avenue New YorkNY10010 United States

The exponential suppression of macroscopic quantum tunneling (MQT) in the number of elements to be reconfigured is an essential element of broken symmetry phases. Slow MQT is also a core bottleneck in quantum algorithms, such as traversing an energy landscape in optimization, and adiabatic state preparation more generally. In this work, we demonstrate the possibility to accelerate MQT through Floquet engineering with the application of a uniform, high frequency transverse drive field. Using the ferromagnetic phase of the transverse field Ising model in one and two dimensions as a prototypical example, we identify three qualitatively distinct regimes as a function of drive strength: (i) for weak drive, the system exhibits exponentially slow MQT alongside robust magnetic order, as expected;(ii) at intermediate drive strength, we find polynomial decay of rates alongside vanishing magnetic order consistent with critical or paramagnetic state;(iii) at very strong drive strengths both the tunnelling rate and time-averaged magnetic order remain finite with increasing system size. We support these claims with extensive full wavefunction and matrix-product state numerical simulations, and theoretical analysis. An experimental test of these results presents a technologically important and novel scientific question accessible on NISQ-era quantum computers. © 2023, CC BY.

关键词： Ising model

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Operational systems, logistics engineering and technology insertion

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NAVAL ENGINEERS JOURNAL 1997年第3期109卷 205-220页

作者： Grubb, MJ Skolnick, A Michael J. Grubb:has perfomzed naval engineering at the Crane Division Naval Surface Warfare Center (NSWC) for more than twenty-five years. He currently the program manager for the Sustainable Hardware and Affordable Readiness Practice Program (SHARP). is a Navy-wide logistics research and development prgram aimed at the successful transiton of proved technologies inot the fleet. SHARP focuses on reducing acquisition performance capability reliability maintainability and readiness of these systems. Mr. Grubb has served as a department director for the past eleven years. His most recent assignment was as director of the Tactical Computer Resources and Test Equipment Department. This organization provided acquisition and in-service engineering support of the Navy's tectical embedded computers priphirals displays and mass memory storage devices. The organization also provided a complete range of product engineering and metrology engineerig services for SSP NevSeaSysCom and the Trident Program. Prior to this appointment Mr. Grubb was deptuy director psysical security programs department and site responsible for program management and system integration of ashore integrated security systems. Mr. Grubb holds a B.S. degree in industrial engineering from Iowa State Universtiy an M.S. degree in industrial engineering from Purdue University and has copleted the course work (Dec.'96 for a master's degree in public and environment affairs at Indiana University-Purdue Univeristy Indianapolis. Dr. Alfred Skolnick operates System Science Consultants (SSC) specilizing in strategic planning technical program definiton technology assessment and engineering analyses on selected matters of national interest. He has taught physics mathematics and management sciences at University of Virginia and Marymount University and is currently adjunct professor of mathematics at Northern Virginia Community College. Form 1985 to 1989 he was president of the American Society of Noval Engineers. Dr. Skolnick served at Applied Physic

In an era of fiscal austerity, downsizing and unforgiving pressure upon human and economic capital, it is an Augean task to identify resources for fresh and creative work. The realities of the day and the practical demands of more immediate fleet needs can often dictate higher priorities. Yet, the Navy must avoid eating its seed corn. Exercising both technical insight and management foresight, the fleet, the R&D community, the Office of the Chief of Naval Operations (OpNav) and the product engineering expertise of the Naval Surface Warfare Center (NSWC) are joined and underway with integrated efforts to marry new, fully demonstrated technologies and operational urgencies. Defense funding today cannot sponsor all work that can be mission-justified over the long term because budgets are insufficient to support product maturation within the classical development cycle. However, by rigorous technical filtering and astute engineering of both marketplace capabilities and currently available components, it is possible in a few select cases to compress and, in effect, integrate advanced development (6.3), engineering development (6.4), weapon procurement (WPN), ship construction (SCN), operation and maintenance (O&M,N) budgetary categories when fleet criticalities and technology opportunities can happily meet. In short, 6.3 funds can be applied directly to ''ripe gateways'' so modern technology is inserted into existing troubled or aging systems, sidestepping the lengthy, traditional development cycle and accelerating practical payoffs to recurrent fleet problems. To produce such constructive results has required a remarkable convergence of sponsor prescience and engineering workforce excellence. The paper describes, extensively, the philosophy of approach, transition strategy, polling of fleet needs, technology assessment, and management team requirements. The process for culling and selecting specific candidate tasks for SHARP sponsorship (matching operational need with t

