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This report provides an introduction to the ensmallen numerical optimization library, as well as a deep dive into the technical details of how it works. The library provides a fast and flexible C++ framework for mathematical optimization of…
Structural equation modelling (SEM) is a multivariate statistical technique for estimating complex relationships between observed and latent variables. Although numerous SEM packages exist, each of them has limitations. Some packages are…
This work introduces ParAMS -- a versatile Python package that aims to make parameterization workflows in computational chemistry and physics more accessible, transparent and reproducible. We demonstrate how ParAMS facilitates the parameter…
Understanding decision-making in clinical environments is of paramount importance if we are to bring the strengths of machine learning to ultimately improve patient outcomes. Several factors including the availability of public data, the…
This article presents an open-source Python package for simulating micro-thermoelectric generators, based on the work by D. Beretta et al. (Sustainable Energy Fuels, 2017). Featuring a user-friendly graphical user interface and robust…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
The online data reduction service reductus transforms measurements in experimental science from laboratory coordinates into physically meaningful quantities with accurate estimation of uncertainties based on instrumental settings and…
Since its launch, TESS has provided high cadence observations for objects across the sky. Although high cadence TESS observations provide a unique possibility to study the rapid time evolution of numerous objects, artifacts in the data make…
anesthetic is a Python package for processing nested sampling runs, and will be useful for any scientist or statistician who uses nested sampling software. anesthetic unifies many existing tools and techniques in an extensible framework…
Magpy is a C++ accelerated Python package for modelling and simulating the magnetic dynamics of nano-sized particles. Nanoparticles are modelled as a system of three-dimensional macrospins and simulated with a set of coupled stochastic…
PySINDy is a Python package for the discovery of governing dynamical systems models from data. In particular, PySINDy provides tools for applying the sparse identification of nonlinear dynamics (SINDy) (Brunton et al. 2016) approach to…
For agentic systems to use external tools to solve complex, long-horizon tasks, we need a large set of diverse and controllable tool-use environments. We introduce SynthTools, a fully LLM-based pipeline spanning the entire lifecycle:…
Reflection in Kotlin is a powerful mechanism to introspect program behavior during its execution at run-time. However, among the variety of practical tasks involving reflection, there are scenarios when the poor performance of run-time…
We present the Explabox: an open-source toolkit for transparent and responsible machine learning (ML) model development and usage. Explabox aids in achieving explainable, fair and robust models by employing a four-step strategy: explore,…
This paper presents maplet, an open-source R package for the creation of highly customizable, fully reproducible statistical pipelines for omics data analysis, with a special focus on metabolomics-based methods. It builds on the…
RevelsMD is a new open source Python library, which uses reduced variance force sampling based estimators to calculate 3D particle densities and radial distribution functions from molecular dynamics simulations. This short note describes…
Since Lorenz's seminal work on a simplified weather model, the numerical analysis of nonlinear dynamical systems has become one of the main subjects of research in physics. Despite of that, there remains a need for accessible, efficient,…
Benchmarking involves designing, running and disseminating rigorous performance assessments of methods, most often for data analysis and software tools, but the process can also be applied to experimental systems. Ideally, a benchmarking…
This paper introduces ROmodel, an open source Python package extending the modeling capabilities of the algebraic modeling language Pyomo to robust optimization problems. ROmodel helps practitioners transition from deterministic to robust…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…