Related papers: Partial Annotation Learning for Biomedical Entity …

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…

Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the…

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…

Supervised machine learning assumes the availability of fully-labeled data, but in many cases, such as low-resource languages, the only data available is partially annotated. We study the problem of Named Entity Recognition (NER) with…

Recognition of biomedical entities from literature is a challenging research focus, which is the foundation for extracting a large amount of biomedical knowledge existing in unstructured texts into structured formats. Using the sequence…

Named entity recognition (NER) is the very first step in the linguistic processing of any new domain. It is currently a common process in BioNLP on English clinical text. However, it is still in its infancy in other major languages, as it…

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…

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…

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…

Most Named Entity Recognition (NER) models operate under the assumption that training datasets are fully labelled. While it is valid for established datasets like CoNLL 2003 and OntoNotes, sometimes it is not feasible to obtain the complete…

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…

Motivation: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network…

The most common Named Entity Recognizers are usually sequence taggers trained on fully annotated corpora, i.e. the class of all words for all entities is known. Partially annotated corpora, i.e. some but not all entities of some types are…

Training a neural network-based biomedical named entity recognition (BioNER) model usually requires extensive and costly human annotations. While several studies have employed multi-task learning with multiple BioNER datasets to reduce…

Biomedical Named Entity Recognition presents significant challenges due to the complexity of biomedical terminology and inconsistencies in annotation across datasets. This paper introduces SRU-NER (Slot-based Recurrent Unit NER), a novel…

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…

FDA Medical Device recalls are critical and time-sensitive events, requiring swift identification of impacted devices to inform the public of a recall event and ensure patient safety. The OpenFDA device recall dataset contains valuable…

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…

Named entity recognition (NER) is a widely applicable natural language processing task and building block of question answering, topic modeling, information retrieval, etc. In the medical domain, NER plays a crucial role by extracting…

Deep neural network models have recently achieved state-of-the-art performance gains in a variety of natural language processing (NLP) tasks (Young, Hazarika, Poria, & Cambria, 2017). However, these gains rely on the availability of large…