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This paper explores articles hosted on the arXiv preprint server with the aim to uncover valuable insights hidden in this vast collection of research. Employing text mining techniques and through the application of natural language…
Since the beginning of COVID pandemic, there have been around 700000 scientific papers published on the subject. A human researcher cannot possibly get acquainted with such a huge text corpus -- and therefore developing AI-based tools to…
As large language models (LLMs) like OpenAI's GPT series continue to make strides, we witness the emergence of artificial intelligence applications in an ever-expanding range of fields. In medicine, these LLMs hold considerable promise for…
In this work, we present the ChemNLP library that can be used for 1) curating open access datasets for materials and chemistry literature, developing and comparing traditional machine learning, transformers and graph neural network models…
Biomedical Information Extraction is an exciting field at the crossroads of Natural Language Processing, Biology and Medicine. It encompasses a variety of different tasks that require application of state-of-the-art NLP techniques, such as…
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…
Digital libraries that maintain extensive textual collections may want to further enrich their content for certain downstream applications, e.g., building knowledge graphs, semantic enrichment of documents, or implementing novel access…
Unstructured text from legal, medical, and administrative sources offers a rich but underutilized resource for research in public health and the social sciences. However, large-scale analysis is hampered by two key challenges: the presence…
Biomedical data is inherently multimodal, comprising physical measurements and natural language narratives. A generalist biomedical AI model needs to simultaneously process different modalities of data, including text and images. Therefore,…
Summary: In anticipation of the individualized proteomics era and the need to integrate knowledge from disease studies, we have augmented our peptide identification software RAId DbS to take into account annotated single amino acid…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
The number of biomedical research articles published has doubled in the past 20 years. Search engine based systems naturally center around searching, but researchers may not have a clear goal in mind, or the goal may be expressed in a query…
Health informatics research is characterized by diverse data modalities, rapid knowledge expansion, and the need to integrate insights across biomedical science, data analytics, and clinical practice. These characteristics make it…
Machine Reading Comprehension (MRC) has become enormously popular recently and has attracted a lot of attention. However, the existing reading comprehension datasets are mostly in English. In this paper, we introduce a Span-Extraction…
Hospital readmission, defined as patients being re-hospitalized shortly after discharge, is a critical concern as it impacts patient outcomes and healthcare costs. Identifying patients at risk of readmission allows for timely interventions,…
Biomedical research results are being published at a high rate, and with existing search engines, the vast amount of published work is usually easily accessible. However, reproducing published results, either experimental data or…
This paper presents AppTechMiner, a rule-based information extraction framework that automatically constructs a knowledge base of all application areas and problem solving techniques. Techniques include tools, methods, datasets or…
We propose SUSIE, a novel summarization method that can work with state-of-the-art summarization models in order to produce structured scientific summaries for academic articles. We also created PMC-SA, a new dataset of academic…
The use of Large Language Models (LLMs) like ChatGPT and DeepSeek for translation and language polishing is a welcome development, reducing the longstanding publishing barrier to non-English speakers. Assessing the uptake of this facility…
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.…