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High resolution peripheral quantitative computed tomography (HR-pQCT) is an imaging technique capable of imaging trabecular bone in-vivo. HR-pQCT has a wide range of applications, primarily focused on bone to improve our understanding of…
In this paper we discuss the theory used in the design of an open source lightmorphic signatures analysis toolkit (LSAT). In addition to providing a core functionality, the software package enables specific optimizations with its modular…
Generation and analysis of time-series data is relevant to many quantitative fields ranging from economics to fluid mechanics. In the physical sciences, structures such as metastable and coherent sets, slow relaxation processes, collective…
One of the most attractive features of R is its linear modeling capabilities. We describe a Python package, salmon, that brings the best of R's linear modeling functionality to Python in a Pythonic way -- by providing composable objects for…
We describe the open-source global fitting package GAMBIT: the Global And Modular Beyond-the-Standard-Model Inference Tool. GAMBIT combines extensive calculations of observables and likelihoods in particle and astroparticle physics with a…
This paper presents McNetKAT, a scalable tool for verifying probabilistic network programs. McNetKAT is based on a new semantics for the guarded and history-free fragment of Probabilistic NetKAT in terms of finite-state, absorbing Markov…
Science depends heavily on reliable and easy-to-use software packages, such as mathematical libraries or data analysis tools. Developing such packages requires a lot of effort, which is too often avoided due to the lack of funding or…
We introduce \texttt{pycobra}, a Python library devoted to ensemble learning (regression and classification) and visualisation. Its main assets are the implementation of several ensemble learning algorithms, a flexible and generic interface…
This paper describes a novel Python package, named causalgraph, for modeling and saving causal graphs embedded in knowledge graphs. The package has been designed to provide an interface between causal disciplines such as causal discovery…
fairseq is an open-source sequence modeling toolkit that allows researchers and developers to train custom models for translation, summarization, language modeling, and other text generation tasks. The toolkit is based on PyTorch and…
Distributed, large-scale quantum computing will need architectures that combine matter-based qubits with photonic links, but today's software stacks target either gate-based chips or linear-optical devices in isolation. We introduce Optyx,…
The purpose of this paper is to show how existing scientific software can be parallelized using a separate thin layer of Python code where all parallel communication is implemented. We provide specific examples on such layers of code, and…
bayesian_pyhf is a Python package that allows for the parallel Bayesian and frequentist evaluation of multi-channel binned statistical models. The Python library pyhf is used to build such models according to the HistFactory framework and…
TorchOptics is an open-source Python library for differentiable Fourier optics simulations, developed using PyTorch to enable GPU-accelerated tensor computations and automatic differentiation. It provides a comprehensive framework for…
In modern-day astronomy, near-infrared, optical, and ultraviolet spectroscopy are indispensable for studying a wide range of phenomena, from measuring black hole masses to analyzing chemical abundances in stellar atmospheres. However,…
Information theory, i.e. the mathematical analysis of information and of its processing, has become a tenet of modern science; yet, its use in real-world studies is usually hindered by its computational complexity, the lack of coherent…
Synthesizer is a fast, flexible, modular, and extensible Python package that empowers astronomers to turn theoretical galaxy models into realistic synthetic observations - including spectra, photometry, images, and spectral cubes - with a…
Interferometric scattering (iSCAT) microscopy is a powerful tool for label-free sensitive detection and imaging of nanoparticles to high spatio-temporal resolution. As it was born out of detection principles central to conventional…
This paper presents PyTSK, a Python toolbox for developing Takagi-Sugeno-Kang (TSK) fuzzy systems. Based on scikit-learn and PyTorch, PyTSK allows users to optimize TSK fuzzy systems using fuzzy clustering or mini-batch gradient descent…
Atomistic models like tight-binding (TB), bond-order potentials (BOP) and classical potentials describe the interatomic interaction in terms of mathematical functions with parameters that need to be adjusted for a particular material. The…