Related papers: A Framework for Reproducible, Interactive Research…
Science has a data management problem, as well as a project management problem. While industrial-grade data science teams have embraced the agile mindset, and adopted or created all kind of tools to create reproducible workflows,…
In the evolving landscape of clinical informatics, the integration and utilization of software tools developed through governmental funding represent a pivotal advancement in research and application. However, the dispersion of these tools…
Rather than using text for scientific research reports, we have proposed developing highly-structured reports with rich semantic models. In this paper, we consider detailed structures for the components of research reports using a modeling…
Patient-trial matching requires reasoning over long, heterogeneous electronic health records (EHRs) and complex eligibility criteria, posing significant challenges for scalability, generalization, and computational efficiency. Existing…
Automatic research with Large Language Models (LLMs) is rapidly gaining importance, driving the development of increasingly complex workflows involving multi-agent systems, planning, tool usage, code execution, and human-agent interaction…
Navigating the vast scientific literature often starts with browsing a paper's abstract. However, when a reader seeks additional information, not present in the abstract, they face a costly cognitive chasm during their dive into the full…
Research must be reproducible in order to make an impact on science and to contribute to the body of knowledge in our field. Yet studies have shown that 70% of research from academic labs cannot be reproduced. In software engineering, and…
The Micropublications semantic model for scientific claims, evidence, argumentation and annotation in biomedical publications, is a metadata model of scientific argumentation, designed to support several key requirements for exchange and…
One of the challenges in machine learning research is to ensure that presented and published results are sound and reliable. Reproducibility, that is obtaining similar results as presented in a paper or talk, using the same code and data…
In this paper, we discuss the approaches we took and trade-offs involved in making a paper on a conceptual topic in pattern recognition research fully reproducible. We discuss our definition of reproducibility, the tools used, how the…
We present an open deep research system for long-form question answering, selected as a winning system in the text-to-text track of the MMU-RAG competition at NeurIPS 2025. The system combines an open-source large language model (LLM) with…
Science depends on collaboration, result reproduction, and the development of supporting software tools. Each of these requires careful management of software versions. We present a unified model for installing, managing, and publishing…
With the exponential increase in online scientific literature, identifying reliable domain-specific data has become increasingly important but also very challenging. Manual data collection and filtering for domain-specific scientific…
Open science movement has established reproducibility, transparency, and validation of research outputs as essential norms for conducting scientific research. It advocates for open access to research outputs, especially research data, to…
Large language models augmented with task-relevant documents have demonstrated impressive performance on knowledge-intensive tasks. However, regarding how to obtain effective documents, the existing methods are mainly divided into two…
In recent years, significant effort has been invested verifying the reproducibility and robustness of research claims in social and behavioral sciences (SBS), much of which has involved resource-intensive replication projects. In this…
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…
An aggregated recursive K-index is proposed as a new scientometric indicator of added value and scientific research output of individual publications. This index can be used instead of or in addition to the H-index (J.E. Hirsch. An index to…
Large-scale replication studies like the Reproducibility Project: Psychology (RP:P) provide invaluable systematic data on scientific replicability, but most analyses and interpretations of the data fail to agree on the definition of…
Reproducibility is a confused terminology. In this paper, I take a fundamental view on reproducibility rooted in the scientific method. The scientific method is analysed and characterised in order to develop the terminology required to…