Related papers: Cross-Domain Data Integration for Named Entity Dis…

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…

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…

Named entity recognition is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the…

Named Entity Recognition (NER) is a machine learning task that traditionally relies on supervised learning and annotated data. Acquiring such data is often a challenge, particularly in specialized fields like medical, legal, and financial…

Named Entity Disambiguation (NED) refers to the task of resolving multiple named entity mentions in a document to their correct references in a knowledge base (KB) (e.g., Wikipedia). In this paper, we propose a novel embedding method…

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…

Developing high-performing systems for detecting biomedical named entities has major implications. State-of-the-art deep-learning based solutions for entity recognition often require large annotated datasets, which is not available in the…

Named Entity Recognition (NER) or the extraction of concepts from clinical text is the task of identifying entities in text and slotting them into categories such as problems, treatments, tests, clinical departments, occurrences (such as…

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…

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)…

Current work in named entity recognition (NER) shows that data augmentation techniques can produce more robust models. However, most existing techniques focus on augmenting in-domain data in low-resource scenarios where annotated data is…

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…

Named entity recognition (NER) for identifying proper nouns in unstructured text is one of the most important and fundamental tasks in natural language processing. However, despite the widespread use of NER models, they still require a…

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…

Named Entity Disambiaguation (NED) is a central task for applications dealing with natural language text. Assume that we have a graph based knowledge base (subsequently referred as Knowledge Graph) where nodes represent various real world…

In medical information extraction, medical Named Entity Recognition (NER) is indispensable, playing a crucial role in developing medical knowledge graphs, enhancing medical question-answering systems, and analyzing electronic medical…

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…

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…

Medical knowledge bases (KBs), distilled from biomedical literature and regulatory actions, are expected to provide high-quality information to facilitate clinical decision making. Entity disambiguation (also referred to as entity linking)…

Biomedical entity linking (EL) consists of named entity recognition (NER) and named entity disambiguation (NED). EL models are trained on corpora labeled by a predefined KB. However, it is a common scenario that only entities within a…