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Multi-task learning (MTL) has achieved remarkable success in natural language processing applications. In this work, we study a multi-task learning model with multiple decoders on varieties of biomedical and clinical natural language…

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…

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 large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA…

Large, pre-trained transformer-based language models such as BERT have drastically changed the Natural Language Processing (NLP) field. We present a survey of recent work that uses these large language models to solve NLP tasks via…

Generative pre-trained transformer (GPT) models have revolutionized the field of natural language processing (NLP) with remarkable performance in various tasks and also extend their power to multimodal domains. Despite their success, large…

Language models pre-trained on biomedical corpora, such as BioBERT, have recently shown promising results on downstream biomedical tasks. Many existing pre-trained models, on the other hand, are resource-intensive and computationally heavy…

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…

Learning time-series representations for discriminative tasks, such as classification and regression, has been a long-standing challenge in the healthcare domain. Current pre-training methods are limited in either unidirectional next-token…

Molecules play a crucial role in biomedical research and discovery, particularly in the field of small molecule drug development. Given the rapid advancements in large language models, especially the recent emergence of reasoning models, it…

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…

In recent years, pre-trained language models (PLMs) achieve the best performance on a wide range of natural language processing (NLP) tasks. While the first models were trained on general domain data, specialized ones have emerged to more…

Contextualized word embeddings derived from pre-trained language models (LMs) show significant improvements on downstream NLP tasks. Pre-training on domain-specific corpora, such as biomedical articles, further improves their performance.…

There is enormous enthusiasm and concerns in using large language models (LLMs) in healthcare, yet current assumptions are all based on general-purpose LLMs such as ChatGPT. This study develops a clinical generative LLM, GatorTronGPT, using…

Specialised pre-trained language models are becoming more frequent in NLP since they can potentially outperform models trained on generic texts. BioBERT and BioClinicalBERT are two examples of such models that have shown promise in medical…

In multilingual healthcare applications, the availability of domain-specific natural language processing(NLP) tools is limited, especially for low-resource languages. Although multilingual bidirectional encoder representations from…

Generative Pre-trained Transformer (GPT) is a state-of-the-art machine learning model capable of generating human-like text through natural language processing (NLP). GPT is trained on massive amounts of text data and uses deep learning…

Pre-trained language models have recently contributed to significant advances in NLP tasks. Recently, multi-modal versions of BERT have been developed, using heavy pre-training relying on vast corpora of aligned textual and image data,…

Biomedical queries have become increasingly prevalent in web searches, reflecting the growing interest in accessing biomedical literature. Despite recent research on large-language models (LLMs) motivated by endeavours to attain generalized…

Pre-trained transformer language models (LMs) have in recent years become the dominant paradigm in applied NLP. These models have achieved state-of-the-art performance on tasks such as information extraction, question answering, sentiment…