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
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TLDR
In this paper, the authors review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data, and their evolution into a flexible interoperability layer between increasingly specialized computational libraries is discussed.Abstract:
Array programming provides a powerful, compact and 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 has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves1 and in the first imaging of a black hole2. Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis. NumPy is the primary array programming library for Python; here its fundamental concepts are reviewed and its evolution into a flexible interoperability layer between increasingly specialized computational libraries is discussed.read more
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Highly accurate protein structure prediction with AlphaFold
John M. Jumper,Richard O. Evans,Alexander Pritzel,Tim Green,Michael Figurnov,Olaf Ronneberger,Kathryn Tunyasuvunakool,Russell Bates,Augustin Žídek,Anna Potapenko,Alex Bridgland,Clemens Meyer,Simon A. A. Kohl,Andrew J. Ballard,Andrew Cowie,Bernardino Romera-Paredes,Stanislav Nikolov,R. D. Jain,Jonas Adler,Trevor Back,Stig Petersen,David Reiman,Ellen Clancy,Michal Zielinski,Martin Steinegger,Michalina Pacholska,Tamas Berghammer,Sebastian Bodenstein,David L. Silver,Oriol Vinyals,Andrew W. Senior,Koray Kavukcuoglu,Pushmeet Kohli,Demis Hassabis +33 more
TL;DR: For example, AlphaFold as mentioned in this paper predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture. But the accuracy is limited by the fact that no homologous structure is available.
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The Observation of Gravitational Waves from a Binary Black Hole Merger
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Journal ArticleDOI
seaborn: statistical data visualization
seaborn: Statistical data visualization
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TL;DR: Seaborn as discussed by the authors is a library for making statistical graphics in Python that provides a high-level interface to matplotlib and integrates closely with pandas data structures, which makes it easy to translate questions about data into graphics that can answer them.
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Cellpose: a generalist algorithm for cellular segmentation
TL;DR: This work introduces a generalist, deep learning-based segmentation method called Cellpose, which can precisely segment cells from a wide range of image types and does not require model retraining or parameter adjustments.
References
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Journal ArticleDOI
The NumPy Array: A Structure for Efficient Numerical Computation
TL;DR: In this article, the authors show how to improve the performance of NumPy arrays through vectorizing calculations, avoiding copying data in memory, and minimizing operation counts, which is a technique similar to the one described in this paper.
Journal ArticleDOI
SciPy 1.0: fundamental algorithms for scientific computing in Python.
Pauli Virtanen,Ralf Gommers,Travis E. Oliphant,Matt Haberland,Matt Haberland,Tyler Reddy,David Cournapeau,Evgeni Burovski,Pearu Peterson,Warren Weckesser,Jonathan Bright,Stefan van der Walt,Matthew Brett,Joshua Wilson,K. Jarrod Millman,Nikolay Mayorov,Andrew Nelson,Eric Jones,Robert Kern,Eric B. Larson,CJ Carey,Ilhan Polat,Yu Feng,Eric Moore,Jake Vanderplas,Denis Laxalde,Josef Perktold,Robert Cimrman,Ian Henriksen,Ian Henriksen,E. A. Quintero,Charles R. Harris,Anne M. Archibald,Antônio H. Ribeiro,Fabian Pedregosa,Paul van Mulbregt,SciPy . Contributors +36 more
TL;DR: SciPy as discussed by the authors is an open-source scientific computing library for the Python programming language, which has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year.
Proceedings ArticleDOI
Data Structures for Statistical Computing in Python
TL;DR: P pandas is a new library which aims to facilitate working with data sets common to finance, statistics, and other related fields and to provide a set of fundamental building blocks for implementing statistical models.
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Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator
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TensorFlow: A system for large-scale machine learning
Martín Abadi,Paul Barham,Jianmin Chen,Zhifeng Chen,Andy Davis,Jeffrey Dean,Matthieu Devin,Sanjay Ghemawat,Geoffrey Irving,Michael Isard,Manjunath Kudlur,Josh Levenberg,Rajat Monga,Sherry Moore,Derek G. Murray,Benoit Steiner,Paul A. Tucker,Vijay K. Vasudevan,Pete Warden,Martin Wicke,Yuan Yu,Xiaoqiang Zheng +21 more
TL;DR: The TensorFlow dataflow model is described and the compelling performance that Tensor Flow achieves for several real-world applications is demonstrated.
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