Array Programming with NumPy
Charles R. Harris,K. Jarrod Millman,Stefan van der Walt,Stefan van der Walt,Ralf Gommers,Pauli Virtanen,David Cournapeau,Eric Wieser,Julian Taylor,Sebastian Berg,Nathaniel J. Smith,Robert Kern,Matti Picus,Stephan Hoyer,Marten H. van Kerkwijk,Matthew Brett,Matthew Brett,Allan Haldane,Jaime Fernández del Río,Mark Wiebe,Mark Wiebe,Pearu Peterson,Pierre Gérard-Marchant,Kevin Sheppard,Tyler Reddy,Warren Weckesser,Hameer Abbasi,Christoph Gohlke,Travis E. Oliphant +28 more
TLDR
How a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data is reviewed.Abstract:
Array programming provides a powerful, compact, expressive syntax for accessing, manipulating, and operating on data in vectors, matrices, and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It plays an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, material science, engineering, finance, and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves and the first imaging of a black hole. Here we show how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring, and analyzing scientific data. NumPy is the foundation upon which the entire scientific Python universe is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Because of its central position in the ecosystem, NumPy increasingly plays the role of an interoperability layer between these new array computation libraries.read more
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Robust Speech Recognition via Large-Scale Weak Supervision
TL;DR: The capabilities of speech processing systems trained simply to predict large amounts of transcripts of audio on the internet are studied, with results that are often competitive with prior fully supervised results but in a zero-shot transfer setting without the need for any fine-tuning.
Journal ArticleDOI
The Astropy Project: Sustaining and Growing a Community-oriented Open-source Project and the Latest Major Release (v5.0) of the Core Package
The Astropy Collaboration,Adrian M. Price-Whelan,Pey Lian Lim,Nicholas Earl,Nathaniel Starkman,Larry Bradley,David L. Shupe,Aarya A. Patil,Lia Corrales,C. E. Brasseur,M. Nöthe,Axel Donath,Erik Tollerud,Brett M. Morris,Adam Ginsburg,Eero Vaher,B. A. Weaver,James Tocknell,William Jamieson,M. H. van Kerkwijk,Thomas P. Robitaille,Bruce Merry,Matteo Bachetti,H. M. Gunther,Tom Aldcroft,Jaime A. Alvarado-Montes,Anne M. Archibald,A. B'odi,Shreyas Bapat,Geert Barentsen,Juanjo Baz'an,Manish J Biswas,Médéric Boquien,D. J. Burke,D Di Cara,Mihai Cara,Kyle E. Conroy,Simon Conseil,Matt Craig,Robert M. Cross,Kelle L. Cruz,Francesco D'Eugenio,Nadia Dencheva,Hadrien A. R. Devillepoix,J. P. Dietrich,Arthur Eigenbrot,Thomas Erben,Leonardo Ferreira,Daniel Foreman-Mackey,R. T. Fox,Nabil Freij,Suyog Garg,Robel Geda,Lauren Glattly,Yash Gondhalekar,Karl D. Gordon,David Grant,Perry Greenfield,A. M. Groener,S. Guest,Sebastián Gurovich,Rasmus Handberg,Akeem Hart,Zac Hatfield-Dodds,Derek Homeier,Griffin Hosseinzadeh,Tim Jenness,Craig Jones,Prajwel Joseph,J. Bryce Kalmbach,Emir Karamehmetoglu,M. Kaluszy'nski,Michaelann Kelley,Nicholas S. Kern,Wolfgang Kerzendorf,Eric W. Koch,Shankar Kulumani,Antony H. Lee,Chun Ly,Zhiyuan Mao,Conor D. MacBride,Jakob M. Maljaars,Demitri Muna,Nellie Appy Murphy,Henrik Norman,R. G. O'Steen,Kyle A. Oman,Camilla Pacifici,Sergio Pascual,J. Pascual-Granado,Rohit R Patil,G. I. Perren,T. E. Pickering,Tanuja Rastogi,Benjamin R. Roulston,Daniel F Ryan,Eli S. Rykoff,J. Sabater,Parikshit Sakurikar,Jesús Busto Salgado,Aniket Sanghi,Nicholas Saunders,V. G. Savchenko,L. C. Schwardt,Michael Seifert-Eckert,Albert J. Shih,A. S. Jain,G. R. Shukla,J. Sick,Chris Simpson,Sudheesh Singanamalla,Leo Singer,Jaladh Singhal,Manodeep Sinha,B. SipHocz,Lee R. Spitler,David Stansby,Ole Streicher,Jani vSumak,John D. Swinbank,Dan S. Taranu,N. B. Tewary,Grant R. Tremblay,Miguel De Val-Borro,Samuel J. Van Kooten,Zlatan Vasovi'c,Shresth Verma,José Vinícius de Miranda Cardoso,Peter K. G. Williams,Tom J. Wilson,Benjamin Winkel,W. M. Wood-Vasey,Rui Xue,Peter Yoachim,Chenchen Zhang,Andrea Zonca +135 more
TL;DR: Astropy as mentioned in this paper is a Python package that provides commonly needed functionality to the astronomical community, such as astronomy, astronomy, and astronomy data visualization, as well as other related projects and packages.
