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Parameterization of interatomic forcefields is a necessary first step in performing molecular dynamics simulations. This is a non-trivial global optimization problem involving quantification of multiple empirical variables against one or…
We introduce Repro, an open-source library which aims at improving the reproducibility and usability of research code. The library provides a lightweight Python API for running software released by researchers within Docker containers which…
Replicability in machine learning (ML) research is increasingly concerning due to the utilization of complex non-deterministic algorithms and the dependence on numerous hyper-parameter choices, such as model architecture and training…
Cloud platforms allow users to execute tasks directly from their web browser and are a key enabling technology not only for commerce but also for computational science. Research software is often developed by scientists with limited…
Science reproducibility is a cornerstone feature in scientific workflows. In most cases, this has been implemented as a way to exactly reproduce the computational steps taken to reach the final results. While these steps are often…
To reproduce eScience, several challenges need to be solved: scientific workflows need to be automated; the involved software versions need to be provided in an unambiguous way; input data needs to be easily accessible; High-Performance…
In recent years, instruction tuning has gained increasing attention and emerged as a crucial technique to enhance the capabilities of Large Language Models (LLMs). To construct high-quality instruction datasets, many instruction processing…
Engineering design optimization seeks to automatically determine the shapes, topologies, or parameters of components that maximize performance under given conditions. This process often depends on physics-based simulations, which are…
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…
To scrutinize notions of computation and time complexity, we introduce and formally define an interactive model for computation that we call it the \emph{computation environment}. A computation environment consists of two main parts: i) a…
Modern rendering libraries provide unprecedented realism, producing real-time photorealistic 3D graphics on commodity hardware. Visual fidelity, however, comes at the cost of increased complexity and difficulty of usage, with many rendering…
Context: Mining software repositories is a popular means to gain insights into a software project's evolution, monitor project health, support decisions and derive best practices. Tools supporting the mining process are commonly applied by…
Software developers create and share code online to demonstrate programming language concepts and programming tasks. Code snippets can be a useful way to explain and demonstrate a programming concept, but may not always be directly…
In this paper we describe EasyInterface, an open-source toolkit for rapid development of web-based graphical user interfaces (GUIs). This toolkit addresses the need of researchers to make their research prototype tools available to the…
Scikit-learn is an increasingly popular machine learning li- brary. Written in Python, it is designed to be simple and efficient, accessible to non-experts, and reusable in various contexts. In this paper, we present and discuss our design…
Processing-in-memory (PIM) promises to alleviate the data movement bottleneck in modern computing systems. However, current real-world PIM systems have the inherent disadvantage that their hardware is more constrained than in conventional…
Running complex sets of machine learning experiments is challenging and time-consuming due to the lack of a unified framework. This leaves researchers forced to spend time implementing necessary features such as parallelization, caching,…
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.…
Over the last decade, there has been growing interest in the assessment of the performance of researchers, research groups, universities and even countries. The assessment of productivity is an instrument to select and promote personnel,…
The need for computational resources grows as computational algorithms gain popularity in different sectors of the scientific community. This search has stimulated the development of several cloud platforms that abstract the complexity of…