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Combined Social and Spatial Coding in a Descending Projection from the Prefrontal Cortex

CELL 2017年第7期171卷 1663-+页

作者： Murugan, Malavika Jang, Hee Jae Park, Michelle Miller, Ellia M. Cox, Julia Taliaferro, Joshua P. Parker, Nathan F. Bhave, Varun Hur, Hong Liang, Yupu Nectow, Alexander R. Pillow, Jonathan W. Witten, Ilana B. Princeton Univ Princeton Neurosci Inst Princeton NJ 08544 USA Princeton Univ Dept Psychol Princeton NJ 08544 USA Princeton Univ Ctr Stat & Machine Learning Princeton NJ 08544 USA Rockefeller Univ CCTS Bioinformat Program New York NY 10065 USA

Social behaviors are crucial to all mammals. Although the prelimbic cortex (PL, part of medial prefrontal cortex) has been implicated in social behavior, it is not clear which neurons are relevant or how they contribute. We found that PL contains anatomically and molecularly distinct subpopulations that target three downstream regions that have been implicated in social behavior: the nucleus accumbens (NAc), amygdala, and ventral tegmental area. Activation of NAc-projecting PL neurons (PL-NAc), but not the other subpopulations, decreased the preference for a social target. To determine what information PL-NAc neurons convey, we selectively recorded from them and found that individual neurons were active during social investigation, but only in specific spatial locations. Spatially specific manipulation of these neurons bidirectionally regulated the formation of a social-spatial association. Thus, the unexpected combination of social and spatial information within the PL-NAc may contribute to social behavior by supporting social-spatial learning.

关键词： social behavior medial prefrontal cortex nucleus accumbens calcium imaging optogenetics

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Transcriptional programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution

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CELL REPORTS 2020年第6期30卷 1767-+页

作者： Aynaud, Marie-Ming Mirabeau, Olivier Gruel, Nadege Grossetete, Sandrine Boeva, Valentina Durand, Simon Surdez, Didier Saulnier, Olivier Zaidi, Sakina Gribkova, Svetlana Fouche, Aziz Kairov, Ulykbek Raynal, Virginie Tirode, Franck Gruenewald, Thomas G. P. Bohec, Mylene Baulande, Sylvain Janoueix-Lerosey, Isabelle Vert, Jean-Philippe Barillot, Emmanuel Delattre, Olivier Zinovyev, Andrei Inst Curie SIREDO Oncol Ctr Quipe Labellisee LNCC INSERMU830 F-75005 Paris France PSL Res Univ Inst Curie Dept Translat Res F-75005 Paris France Univ Paris 05 CNRS Inst Cochin INSERMUMR 8104U1016UMR S1016 F-75014 Paris France Swiss Fed Inst Technol Inst Machine Learning Swiss Inst Bioinformat SIB Dept Comp Sci CH-8092 Zurich Switzerland INSERM U900 F-75005 Paris France PSL Res Univ Mines ParisTech CBIO Ctr Computat Biol F-75006 Paris France PSL Res Univ Inst Curie F-75005 Paris France Univ Paris 07 F-75013 Paris France Ecole Normale Super Paris Saclay F-94230 Cachan France Nazarbayev Univ Natl Lab Astana Ctr Life Sci Lab Bioinformat & Syst Biol Nur Sultan Kazakhstan Univ Claude Bernard Lyon 1 Univ Lyon CNRS 5286 INSERMU1052Canc Res Ctr Lyon F-69008 Lyon France Inst Curie NGS Platform F-75005 Paris France Brain Team F-75009 Paris France Lunenfeld Tanenbaum Res Inst Toronto ON M5G 1X5 Canada Hosp Sick Children Dev & Stem Cell Biol Program Toronto ON M5G 0A4 Canada Hosp Sick Children Arthur & Sonia Labatt Brain Tumour Res Ctr Toronto ON M5G 0A4 Canada Ludwig Maximilians Univ Munchen Inst Pathol Max Eder Res Grp Pediat Sarcoma Biol Fac Med Munich Germany German Canc Consortium DKTK Partner Site Munich Munich Germany German Canc Res Ctr Heidelberg Germany

