Related papers: A large dataset of software mentions in the biomed…
Despite the importance of scientific software for research, it is often not formally recognized and rewarded. This is especially true for foundational libraries, which are hidden below packages visible to the users (and thus doubly hidden,…
Datasets collecting software mentions from scholarly publications can potentially be used for research into the software that has been used in the published research, as well as into the practice of software citation. Recently, new software…
Knowledge about software used in scientific investigations is important for several reasons, for instance, to enable an understanding of provenance and methods involved in data handling. However, software is usually not formally cited, but…
PubMed is an essential resource for the medical domain, but useful concepts are either difficult to extract or are ambiguated, which has significantly hindered knowledge discovery. To address this issue, we constructed a PubMed knowledge…
Motivation: Named Entity Recognition (NER) is a key task to support biomedical research. In Biomedical Named Entity Recognition (BioNER), obtaining high-quality expert annotated data is laborious and expensive, leading to the development of…
Medical imaging papers often focus on methodology, but the quality of the algorithms and the validity of the conclusions are highly dependent on the datasets used. As creating datasets requires a lot of effort, researchers often use…
In many academic disciplines, software is created during the research process or for a research purpose. The crucial role of software for research is increasingly acknowledged. The application of software engineering to research software…
We present a scalable, AI-powered system that identifies and extracts evidence-based behavioral nudges from unstructured biomedical literature. Nudges are subtle, non-coercive interventions that influence behavior without limiting choice,…
Papers, patents, and clinical trials are essential scientific resources in biomedicine, crucial for knowledge sharing and dissemination. However, these documents are often stored in disparate databases with varying management standards and…
The recognition of dataset names is a critical task for automatic information extraction in scientific literature, enabling researchers to understand and identify research opportunities. However, existing corpora for dataset mention…
Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the…
Automatically locating named entities in natural language text - named entity recognition - is an important task in the biomedical domain. Many named entity mentions are ambiguous between several bioconcept types, however, causing text…
This paper presents the formal release of MedMentions, a new manually annotated resource for the recognition of biomedical concepts. What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts…
The explosive growth of AI and machine learning literature -- with venues like NeurIPS and ICLR now accepting thousands of papers annually -- has made comprehensive citation coverage increasingly difficult for researchers. While citation…
Named-entity recognition (NER) is fundamental to extracting structured information from the >80% of healthcare data that resides in unstructured clinical notes and biomedical literature. Despite recent advances with large language models,…
Automatically extracting organization names from the affiliation sentences of articles related to biomedicine is of great interest to the pharmaceutical marketing industry, health care funding agencies and public health officials. It will…
There has been rapid growth in biomedical literature, yet capturing the heterogeneity of the bibliographic information of these articles remains relatively understudied. Although graph mining research via heterogeneous graph neural networks…
Datasets are critical for scientific research, playing an important role in replication, reproducibility, and efficiency. Researchers have recently shown that datasets are becoming more important for science to function properly, even…
Tools to explore scientific literature are essential for scientists, especially in biomedicine, where about a million new papers are published every year. Many such tools provide users the ability to search for specific entities (e.g.…
As a major social media platform, Twitter publishes a large number of user-generated text (tweets) on a daily basis. Mining such data can be used to address important social, public health, and emergency management issues that are…