Related papers: Domain specific BERT representation for Named Enti…

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…

Developing high-performance entity normalization algorithms that can alleviate the term variation problem is of great interest to the biomedical community. Although deep learning-based methods have been successfully applied to biomedical…

The task of Named Entity Recognition (NER) is an important component of many natural language processing systems, such as relation extraction and knowledge graph construction. In this work, we present a simple and effective approach for…

Named entity recognition (NER) models generally perform poorly when large training datasets are unavailable for low-resource domains. Recently, pre-training a large-scale language model has become a promising direction for coping with the…

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…

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…

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)…

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…

Pre-trained models such as BERT are widely used in NLP tasks and are fine-tuned to improve the performance of various NLP tasks consistently. Nevertheless, the fine-tuned BERT model trained on our protocol corpus still has a weak…

The Bidirectional Encoder Representations from Transformers (BERT) model has achieved the state-of-the-art performance for many natural language processing (NLP) tasks. Yet, limited research has been contributed to studying its…

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…

Recent advances in language representation using neural networks have made it viable to transfer the learned internal states of a trained model to downstream natural language processing tasks, such as named entity recognition (NER) and…

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…

This paper presents a framework for Named Entity Recognition (NER) leveraging the Bidirectional Encoder Representations from Transformers (BERT) model in natural language processing (NLP). NER is a fundamental task in NLP with broad…

Contextual word embedding models such as ELMo (Peters et al., 2018) and BERT (Devlin et al., 2018) have dramatically improved performance for many natural language processing (NLP) tasks in recent months. However, these models have been…

Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained…

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…

This paper presents an iterative approach to performing Scientific Named Entity Recognition (SciNER) using BERT-based models. We leverage transfer learning to fine-tune pretrained models with a small but high-quality set of manually…

Named Entity Recognition (NER) and Relation Extraction (RE) are essential tools in distilling knowledge from biomedical literature. This paper presents our findings from participating in BioNLP Shared Tasks 2019. We addressed Named Entity…