Related papers: A Byte-sized Approach to Named Entity Recognition

Named entity recognition (NER) is a fundamental task in natural language processing that aims to identify and classify named entities in text. However, span-based methods for NER typically assign entity types to text spans, resulting in an…

Disease name recognition and normalization, which is generally called biomedical entity linking, is a fundamental process in biomedical text mining. Recently, neural joint learning of both tasks has been proposed to utilize the mutual…

Supervised models trained to predict properties from representations have been achieving high accuracy on a variety of tasks. For instance, the BERT family seems to work exceptionally well on the downstream task from NER tagging to the…

The aim of Named Entity Recognition (NER) is to identify references of named entities in unstructured documents, and to classify them into pre-defined semantic categories. NER often aids from added background knowledge in the form of…

Entity linking (EL) for biomedical text is typically benchmarked on English-only corpora with flat mentions, leaving the more realistic scenario of nested and multilingual mentions largely unexplored. We present our system for the BioNNE…

Named entity recognition (NER) identifies typed entity mentions in raw text. While the task is well-established, there is no universally used tagset: often, datasets are annotated for use in downstream applications and accordingly only…

Subword tokenization methods like Byte Pair Encoding (BPE) are widely used in large language models due to their balance of vocabulary compactness and representational power. However, they suffer from inefficiencies in representing rare…

Here we present the training and evaluation of NanoNER, a Named Entity Recognition (NER) model for Nanobiology. NER consists in the identification of specific entities in spans of unstructured texts and is often a primary task in Natural…

Named Entity Recognition (NER) encounters the challenge of unbalanced labels, where certain entity types are overrepresented while others are underrepresented in real-world datasets. This imbalance can lead to biased models that perform…

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…

Byte-Pair Encoding (BPE) has become a widely adopted subword tokenization method in modern language models due to its simplicity and strong empirical performance across downstream tasks. However, applying BPE to unsegmented languages such…

Biomedical entity linking is the task of identifying mentions of biomedical concepts in text documents and mapping them to canonical entities in a target thesaurus. Recent advancements in entity linking using BERT-based models follow a…

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…

Named entity disambiguation (NED), which involves mapping textual mentions to structured entities, is particularly challenging in the medical domain due to the presence of rare entities. Existing approaches are limited by the presence of…

Named Entity Recognition seeks to extract substrings within a text that name real-world objects and to determine their type (for example, whether they refer to persons or organizations). In this survey, we first present an overview of…

In this paper, we study a novel approach for named entity recognition (NER) and mention detection in natural language processing. Instead of treating NER as a sequence labelling problem, we propose a new local detection approach, which rely…

Weak supervision has shown promising results in many natural language processing tasks, such as Named Entity Recognition (NER). Existing work mainly focuses on learning deep NER models only with weak supervision, i.e., without any human…

We consider the problem of Named Entity Recognition (NER) on biomedical scientific literature, and more specifically the genomic variants recognition in this work. Significant success has been achieved for NER on canonical tasks in recent…

What are the units of text that we want to model? From bytes to multi-word expressions, text can be analyzed and generated at many granularities. Until recently, most natural language processing (NLP) models operated over words, treating…

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…