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Code-switching, or alternating between languages within a single conversation, presents challenges for multilingual language models on NLP tasks. This research investigates if pre-training Multilingual BERT (mBERT) on code-switched datasets…

Efficient text classification is essential for handling the increasing volume of academic publications. This study explores the use of pre-trained language models (PLMs), including BERT, SciBERT, BioBERT, and BlueBERT, fine-tuned on the Web…

The Biocreative VII Track-2 challenge consists of named entity recognition, entity-linking (or entity-normalization), and topic indexing tasks -- with entities and topics limited to chemicals for this challenge. Named entity recognition is…

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…

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…

Objective: To comparatively evaluate several transformer model architectures at identifying protected health information (PHI) in the i2b2/UTHealth 2014 clinical text de-identification challenge corpus. Methods: The i2b2/UTHealth 2014…

We study the problem of incorporating prior knowledge into a deep Transformer-based model,i.e.,Bidirectional Encoder Representations from Transformers (BERT), to enhance its performance on semantic textual matching tasks. By probing and…

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…

In this research, we explored the improvement in terms of multi-class disease classification via pre-trained language models over Medical-Abstracts-TC-Corpus that spans five medical conditions. We excluded non-cancer conditions and examined…

Medical text learning has recently emerged as a promising area to improve healthcare due to the wide adoption of electronic health record (EHR) systems. The complexity of the medical text such as diverse length, mixed text types, and full…

The computational prediction and design of peptide binders targeting specific linear epitopes is crucial in biological and biomedical research, yet it remains challenging due to their highly dynamic nature and the scarcity of experimentally…

The Transformer architecture and transfer learning have marked a quantum leap in natural language processing, improving the state of the art across a range of text-based tasks. This paper examines how these advancements can be applied to…

Large pretrained Transformer-based language models like BERT and GPT have changed the landscape of Natural Language Processing (NLP). However, fine tuning such models still requires a large number of training examples for each target task,…

This paper describes our study on using mutilingual BERT embeddings and some new neural models for improving sequence tagging tasks for the Vietnamese language. We propose new model architectures and evaluate them extensively on two named…

Exploiting label hierarchies has become a promising approach to tackling the zero-shot multi-label text classification (ZS-MTC) problem. Conventional methods aim to learn a matching model between text and labels, using a graph encoder to…

Recent approaches based on artificial neural networks (ANNs) have shown promising results for named-entity recognition (NER). In order to achieve high performances, ANNs need to be trained on a large labeled dataset. However, labels might…

Natural Language Processing (NLP) has witnessed a transformative leap with the advent of transformer-based architectures, which have significantly enhanced the ability of machines to understand and generate human-like text. This paper…

Newly-introduced deep learning architectures, namely BERT, XLNet, RoBERTa and ALBERT, have been proved to be robust on several NLP tasks. However, the datasets trained on these architectures are fixed in terms of size and generalizability.…

Small and imbalanced datasets commonly seen in healthcare represent a challenge when training classifiers based on deep learning models. So motivated, we propose a novel framework based on BioBERT (Bidirectional Encoder Representations from…

Accurate medical time series (MedTS) classification is essential for effective clinical diagnosis, yet remains challenging due to complex multi-channel temporal dependencies, information redundancy, and label scarcity. While…