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Linear Mixed-Effects (LME) models are a fundamental tool for modeling correlated data, including cohort studies, longitudinal data analysis, and meta-analysis. Design and analysis of variable selection methods for LMEs is more difficult…
Thermodynamic models are often vital when characterising complex systems, particularly natural gas, electrolyte, polymer, pharmaceutical and biological systems. However, their implementations have historically been abstruse and cumbersome,…
This paper proposes the Proximal Iteratively REweighted (PIRE) algorithm for solving a general problem, which involves a large body of nonconvex sparse and structured sparse related problems. Comparing with previous iterative solvers for…
The characterization of exoplanet requires reliable determination of the fundamental parameters of their host stars. Spectral fitting plays an important role in this process. For the majority of stellar parameters matching synthetic spectra…
We present a suite of packages in R, Python, Julia, and C++ that efficiently solve the Sorted L-One Penalized Estimation (SLOPE) problem. The packages feature a highly efficient hybrid coordinate descent algorithm that fits generalized…
Current multi-physics Finite Element Method (FEM) solvers are complex systems in terms of both their mathematical complexity and lines of code. This paper proposes a skeleton generic FEM solver, named MetaFEM, in total about 5,000 lines of…
MLJ (Machine Learing in Julia) is an open source software package providing a common interface for interacting with machine learning models written in Julia and other languages. It provides tools and meta-algorithms for selecting, tuning,…
This paper proposes Scalene, a profiler specialized for Python. Scalene combines a suite of innovations to precisely and simultaneously profile CPU, memory, and GPU usage, all with low overhead. Scalene's CPU and memory profilers help…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
SfePy (Simple Finite Elements in Python) is a framework for solving various kinds of problems (mechanics, physics, biology, ...) described by partial differential equations in two or three space dimensions by the finite element method. The…
Integrals involving highly oscillatory Bessel functions are notoriously challenging to compute using conventional integration techniques. While several methods are available, they predominantly cater to integrals with at most a single…
This paper reports the development of a Python Non-Uniform Fast Fourier Transform (PyNUFFT) package, which accelerates non-Cartesian image reconstruction on heterogeneous platforms. Scientific computing with Python encompasses a mature and…
The lepton propagator PROPOSAL is a Monte-Carlo Simulation library written in C++, propagating high energy muons and other charged particles through large distances of media. In this article, a restructuring of the code is described, which…
The Python package pylimer-tools is a comprehensive toolkit for computational studies of polymer networks, particularly bead-spring networks. The package provides functionality to generate polymer networks using Monte Carlo (MC) procedures…
\textsc{Pykat} is a Python package which extends the popular optical interferometer modelling software \textsc{Finesse}. It provides a more modern and efficient user interface for conducting complex numerical simulations, as well as…
This is a companion Focus Demonstration article to the PyMUSE python package, demonstrating its usage and utilities for VLT/MUSE data analysis, that include a wide range of options for spectra extractions, the creation of different types of…
We present SPIKE (Spectrometry Processing Innovative KErnel), an open-source Python package dedicated to Fourier spectroscopies. It provides basic functionalities such as apodisation, a complete set of Fourier transforms, phasing for NMR),…
The Isabelle/PIDE platform addresses the question whether proof assistants of the LCF family are suitable as technological basis for educational tools. The traditionally strong logical foundations of systems like HOL, Coq, or Isabelle have…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
Spectral line observations are an indispensable tool to remotely probe the physical and chemical conditions throughout the universe. Modelling their behaviour is a computational challenge that requires dedicated software. In this paper, we…