Related papers: A Framework for Reproducible, Interactive Research…
Many research groups aspire to make data and code FAIR and reproducible, yet struggle because the data and code life cycles are disconnected, executable environments are often missing from published work, and technical skill requirements…
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
The reproducibility of scientific articles is central to the advancement of science. Despite this importance, evaluating reproducibility remains challenging due to the scarcity of ground truth data. Predictive models can address this…
An essential part of research and scientific communication is researchers' ability to reproduce the results of others. While there have been increasing standards for authors to make data and code available, many of these files are hard to…
Many interesting data sets available on the Internet are of a medium size---too big to fit into a personal computer's memory, but not so large that they won't fit comfortably on its hard disk. In the coming years, data sets of this…
The trend toward open science increases the pressure on authors to provide access to the source code and data they used to compute the results reported in their scientific papers. Since sharing materials reproducibly is challenging, several…
Reproducibility should be a cornerstone of science as it enables validation and reuse. In recent years, the scientific community and the general public became increasingly aware of the reproducibility crisis, i.e. the wide-spread inability…
Computational reproducibility of scientific results, that is, the execution of a computational experiment (e.g., a script) using its original settings (data, code, etc.), should always be possible. However, reproducibility has become a…
The reproducibility of scientific research has become a point of critical concern. We argue that openness and transparency are critical for reproducibility, and we outline an ecosystem for open and transparent science that has emerged…
The high incidence of irreproducible research has led to urgent appeals for transparency and equitable practices in open science. For the scientific disciplines that rely on computationally intensive analyses of large data sets, a granular…
Background. Effectively communicating complex statistical model outputs is a major challenge in public health. This study introduces the FARSI approach (Fast, Accessible, Reliable, Secure, Informative) as a framework to enhance the…
Digital computational outputs are now ubiquitous in the research workflow and the way in which these data are stored and cataloged is becoming more standardized across fields of research. However, even with accessible data and code, the…
This paper explores the significant impact of AI-based medical devices, including wearables, telemedicine, large language models, and digital twins, on clinical decision support systems. It emphasizes the importance of producing outcomes…
This paper introduces reproducible research, and explains its importance, benefits and challenges. Some important tools for conducting reproducible research in Transportation Research are also introduced. Moreover, the source code for…
This paper investigates the conceptual relationship between openness and reproducibility using a model-centric approach, heavily informed by probability theory and statistics. We first clarify the concepts of reliability, auditability,…
The Internet has become a very powerful platform where diverse medical information are expressed daily. Recently, a huge growth is seen in searches like symptoms, diseases, medicines, and many other health related queries around the globe.…
As computational analysis becomes increasingly more complex in health research, transparent sharing of analytical code is vital for reproducibility and trust. This practical guide, aligned to open science practices, outlines actionable…
This article presents our steps to integrate complex and partly unstructured medical data into a clinical research database with subsequent decision support. Our main application is an integrated faceted search tool, accompanied by the…
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…
This study applies Large Language Models (LLMs) to two foundational Electronic Health Record (EHR) data science tasks: structured data querying (using programmatic languages, Python/Pandas) and information extraction from unstructured…