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Background and Objective: Deep learning enables tremendous progress in medical image analysis. One driving force of this progress are open-source frameworks like TensorFlow and PyTorch. However, these frameworks rarely address issues…

With the recent rapid progress in the study of deep generative models (DGMs), there is a need for a framework that can implement them in a simple and generic way. In this research, we focus on two features of DGMs: (1) deep neural networks…

PyArmadillo is a linear algebra library for the Python language, with the aim of closely mirroring the programming interface of the widely used Armadillo C++ library, which in turn is deliberately similar to Matlab. PyArmadillo hence…

Just like the scientific data they generate, simulation workflows for research should be findable, accessible, interoperable, and reusable (FAIR). However, while significant progress has been made towards FAIR data, the majority of science…

Scientific research frequently involves the use of computational tools and methods. Providing thorough documentation, open-source code, and data -- the creation of reproducible computational research -- helps others understand a…

Pyqcm is a Python/C++ library that implements a few quantum cluster methods with an exact diagonalization impurity solver. Quantum cluster methods are used in the study of strongly correlated electrons to provide an approximate solution to…

Fast numerical libraries have been a cornerstone of scientific computing for decades, but this comes at a price. Programs may be tied to vendor specific software ecosystems resulting in polluted, non-portable code. As we enter an era of…

Libraries for supervised classification have enabled the wide-spread usage of machine learning methods. Existing libraries, such as scikit-learn, caret, and mlpack, implement techniques based on the classical empirical risk minimization…

Ligands entering a protein binding pocket essentially compete with water molecules for binding to the protein. Hence, the location and thermodynamic properties of water molecules in protein structures have gained increased attention in the…

Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…

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…

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…

As computer systems become more and more complex, software and tools lag more and more behind. This is especially true for scientific software that often demands high performance, and thus needs to take advantage of parallelisms, memory…

Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this…

DeeProb-kit is a unified library written in Python consisting of a collection of deep probabilistic models (DPMs) that are tractable and exact representations for the modelled probability distributions. The availability of a representative…

Pykg2vec is an open-source Python library for learning the representations of the entities and relations in knowledge graphs. Pykg2vec's flexible and modular software architecture currently implements 16 state-of-the-art knowledge graph…

Large language models (LLMs) have become a dominant and important tool for NLP researchers in a wide range of tasks. Today, many researchers use LLMs in synthetic data generation, task evaluation, fine-tuning, distillation, and other…

This paper presents gnss_lib_py, a Python library used to parse, analyze, and visualize data from a variety of GNSS (Global Navigation Satellite Systems) data sources. The gnss_lib_py library's ease of use, modular capabilities, testing…

Ordinary Differential Equations (ODE) are used throughout science where the capture of rates of change in states is sought. While both pieces of commercial and open software exist to study such systems, their efficient and accurate usage…

Organizations have realized the importance of data analysis and its benefits. This in combination with Machine Learning algorithms has allowed to solve problems more easily, making these processes less time-consuming. Neural networks are…