关键词： Naval vessels

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TAROGE-M: Antarctic High-Mountain Radio Antenna Array for Detecting Ultra-High Energy ANITA Anomalous Events 38

TAROGE-M: Antarctic High-Mountain Radio Antenna Array for De...

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38th International Cosmic Ray Conference, ICRC 2023

作者： Wang, Shih-Hao Chen, Pisin Chen, Yaocheng Chen, Ying-Chih Choi, Taejin Ham, Young-Bae Hsu, Shih-Ying Huang, Jian-Jung Huang, MingHuey A. Jee, Geonhwa Jung, Jongil Kim, Jieun Kuo, Chung-Yun Kwon, Hyuck-Jin Lee, Changsup Leung, Chung-Hei Liu, Tsung-Che Nam, Jiwoo Shiao, Yu-Shao J. Shin, Bok-Kyun Su, Shih-Chieh Wang, Min-Zu Wang, Shih-Hao Wang, Yu-Hsin Anker, Astrid Barwick, Steven W. Besson, Dave Z. Bouma, Sjoerd Cataldo, Maddalena Gaswint, Geoffrey Glaser, Christian Hallmann, Steffen Hanson, Jordan C. Henrichs, Jakob Kleinfelder, Stuart A. Lahmann, Robert Meyers, Zachary S. Nelles, Anna Novikov, Alexander Paul, Manuel P. Pyras, Lilly Persichilli, Christopher Plaisier, Ilse Rice-Smith, Ryan Seikh, Mohammad F. H. Tatar, Joulien Welling, Christoph Zhao, Leshan Department of Physics National Taiwan University Taipei10617 Taiwan Leung Center for Cosmology and Particle Astrophysics National Taiwan University Taipei10617 Taiwan Kavli Institute for Particle Astrophysics and Cosmology SLAC National Accelerator Laboratory Stanford University StanfordCA94305 United States Division of Atmospheric Sciences Korea Polar Research Institute Incheon Korea Republic of Department of Polar Science Korea University of Science and Technology Daejeon Korea Republic of Department of Energy Engineering National United University Miaoli Taiwan Department of Astronomy Space Science and Geology Chungnam National University Daejeon34134 Korea Republic of Department of Physics and Astronomy University of Delaware NewarkDE19716 United States Department of Electrophysics National Yang Ming Chiao Tung University Hsinchu300 Taiwan Department of applied physics National Pingtung university Pingtung900 Taiwan Chung Cheng Institute of Technology National Defense University Taoyuan335 Taiwan Undergraduate Degree Program of Systems Engineering and Technology National Yang Ming Chiao Tung University Hsinchu300 Taiwan National Nano Device Laboratories Hsinchu300 Taiwan Ulsan National Institute of Science and Technology Ulsan44919 Korea Republic of Institute of Astronomy and Astrophysics Academia Sinica Astronomy-Mathematics Building No. 1 Sec. 4 Roosevelt Rd. Taipei10617 Taiwan Department of Physics and Astronomy University of California IrvineCA92697 United States Department of Physics and Astronomy University of Kansas LawrenceKS66045 United States DESY Zeuthen15738 Germany ECAP Friedrich-Alexander-Universität Erlangen-Nürnberg Erlangen91058 Germany Uppsala University Department of Physics and Astronomy UppsalaSE-752 37 Sweden Whittier College Department of Physics WhittierCA90602 United States Department of Electrical Engineering and Computer Science University of California IrvineCA92697 United States Resea