Journal ArticleDOI
Squidpy: a scalable framework for spatial omics analysis
Giovanni Palla,Hannah Spitzer,Michal Klein,David Fischer,A. C. Schaar,L. B. Kuemmerle,Sergei Rybakov,Ignacio L. Ibarra,Olle Holmberg,I H Virshup,Mohammad Lotfollahi,Sabrina Richter,Fabian J. Theis +12 more
TL;DR: Squid as discussed by the authors is a Python framework that brings together tools from omics and image analysis to enable scalable description of spatial molecular data, such as transcriptome or multivariate proteins. Squidpy provides efficient infrastructure and numerous analysis methods that allow to efficiently store, manipulate and interactively visualize spatial omics data.
Journal ArticleDOI
First Sagittarius A* Event Horizon Telescope Results. III. Imaging of the Galactic Center Supermassive Black Hole
Event Horizon Telescope Collaboration,Kazunori Akiyama,A. Alberti,Walter Alef,Juan-Carlos Algaba,Richard Anantua,Keiichi Asada,Rebecca Azulay,Uwe Bach,A-K. Baczko,David Ball,Mislav Baloković,John E. Barrett,M. Bauböck,Bradford Benson,Dan Bintley,Lindy Blackburn,Ray Blundell,Katherine L. Bouman,Geoffrey C. Bower,Hope Boyce,Michael Kremer,Christiaan D. Brinkerink,Roger Brissenden,Silke Britzen,Avery E. Broderick,Dominique Broguiere,Thomas Bronzwaer,Sandra Bustamante,Do-Young Byun,John E. Carlstrom,Chiara Ceccobello,Andrew Chael,Chi-kwan Chan,Koushik Chatterjee,Shami Chatterjee,Ming-Tang Chen,Y. Chen 陈,Xiaopeng Cheng,Ilje Cho,Pierre Christian,Nicholas S. Conroy,John Conway,James M. Cordes,T. M. Crawford,Geoffrey B. Crew,Alejandro Cruz-Osorio,Y. Cui 崔,Jordy Davelaar,M. De Laurentis,Roger Deane,Jessica Dempsey,Gregory Desvignes,Jason Dexter,Vedant Dhruv,Sheperd S. Doeleman,Shawn M. Dougal,Sergio A. Dzib,R. P. Eatough,Razieh Emami,Heino Falcke,Joseph R. Farah,Vincent L. Fish,Ed Fomalont,H. A. Ford,Raquel Fraga-Encinas,William T. Freeman,Per Friberg,Christian M. Fromm,Antonio Fuentes,Peter Galison,Charles F. Gammie,R. García,Olivier Gentaz,Boris Georgiev,Ciriaco Goddi,Roman Gold,Arturo I. Gómez-Ruiz,J. A. Gomez,M. Gu 顾,Mark Gurwell,Kazuhiro Hada,Daryl Haggard,Kari Haworth,Michael Pecht,Ronald Hesper,D. Heumann,L. Ho 何,Paul T. P. Ho,Mareki Honma,Chih-Wei Locutus Huang,L. Huang 黄,David H. Hughes,Shiro Ikeda,Caterina M. V. Impellizzeri,Makoto Inoue,Sara Issaoun,David J. James,Buell T. Jannuzi,Michael Janssen,Britton Jeter,Wu 悟 Jiang 江,A. Jiménez-Rosales,Michael D. Johnson,Svetlana G. Jorstad,Abhishek V. Joshi,Taehyun Jung,Mansour Karami,Ramesh Karuppusamy,Tomohisa Kawashima,Garrett K. Keating,Mark Kettenis,Dong-Jin Kim,Jae-Young Kim,Jongsoo Kim,Junhan Kim,Motoki Kino,Jun Yi Koay,Prashant Kocherlakota,Yutaro Kofuji,Patrick M. Koch,Shoko Koyama,Carsten Kramer,Michael Kramer,Thomas P. Krichbaum,C. Y. Kuo,N Bella,Tod R. Lauer,Daeyoung Lee,Sang-Sung Lee,Po Kin Leung,Aviad Levis,Z. Li 李,Rocco Lico,Greg Lindahl,Michael Lindqvist,Mikhail M. Lisakov,J. Liu 刘,Kuo Liu,Elisabetta Liuzzo,W. Lo,Andrei Lobanov,Laurent Loinard,C. Lonsdale,R. Lu 路,J. Mao 毛,Nicola Marchili,Sera Markoff,Daniel P. Marrone,Alan P. Marscher,Ivan