Related papers: Biomedical Entity Linking for Dutch: Fine-tuning a…

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…

The Biocreative VII Track-2 challenge consists of named entity recognition, entity-linking (or entity-normalization), and topic indexing tasks -- with entities and topics limited to chemicals for this challenge. Named entity recognition is…

This study proposes a medical entity extraction method based on Transformer to enhance the information extraction capability of medical literature. Considering the professionalism and complexity of medical texts, we compare the performance…

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.…

Recent advances in natural language processing (NLP) have been driven bypretrained language models like BERT, RoBERTa, T5, and GPT. Thesemodels excel at understanding complex texts, but biomedical literature, withits domain-specific…

Biological relation networks contain rich information for understanding the biological mechanisms behind the relationship of entities such as genes, proteins, diseases, and chemicals. The vast growth of biomedical literature poses…

Entity linking, the task of mapping textual mentions to known entities, has recently been tackled using contextualized neural networks. We address the question whether these results -- reported for large, high-quality datasets such as…

Biomedical entity linking and event extraction are two crucial tasks to support text understanding and retrieval in the biomedical domain. These two tasks intrinsically benefit each other: entity linking disambiguates the biomedical…

Progress in biomedical Named Entity Recognition (NER) and Entity Linking (EL) is currently hindered by a fragmented data landscape, a lack of resources for building explainable models, and the limitations of semantically-blind evaluation…

Biomedical entity linking maps textual mentions to concepts in structured knowledge bases such as UMLS or SNOMED CT. Most existing systems link each mention independently, using only the mention or its surrounding sentence. This ignores…

Whilst there has been growing progress in Entity Linking (EL) for general language, existing datasets fail to address the complex nature of health terminology in layman's language. Meanwhile, there is a growing need for applications that…

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…

Pretrained language models have shown success in many natural language processing tasks. Many works explore incorporating knowledge into language models. In the biomedical domain, experts have taken decades of effort on building large-scale…

Medical Entity Recognition (MedER) is an essential NLP task for extracting meaningful entities from the medical corpus. Nowadays, MedER-based research outcomes can remarkably contribute to the development of automated systems in the medical…

Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language…

The availability of biomedical text data and advances in natural language processing (NLP) have made new applications in biomedical NLP possible. Language models trained or fine tuned using domain specific corpora can outperform general…

Biomedical text mining is becoming increasingly important as the number of biomedical documents and web data rapidly grows. Recently, word representation models such as BERT has gained popularity among researchers. However, it is difficult…

Successful biomedical relation extraction can provide evidence to researchers and clinicians about possible unknown associations between biomedical entities, advancing the current knowledge we have about those entities and their inherent…

This paper shines a light on the potential of definition-based semantic models for detecting idiomatic and semi-idiomatic multiword expressions (MWEs) in clinical terminology. Our study focuses on biomedical entities defined in the UMLS…

Advances in natural language processing techniques, such as named entity recognition and normalization to widely used standardized terminologies like UMLS or SNOMED-CT, along with the digitalization of electronic health records, have…