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Process Reward Models (PRMs) have emerged as a powerful tool for providing step-level feedback when evaluating the reasoning of Large Language Models (LLMs), which frequently produce chains of thought (CoTs) containing errors even when the…
Understanding astrophysical and cosmological processes can be challenging due to their complexity and lack of intuitive analogies. To address this, we present \texttt{AstronomyCalc}, a Python package specifically designed to aid…
Exoplanet science often involves using the system parameters of real exoplanets for tasks such as simulations, fitting routines, and target selection for proposals. Several exoplanet catalogues are already well established but often lack a…
Python for Power System Analysis (PyPSA) is a free software toolbox for simulating and optimising modern electrical power systems over multiple periods. PyPSA includes models for conventional generators with unit commitment, variable…
Time-to-event (survival) analysis models the time until a pre-specified event occurs. When time is measured in discrete units or rounded into intervals, standard continuous-time models can yield biased estimators. In addition, the event of…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
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…
Accurate and efficient simulation tools are essential in robotics, enabling the visualization of system dynamics and the validation of control laws before committing resources to physical experimentation. Developing physically accurate…
pyGDM is a python toolkit for electro-dynamical simulations in nano-optics based on the Green Dyadic Method (GDM). In contrast to most other coupled-dipole codes, pyGDM uses a generalized propagator, which allows to cost-efficiently solve…
Metadata and comments are critical elements of any software development process. In this paper, we explain how metadata and comments in source code can play an essential role in comprehending software. We introduce a Python-based…
Mathematical modelling allows us to concisely describe fundamental principles in biology. Analysis of models can help to both explain known phenomena, and predict the existence of new, unseen behaviours. Model analysis is often a complex…
We present PyRigi, a novel Python package designed to study the rigidity properties of graphs and frameworks. Among many other capabilities, PyRigi can determine whether a graph admits only finitely many ways, up to isometries, of being…
Data cubes are used for analyzing large data sets usually contained in data warehouses. The most popular data cube tools use graphical user interfaces (GUI) to do the data analysis. Traditionally this was fine since data analysts were not…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
Dynamical systems see widespread use in natural sciences like physics, biology, chemistry, as well as engineering disciplines such as circuit analysis, computational fluid dynamics, and control. For simple systems, the differential…
Firedrake is a new tool for automating the numerical solution of partial differential equations. Firedrake adopts the domain-specific language for the finite element method of the FEniCS project, but with a pure Python runtime-only…
Many problems in science and engineering can be represented by a set of partial differential equations (PDEs) through mathematical modeling. Mechanism-based computation following PDEs has long been an essential paradigm for studying topics…
We propose PyTorchGeoNodes, a differentiable module for reconstructing 3D objects and their parameters from images using interpretable shape programs. Unlike traditional CAD model retrieval, shape programs allow reasoning about semantic…
Research into the processes of photoionised nebulae plays a significant part in our understanding of stellar evolution. It is extremely difficult to visually represent or model ionised nebula, requiring astronomers to employ sophisticated…
Developing web-based GIS applications, commonly known as CyberGIS dashboards, for querying and visualizing GIS data in environmental research often demands repetitive and resource-intensive efforts. While Generative AI offers automation…