Marti-Vidal,Satoki Matsushita,Lynn D. Matthews,Lia Medeiros,Karl M. Menten,Daniel Michalik,Izumi Mizuno,Yosuke Mizuno,James M. Moran,Kotaro Moriyama,Monika Moscibrodzka,Cornelia Müller,Alejandro Mus,Gibwa Musoke,Ioannis Myserlis,A. Nadolski,Hiroshi Nagai,Neil M. Nagar,Masanori Nakamura,Ramesh Narayan,Gopal Narayanan,Iniyan Natarajan,Antonios Nathanail,Santiago Navarro Fuentes,Joseph Neilsen,R. Neri,Chunchong Ni,A. Noutsos,Michael A. Nowak,Junghwan Oh,Hiroki Okino,Hector Olivares,Gisela N. Ortiz-León,Tomoaki Oyama,Feryal Özel,Daniel C. M. Palumbo,G. F. Paraschos,Jong-Ho Park,Harriet Parsons,Nimesh A. Patel,Ue Li Pen,Dominic W. Pesce,Vincent Piétu,Richard L. Plambeck,Aleksandar Popstefanija,Oliver Porth,Felix M. Pötzl,Ben Prather,Jorge A. Preciado-López,Dimitrios Psaltis,Hung-Yi Pu,Venkatessh Ramakrishnan,Ramprasad Rao,Mark G. Rawlings,Alexander W. Raymond,Luciano Rezzolla,Angelo Ricarte,Bart Ripperda,Freek Roelofs,Alan E. E. Rogers,E. Ros,C. Romero-Canizales,Arash Roshanineshat,Helge Rottmann,Alan L. Roy,Ignacio Ruiz,Chet Ruszczyk,Kazi L.J. Rygl,S. Sánchez,D. Sánchez-Argüelles,M. Sánchez-Portal,Mahito Sasada,Kaushik Satapathy,Tuomas Savolainen,F. Peter Schloerb,Jonathan F. Schonfeld,Karl Schuster,Lijing Shao,Z. Shen 沈,Des Small,Bong Won Sohn,Jason SooHoo,Kamal Souccar,H. Sun 孙,Fumie Tazaki,Alexandra J. Tetarenko,Paul Tiede,Remo P. J. Tilanus,Michael Titus,Pablo Torne,Efthalia Traianou,Tyler Trent,Sascha Trippe,Matthew Turk,I. van Bemmel,H. J. van Langevelde,Daniel R. van Rossum,J. Vos,Jan Wagner,Derek Ward-Thompson,John F. C. Wardle,Jonathan Weintroub,Norbert Wex,Robert Wharton,Maciek Wielgus,Kaj Wiik,Gunther Witzel,Michael F. Wondrak,George N. Wong,Q. Wu 吴,Paul Yamaguchi,Doosoo Yoon,André Young,Ken H. Young,Ziri Younsi,F. Yuan 袁,Y. Yuan 袁,J. A. Zensus,Shuo Zhang,Guang-Yao Zhao,Shan-Shan 杉杉 Zhao 赵 +270 more
TL;DR: In this article , the authors presented the first event-horizon-scale images and spatiotemporal analysis of Sgr A* taken with the Event Horizon Telescope in 2017 April at a wavelength of 1.3 mm.
Journal ArticleDOI
Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging
Michele Gabriele,Hugo B. Brandão,Simon Grosse-Holz,Asmita Jha,Gina M. Dailey,Claudia Cattoglio,Tsung-Han S. Hsieh,Leonid A. Mirny,Christoph Peter Gerhard Zechner,Anders J. Hansen +9 more
TL;DR: The results establish that the Fbn2 TAD is highly dynamic, and about 92% of the time, cohesin-extruded loops exist within the TAD without bridging both CTCF boundaries, which suggests that single CTCf boundaries, rather than the fully C TCF-CTCF looped state, may be the primary regulators of functional interactions.
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TL;DR: Astropy as discussed by the authors is a Python package for astronomy-related functionality, including support for domain-specific file formats such as flexible image transport system (FITS) files, Virtual Observatory (VO) tables, common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions.
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