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The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
PEPit is a Python package aiming at simplifying the access to worst-case analyses of a large family of first-order optimization methods possibly involving gradient, projection, proximal, or linear optimization oracles, along with their…
The minimum spanning tree (MST), a graph constructed from a distribution of points, draws lines between pairs of points so that all points are linked in a single skeletal structure that contains no loops and has minimal total edge length.…
Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a…
In deterministic optimization, it is typically assumed that all problem parameters are fixed and known. In practice, however, some parameters may be a priori unknown but can be estimated from contextual information. A typical…
Mathematical modeling is a powerful tool in rheology, and we present pyRheo, an open-source package for Python designed to streamline the analysis of creep, stress relaxation, oscillation, and rotation tests. pyRheo contains a comprehensive…
DIETER is an open-source power sector model designed to analyze future settings with very high shares of variable renewable energy sources. It minimizes overall system costs, including fixed and variable costs of various generation,…
With the rapid development of large language models (LLMs), more and more researchers have paid attention to information extraction based on LLMs. However, there are still some spaces to improve in the existing related methods. First,…
There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent…
For scientific knowledge to be findable, accessible, interoperable, and reusable, it needs to be machine-readable. Moving forward from post-publication extraction of knowledge, we adopted a pre-publication approach to write research…
We present an open source Python 3 library aimed at practitioners of molecular simulation, especially Monte Carlo simulation. The aims of the library are to facilitate the generation of simulation data for a wide range of problems; and to…
Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still…
The usage of the high-level scripting language Python has enabled new mechanisms for data interrogation, discovery and visualization of scientific data. We present yt, an open source, community-developed astrophysical analysis and…
Information theory has been taken as a prospective tool for quantifying the complexity of complex networks. In this paper, we first study the information entropy or uncertainty of a path using the information theory. Then we apply the path…
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…
We present PyXtal, a new package based on the Python programming language, used to generate structures with specific symmetry and chemical compositions for both atomic and molecular systems. This soft ware provides support for various…
As camera pixel arrays have grown larger and faster, and optical microscopy techniques ever more refined, there has been an explosion in the quantity of data acquired during routine light microcopy. At the single-molecule level, analysis…
Recent deep learning methods for fMRI-based diagnosis have achieved promising accuracy by modeling functional connectivity networks. However, standard approaches often struggle with noisy interactions, and conventional post-hoc attribution…
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…
Understanding how the brain functions is one of the biggest challenges of our time. The analysis of experimentally recorded neural firing patterns (spike trains) plays a crucial role in addressing this problem. Here, the PySpike library is…