EWSR1-FLI1, the chimeric oncogene specific for Ewing sarcoma (EwS), induces a cascade of signaling events leading to cell transformation. However, it remains elusive how genetically homogeneous EwS cells can drive the heterogeneity of transcriptional programs. Here, we combine independent component analysis of single-cell RNA sequencing data from diverse cell types and model systems with time-resolved mapping of EWSR1-FLI1 binding sites and of open chromatin regions to characterize dynamic cellular processes associated with EWSR1-FLI1 activity. We thus define an exquisitely specific and direct enhancer-driven EWSR1-FLI1 program. In EwS tumors, cell proliferation and strong oxidative phosphorylation metabolism are associated with a well-defined range of EWSR1-FLI1 activity. In contrast, a subpopulation of cells from below and above the intermediary EWSR1-FLI1 activity is characterized by increased hypoxia. Overall, our study reveals sources of intratumoral heterogeneity within EwS tumors.

关键词： single-cell RNA-sequencing Ewing sarcoma EWSR1-FLI1 intratumor heterogeneity patient-derived xenografts Independent Component Analysis time series transcriptomics

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The SCUBA-2 Large eXtragalactic Survey: 850 μm map, catalogue and the bright-end number counts of the XMM-LSS field

arXiv

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arXiv 2023年

作者： Garratt, T.K. Geach, J.E. Tamura, Y. Coppin, K.E.K. Franco, M. Ao, Y. Chen, C.-C. Cheng, C. Clements, D.L. Dai, Y.S. Dannerbauer, H. Greve, T.R. Hatsukade, B. Hwang, H.S. Jiang, L. Kohno, K. Koprowski, M.P. Michalowski, M.J. Sawicki, M. Scott, D. Shim, H. Takeuchi, T.T. Wang, W.-H. Xue, Y.Q. Yang, C. Centre for Astrophysics Research University of Hertfordshire HatfieldAL10 9AB United Kingdom Division of Particle and Astrophysical Science Nagoya University Aichi Nagoya464-8602 Japan Purple Mountain Observatory Key Laboratory for Radio Astronomy Chinese Academy of Sciences 10 Yuanhua Road Nanjing210023 China School of Astronomy and Space Science University of Science and Technology of China Anhui Hefei230026 China Academia Sinica Institute of Astronomy and Astrophysics No. 1 Section 4 Roosevelt Road Taipei10617 Taiwan Chinese Academy of Sciences South America Center for Astronomy National Astronomical Observatories CAS Beijing100101 China Imperial College London Blackett Lab Prince Consort Road LondonSW7 2AZ United Kingdom National Astronomical Observatories Chinese Academy of Sciences 20A Datun RoadChaoyang District Beijing100101 China Tenerife La LagunaE-38205 Spain Universidad de La Laguna Dpto. Astrofísica Tenerife La LagunaE-38206 Spain National Space Institute DTU Space Technical University of Denmark Elektrovej 327 Kgs. LyngbyDK-2800 Denmark Department of Physics and Astronomy University College London Gower Street LondonWC1E 6BT United Kingdom Institute of Astronomy Graduate School of Science The University of Tokyo 2-21-1 Osawa Tokyo Mitaka181-0015 Japan Astronomy Program Department of Physics and Astronomy Seoul National University 1 Gwanak-ro Gwanak-gu Seoul08826 Korea Republic of SNU Astronomy Research Center Astronomy Program Seoul National University 1 Gwanak-ro Gwanak-gu Seoul08826 Korea Republic of Kavli Institute for Astronomy and Astrophysics Peking University No. 5 Yiheyuan Road Haidian District Beijing100871 China Institute of Astronomy Faculty of Physics Astronomy and Informatics Nicolaus Copernicus University Grudziadzka 5 Torun87-100 Poland Astronomical Observatory Institute Faculty of Physics Adam Mickiewicz University ul. Sloneczna 36 Poznań60-286 Poland Department of Astronomy and P

