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This paper proposes a procedure to execute external source codes from a LaTeX document and include the calculation outputs in the resulting Portable Document Format (pdf) file automatically. It integrates programming tools into the LaTeX…
Reproducibility is increasingly important to statistical research, but many details are often omitted from the published version of complex statistical analyses. A reader's comprehension is limited to what the author concludes, without…
We propose a Makefile for developing containerized $\LaTeX$ technical documents. The Makefile allows the author to execute the code that generates variables, tables and figures (results), which are then used during the $\LaTeX$ compilation,…
Academic documents stored in PDF format can be transformed into plain text structured markup languages to enhance accessibility and enable scalable digital library workflows. Markup languages allow for easier updates and customization,…
The large-scale training of multi-modal models on data scraped from the web has shown outstanding utility in infusing these models with the required world knowledge to perform effectively on multiple downstream tasks. However, one downside…
Reproducible document standards, like R Markdown, facilitate the programmatic creation of documents whose content is itself programmatically generated. While these documents are generally not complete in the sense that they will not include…
Recent advances in large language models (LLMs) have enabled AI agents to autonomously generate scientific proposals, conduct experiments, author papers, and perform peer reviews. Yet this flood of AI-generated research content collides…
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…
Transforming scientific papers into multimodal presentation content is essential for research dissemination but remains labor intensive. Existing automated solutions typically treat each format as an isolated downstream task, leading to…
Today's peer review process for scientific articles is unnecessarily opaque and offers few incentives to referees. Likewise, the publishing process is unnecessarily inefficient and its results are only rarely made freely available to the…
We introduce Texar, an open-source toolkit aiming to support the broad set of text generation tasks that transform any inputs into natural language, such as machine translation, summarization, dialog, content manipulation, and so forth.…
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…
Tool use has turned large language models (LLMs) into powerful agents that can perform complex multi-step tasks by dynamically utilising external software components. However, these tools must be implemented in advance by human developers,…
Recent advances in artificial intelligence (AI) have accelerated the growth of both human-authored and AI-generated research outputs, placing increasing strain on traditional academic publishing systems and challenging the scalability of…
LLM-agents are increasingly used to accelerate the progress of scientific research. Yet a persistent bottleneck is data access: agents not only lack readily available tools for retrieval, but also have to work with unstrcutured,…
Scientific software is one of the key elements for reproducible research. However, classic publications and related scientific software are typically not (sufficiently) linked, and it lacks tools to jointly explore these artefacts. In this…
The emergence of R, a freely available data analysis environment, brought to the researcher in any science field a set of well-concerted instruments of immense power and low cost. In botany and zoology, these instruments could be used, for…
Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…
Preprints are essential for the timely and open dissemination of research. arXiv, the most widely used preprint service, takes the idea of open science one step further by not only publishing the actual preprints but also LaTeX sources and…
Although a standard in natural science, reproducibility has been only episodically applied in experimental computer science. Scientific papers often present a large number of tables, plots and pictures that summarize the obtained results,…