Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

SciPy 1.0: fundamental algorithms for scientific computing in Python

Journal Article · · Nature Methods
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [9];  [11];  [12];  [9];  [13];  [14];  [15];  [15];  [16];  [17] more »;  [18];  [19];  [20];  [16];  [21];  [22];  [23];  [24];  [25];  [26];  [27];  [28];  [29];  [29] « less
  1. Univ. of Jyväskylä, (Finland)
  2. Quansight LLC, Austin, TX (United States)
  3. Brigham Young Univ., Provo, UT (United States); Quansight LLC, Austin, TX (United States); Mayo Clinic, Rochester, MN (United States); Enthought, Inc., Austin, TX (United States); Anaconda Inc., Austin, TX (United States)
  4. California Polytechnic State Univ. (CalPoly), San Luis Obispo, CA (United States); Univ. of California, Los Angeles, CA (United States)
  5. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  6. Independent Researcher, Tokyo (Japan)
  7. National Research Univ., Moscow (Russian Federation)
  8. Tallinn Techincal Univ. (Estonia)
  9. Univ. of California, Berkeley, CA (United States)
  10. Independent Researcher, New York, NY (United States)
  11. Univ. of Birmingham (United Kingdom)
  12. Independant Researcher, San Francisco, CA (United States)
  13. WayRay LLC, Moscow (Russian Federation). Skolkovo Innovation Center
  14. Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia)
  15. Enthought, Inc., Austin, TX (United States)
  16. Univ. of Washington, Seattle, WA (United States)
  17. Univ. of Massachusetts, Amherst, MA (United States)
  18. Independent Research, Amsterdam (Netherlands)
  19. Univ. of California (United States)
  20. Bruker Biospin Corp., Billerica, MA (United States)
  21. Independent Research, Toulouse (France)
  22. Independent Researcher, Montreal, QC (France)
  23. Univ. of West Bohemia, Plzeň (Czech Republic)
  24. Brigham Young Univ., Provo, UT (United States); Univ. of Texas, Austin, TX (United States); Anaconda Inc., Austin, TX (United States)
  25. Independent Researcher, Belmont, MA (United States)
  26. Space Dynamics Lab., North Logan, UT (United States)
  27. Anton Pannekoek Inst., Amsterdam, (Netherlands)
  28. Univ. Federal de Minas Gerais, Belo Horizonte (Brazil)
  29. Google LLC, Montreal, QC (Canada)
+ Show Author Affiliations

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.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE
Contributing Organization:
SciPy 1.0 Contributors
Grant/Contract Number:
89233218CNA000001
OSTI ID:
1659198
Report Number(s):
LA-UR--19-29085
Journal Information:
Nature Methods, Journal Name: Nature Methods Journal Issue: 3 Vol. 17; ISSN 1548-7091
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

References (73)