We present 850 μm imaging of the XMM-LSS field observed for 170 hours as part of the James Clerk Maxwell Telescope SCUBA-2 Large eXtragalactic Survey (S2LXS). S2LXS XMM-LSS maps an area of 9 deg2, reaching a moderate depth of 1σ 4 mJy beam−1. This is the largest contiguous area of extragalactic sky mapped by JCMT at 850 μm to date. The wide area of the S2LXS XMM-LSS survey allows us to probe the ultra-bright (S850μm & 15 mJy), yet rare submillimetre population. We present the S2LXS XMM-LSS catalogue, which comprises 40 sources detected at >5σ significance, with deboosted flux densities in the range of 7 mJy to 48 mJy. We robustly measure the bright-end of the 850 μm number counts at flux densities >7 mJy, reducing the Poisson errors compared to existing measurements. The S2LXS XMM-LSS observed number counts show the characteristic upturn at bright fluxes, expected to be motivated by local sources of submillimetre emission and high-redshift strongly lensed galaxies. We find that the observed 850 μm number counts are best reproduced by model predictions that include either strong lensing or source blending from a 15 arcsec beam, indicating that both may make an important contribution to the observed over-abundance of bright single dish 850 μm selected sources. We make the S2LXS XMM-LSS 850 μm map and >5σ catalogue presented here publicly available. Copyright © 2023, The Authors. All rights reserved.

关键词： Blending

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EMPRESS. IX. Extremely Metal-poor Galaxies are Very Gas-rich Dispersion-dominated Systems: Will the James Webb Space Telescope Witness Gaseous Turbulent High-z Primordial Galaxies?

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ASTROPHYSICAL JOURNAL 2023年第2期951卷 102-102页

作者： Isobe, Yuki Ouchi, Masami Nakajima, Kimihiko Ozaki, Shinobu Bouche, Nicolas F. Wise, John H. Xu, Yi Emsellem, Eric Kusakabe, Haruka Hattori, Takashi Nagao, Tohru Chiaki, Gen Fukushima, Hajime Harikane, Yuichi Hayashi, Kohei Hirai, Yutaka Kim, Ji Hoon Maseda, Michael V. Nagamine, Kentaro Shibuya, Takatoshi Sugahara, Yuma Yajima, Hidenobu Aoyama, Shohei Fujimoto, Seiji Fukushima, Keita Hatano, Shun Inoue, Akio K. Ishigaki, Tsuyoshi Kawasaki, Masahiro Kojima, Takashi Komiyama, Yutaka Koyama, Shuhei Koyama, Yusei Lee, Chien-Hsiu Matsumoto, Akinori Mawatari, Ken Moriya, Takashi J. Motohara, Kentaro Murai, Kai Nishigaki, Moka Onodera, Masato Ono, Yoshiaki Rauch, Michael Saito, Tomoki Sasaki, Rin Suzuki, Akihiro Takeuchi, Tsutomu T. Umeda, Hiroya Umemura, Masayuki Watanabe, Kuria Yabe, Kiyoto Zhang, Yechi Univ Tokyo Inst Cosm Ray Res 5-1-5 Kashiwanoha Kashiwa Chiba 2778582 Japan Univ Tokyo Grad Sch Sci Dept Phys 7-3-1 HongoBunkyo Tokyo 1130033 Japan Natl Astron Observ Japan 2-21-1 Osawa Mitaka Tokyo 1818588 Japan Univ Tokyo Kavli Inst Phys & Math Universe WPI Kashiwa Chiba 2778583 Japan Univ Lyon 1 Univ Lyon Ctr Rech Astrophys Lyon ENS LyonCNRSUMR 5574 F-69230 St Genis Laval France Georgia Inst Technol Ctr Relativist Astrophys Sch Phys Atlanta GA 30332 USA Univ Tokyo Grad Sch Sci Dept Astron 7-3-1 HongoBunkyo Tokyo 1130033 Japan European Southern Observ Karl Schwarzschild Str 2 D-85748 Garching Germany Univ Geneva Observ Geneve 51 Ch Maillettes CH-1290 Versoix Switzerland Natl Inst Nat Sci NINS Natl Astron Observ Japan Subaru Telescope 650 North Aohoku Pl Hilo HI 96720 USA Ehime Univ Res Ctr Space & Cosm Evolut Bunkyo Cho 2-5 Matsuyama Ehime 7908577 Japan Univ Tsukuba Ctr Computat Sci Ten Nodai 1-1-1 Tsukuba Ibaraki 3058577 Japan UCL Dept Phys & Astron Gower St London WC1E 6BT England Ichinoseki Coll Natl Inst Technol Ichinoseki 0218511 Japan Tohoku Univ Astron Inst 6-3 AobaAoba Ku Sendai Miyagi 9808578 Japan Univ Notre Dame Dept Phys & Astron 225 Nieuwland Sci Hall Notre Dame IN 46556 USA Seoul Natl Univ Dept Phys & Astron Astron Program 1 Gwanak Ro Seoul 08826 South Korea Seoul Natl Univ SNU Astron Res Ctr 1 Gwanak Ro Seoul 08826 South Korea Univ Wisconsin Dept Astron 475 N Charter St Madison WI 53706 USA Osaka Univ Grad Sch Sci Dept Earth & Space Sci Theoret Astrophys 1-1 Machikaneyama Toyonaka Osaka 5600043 Japan Univ Nevada Dept Phys & Astron 4505 S Maryland Pkwy Las Vegas NV 89154 USA Kitami Inst Technol 165 Koen Cho Kitami Hokkaido 0908507 Japan Waseda Univ Waseda Res Inst Sci & Engn Fac Sci & Engn 3-4-1 OkuboShinjuku Tokyo 1698555 Japan Chiba Univ Inst Management & Informat Technol 1-33 Yayoi Cho Chiba 2638522 Japan Cosm DAWN Ctr Copenhagen Denmark Univ Copenhagen Niels Bohr Inst Lyngbyvej 2

