Related papers: A large dataset of software mentions in the biomed…
Recent research advances achieve human-level accuracy for de-identifying free-text clinical notes on research datasets, but gaps remain in reproducing this in large real-world settings. This paper summarizes lessons learned from building a…
Medical entity linking is the task of identifying and standardizing medical concepts referred to in an unstructured text. Most of the existing methods adopt a three-step approach of (1) detecting mentions, (2) generating a list of candidate…
miRNA mRNA relations are closely linked to several biological processes and disease mechanisms In a recent study we tested the performance of large language models LLMs on extracting miRNA mRNA relations from PubMed PubMedBERT achieved the…
Manually curated biomedical repositories -- spanning bioactivity, genomics, and chemistry -- are expensive to maintain, lag behind primary literature, and discard experimental context, obscuring nuances needed to assess data correctness and…
In the field of Computer Science, conference and workshop papers serve as important contributions, carrying substantial weight in research assessment processes, compared to other disciplines. However, a considerable number of these papers…
Despite the growing scale of medical Vision-Language datasets, the impact of dataset quality on model performance remains under-explored. We introduce Open-PMC, a high-quality medical dataset from PubMed Central, containing 2.2 million…
We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for…
Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on…
Knowledge about the software used in scientific investigations is necessary for different reasons, including provenance of the results, measuring software impact to attribute developers, and bibliometric software citation analysis in…
Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows. The reproducibility of…
Biomedical named entity recognition (NER) presents unique challenges due to specialized vocabularies, the sheer volume of entities, and the continuous emergence of novel entities. Traditional NER models, constrained by fixed taxonomies and…
$\textbf{Objective}$ Develop an automatic diagnostic system which only uses textual admission information from Electronic Health Records (EHRs) and assist clinicians with a timely and statistically proved decision tool. The hope is that the…
This paper describes the system submitted to the SOMD 2026 Shared Task for Cross-Document Coreference Resolution (CDCR) of software mentions. Our approach addresses the challenge of identifying and clustering inconsistent software mentions…
Accurate extraction of breast cancer patients' phenotypes is important for clinical decision support and clinical research. Current models do not take full advantage of cancer domain-specific corpus, whether pre-training Bidirectional…
Biomedical knowledge resources often either preserve evidence as unstructured text or compress it into flat triples that omit study design, provenance, and quantitative support. Here we present EvidenceNet, a disease-specific dataset of…
Scientific document embeddings contain a variety of rich features which can be harnessed for downstream tasks such as recommendation, ranking, and clustering. We explore which tangible insights can be drawn from scientific document…
This study is dedicated to exploring the application of prompt learning methods to advance Named Entity Recognition (NER) within the medical domain. In recent years, the emergence of large-scale models has driven significant progress in NER…
Proper citation is of great importance in academic writing for it enables knowledge accumulation and maintains academic integrity. However, citing properly is not an easy task. For published scientific entities, the ever-growing academic…
We introduce the General Index of Software Engineering Papers, a dataset of fulltext-indexed papers from the most prominent scientific venues in the field of Software Engineering. The dataset includes both complete bibliographic information…
Recently, considerable literature has grown up around the theme of few-shot named entity recognition (NER), but little published benchmark data specifically focused on the practical and challenging task. Current approaches collect existing…