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Robust advances in interactome analysis demand comprehensive, non-redundant and consistently annotated datasets. By non-redundant, we mean that the accounting of evidence for every interaction should be faithful: each independent…

As AI agents increasingly contribute to code development and maintenance, there is still limited empirical evidence on the quality and risk characteristics of their changes in real-world projects, particularly for refactoring-oriented…

Software engineers regularly use JavaScript and Python for both front-end and back-end automation tasks. On top of JavaScript and Python, there are several frameworks to facilitate automation tasks further. Some of these frameworks are Node…

Modern software programs are built on stacks that are often undergoing changes that introduce updates and improvements, but may also break any project that depends upon them. In this paper we explore the use of Large Language Models (LLMs)…

Open-source simulation frameworks are evolving rapidly to provide accessible tools for the numerical solution of partial differential equations. Modern finite element (FEM) software such as FEniCS, Firedrake, or dune-fem alleviates the need…

We have developed PyTIE (Python Topological Indices Expressions) which is defined as the collections of Python packages such as PyTIE D, PyTIE DS, PyTIE SMS DE, and PyTIE SMS DSE, which are open-source software packages and cross-platform…

Desktop GIS applications, such as ArcGIS and QGIS, provide tools essential for conducting suitability analysis, an activity that is central in formulating a land-use plan. But, when it comes to building complicated land-use suitability…

rigidPy is a Python package that provides a set of tools necessary for studying rigidity and mechanical response in spring networks. It also includes suitable modules for generating new realizations of networks with applications in glassy…

We introduce PyPulse, a Python package for imputation of biosignals in both clinical and wearable sensor settings. Missingness is commonplace in these settings and can arise from multiple causes, such as insecure sensor attachment or data…

Software libraries are central to the functionality, security, and maintainability of modern code. As developers increasingly turn to Large Language Models (LLMs) to assist with programming tasks, understanding how these models recommend…

A Software Bill of Materials (SBOM) is becoming an essential tool for effective software dependency management. An SBOM is a list of components used in software, including details such as component names, versions, and licenses. Using…

With the recent advances in AI programming assistants such as GitHub Copilot, programming is not limited to classical programming languages anymore--programming tasks can also be expressed and solved by end-users in natural text. Despite…

Automating C-to-Rust migration is critical for improving software security without sacrificing performance. Traditional rule-based methods struggle with diverse C idioms, often producing rigid and unidiomatic Rust code. Large Language…

Instruction tuning is essential for aligning large language models (LLMs) to downstream tasks and commonly relies on large, diverse corpora. However, small, high-quality subsets, known as coresets, can deliver comparable or superior…

As the field of data science continues to grow, there will be an ever-increasing demand for tools that make machine learning accessible to non-experts. In this paper, we introduce the concept of tree-based pipeline optimization for…

Runtime verification (RV) now scales for testing thousands of open-source Java projects, helping find hundreds of bugs. The popular Python ecosystem could use such benefits. But, today's Python RV systems are limited to a domain or…

The online data reduction service reductus transforms measurements in experimental science from laboratory coordinates into physically meaningful quantities with accurate estimation of uncertainties based on instrumental settings and…

PyUnfold is a Python package for incorporating imperfections of the measurement process into a data analysis pipeline. In an ideal world, we would have access to the perfect detector: an apparatus that makes no error in measuring a desired…

Recent years have seen a rise in the popularity of quality diversity (QD) optimization, a branch of optimization that seeks to find a collection of diverse, high-performing solutions to a given problem. To grow further, we believe the QD…

Recent surge in Large Language Model (LLM) availability has opened exciting avenues for research. However, efficiently interacting with these models presents a significant hurdle since LLMs often reside on proprietary or self-hosted API…