We present kinematics of six local extremely metal-poor galaxies (EMPGs) with low metallicities (0.016-0.098 Z (& ODOT;)) and low stellar masses (10(4.7)-10(7.6) M (& ODOT;)). Taking deep medium/high-resolution (R & SIM;7500) integral-field spectra with 8.2 m Subaru, we resolve the small inner velocity gradients and dispersions of the EMPGs with H & alpha;emission. Carefully masking out substructures originating by inflow and/or outflow, we fit three-dimensional disk models to the observed H & alpha;flux, velocity, and velocity dispersion maps. All the EMPGs show rotational velocities (v (rot)) of 5-23 km s(-1) smaller than the velocity dispersions (& sigma;(0)) of 17-31 km s(-1), indicating dispersion-dominated (v (rot)/& sigma;(0) = 0.29-0.80 < 1) systems affected by inflow and/or outflow. Except for two EMPGs with large uncertainties, we find that the EMPGs have very large gas-mass fractions of f (gas) & SIME;0.9-1.0. Comparing our results with other H & alpha;kinematics studies, we find that v (rot)/& sigma;(0) decreases and f (gas) increases with decreasing metallicity, decreasing stellar mass, and increasing specific star formation rate. We also find that simulated high-z (z & SIM;7) forming galaxies have gas fractions and dynamics similar to the observed EMPGs. Our EMPG observations and the simulations suggest that primordial galaxies are gas-rich dispersion-dominated systems, which would be identified by the forthcoming James Webb Space Telescope observations at z & SIM;7.

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"I know it when I see it". Visualization and Intuitive Interpretability

arXiv

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arXiv 2017年

作者： Offert, Fabian Machine Learning and the Arts Research Group Media Arts and Technology Program University of California Santa Barbara United States

Most research on the interpretability of machine learning systems focuses on the development of a more rigorous notion of interpretability. I suggest that a better understanding of the deficiencies of the intuitive notion of interpretability is needed as well. I show that visualization enables but also impedes intuitive interpretability, as it presupposes two levels of technical pre-interpretation: dimensionality reduction and regularization. Furthermore, I argue that the use of positive concepts to emulate the distributed semantic structure of machine learning models introduces a significant human bias into the model. As a consequence, I suggest that, if intuitive interpretability is needed, singular representations of internal model states should be avoided. Copyright © 2017, The Authors. All rights reserved.

关键词： Visualization

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Evaluation of Spatial Generalization Characteristics of a Robust Classifier as Applied to Coral Reef Habitats in Remote Islands of the Pacific Ocean

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REMOTE SENSING 2018年第11期10卷 1774-1774页

作者： Gapper, Justin J. El-Askary, Hesham Linstead, Erik Piechota, Thomas Chapman Univ Schmid Coll Sci & Technol Computat & Data Sci Grad Program Orange CA 92866 USA Chapman Univ Ctr Excellence Earth Syst Modeling & Observat Orange CA 92866 USA Chapman Univ Schmid Coll Sci & Technol Orange CA 92866 USA Alexandria Univ Fac Sci Dept Environm Sci Alexandria 21522 Egypt Chapman Univ Machine Learning & Assist Technol Lab MLAT Orange CA 92866 USA

