21 papers · ranked by Valyu relevance
C. R. Harris, K. Jarrod Millman, Stéfan van der Walt, Ralf Gommers + 22 more
'Pauli Virtanen' 'David Cournapeau' 'Eric Wieser' 'Julian Taylor' 'Sebastian Berg' 'Nathaniel J. Smith' 'Robert Kern' 'Matti Picus' 'Stephan Hoyer' 'M. H. van Kerkwijk' 'Matthew Brett' 'Allan Haldane' 'Jaime Fernández del Río' 'Mark Wiebe' 'Pearu Peterson' 'P Gerard-Marchant' 'Kevin Sheppard' 'Tyler Reddy' 'Warren…
Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers + 22 more
'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' 'Allan Haldane' 'Jaime Fernández del Río' 'Mark Wiebe' 'Pearu Peterson' 'Pierre Gérard-Marchant' 'Kevin Sheppard'…
Oscar Castro, Pierrick Bruneau, Jean-Sébastien Sottet, Dario Torregrossa
'Dario Torregrossa'] Python has become the prime language for application development in the Data Science and Machine Learning domains. However, data scientists are not necessarily experienced programmers. While Python lets them quickly implement their algorithms, when moving at scale, computation efficiency becomes…
Knut Rand, Ivar Grytten, Milena Pavlovic, Chakravarthi Kanduri + 1 more
Python is a popular and widespread programming language for scientific computing, in large part due to the powerful array programming library NumPy, which makes it easy to write clean, vectorized and efficient code for handling large datasets. A challenge with using array programming for biological data is that the…
Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland + 107 more
'Tyler Reddy' 'David Cournapeau' 'Evgeni Burovski' 'Pearu Peterson' 'Warren Weckesser' 'Jonathan Bright' 'Stéfan van der Walt' 'Matthew Brett' 'Joshua Wilson' 'K. Jarrod Millman' 'Nikolay Mayorov' 'Andrew Nelson' 'Eric D. Jones' 'Robert Kern' 'Eric R. Larson' 'CJ Carey' 'İlhan Polat' 'Yu Feng' 'Eric Moore' 'Jake…
Srinath Kailasa, Tingyu Wang, Lorena A. Barba, Timo Betcke
—Numba is a game-changing compiler for high-performance computing with Python. It produces machine code that runs outside of the single-threaded Python interpreter and that fully utilizes the resources of modern CPUs. This means support for parallel multithreading and auto-vectorization if available, as with compiled…
Maximilian H. Kriebel, Paweł Tecmer, Marta Gałyńska, Aleksandra Leszczyk + 1 more
Coupled-Cluster Implementations: A Comparison Between CPUs and GPUs Authors: Maximilian H. Kriebel, Paweł Tecmer, Marta Gałyńska, Aleksandra Leszczyk, Katharina Boguslawski In this work, we benchmark several Python routines for time and memory requirements to identify the optimal choice of the tensor contraction…
Ralf Biehl, Alejandro Fernandez-Martinez
The aim of Jscatter is the processing of experimental data and physical models with the focus to enable the user to develop/modify their own models and use them within experimental data evaluation. The basic structures dataArray and dataList contain matrix-like data of different size including attributes to store…
Laurent P. René de Cotret, Martin R. Otto, Mark J. Stern, Bradley J. Siwick
This paper details a software ecosystem comprising three free and open-source Python packages for processing raw ultrafast electron scattering (UES) data and interactively exploring the processed data. The first package, iris, is graphical user-interface program and library for interactive exploration of UES data.…
Eilif Muller, James A. Bednar, Markus Diesmann, Marc-Oliver Gewaltig + 2 more
'Michael Hines' 'Andrew P. Davison'] This Research Topic of Frontiers in Neuroinformatics is dedicated to the memory of Rolf Kötter (1961-2010), who was the Frontiers Associate Editor responsible for this Research Topic, and who gave us considerable support and encouragement during the process of conceiving and…
Brandon M. Pardi, Syeda Tajin Ahmed, Silvia Jonguitud Flores, Warren Flores + 3 more
Here, we present a Python based software that allows for the rapid visualization, data mining, and basic model applications of quartz crystal microbalance with dissipation data. Our implementation begins with a Tkinter GUI to prompt the user for all required information, such as file name/location, selection of…
Yajushi Khurana, Keisuke Ishihara
Three-dimensional biological morphologies encode functional and physiological state, yet the directional, orientational, and topological properties of these shapes are rarely captured by morphometric tools available for bioimage analysis. Minkowski tensors are mathematically rigorous tensor-valued measures that encode…
Fabian Woller, Lis Arend, Christian Fuchsberger, Markus List + 1 more
For each supported test, the output is represented by a Python dictionary that stores data matrices with the user-requested output (P-values, adjusted P-values, and/or effect sizes). We store output matrices as 2-dimensional objects of the same type as the input data (i.e., as NumPy arrays, PyTorch tensors, or pandas…
Patrick Ropp, Aaron Friedman, Jacob D. Durrant
Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with dependencies and compilers. This presents a barrier that can hinder the otherwise broad adoption of new tools. We…
Svenn-Arne Dragly, Milad Hobbi Mobarhan, Mikkel Lepperød, Simen Tennøe + 3 more
Natural sciences generate an increasing amount of data in a wide range of formats developed by different research groups and commercial companies. At the same time there is a growing desire to share data along with publications in order to enable reproducible research. Open formats have publicly available…
Wouter De Coster, Svenn D’Hert, Darrin T. Schultz, Marc Cruts + 1 more
Summary: Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Availability and Implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 Licence. The source code can…
Lucian Chan, Geoffrey Hutchison, Garrett Morris
Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here…
Authors not listed
nDTomo is a Python-based software suite for the simulation, reconstruction and analysis of X-ray chemical imaging and computed tomography data. It provides a collection of Python function-based tools designed for accessibility and education as well as a graphical user interface (GUI). Prioritising transparency and ease…
Authors not listed
Solving optimization problems, especially for nonlinear and constrained systems, is a challenge. Decades of specialized algorithms have been developed for general and special cases of root finding, minimization (including constraints), for parameter estimation, and mapping connected spaces. These approaches typically…
Authors not listed
Inverse problems, where we seek the values of inputs to a model that lead to a desired set of outputs, are a challenges subset of problems in science and engineering. In this work we demonstrate the use of two generative AI methods to solve inverse problems. We compare this approach to two more conventional approaches…
I. Osborne, J. Pivarski, Ioana Ifrim, Angus Hollands + 1 more
'Henry Schreiner'] > Abstract. Awkward Array is a library for performing NumPy-like computations on nested, variable-sized data, enabling array-oriented programming on arbitrary data structures in Python. However, imperative (procedural) solutions can sometimes be easier to write or faster to run. Performant imperative…