FFT algorithms for vector computers journal August 1984
Large-scale dynamics of perceptual decision information across human cortex journal October 2020
The guide to available mathematical software problem classification system 1 journal January 1991
GW150914: First results from the search for binary black hole coalescence with Advanced LIGO journal June 2016
CODATA recommended values of the fundamental physical constants: 2014 journal September 2016
NetCDF: an interface for scientific data access journal July 1990
Solving the Trust-Region Subproblem using the Lanczos Method journal January 1999
An overview of SuperLU: Algorithms, implementation, and user interface journal September 2005
ALGORITHM 644: a portable package for Bessel functions of a complex argument and nonnegative order journal January 1987
From FATS to feets: Further improvements to an astronomical feature extraction tool based on machine learning preprint January 2018
Analysis of approximate nearest neighbor searching with clustered point sets preprint January 1999
Probabilistic programming in Python using PyMC3 posted_content January 2016
The Mosek Interior Point Optimizer for Linear Programming: An Implementation of the Homogeneous Algorithm book January 2000
A Direct Search Optimization Method That Models the Objective and Constraint Functions by Linear Interpolation book January 1994
The nonlinear programming method of Wilson, Han, and Powell with an augmented Lagrangian type line search function: Part 1: Convergence analysis journal February 1982
The nonlinear programming method of Wilson, Han, and Powell with an augmented Lagrangian type line search function: Part 2: An efficient implementation with linear least squares subproblems journal February 1982
A New Algorithm for Unconstrained Optimization book January 1970
FFT algorithms for vector computers journal August 1984
Direct search algorithms for optimization calculations journal January 1998
Differential Evolution – A Simple and Efficient Heuristic for global Optimization over Continuous Spaces journal January 1997
Collaborative software development made easy journal October 2017
CASSPER is a semantic segmentation-based particle picking algorithm for single-particle cryo-electron microscopy journal February 2021
CODATA Recommended Values of the Fundamental Physical Constants: 2014 journal December 2016
Finding scientific topics journal February 2004
On the convergence of a sequential quadratic programming method with an augmented lagrangian line search function journal January 1983
trlib : a vector-free implementation of the GLTR method for iterative solution of the trust region problem journal November 2017
emcee : The MCMC Hammer
  • Foreman-Mackey, Daniel; Hogg, David W.; Lang, Dustin
  • Publications of the Astronomical Society of the Pacific, Vol. 125, Issue 925 https://doi.org/10.1086/670067
journal March 2013
The Clustering Characteristics of h I-Selected Galaxies from the 40% Alfalfa Survey journal April 2012
The LIGO Open Science Center journal May 2015
An efficient method for finding the minimum of a function of several variables without calculating derivatives journal February 1964
A Simplex Method for Function Minimization journal January 1965
Characterization of structures from X-ray scattering data using genetic algorithms
  • Wormington, Matthew; Panaccione, Charles; Matney, Kevin M.
  • Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences, Vol. 357, Issue 1761 https://doi.org/10.1098/rsta.1999.0469
journal October 1999
GW150914: First results from the search for binary black hole coalescence with Advanced LIGO journal June 2016
Observation of Gravitational Waves from a Binary Black Hole Merger journal February 2016
GW170817: Observation of Gravitational Waves from a Binary Neutron Star Inspiral journal October 2017
Guest Editor's Introduction: Python: Batteries Included journal January 2007
Cython: The Best of Both Worlds journal March 2011
Python: An Ecosystem for Scientific Computing journal March 2011
Mayavi: 3D Visualization of Scientific Data journal March 2011
Python for Scientists and Engineers journal March 2011
The NumPy Array: A Structure for Efficient Numerical Computation journal March 2011
Monotone Piecewise Cubic Interpolation journal April 1980
The Conjugate Gradient Method and Trust Regions in Large Scale Optimization journal June 1983
Newton-Type Minimization via the Lanczos Method journal August 1984
Computing a Trust Region Step journal September 1983
A Limited Memory Algorithm for Bound Constrained Optimization journal September 1995
ARPACK Users' Guide book January 1998
Trust Region Methods book January 2000
Solving the Trust-Region Subproblem using the Lanczos Method journal January 1999
Tracing the meta-level: PyPy's tracing JIT compiler
  • Bolz, Carl Friedrich; Cuni, Antonio; Fijalkowski, Maciej
  • Proceedings of the 4th workshop on the Implementation, Compilation, Optimization of Object-Oriented Languages and Programming Systems - ICOOOLPS '09 https://doi.org/10.1145/1565824.1565827
conference January 2009
The quickhull algorithm for convex hulls journal December 1996
Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization journal December 1997
Numba: a LLVM-based Python JIT compiler conference January 2015
A New Method of Interpolation and Smooth Curve Fitting Based on Local Procedures journal October 1970
GW150914: First results from the search for binary black hole coalescence with Advanced LIGO text January 2016
GW170817: Observation of Gravitational Waves from a Binary Neutron Star Inspiral other January 2017
Python in neuroscience text January 2015
User guide for MINPACK-1. [In FORTRAN] report August 1980
Sparse: A more modern sparse array library conference January 2018
Circumventing The Linker: Using SciPy's BLAS and LAPACK Within Cython conference January 2015
Statsmodels: Econometric and Statistical Modeling with Python conference January 2010
Python in neuroscience journal April 2015
The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package journal August 2018
First M87 Event Horizon Telescope Results. III. Data Processing and Calibration journal April 2019
GW150914: First results from the search for binary black hole coalescence with Advanced LIGO text January 2016
GW170817: Observation of Gravitational Waves from a Binary Neutron Star Inspiral text January 2017
GW170817: Observation of gravitational waves from a binary neutron star inspiral text January 2017
Codata Recommended Values Of The Fundamental Physical Constants: 2014 text January 2015
Numerical Python ("Numeric") manual text January 2001
Numerical Python ("Numeric") manual text January 2001
SymPy: symbolic computing in Python journal January 2017
Probabilistic programming in Python using PyMC3 journal January 2016
scikit-image: image processing in Python journal January 2014

