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Despite recent advances in natural language processing, many statistical models for processing text perform extremely poorly under domain shift. Processing biomedical and clinical text is a critically important application area of natural…
Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…
WorkingWiki is a software extension for the popular MediaWiki platform that makes a wiki into a powerful environment for collaborating on publication-quality manuscripts and software projects. Developed in Jonathan Dushoff's theoretical…
Scientific workflow management systems offer features for composing complex computational pipelines from modular building blocks, for executing the resulting automated workflows, and for recording the provenance of data products resulting…
This technical report introduces Docling, an easy to use, self-contained, MIT-licensed open-source package for PDF document conversion. It is powered by state-of-the-art specialized AI models for layout analysis (DocLayNet) and table…
SciLaD is a novel, large-scale dataset of scientific language constructed entirely using open-source frameworks and publicly available data sources. It comprises a curated English split containing over 10 million scientific publications and…
The use of several open source scientific packages in the Schr\"odinger Materials Science Suite will be discussed. A typical workflow for materials discovery will be described, discussing how open source packages have been incorporated at…
The number of Language Models (LMs) dedicated to processing scientific text is on the rise. Keeping pace with the rapid growth of scientific LMs (SciLMs) has become a daunting task for researchers. To date, no comprehensive surveys on…
In the field of computational science and engineering, workflows often entail the application of various software, for instance, for simulation or pre- and postprocessing. Typically, these components have to be combined in arbitrarily…
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 Scholarly Document Processing (SDP) workshop is to encourage more efforts on natural language understanding of scientific task. It contains three shared tasks and we participate in the LongSumm shared task. In this paper, we describe…
Managing issue reports is essential for the evolution and maintenance of software systems. However, manual issue management tasks such as triaging, prioritizing, localizing, and resolving issues are highly resource-intensive for projects…
Science is conducted collaboratively, often requiring knowledge sharing about computational experiments. When experiments include only datasets, they can be shared using Uniform Resource Identifiers (URIs) or Digital Object Identifiers…
Scientific papers make claims about prior work backed by citations. Verifying those citations at scale (that each cited paper exists, says what the citation claims, and is itself reliable) is structurally beyond what human review can…
Scientific reasoning poses an excessive challenge for even the most advanced Large Language Models (LLMs). To make this task more practical and solvable for LLMs, we introduce a new task setting named tool-augmented scientific reasoning.…
The rapid growth of scientific literature has made manual extraction of structured knowledge increasingly impractical. To address this challenge, we introduce SCILIRE, a system for creating datasets from scientific literature. SCILIRE has…
This paper proposes a software repository model together with associated tooling and consists of several complex, open-source GUI driven applications ready to be used in empirical software research. We start by providing the rationale for…
The transfer learning toolkit wraps the codes of 17 transfer learning models and provides integrated interfaces, allowing users to use those models by calling a simple function. It is easy for primary researchers to use this toolkit and to…
This paper provides an overview of prominent deep learning toolkits and, in particular, reports on recent publications that contributed open source software for implementing tasks that are common in intelligent user interfaces (IUI). We…
In this work, we present scikit-fingerprints, a Python package for computation of molecular fingerprints for applications in chemoinformatics. Our library offers an industry-standard scikit-learn interface, allowing intuitive usage and easy…