Related papers: Clinical-Longformer and Clinical-BigBird: Transfor…

Objective: Clinical knowledge enriched transformer models (e.g., ClinicalBERT) have state-of-the-art results on clinical NLP (natural language processing) tasks. One of the core limitations of these transformer models is the substantial…

Transformers-based models, such as BERT, have been one of the most successful deep learning models for NLP. Unfortunately, one of their core limitations is the quadratic dependency (mainly in terms of memory) on the sequence length due to…

Recently, pretrained language models based on BERT have been introduced for the French biomedical domain. Although these models have achieved state-of-the-art results on biomedical and clinical NLP tasks, they are constrained by a limited…

BERT has shown a lot of sucess in a wide variety of NLP tasks. But it has a limitation dealing with long inputs due to its attention mechanism. Longformer, ETC and BigBird addressed this issue and effectively solved the quadratic dependency…

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…

Transformer-based masked language models such as BERT, trained on general corpora, have shown impressive performance on downstream tasks. It has also been demonstrated that the downstream task performance of such models can be improved by…

BERT, which stands for Bidirectional Encoder Representations from Transformers, is a recently introduced language representation model based upon the transfer learning paradigm. We extend its fine-tuning procedure to address one of its…

Self-attention has emerged as a vital component of state-of-the-art sequence-to-sequence models for natural language processing in recent years, brought to the forefront by pre-trained bi-directional Transformer models. Its effectiveness is…

Recent advances in natural language processing (NLP) have been driven bypretrained language models like BERT, RoBERTa, T5, and GPT. Thesemodels excel at understanding complex texts, but biomedical literature, withits domain-specific…

Large-scale transformer-based models like the Bidirectional Encoder Representations from Transformers (BERT) are widely used for Natural Language Processing (NLP) applications, wherein these models are initially pre-trained with a large…

Encoder-based transformer models are central to biomedical and clinical Natural Language Processing (NLP), as their bidirectional self-attention makes them well-suited for efficiently extracting structured information from unstructured text…

Pre-trained Transformer-based models have achieved state-of-the-art performance for various Natural Language Processing (NLP) tasks. However, these models often have billions of parameters, and, thus, are too resource-hungry and…

Several biomedical language models have already been developed for clinical language inference. However, these models typically utilize general vocabularies and are trained on relatively small clinical corpora. We sought to evaluate the…

Objectives: To adapt and evaluate a deep learning language model for answering why-questions based on patient-specific clinical text. Materials and Methods: Bidirectional encoder representations from transformers (BERT) models were trained…

Transformer models have achieved great success across many NLP problems. However, previous studies in automated ICD coding concluded that these models fail to outperform some of the earlier solutions such as CNN-based models. In this paper…

Pretrained language models such as Bidirectional Encoder Representations from Transformers (BERT) have achieved state-of-the-art performance in natural language processing (NLP) tasks. Recently, BERT has been adapted to the biomedical…

Transformer-based models are unable to process long sequences due to their self-attention operation, which scales quadratically with the sequence length. To address this limitation, we introduce the Longformer with an attention mechanism…

We present a Three-level Hierarchical Transformer Network (3-level-HTN) for modeling long-term dependencies across clinical notes for the purpose of patient-level prediction. The network is equipped with three levels of Transformer-based…

Pre-trained Transformers currently dominate most NLP tasks. They impose, however, limits on the maximum input length (512 sub-words in BERT), which are too restrictive in the legal domain. Even sparse-attention models, such as Longformer…

Recent years have witnessed a substantial increase in the use of deep learning to solve various natural language processing (NLP) problems. Early deep learning models were constrained by their sequential or unidirectional nature, such that…