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Natural language processing (NLP) applications such as named entity recognition (NER) for low-resource corpora do not benefit from recent advances in the development of large language models (LLMs) where there is still a need for larger…

Training and evaluating language models increasingly requires the construction of meta-datasets --diverse collections of curated data with clear provenance. Natural language prompting has recently lead to improved zero-shot generalization…

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…

We present the construction of an annotated corpus of PubMed abstracts reporting about positive, negative or neutral effects of treatments or substances. Our ultimate goal is to annotate one sentence (rationale) for each abstract and to use…

Clinical decision-making requires synthesizing heterogeneous evidence, including patient histories, clinical guidelines, and trajectories of comparable cases. While large language models (LLMs) offer strong reasoning capabilities, they…

Topic modelling is a pivotal unsupervised machine learning technique for extracting valuable insights from large document collections. Existing neural topic modelling methods often encode contextual information of documents, while ignoring…

Creating scientific publications is a complex process, typically composed of a number of different activities, such as designing the experiments, data preparation, programming software and writing and editing the manuscript. The information…

Large-scale data sets on scholarly publications are the basis for a variety of bibliometric analyses and natural language processing (NLP) applications. Especially data sets derived from publication's full-text have recently gained…

Many questions in computational social science rely on datasets assembled from heterogeneous online sources, a process that is often labor-intensive, costly, and difficult to reproduce. Recent advances in large language models enable…

This paper conducts a comprehensive investigation into applying large language models, particularly on BioBERT, in healthcare. It begins with thoroughly examining previous natural language processing (NLP) approaches in healthcare, shedding…

The processing of entities in natural language is essential to many medical NLP systems. Unfortunately, existing datasets vastly under-represent the entities required to model public health relevant texts such as health advice often found…

The surging amount of biomedical literature & digital clinical records presents a growing need for text mining techniques that can not only identify but also semantically relate entities in unstructured data. In this paper we propose a text…

Biomedical evidence synthesis relies on accurate extraction of methodological, laboratory, and outcome variables from full-text research articles, yet these variables are embedded in complex scientific PDFs that make manual abstraction…

Curating, processing, and combining large-scale medical imaging datasets from national studies is a non-trivial task due to the intense computation and data throughput required, variability of acquired data, and associated financial…

There are a few challenges related to the task of biomedical named entity recognition, which are: the existing methods consider a fewer number of biomedical entities (e.g., disease, symptom, proteins, genes); and these methods do not…

Relevant information in documents is often summarized in tables, helping the reader to identify useful facts. Most benchmark datasets support either document layout analysis or table understanding, but lack in providing data to apply both…

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts…

The field of Natural Language Processing (NLP) is growing rapidly, with new research published daily along with an abundance of tutorials, codebases and other online resources. In order to learn this dynamic field or stay up-to-date on the…

Applying Machine learning to domains like Earth Sciences is impeded by the lack of labeled data, despite a large corpus of raw data available in such domains. For instance, training a wildfire classifier on satellite imagery requires…

Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations.…