Cited By (111)

The efficacy of event isotropy as an event shape observable journal July 2021
On proportional volume sampling for experimental design in general spaces journal December 2022
Mixed Deep Gaussian Mixture Model: a clustering model for mixed datasets journal October 2021
Detecting dispersed radio transients in real time using convolutional neural networks journal January 2022
Robust Optimization and Validation of Echo State Networks for learning chaotic dynamics journal October 2021
Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling journal July 2021
Predicting the need for intubation in the first 24 h after critical care admission using machine learning approaches journal December 2020
Site-selective dynamics of azidolysozyme journal April 2021
Toolkit for scalar fields in universes with finite-dimensional Hilbert space journal November 2022
Discovery of multi-operon colinear syntenic blocks in microbial genomes journal July 2020
Phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories revealed by AI-MiXeR journal June 2020
Searching for QCD instantons at hadron colliders journal January 2021
Learning Interpretable Feature Context Effects in Discrete Choice conference August 2021
Voluntary modification of rapid tactile-motor responses during reaching differs from its visuomotor counterpart journal July 2020
iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists journal July 2021
3D diffractive imaging of nanoparticle ensembles using an x-ray laser journal December 2020
City size and the spreading of COVID-19 in Brazil journal September 2020
A city of cities: Measuring how 15-minutes urban accessibility shapes human mobility in Barcelona journal May 2021
datasets - Mechanism of optimal time-course COVID-19 vaccine prioritization based on non-Markovian steady-state prediction dataset January 2021
Optimization by moving ridge functions: derivative-free optimization for computationally intensive functions journalarticle January 2022
Reconstructing aspects of human embryogenesis with pluripotent stem cells text January 2021
Re-evaluating Evaluation in Text Summarization conference January 2020
Classification of hierarchical text using geometric deep learning: the case of clinical trials corpus conference January 2021
Cherenkov Telescope Array sensitivity to branon dark matter models
  • Aguirre-Santaella, Alejandra; Sánchez-Conde, M. A.; Gammaldi, V.
  • Proceedings of 37th International Cosmic Ray Conference — PoS(ICRC2021) https://doi.org/10.22323/1.395.0507
conference July 2021
Condition Monitoring of Drive Trains by Data Fusion of Acoustic Emission and Vibration Sensors other January 2021
Findings of the WMT 2020 Biomedical Translation Shared Task: Basque, Italian and Russian as New Additional Languages text January 2020
Intelligent Planning and Research on Urban Traffic Congestion journal November 2021
Inertial Measurement of Head Tilt in Rodents: Principles and Applications to Vestibular Research journal September 2021
A spiking neural network (SNN) for detecting high frequency oscillations (HFOs) in the intraoperative ECoG text January 2021
Localized Geometric Moves to Compute Hyperbolic Structures on Triangulated 3-Manifolds text January 2022
g2pM: A Neural Grapheme-to-Phoneme Conversion Package for Mandarin Chinese Based on a New Open Benchmark Dataset preprint January 2020
A scaling theory of armed conflict avalanches text January 2020
Heterogeneity in susceptibility dictates the order of epidemiological models preprint January 2020
Inference, prediction and optimization of non-pharmaceutical interventions using compartment models: the PyRoss library preprint January 2020
Photometric Data-driven Classification of Type Ia Supernovae in the Open Supernova Catalog text January 2020
$\textsf{Xsec}$: the cross-section evaluation code text January 2020
Deep Learning modeling of Limit Order Book: a comparative perspective preprint January 2020
Unsupervised Learning of Solutions to Differential Equations with Generative Adversarial Networks preprint January 2020