This study was an evaluation of the spectral signature generalization properties of coral across four remote Pacific Ocean reefs. The sites under consideration have not been the subject of previous studies for coral classification using remote sensing data. Previous research regarding using remote sensing to identify reefs has been limited to in-situ assessment, with some researchers also performing temporal analysis of a selected area of interest. This study expanded the previous in-situ analyses by evaluating the ability of a basic predictor, Linear Discriminant Analysis (LDA), trained on Depth Invariant Indices calculated from the spectral signature of coral in one location to generalize to other locations, both within the same scene and in other scenes. Three Landsat 8 scenes were selected and masked for null, land, and obstructed pixels, and corrections for sun glint and atmospheric interference were applied. Depth Invariant Indices (DII) were then calculated according to the method of Lyzenga and an LDA classifier trained on ground truth data from a single scene. The resulting LDA classifier was then applied to other locations and the coral classification accuracy evaluated. When applied to ground truth data from the Palmyra Atoll location in scene path/row 065/056, the initial model achieved an accuracy of 80.3%. However, when applied to ground truth observations from another location within the scene, namely, Kingman Reef, it achieved an accuracy of 78.6%. The model was then applied to two additional scenes (Howland Island and Baker Island Atoll), which yielded an accuracy of 69.2% and 71.4%, respectively. Finally, the algorithm was retrained using data gathered from all four sites, which produced an overall accuracy of 74.1%.

关键词： coral detection classification spectral signature expansion benthic habitat mapping Landsat 8

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The Spatiotemporal Organization of the Striatum Encodes Action Space

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NEURON 2017年第5期95卷 1171-+页

作者： Klaus, Andreas Martins, Gabriela J. Paixao, Vitor B. Zhou, Pengcheng Paninski, Liam Costa, Rui M. Champalimaud Fdn Champalimaud Neurosci Program P-1400038 Lisbon Portugal Carnegie Mellon Univ Ctr Neural Basis Cognit Pittsburgh PA 15213 USA Carnegie Mellon Univ Machine Learning Dept Pittsburgh PA 15213 USA Columbia Univ Dept Stat New York NY 10027 USA Columbia Univ Dept Neurosci Zuckerman Mind Brain Behav Inst New York NY 10027 USA

Activity in striatal direct-and indirect-pathway spiny projection neurons (SPNs) is critical for proper movement. However, little is known about the spatiotemporal organization of this activity. We investigated the spatiotemporal organization of SPN ensemble activity in mice during self-paced, natural movements using microendoscopic imaging. Activity in both pathways showed predominantly local but also some long-range correlations. Using a novel approach to cluster and quantify behaviors based on continuous accelerometer and video data, we found that SPN ensembles active during specific actions were spatially closer and more correlated overall. Furthermore, similarity between different actions corresponded to the similarity between SPN ensemble patterns, irrespective of movement speed. Consistently, the accuracy of decoding behavior from SPN ensemble patterns was directly related to the dissimilarity between behavioral clusters. These results identify a predominantly local, but not spatially compact, organization of direct- and indirect-pathway SPN activity that maps action space independently of movement speed.

关键词： basal ganglia direct pathway indirect pathway caudate putamen calcium imaging neural correlation population activity action space behavior decoding

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Author Correction: Concordance of randomised controlled trials for artificial intelligence interventions with the CONSORT-AI reporting guidelines

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Nature communications 2024年第1期15卷 6376页

