Related papers: Augmenting Biomedical Named Entity Recognition wit…

Biomedical entity linking (BioEL) has achieved remarkable progress with the help of pre-trained language models. However, existing BioEL methods usually struggle to handle rare and difficult entities due to long-tailed distribution. To…

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) systems that perform well require task-related and manually annotated datasets. However, they are expensive to develop, and are thus limited in size. As there already exists a large number of NER datasets that…

Named-entities are inherently multilingual, and annotations in any given language may be limited. This motivates us to consider polyglot named-entity recognition (NER), where one model is trained using annotated data drawn from more than…

In this paper, we present our system for the BioNNE English track, which aims to extract 8 types of biomedical nested named entities from biomedical text. We use a large language model (Mixtral 8x7B instruct) and ScispaCy NER model to…

This paper conducts a comprehensive investigation into applying large language models, particularly on BioBERT, in healthcare. It begins with thoroughly examining previous natural language processing (NLP) approaches in healthcare, shedding…

We compare three simple and popular approaches for NER: 1) SEQ (sequence-labeling with a linear token classifier) 2) SeqCRF (sequence-labeling with Conditional Random Fields), and 3) SpanPred (span-prediction with boundary token…

When combined with In-Context Learning, a technique that enables models to adapt to new tasks by incorporating task-specific examples or demonstrations directly within the input prompt, autoregressive language models have achieved good…

Deep neural models for named entity recognition (NER) have shown impressive results in overcoming label scarcity and generalizing to unseen entities by leveraging distant supervision and auxiliary information such as explanations. However,…

Named Entity Recognition (NER) aims to extract and classify entity mentions in the text into pre-defined types (e.g., organization or person name). Recently, many works have been proposed to shape the NER as a machine reading comprehension…

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…

Entities lie in the heart of biomedical natural language understanding, and the biomedical entity linking (EL) task remains challenging due to the fine-grained and diversiform concept names. Generative methods achieve remarkable…

Named entity recognition has been extensively studied on English news texts. However, the transfer to other domains and languages is still a challenging problem. In this paper, we describe the system with which we participated in the first…

This study proposes a medical entity extraction method based on Transformer to enhance the information extraction capability of medical literature. Considering the professionalism and complexity of medical texts, we compare the performance…

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing…

Nested Named Entity Recognition (NNER) focuses on addressing overlapped entity recognition. Compared to Flat Named Entity Recognition (FNER), annotated resources are scarce in the corpus for NNER. Data augmentation is an effective approach…

Recently, neural methods have achieved state-of-the-art (SOTA) results in Named Entity Recognition (NER) tasks for many languages without the need for manually crafted features. However, these models still require manually annotated…

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…

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…

As opposed to general English, many concepts in biomedical terminology have been designed in recent history by biomedical professionals with the goal of being precise and concise. This is often achieved by concatenating meaningful…