Finite Versus Infinite Neural Networks: an Empirical Study preprint January 2020
Manifold-adaptive dimension estimation revisited text January 2020
PyMGRIT: A Python Package for the parallel-in-time method MGRIT preprint January 2020
A Quantum-Inspired Algorithm for the Factorized Form of Unitary Coupled Cluster Theory preprint January 2020
No COVID-19 Climate Silver Lining in the US Power Sector text January 2020
Non-intrusive double-greedy parametric model reduction by interpolation of frequency-domain rational surrogates text January 2020
Adaptive Sampling of Pareto Frontiers with Binary Constraints Using Regression and Classification preprint January 2020
Analysis of Seismic Inversion with Optimal Transportation and Softplus Encoding text January 2020
Discovering causal factors of drought in Ethiopia preprint January 2020
A parallel algorithm for solving linear parabolic evolution equations text January 2020
Leader: Prefixing a Length for Faster Word Vector Serialization preprint January 2020
Obey validity limits of data-driven models text January 2020
Penalty methods for variational quantum eigensolver text January 2020
Reverse engineering learned optimizers reveals known and novel mechanisms preprint January 2020
X-ray dark-field signal reduction due to hardening of the visibility spectrum preprint January 2020
Learning outside the Black-Box: The pursuit of interpretable models text January 2020
Constrained, Global Optimization of Functions with Lipschitz Continuous Gradients preprint January 2020
Comparison between the Thomas-Fermi and Hartree-Fock-Bogoliubov Methods in the Inner Crust of a Neutron Star: The Role of Pairing Correlations text January 2020
Deterministic Certification to Adversarial Attacks via Bernstein Polynomial Approximation preprint January 2020
On the Optimization of Approximate Control Variates with Parametrically Defined Estimators preprint January 2020
Learning the Evolution of the Universe in N-body Simulations preprint January 2020
Can we learn where people come from? Retracing of origins in merging situations preprint January 2020
Solving Differential Equations via Continuous-Variable Quantum Computers preprint January 2020
Spatio-temporal methods for estimating subsurface ocean thermal response to tropical cyclones preprint January 2020
Solving Quadratic Unconstrained Binary Optimization with divide-and-conquer and quantum algorithms preprint January 2021
Neutron-Induced, Single-Event Effects on Neuromorphic Event-based Vision Sensor: A First Step Towards Space Applications text January 2021
A Probabilistic Taylor Expansion with Applications in Filtering and Differential Equations preprint January 2021
The Gene Mover's Distance: Single-cell similarity via Optimal Transport preprint January 2021
First-principles characterization of the magnetic properties of Cu$_2$(OH)$_3$Br text January 2021
A single-layer based numerical method for the slender body boundary value problem text January 2021
Sarc-Graph: Automated segmentation, tracking, and analysis of sarcomeres in hiPSC-derived cardiomyocytes text January 2021
A Ranking Approach to Fair Classification text January 2021
Detecting Extraneous Content in Podcasts preprint January 2021
DI2: prior-free and multi-item discretization ofbiomedical data and its applications preprint January 2021
Nondeterminism and Instability in Neural Network Optimization preprint January 2021
Assessing the impact of transient orbital resonances text January 2021
The Old and the New: Can Physics-Informed Deep-Learning Replace Traditional Linear Solvers? preprint January 2021
A Review & Framework for Modeling Complex Engineered System Development Processes preprint January 2021
YOLinO: Generic Single Shot Polyline Detection in Real Time preprint January 2021
Linear-Time Probabilistic Solutions of Boundary Value Problems preprint January 2021
yaglm: a Python package for fitting and tuning generalized linear models that supports structured, adaptive and non-convex penalties preprint January 2021
Machine Learning for CUDA+MPI Design Rules preprint January 2022
