Author
Pearu Peterson
Bio: Pearu Peterson is an academic researcher from Tallinn University of Technology. The author has contributed to research in topics: Python (programming language) & Soliton. The author has an hindex of 18, co-authored 37 publications receiving 21177 citations.
Papers
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University of Jyväskylä1, California Polytechnic State University2, University of California, Los Angeles3, Los Alamos National Laboratory4, National Research University – Higher School of Economics5, University of California, Berkeley6, University of Birmingham7, Australian Nuclear Science and Technology Organisation8, University of Washington9, University of Massachusetts Amherst10, University of West Bohemia11, University of Texas at Austin12, Brigham Young University13, Universidade Federal de Minas Gerais14, Google15
TL;DR: SciPy as discussed by the authors is an open source scientific computing library for the Python programming language, which includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics.
Abstract: SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging scientific algorithms in the Python programming language, with more than 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories, and millions of downloads per year. This includes usage of SciPy in almost half of all machine learning projects on GitHub, and usage by high profile projects including LIGO gravitational wave analysis and creation of the first-ever image of a black hole (M87). The library includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics. In this work, we provide an overview of the capabilities and development practices of the SciPy library and highlight some recent technical developments.
12,774 citations
University of California, Berkeley1, Stellenbosch University2, University of Jyväskylä3, University of Cambridge4, Google5, University of Toronto6, University of Birmingham7, Temple University8, Amazon.com9, University of British Columbia10, University of Georgia11, University of Oxford12, Los Alamos National Laboratory13, University of California, Irvine14
TL;DR: 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.
7,624 citations
University of Jyväskylä1, California Polytechnic State University2, University of California, Los Angeles3, Los Alamos National Laboratory4, National Research University – Higher School of Economics5, University of California, Berkeley6, University of Birmingham7, Australian Nuclear Science and Technology Organisation8, University of Washington9, University of Massachusetts Amherst10, University of West Bohemia11, Brigham Young University12, University of Texas at Austin13, Universidade Federal de Minas Gerais14, Google15
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.
Abstract: SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy 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. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.
6,244 citations
University of California, Berkeley1, Stellenbosch University2, University of Jyväskylä3, University of Cambridge4, Google5, University of Toronto6, University of Birmingham7, Temple University8, University of British Columbia9, Amazon.com10, University of Georgia11, University of Oxford12, Los Alamos National Laboratory13, University of California, Irvine14
TL;DR: 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.
4,342 citations
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28 Oct 2017
TL;DR: An automatic differentiation module of PyTorch is described — a library designed to enable rapid research on machine learning models that focuses on differentiation of purely imperative programs, with a focus on extensibility and low overhead.
Abstract: In this article, we describe an automatic differentiation module of PyTorch — a library designed to enable rapid research on machine learning models. It builds upon a few projects, most notably Lua Torch, Chainer, and HIPS Autograd [4], and provides a high performance environment with easy access to automatic differentiation of models executed on different devices (CPU and GPU). To make prototyping easier, PyTorch does not follow the symbolic approach used in many other deep learning frameworks, but focuses on differentiation of purely imperative programs, with a focus on extensibility and low overhead. Note that this preprint is a draft of certain sections from an upcoming paper covering all PyTorch features.
13,268 citations
University of Jyväskylä1, University of California, Los Angeles2, California Polytechnic State University3, Los Alamos National Laboratory4, National Research University – Higher School of Economics5, University of California, Berkeley6, University of Birmingham7, Australian Nuclear Science and Technology Organisation8, University of Washington9, University of Massachusetts Amherst10, University of West Bohemia11, Brigham Young University12, University of Texas at Austin13, Universidade Federal de Minas Gerais14, Google15
TL;DR: SciPy as discussed by the authors is an open source scientific computing library for the Python programming language, which includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics.
Abstract: SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging scientific algorithms in the Python programming language, with more than 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories, and millions of downloads per year. This includes usage of SciPy in almost half of all machine learning projects on GitHub, and usage by high profile projects including LIGO gravitational wave analysis and creation of the first-ever image of a black hole (M87). The library includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics. In this work, we provide an overview of the capabilities and development practices of the SciPy library and highlight some recent technical developments.
12,774 citations
Posted Content•
TL;DR: PyTorch as discussed by the authors is a machine learning library that provides an imperative and Pythonic programming style that makes debugging easy and is consistent with other popular scientific computing libraries, while remaining efficient and supporting hardware accelerators such as GPUs.
Abstract: Deep learning frameworks have often focused on either usability or speed, but not both. PyTorch is a machine learning library that shows that these two goals are in fact compatible: it provides an imperative and Pythonic programming style that supports code as a model, makes debugging easy and is consistent with other popular scientific computing libraries, while remaining efficient and supporting hardware accelerators such as GPUs.
In this paper, we detail the principles that drove the implementation of PyTorch and how they are reflected in its architecture. We emphasize that every aspect of PyTorch is a regular Python program under the full control of its user. We also explain how the careful and pragmatic implementation of the key components of its runtime enables them to work together to achieve compelling performance.
We demonstrate the efficiency of individual subsystems, as well as the overall speed of PyTorch on several common benchmarks.
12,767 citations
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.
Abstract: Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort1–4, the structures of around 100,000 unique proteins have been determined5, but this represents a small fraction of the billions of known protein sequences6,7. Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence—the structure prediction component of the ‘protein folding problem’8—has been an important open research problem for more than 50 years9. Despite recent progress10–14, existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14)15, demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm. AlphaFold predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture.
10,601 citations
Proceedings Article•
01 Jan 2019
TL;DR: This paper details the principles that drove the implementation of PyTorch and how they are reflected in its architecture, and explains how the careful and pragmatic implementation of the key components of its runtime enables them to work together to achieve compelling performance.
Abstract: Deep learning frameworks have often focused on either usability or speed, but not both. PyTorch is a machine learning library that shows that these two goals are in fact compatible: it was designed from first principles to support an imperative and Pythonic programming style that supports code as a model, makes debugging easy and is consistent with other popular scientific computing libraries, while remaining efficient and supporting hardware accelerators such as GPUs. In this paper, we detail the principles that drove the implementation of PyTorch and how they are reflected in its architecture. We emphasize that every aspect of PyTorch is a regular Python program under the full control of its user. We also explain how the careful and pragmatic implementation of the key components of its runtime enables them to work together to achieve compelling performance. We demonstrate the efficiency of individual subsystems, as well as the overall speed of PyTorch on several commonly used benchmarks.
10,045 citations