TAROGE-M is a radio antenna array atop ∼ 2.7 km-high Mt. Melbourne in Antarctica for detecting ultra-high energy (UHE, E > 1017 eV) air showers in near-horizontal directions. Besides the detection of cosmic rays and Earth-skimming tau neutrinos, its primary goal is to reproduce the discovery and verify the origin of so-called ANITA anomalous events, having feature of upward-going UHE air showers but cannot be explained by tau neutrinos. The detection concept takes advantages of a high altitude for a broad view toward the horizon;strong and near-vertical geomagnetic field for enhancing the radio signal;and quiet radio environment in Antarctica. Its relatively simple design and high duty cycle make it easily to be extended and thus to achieve an exposure competitive with ANITA experiments within a few years. The first TAROGE-M station operating at 180-450 MHz frequencies deployed in 2020 detected seven UHE cosmic ray events within 25.3-day livetime. The events have a mean energy of ∼ 1 EeV and an estimated flux consistent with other experiments, and validate the station as an UHE particle detector. In 2022-2023 season, the system was upgraded for a robust long-term operation, with a more detailed calibration with a drone-borne pulser. We also discuss the planned upgrade, including the implementation of interferometric trigger, which is expected to increase the cosmic ray and tau neutrino acceptances by a factor of 10 at 0.1 EeV, corresponding to a lower energy threshold by a factor of 3. © Copyright owned by the author(s) under the terms of the Creative Commons.

关键词： Cosmic rays

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Autonomous Multi-Modal Chemical Tomography using Bayesian Optimization

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Microscopy and Microanalysis 2024年第SUPPLEMENT_1期30卷

作者： Millsaps, William Schwartz, Jonathan Manassa, Jason Wendy Di, Zichao Jiang, Yi Hovden, Robert Department of Nuclear Engineering Radiological Sciences University of Michigan Ann Arbor MI US Chan Zuckerberg Imaging Institute Redwood City CA USA Department of Materials Science and Engineering University of Michigan Ann Arbor MI US Mathematics and Computer Science Division Argonne National Laboratory Lemont IL US Advanced Photon Source Facility Argonne National Laboratory Lemont IL US Applied Physics Program University of Michigan Ann Arbor MI US

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Classification of datasets with imputed missing values: does imputation quality matter?

arXiv

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arXiv 2022年

作者： Shadbahr, Tolou Roberts, Michael Stanczuk, Jan Gilbey, Julian Teare, Philip Dittmer, Sören Thorpe, Matthew Torné, Ramon Viñas Sala, Evis Lió, Pietro Patel, Mishal Rudd, James H.F. Mirtti, Tuomas Rannikko, Antti Sakari Aston, John A.D. Tang, Jing Schönlieb, Carola-Bibiane Selby, Ian Breger, Anna Weir-McCall, Jonathan R. Gkrania-Klotsas, Effrossyni Korhonen, Anna Jefferson, Emily Langs, Georg Yang, Guang Prosch, Helmut Preller, Jacobus Stanczuk, Jan Babar, Judith Sánchez, Lorena Escudero Wassin, Marcel Holzer, Markus Walton, Nicholas Research Program in Systems Oncology Faculty of Medicine University of Helsinki Helsinki Finland Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge United Kingdom Data Science & Artificial Intelligence AstraZeneca Cambridge United Kingdom Department of Mathematics University of Manchester Manchester United Kingdom Department of Computer Science and Technology University of Cambridge Cambridge United Kingdom Department of Radiology University of Cambridge Cambridge United Kingdom Clinical Pharmacology & Safety Sciences AstraZeneca Cambridge United Kingdom Department of Medicine University of Cambridge Cambridge United Kingdom Department of Pathology University of Helsinki Helsinki University Hospital Finland iCAN-Digital Precision Cancer Medicine Flagship Helsinki Finland Department of Urology University of Helsinki Helsinki University Hospital Helsinki Finland Department of Pure Mathematics and Mathematical Statistics University of Cambridge Cambridge United Kingdom ZeTeM University of Bremen Bremen Germany Faculty of Mathematics University of Vienna Austria Royal Papworth Hospital Cambridge Royal Papworth Hospital NHS Foundation Trust Cambridge United Kingdom Addenbrooke’s Hospital Cambridge University Hospitals NHS Trust Cambridge United Kingdom Language Technology Laboratory University of Cambridge Cambridge United Kingdom Population Health and Genomics School of Medicine University of Dundee Dundee United Kingdom Department of Biomedical Imaging and Image-guided Therapy Computational Imaging Research Lab Medical University of Vienna Vienna Austria National Heart and Lung Institute Imperial College London London United Kingdom Contextflow GmbH Vienna Austria Institute of Astronomy University of Cambridge Cambridge United Kingdom

