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Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
Today, software systems have a significant role in various domains among which are healthcare, entertainment, transport and logistics, and many more. It is only natural that with this increasing dependency on software, the number of…
Software repositories are an essential source of information for software engineering research on topics such as project evolution and developer collaboration. Appropriate mining tools and analysis pipelines are therefore an indispensable…
Software engineering is knowledge-intensive and requires software developers to continually search for knowledge, often on community question answering platforms such as Stack Overflow. Such information sharing platforms do not exist in…
Computational physics increasingly depends on large simulation datasets generated by software that remains under active development for many years. In such settings, reproducibility requires not only well documented data but also explicit…
Scientific document embeddings contain a variety of rich features which can be harnessed for downstream tasks such as recommendation, ranking, and clustering. We explore which tangible insights can be drawn from scientific document…
Software is an important tool for scholarly work, but software produced for research is in many cases not easily identifiable or discoverable. A potential first step in linking research and software is software identification. In this paper…
The lack of predictability of citation-based measures frequently used to gauge impact, from impact factors to short-term citations, raises a fundamental question: Is there long-term predictability in citation patterns? Here, we derive a…
Citation recommendation systems for the scientific literature, to help authors find papers that should be cited, have the potential to speed up discoveries and uncover new routes for scientific exploration. We treat this task as a ranking…
The rapid advancement of Large Language Models (LLMs) is reshaping software engineering by profoundly influencing coding, documentation, and system maintenance practices. As these tools become deeply embedded in developers' daily workflows,…
The Web is our primary source of all kinds of information today. This includes information about software as well as associated materials, like source code, documentation, related publications and change logs. Such data is of particular…
Reproducibility in research remains hindered by complex systems involving data, models, tools, and algorithms. Studies highlight a reproducibility crisis due to a lack of standardized reporting, code and data sharing, and rigorous…
In this research, we present a comprehensive, longitudinal empirical summary of the R package ecosystem, including not just CRAN, but also Bioconductor and GitHub. We analyze more than 25,000 packages, 150,000 releases, and 15 million files…
Citations in science are being studied from several perspectives, among which approaches such as scientometrics and science of science. In this chapter I briefly review some of the literature on citations, citation distributions and models…
Failure studies are important in revealing the root causes, behaviors, and life cycle of defects in software systems. These studies either focus on understanding the characteristics of defects in specific classes of systems or the…
Authorship of scientific articles has profoundly changed from early science until now. If once upon a time a paper was authored by a handful of authors, scientific collaborations are much more prominent on average nowadays. As authorship…
This paper presents an analysis of the Overton policy document database, describing the makeup of materials indexed and the nature in which they cite academic literature. We report on various aspects of the data, including growth,…
To remain viable and thrive, software organizations must rapidly adapt to frequent, and often rather far-ranging, changes to their operational context. These changes typically concern many factors, including the nature of the organization's…
Despite potential benefits in Software Engineering (SE), adoption of software modelling in industry is low. Technical issues such as tool support have gained significant research before, but individual guidance and training have received…
The citations process for scientific papers has been studied extensively. But while the citations accrued by authors are the sum of the citations of their papers, translating the dynamics of citation accumulation from the paper to the…