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Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
Domain experts can play a crucial role in guiding data scientists to optimize machine learning models while ensuring contextual relevance for downstream use. However, in current workflows, such collaboration is challenging due to differing…
We present PRETUS -a Plugin-based Real Time UltraSound software platform for live ultrasound image analysis and operator support. The software is lightweight; functionality is brought in via independent plug-ins that can be arranged in…
We introduce a novel software abstraction termed "model caller," acting as an intermediary for AI and ML model calling, advocating its transformative utility beyond existing model-serving frameworks. This abstraction offers multiple…
Computational models can provide significant insight into the operation mechanisms and deficiencies of photovoltaic solar cells. Solcore is a modular set of computational tools, written in Python 3, for the design and simulation of…
Simulation is a foundational tool for the analysis and testing of cyber-physical systems (CPS), underpinning activities such as algorithm development, runtime monitoring, and system verification. As CPS grow in complexity and scale,…
CurvPy is an open-source Python library for automated curve fitting and regression analysis, aiming to make advanced statistical and machine learning techniques more accessible. This paper explores the mathematical foundations and…
Small multiples are miniature representations of visual information used generically across many domains. Handling large numbers of small multiples imposes challenges on many analytic tasks like inspection, comparison, navigation, or…
The purpose of this work is to highlight the content of the Microsoft Recommenders repository and show how it can be used to reduce the time involved in developing recommender systems. The open source repository provides python utilities to…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
We present Simphony, a free and open-source software toolbox for abstracting and simulating photonic integrated circuits, implemented in Python. The toolbox is both fast and easily extensible; plugins can be written to provide compatibility…
User simulation is a valuable methodology for evaluation in Information Retrieval (IR), enabling low-cost experimentation and counterfactual analysis. However, existing simulation frameworks are primarily code-centric libraries that require…
Selecting the right compiler optimisations has a severe impact on programs' performance. Still, the available optimisations keep increasing, and their effect depends on the specific program, making the task human intractable. Researchers…
The reproducibility of software environments is a critical concern in modern software engineering, with ramifications ranging from the effectiveness of collaboration workflows to software supply chain security and scientific…
Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated datasets. Being able to easily access and utilise these is crucial for…
Software frameworks for neural networks play a key role in the development and application of deep learning methods. In this paper, we introduce the Chainer framework, which intends to provide a flexible, intuitive, and high performance…
ControlBurn is a Python package to construct feature-sparse tree ensembles that support nonlinear feature selection and interpretable machine learning. The algorithms in this package first build large tree ensembles that prioritize basis…
Software module clustering is an unsupervised learning method used to cluster software entities (e.g., classes, modules, or files) with similar features. The obtained clusters may be used to study, analyze, and understand the software…
In the past decade, enormous progress has been made in advancing the state-of-the-art in bioimage analysis - a young computational field that works in close collaboration with the life sciences on the quantitative analysis of scientific…
The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…