Classifying samples in incomplete datasets is a common aim for machine learning practitioners, but is non-trivial. Missing data is found in most real-world datasets and these missing values are typically imputed using established methods, followed by classification of the now complete, imputed, samples. The focus of the machine learning researcher is then to optimise the downstream classification performance. In this study, we highlight that it is imperative to consider the quality of the imputation. We demonstrate how the commonly used measures for assessing quality are flawed and propose a new class of discrepancy scores which focus on how well the method recreates the overall distribution of the data. To conclude, we highlight the compromised interpretability of classifier models trained using poorly imputed data. All code and data used in this paper are also released publicly at [inserted upon publication]. © 2022, CC BY.

关键词： Classification (of information)

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Training of Physical Neural Networks

arXiv

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arXiv 2024年

作者： Momeni, Ali Rahmani, Babak Scellier, Benjamin Wright, Logan G. McMahon, Peter L. Wanjura, Clara C. Li, Yuhang Skalli, Anas Berloff, Natalia G. Onodera, Tatsuhiro Oguz, Ilker Morichetti, Francesco del Hougne, Philipp Le Gallo, Manuel Sebastian, Abu Mirhoseini, Azalia Zhang, Cheng Marković, Danijela Brunner, Daniel Moser, Christophe Gigan, Sylvain Marquardt, Florian Ozcan, Aydogan Grollier, Julie Liu, Andrea J. Psaltis, Demetri Alù, Andrea Fleury, Romain Lausanne Switzerland Microsoft Research 198 Cambridge Science Park CambridgeCB4 0AB United Kingdom Rain AI San Francisco United States Department of Applied Physics Yale University CT United States School of Applied and Engineering Physics Cornell University IthacaNY14853 United States Max Planck Institute for the Science of Light Staudtstraße 2 Erlangen91058 Germany Department of Electrical and Computer Engineering University of California Los AngelesCA90095 United States FEMTO-ST Institute Optics Department CNRS University Bourgogne Franche-Comté Besançon25030 Cedex France Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge United Kingdom NTT Physics and Informatics Laboratories NTT Research Inc. Sunnyvale United States Lausanne Switzerland Dipartimento di Elettronica Informazione e Bioingegneria Politecnico di Milano Milan Italy Univ Rennes CNRS IETR UMR 6164 RennesF-35000 France IBM Research Europe– Zurich Rüschlikon8803 Switzerland Department of Computer Science Stanford University United States Google DeepMind 1600 Amphitheatre Parkway Mountain ViewCA94043 United States Unité Mixte de Physique CNRS/Thales CNRS Thales Université Paris-Saclay Palaiseau France Laboratoire Kastler Brossel Sorbonne Université École Normale Supérieure Collège de France CNRS UMR 8552 Paris France Laboratoire Albert Fert CNRS Thales UniversitéParis-Saclay Palaiseau91767 France Department of Physics and Astronomy University of Pennsylvania PhiladelphiaPA19104 United States Lausanne Switzerland Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Physics Program Graduate Center City University of New York New YorkNY10016 United States

