Related papers: Domain specific BERT representation for Named Enti…

This paper describes our submission on the COVID-19 literature annotation task at Biocreative VII. We proposed an approach that exploits the knowledge of the globally non-optimal weights, usually rejected, to build a rich representation of…

Objective: This study quantifies the capabilities of GPT-3.5 and GPT-4 for clinical named entity recognition (NER) tasks and proposes task-specific prompts to improve their performance. Materials and Methods: We evaluated these models on…

This paper presents new state-of-the-art models for three tasks, part-of-speech tagging, syntactic parsing, and semantic parsing, using the cutting-edge contextualized embedding framework known as BERT. For each task, we first replicate and…

We introduce a new language representation model called BERT, which stands for Bidirectional Encoder Representations from Transformers. Unlike recent language representation models, BERT is designed to pre-train deep bidirectional…

The delivery of appropriate targeted therapies to cancer patients requires the complete analysis of the molecular profiling of tumors and the patient's clinical characteristics in the context of existing knowledge and recent findings…

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…

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…

The rapidly increasing volume of electronic health record (EHR) data underscores a pressing need to unlock biomedical knowledge from unstructured clinical texts to support advancements in data-driven clinical systems, including patient…

The success of pre-trained word embeddings has motivated its use in tasks in the biomedical domain. The BERT language model has shown remarkable results on standard performance metrics in tasks such as Named Entity Recognition (NER) and…

Motivation: The proliferation of Biomedical research articles has made the task of information retrieval more important than ever. Scientists and Researchers are having difficulty in finding articles that contain information relevant to…

In this work, we represent Lex-BERT, which incorporates the lexicon information into Chinese BERT for named entity recognition (NER) tasks in a natural manner. Instead of using word embeddings and a newly designed transformer layer as in…

More recently, Bidirectional Encoder Representations from Transformers (BERT) was proposed and has achieved impressive success on many natural language processing (NLP) tasks such as question answering and language understanding, due mainly…

Deep neural network models have been very successfully applied to Natural Language Processing (NLP) and Image based tasks. Their application to network analysis and management tasks is just recently being pursued. Our interest is in…

In biomedical literature, it is common for entity boundaries to not align with word boundaries. Therefore, effective identification of entity spans requires approaches capable of considering tokens that are smaller than words. We introduce…

Entity and relation extraction is the necessary step in structuring medical text. However, the feature extraction ability of the bidirectional long short term memory network in the existing model does not achieve the best effect. At the…

We evaluate named entity representations of BERT-based NLP models by investigating their robustness to replacements from the same typed class in the input. We highlight that on several tasks while such perturbations are natural, state of…

Named Entity Recognition (NER) is a fundamental Natural Language Processing (NLP) task to extract entities from unstructured data. The previous methods for NER were based on machine learning or deep learning. Recently, pre-training models…

Motivation: Named Entity Recognition (NER) is a key task to support biomedical research. In Biomedical Named Entity Recognition (BioNER), obtaining high-quality expert annotated data is laborious and expensive, leading to the development of…

Named entity recognition (NER) is the task to identify mentions of rigid designators from text belonging to predefined semantic types such as person, location, organization etc. NER always serves as the foundation for many natural language…

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…