Related papers: How Do Your Biomedical Named Entity Recognition Mo…

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)…

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) is a fundamental task of Biomedical Natural Language Processing for extracting relevant information from biomedical texts, such as clinical records, scientific publications, and electronic health…

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…

Biomedical entity linking aims to map biomedical mentions, such as diseases and drugs, to standard entities in a given knowledge base. The specific challenge in this context is that the same biomedical entity can have a wide range of names,…

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…

In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing…

When performing named entity recognition (NER), entity length is variable and dependent on a specific domain or dataset. Pre-trained language models (PLMs) are used to solve NER tasks and tend to be biased toward dataset patterns such as…

This study evaluated the effect of BioBERT in medical text processing for the task of medical named entity recognition. Through comparative experiments with models such as BERT, ClinicalBERT, SciBERT, and BlueBERT, the results showed that…

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…

Biomedical Named Entity Recognition (BioNER), task6 in BioASQ (A challenge in large-scale biomedical semantic indexing and question answering), is crucial for extracting information from scientific literature but faces hurdles such as…

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…

This study is dedicated to exploring the application of prompt learning methods to advance Named Entity Recognition (NER) within the medical domain. In recent years, the emergence of large-scale models has driven significant progress in NER…

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…

Although deep learning techniques have shown significant achievements, they frequently depend on extensive amounts of hand-labeled data and tend to perform inadequately in few-shot scenarios. The objective of this study is to devise a…

Named Entity Recognition (NER) is a challenging and widely studied task that involves detecting and typing entities in text. So far,NER still approaches entity typing as a task of classification into universal classes (e.g. date, person, or…

Biomedical Named Entity Recognition (BioNER) is a crucial step for analyzing Biomedical texts, which aims at extracting biomedical named entities from a given text. Different supervised machine learning algorithms have been applied for…

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base (KB). A popular approach to the task are name-based methods, i.e. those identifying the most appropriate name in the KB for a given mention, either…

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…

Incorporating external knowledge into Named Entity Recognition (NER) systems has been widely studied in the generic domain. In this paper, we focus on clinical domain where only limited data is accessible and interpretability is important.…