Related papers: NEMO: Extraction and normalization of organization…
Accurate affiliation matching, which links affiliation strings to standardized organization identifiers, is critical for improving research metadata quality, facilitating comprehensive bibliometric analyses, and supporting data…
Acknowledgments in scientific papers may give an insight into aspects of the scientific community, such as reward systems, collaboration patterns, and hidden research trends. The aim of the paper is to evaluate the performance of different…
Similarity network construction is a fundamental step in many approaches to community detection in biomedical analysis. It is utilised both in the creation of network structures from non-relational data and as a processing step in…
Named Entity Recognition (NER) is an important task in natural language processing that aims to identify and extract key entities from unstructured text. We present a novel application of NER in plasma physics research articles and address…
Accurate recognition of biomedical named entities is critical for medical information extraction and knowledge discovery. However, existing methods often struggle with nested entities, entity boundary ambiguity, and cross-lingual…
Existing fact-checking models for biomedical claims are typically trained on synthetic or well-worded data and hardly transfer to social media content. This mismatch can be mitigated by adapting the social media input to mimic the focused…
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…
Acknowledgments in scientific papers may give an insight into aspects of the scientific community, such as reward systems, collaboration patterns, and hidden research trends. The aim of the paper is to evaluate the performance of different…
In this paper, we present our system for the BioNNE English track, which aims to extract 8 types of biomedical nested named entities from biomedical text. We use a large language model (Mixtral 8x7B instruct) and ScispaCy NER model to…
We present a novel algorithm and validation method for disambiguating author names in very large bibliographic data sets and apply it to the full Web of Science (WoS) citation index. Our algorithm relies only upon the author and citation…
Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations…
Understanding the meaning of text often involves reasoning about entities and their relationships. This requires identifying textual mentions of entities, linking them to a canonical concept, and discerning their relationships. These tasks…
Information Extraction (IE), encompassing Named Entity Recognition (NER), Named Entity Linking (NEL), and Relation Extraction (RE), is critical for transforming the rapidly growing volume of scientific publications into structured,…
Training a Named Entity Recognition (NER) model often involves fixing a taxonomy of entity types. However, requirements evolve and we might need the NER model to recognize additional entity types. A simple approach is to re-annotate entire…
The metadata about scientific experiments published in online repositories have been shown to suffer from a high degree of representational heterogeneity---there are often many ways to represent the same type of information, such as a…
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: Biomedical named-entity normalization involves connecting biomedical entities with distinct database identifiers in order to facilitate data integration across various fields of biology. Existing systems for biomedical named…
In the domain of Natural Language Processing (NLP), Named Entity Recognition (NER) stands out as a pivotal mechanism for extracting structured insights from unstructured text. This manuscript offers an exhaustive exploration into the…
Information extraction techniques, including named entity recognition (NER) and relation extraction (RE), are crucial in many domains to support making sense of vast amounts of unstructured text data by identifying and connecting relevant…
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…