Physical neural networks (PNNs) are a class of neural-like networks that leverage the properties of physical systems to perform computation. While PNNs are so far a niche research area with small-scale laboratory demonstrations, they are arguably one of the most underappreciated important opportunities in modern artificial intelligence (AI). Could we train AI models 1000x larger than current ones? Could we do this and also have them perform inference locally and privately on edge devices, such as smartphones or sensors? Research over the past few years has shown that the answer to all these questions is likely "textityes, with enough research": PNNs could one day radically change what is possible and practical for AI systems. To do this will however require rethinking both how AI models work, and how they are trained – primarily by considering the problems through the constraints of the underlying hardware physics. To train PNNs at large scale, many methods including backpropagation-based and backpropagation-free approaches are now being explored. These methods have various trade-offs, and so far no method has been shown to scale to the same scale and performance as the backpropagation algorithm widely used in deep learning today. However, this is rapidly changing, and a diverse ecosystem of training techniques provides clues for how PNNs may one day be utilized to create both more efficient realizations of current-scale AI models, and to enable unprecedented-scale models. Copyright © 2024, The Authors. All rights reserved.

关键词： Deep learning

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Building Ramps and Pathways to Data science in K-12, Minority-Serving Institutions, and Two-Year Colleges

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Scatterplot 2024年第1期1卷

作者： Rachel Saidi Helen Burn Ben Baumer Jason Black Debzani Deb Zarek Drozda a Math Statistics and Data Science Department Montgomery College – Rockville Campus Rockville MD USA b Mathematics Department Highline College Des Moines Washington Des Moines WA USA c Statistical and Data Sciences Department Smith College Northampton MA USA d School of Business and Interdisciplinary Center for Creativity and Innovation (ICCI) Florida A&M University Tallahassee FL USA e Computer Science Department Center for Applied Data Science (CADS) Winston-Salem State University Winston-Salem NC USA f Data Science 4 Everyone (DS4E) Program University of Chicago Chicago IL USA

Global demand for data scientists and analysts is on a trajectory of sustained growth, underscoring the need to expand enrollment of students in data science and data analytics courses and programs. This article explores diverse pathways to data science for various groups, including high school students, those in two-year colleges, and students in small colleges and minority-serving institutions. This article identifies opportunities and challenges associated with pursuing data science for students in these sectors, including factors such as building partnerships and awareness of the field and difficulties in establishing articulation agreements between institutions. The authors, representing various organizations participating in a panel discussion at the 2023 Data science Leadership Summit of the Academic Data science Alliance (ADSA), share insights into efforts to develop nontraditional pathways, serving as a resource for schools, colleges, and organizations contemplating creation of data science programs. The panelists’ combined experience spans work with a broad range of organizations including ADSA, American mathematics Association of Two-Year Colleges, American Statistical Association, Data science for Everyone, the Department of Education, HBCU Data science Consortium, Mathematical Association of America, National Academies of science, Engineering, and Medicine, HBCU Data science Consortium, National science Foundation, and StatPREP.

关键词： Data science pathways access K-12 minority-serving institution two-year college

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DeePMD-kit v2: A software package for Deep Potential models

arXiv

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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

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Chemical Electron Tomography at Lower Dose and Higher Resolution

引用

Microscopy and Microanalysis 2024年第SUPPLEMENT_1期30卷

作者： Hovden, Robert Schwartz, Jonathan Sung, Suk Hyun Di, Zichao Wendy Jiang, Yi Manassa, Jason Pietryga, Jacob Qian, Yiwen Cho, Min Gee Rowell, Jonathan L Zheng, Huihuo Robinson, Richard D Gu, Junsi Kirilin, Alexey Rozeveld, Steve Ercius, Peter Scott, Mary Department of Materials Science and Engineering University of Michigan Ann Arbor MI Applied Physics Program University of Michigan Ann Arbor MI Chan Zuckerberg Initiative Redwood City CA Rowland Institute at Harvard Cambridge MA. Mathematics and Computer Science Division Argonne National Laboratory Lemont IL Advanced Photon Source Facility Argonne National Laboratory Lemont IL Department of Materials Science and Engineering U.C. Berkeley Berkeley CA National Center for Electron Microscopy Molecular Foundry Berkeley CA Department of Chemistry and Chemical Biology Cornell University Ithaca NY Argonne Leadership Computing Facility Argonne National Laboratory Lemont IL Dow Chemical Co. Terneuzen Netherlands Dow Chemical Co. Midland MI

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