Related papers: BioNerFlair: biomedical named entity recognition u…

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…

We present a weakly-supervised data augmentation approach to improve Named Entity Recognition (NER) in a challenging domain: extracting biomedical entities (e.g., proteins) from the scientific literature. First, we train a neural NER (NNER)…

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…

Recognizing spans of biomedical concepts and their types (e.g., drug or gene) in free text, often called biomedical named entity recognition (NER), is a basic component of information extraction (IE) pipelines. Without a strong NER…

In recent years, with the growing amount of biomedical documents, coupled with advancement in natural language processing algorithms, the research on biomedical named entity recognition (BioNER) has increased exponentially. However, BioNER…

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…

Named entity recognition (NER) is a fundamental part of extracting information from documents in biomedical applications. A notable advantage of NER is its consistency in extracting biomedical entities in a document context. Although…

The growth rate in the amount of biomedical documents is staggering. Unlocking information trapped in these documents can enable researchers and practitioners to operate confidently in the information world. Biomedical NER, the task of…

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…

Prevalent solution for BioNER involves using representation learning techniques coupled with sequence labeling. However, such methods are inherently task-specific, demonstrate poor generalizability, and often require dedicated model for…

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…

Biomedical named entity recognition (NER) is a fundamental task in text mining of medical documents and has many applications. Deep learning based approaches to this task have been gaining increasing attention in recent years as their…

Biomedical named entity recognition (BioNER) seeks to automatically recognize biomedical entities in natural language text, serving as a necessary foundation for downstream text mining tasks and applications such as information extraction…

Large language models (LLMs) have demonstrated dominating performance in many NLP tasks, especially on generative tasks. However, they often fall short in some information extraction tasks, particularly those requiring domain-specific…

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…

Background and Objective: Biomedical Named Entity Recognition (BioNER) is a foundational task in medical informatics, crucial for downstream applications like drug discovery and clinical trial matching. However, adapting general-domain…

Background: Finding biomedical named entities is one of the most essential tasks in biomedical text mining. Recently, deep learning-based approaches have been applied to biomedical named entity recognition (BioNER) and showed promising…

Most existing methods for biomedical entity recognition task rely on explicit feature engineering where many features either are specific to a particular task or depends on output of other existing NLP tools. Neural architectures have been…

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…

Supervised named entity recognition (NER) in the biomedical domain depends on large sets of annotated texts with the given named entities. The creation of such datasets can be time-consuming and expensive, while extraction of new entities…