作者： Alexander P L Martindale Carrie D Llewellyn Richard O de Visser Benjamin Ng Victoria Ngai Aditya U Kale Lavinia Ferrante di Ruffano Robert M Golub Gary S Collins David Moher Melissa D McCradden Lauren Oakden-Rayner Samantha Cruz Rivera Melanie Calvert Christopher J Kelly Cecilia S Lee Christopher Yau An-Wen Chan Pearse A Keane Andrew L Beam Alastair K Denniston Xiaoxuan Liu Brighton and Sussex Medical School Brighton UK. Department of Primary Care and Public Health Brighton and Sussex Medical School Brighton UK. Birmingham and Midland Eye Centre Sandwell and West Birmingham NHS Trust Birmingham UK. Christ Church University of Oxford Oxford UK. University College London Medical School London UK. Institute of Inflammation and Ageing University of Birmingham Birmingham UK. University Hospitals Birmingham NHS Foundation Trust Birmingham UK. National Institute for Health and Care Research (NIHR) Birmingham Biomedical Research Centre University of Birmingham Birmingham UK. York Health Economics Consortium University of York Birmingham UK. Northwestern University Feinberg School of Medicine Chicago Illinois USA. Centre for Statistics in Medicine//UK EQUATOR Centre Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK. Centre for Journalology Clinical Epidemiology Program Ottawa Hospital Research Institute Ottowa Canada. Department of Bioethics The Hospital for Sick Children Toronto Canada. Genetics & Genome Biology Research Program Peter Gilgan Centre for Research & Learning Toronto Canada. Division of Clinical and Public Health Dalla Lana School of Public Health Toronto Canada. Australian Institute for Machine Learning University of Adelaide Adelaide Australia. Birmingham Health Partners Centre for Regulatory Science and Innovation University of Birmingham Birmingham UK. Centre for Patient Reported Outcomes Research (CPROR) Institute of Applied Health Research College of Medical and Dental Sciences University of Birmingham Birmingham UK. NIHR Applied Research Collaboration (ARC) West Midlands University of Birmingham Birmingham UK. NIHR Blood and Transplant Research Unit (BTRU) in Precision Transplant and Cellular Therapeutics University of Birmingham Birmingham UK. Google Health London UK. University of Washington Seattle WA USA. Nuffield Department of Women's and Rep

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Reflections on the past two decades of neuroscience

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NATURE REVIEWS NEUROSCIENCE 2020年第10期21卷 524-534页

作者： Bassett, Danielle S. Cullen, Kathleen E. Eickhoff, Simon B. Farah, Martha J. Goda, Yukiko Haggard, Patrick Hu, Hailan Hurd, Yasmin L. Josselyn, Sheena A. Khakh, Baljit S. Knoblich, Juergen A. Poirazi, Panayiota Poldrack, Russell A. Prinz, Marco Roelfsema, Pieter R. Spires-Jones, Tara L. Sur, Mriganka Ueda, Hiroki R. Univ Penn Dept Bioengn Philadelphia PA 19104 USA Univ Penn Dept Elect & Syst Engn Philadelphia PA 19104 USA Univ Penn Dept Phys & Astron Philadelphia PA 19104 USA Univ Penn Dept Neurol Philadelphia PA 19104 USA Univ Penn Dept Psychiat Philadelphia PA 19104 USA Santa Fe Inst Santa Fe NM 87501 USA Johns Hopkins Univ Dept Biomed Engn Baltimore MD 21218 USA Johns Hopkins Univ Dept Otolaryngol Head & Neck Surg Baltimore MD 21218 USA Johns Hopkins Univ Dept Neurosci Baltimore MD 21218 USA Heinrich Heine Univ Dusseldorf Med Fac Inst Syst Neurosci Dusseldorf Germany Res Ctr Julich Inst Neurosci & Med Brain & Behav INM 7 Julich Germany Univ Penn Ctr Neurosci & Soc Philadelphia PA 19104 USA RIKEN Ctr Brain Sci Lab Synapt Plast & Connect Wako Saitama Japan UCL Inst Cognit Neurosci London England Zhejiang Univ Sch Med Dept Psychiat Sch Brain Sci & Brain MedAffiliated Hosp 1 Hangzhou Peoples R China MOE Frontier Res Ctr Brain Brain Machine Integrat Zhejiang Lab Syst & Precis Med Hangzhou Peoples R China Icahn Sch Med Mt Sinai Dept Psychiat Addict Inst Mt Sinai New York NY 10029 USA Icahn Sch Med Mt Sinai Dept Neurosci Addict Inst Mt Sinai New York NY 10029 USA Hosp Sick Children Program Neurosci & Mental Hlth Toronto ON Canada Univ Toronto Physiol Dept Psychol Toronto ON Canada Univ Toronto Inst Med Sci Toronto ON Canada Canadian Inst Adv Res CIFAR Brain Mind & Consciousness Program Toronto ON Canada Univ Calif Los Angeles David Geffen Sch Med Dept Psychol Los Angeles CA 90095 USA Austrian Acad Sci IMBA Inst Mol Biotechnol Vienna BioCtr VBC Vienna Austria Fdn Res & Technol Hellas FORTH Inst Mol Biol & Biotechnol IMBB Iraklion Crete Greece Stanford Univ Dept Psychol Stanford CA 94305 USA Univ Freiburg Med Fac Inst Neuropathol Freiburg Germany Univ Freiburg Signalling Res Ctr BIOSS & CIBSS Freiburg Germany Univ Freiburg Ctr Basics NeuroModulat NeuroModulBasics Fac Med Freiburg Germany Netherlands Inst Neurosci Dept Vis & Cog

