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Python applications depend on third-party native libraries that may be vendored within package distributions or installed on the host system. When vulnerabilities are discovered in these native libraries, determining which Python packages…

Nearly every popular programming language comes with one or more package managers. The software packages distributed by such package managers form large software ecosystems. These packaging ecosystems contain a large number of package…

One of the most powerful features of R is its infrastructure for contributed code. The built-in package manager and complementary repositories provide a great system for development and exchange of code, and have played an important role in…

Dynamic graph embedding has emerged as an important technique for modeling complex time-evolving networks across diverse domains. While transformer-based models have shown promise in capturing long-range dependencies in temporal graph data,…

Distributed collaborative software development tends to make artifacts and decisions inconsistent and uncertain. We try to solve this problem by providing an information repository to reflect the state of works precisely, by managing the…

The Model Context Protocol (MCP) has recently emerged as a standardized interface for connecting language models with external tools and data. As the ecosystem rapidly expands, the lack of a structured, comprehensive view of existing MCP…

Open-source software supply chain security relies heavily on assessing affected versions of library vulnerabilities. While prior studies have leveraged exploits for verifying vulnerability affected versions, they point out a key limitation…

This paper describes a data-driven framework to parse musical sequences into dependency trees, which are hierarchical structures used in music cognition research and music analysis. The parsing involves two steps. First, the input sequence…

In Open Source Software, resources of any project are open for reuse by introducing dependencies or copying the resource itself. In contrast to dependency-based reuse, the infrastructure to systematically support copy-based reuse appears to…

Discovering temporal lagged and inter-dependencies in multivariate time series data is an important task. However, in many real-world applications, such as commercial cloud management, manufacturing predictive maintenance, and portfolios…

As the complexity and size of software projects increases in real-world environments, maintaining and creating maintainable and dependable code becomes harder and more costly. Refactoring is considered as a method for enhancing the internal…

Long lived software projects encompass a large number of artifacts, which undergo many revisions throughout their history. Empirical software engineering researchers studying software evolution gather and collect datasets with millions of…

Large Language Models have advanced automated software development, however, it remains a challenge to correctly infer dependencies, namely, identifying the internal components and external packages required for a repository to successfully…

Dependency networks (Heckerman et al., 2000) are potential probabilistic graphical models for systems comprising a large number of variables. Like Bayesian networks, the structure of a dependency network is represented by a directed graph,…

Delivering a reproducible environment along with complex and up-to-date software stacks on thousands of distributed and heterogeneous worker nodes is a critical task. The CernVM-File System (CVMFS) has been designed to help various…

Feature models are widely used to capture the configuration space of software systems. Although automated reasoning has been studied for detecting problematic features and supporting configuration tasks, significantly less attention has…

We present a repository decomposition system that converts large software repositories into a vectorized knowledge graph which mirrors project architectural and semantic structure, capturing semantic relationships and allowing a significant…

Much of the current software depends on open-source components, which in turn have complex dependencies on other open-source libraries. Vulnerabilities in open source therefore have potentially huge impacts. The goal of this work is to get…

Graphs are fundamental data structures which concisely capture the relational structure in many important real-world domains, such as knowledge graphs, physical and social interactions, language, and chemistry. Here we introduce a powerful…

Large language models (LLMs) have developed rapidly in recent years, revolutionizing various fields. Despite their widespread success, LLMs heavily rely on external code dependencies from package management systems, creating a complex and…