Shell model for stratified convection: implications for the solar convective conundrum preprint January 2022
Learning to denoise historical music text January 2020
Utilizing cosmic-ray positron and electron observations to probe the averaged properties of Milky Way pulsars dataset January 2021
Additional file 1 of DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy dataset January 2021
Additional file 6 of Modeling the temporal dynamics of cervicovaginal microbiota identifies targets that may promote reproductive health dataset January 2021
Additional file 7 of Modeling the temporal dynamics of cervicovaginal microbiota identifies targets that may promote reproductive health audiovisual January 2021
Additional file 2 of OmicsOne: associate omics data with phenotypes in one-click dataset January 2021
Additional file 3 of OmicsOne: associate omics data with phenotypes in one-click dataset January 2021
Additional file 4 of OmicsOne: associate omics data with phenotypes in one-click dataset January 2021
Additional file 2 of pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls dataset January 2023
Additional file 1 of A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome dataset January 2023
Additional file 1 of Protein length distribution is remarkably uniform across the tree of life dataset January 2023
Additional file 3 of Protein length distribution is remarkably uniform across the tree of life dataset January 2023
Additional file 4 of Protein length distribution is remarkably uniform across the tree of life dataset January 2023
Additional file 5 of Protein length distribution is remarkably uniform across the tree of life dataset January 2023
Additional file 6 of Protein length distribution is remarkably uniform across the tree of life dataset January 2023
Additional file 7 of Protein length distribution is remarkably uniform across the tree of life dataset January 2023
Additional file 1 of Highly accelerated free-breathing real-time myocardial tagging for exercise cardiovascular magnetic resonance image January 2023
Additional file 1 of Plasma indole-3-aldehyde as a novel biomarker of acute kidney injury after cardiac surgery: a reanalysis using prospective metabolomic data dataset January 2023
Additional file 1 of Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set dataset January 2023
Additional file 1 of Dashing Growth Curves: a web application for rapid and interactive analysis of microbial growth curves dataset January 2024
Additional file 1 of Dimension reduction and outlier detection of 3-D shapes derived from multi-organ CT images dataset January 2024
Additional file 1 of Transcriptional profiling of peripheral blood mononuclear cells identifies inflammatory phenotypes in Ataxia Telangiectasia image January 2024
Additional file 1 of Mitochondrial genome plasticity of mammalian species dataset January 2024
Additional file 1 of Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages image January 2024
Squidpy: a scalable framework for spatial single cell analysis collection January 2021
Controlled beams of shock-frozen, isolated, biological and artificial nanoparticles journal March 2020
Variant effect predictions capture some aspects of deep mutational scanning experiments journal March 2020
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome journal June 2020
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome text January 2020
Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments journal January 2020

Similar Records

Experiences using SciPy for computer vision research
Journal Article · Mon Dec 31 23:00:00 EST 2007 · OSTI ID:964975
First time experiences using SciPy for computer vision research
Journal Article · Mon Dec 31 23:00:00 EST 2007 · OSTI ID:964968
The Python ARM Radar Toolkit (Py-ART), a library for working with weather radar data in the Python programming language
Journal Article · Mon Jul 18 00:00:00 EDT 2016 · Journal of Open Research Software · OSTI ID:1339572

Related Subjects

97 MATHEMATICS AND COMPUTING
Computational Physics
Data Structures and Algorithms
Mathematical Software
Software Engineering