The first issue ofNature Reviews Neurosciencewas published 20 years ago, in 2000. To mark this anniversary, in this Viewpoint article we asked a selection of researchers from across the field who have authored pieces published in the journal in recent years for their thoughts on notable and interesting developments in neuroscience, and particularly in their areas of the field, over the past two decades. They also provide some thoughts on current lines of research and questions that excite them.

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DeePMD-kit v2: A software package for deep potential models

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JOURNAL OF CHEMICAL PHYSICS 2023年第5期159卷 054801-054801页

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marian 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, Sigbjorn Loland 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. E, Weinan Car, Roberto Zhang, Linfeng Wang, Han Rutgers State Univ Inst Quantitat Biomed Lab Biomol Simulat Res Piscataway NJ 08854 USA Rutgers State Univ Dept Chem & Chem Biol Piscataway NJ 08854 USA AI Sci Inst Beijing 100080 Peoples R China DP Technol Beijing 100080 Peoples R China Peking Univ Acad Adv Interdisciplinary Studies Beijing 100871 Peoples R China Peking Univ Coll Engn HEDPS CAPT Beijing 100871 Peoples R China Hunan Univ Coll Elect & Informat Engn Changsha Peoples R China Peking Univ Yuanpei Coll Beijing 100871 Peoples R China Princeton Univ Program Appl & Computat Math Princeton NJ 08540 USA Comenius Univ Dept Expt Phys Mlynska Dolina F2 Bratislava 84248 Slovakia Tsinghua Univ Inst Interdisciplinary Informat Sci Ctr Quantum Informat Beijing 100084 Peoples R China Peking Univ Ctr Data Sci Beijing 100871 Peoples R China ByteDance Res Zhonghang Plaza43 North 3rd Ring West Rd Beijing Peoples R China Peking Univ Coll Chem & Mol Engn Beijing 100871 Peoples R China Baidu Inc Beijing Peoples R China Westlake Univ Sch Life Sci Key Lab Struct Biol Zhejiang Prov Hangzhou Zhejiang Peoples R China Westlake Lab Life Sci & Biomed Westlake AI Therapeut Lab Hangzhou Zhejiang Peoples R China Princeton Univ Dept Chem Princeton NJ 08544 USA SISSA I-34136 Trieste Italy Ecole Polytech Fed Lausanne Inst Mat Lab Computat Sci & Modeling CH-1015 Lausanne Switzerland Natl Univ Def Technol Dept Phys Changsha 410073 Hunan Peoples R China Chinese Acad Sci Inst Comp Technol State Key Lab Processors Beijing Peoples R China Univ Chinese Acad Sci Beijing Peoples R China Peking Univ Sch Elect Engn & Comp Sci Beijing 100871 Peoples R China Univ Tokyo Dept Chem Syst Engn 7-3-1 HongoBunkyo Ku Tokyo 1138656 Japan Univ Oslo Hylleraas Ctr Quantum Mol Sci POB 1033 Blindern N-0315 Oslo Norway Univ Oslo Dept Chem POB 1033 Blindern N-0315 Oslo Norway Peking Univ Wangxuan Inst Comp Technol Beijing 100871 Peoples R China East China Normal Univ Shanghai Engn Res Ctr Mol Therapeut & New Drug Dev S

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials 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, DP-range correction, DP long range, graphics processing unit support for customized operators, model compression, non-von Neumann molecular dynamics, and improved usability, including documentation, compiled binary packages, graphical user interfaces, and application programming interfaces. This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, this article presents a comprehensive procedure for conducting molecular dynamics as a representative application, benchmarks the accuracy and efficiency of different models, and discusses ongoing developments.

关键词： Molecular dynamics

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