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Previous work on document-level NMT usually focuses on limited contexts because of degraded performance on larger contexts. In this paper, we investigate on using large contexts with three main contributions: (1) Different from previous…

Rare diseases, including Inborn Errors of Metabolism (IEM), pose significant diagnostic challenges. Case reports serve as key but computationally underutilized resources to inform diagnosis. Clinical dense information extraction refers to…

Background: Machine learning methods for clinical named entity recognition and entity normalization systems can utilize both labeled corpora and Knowledge Graphs (KGs) for learning. However, infrequently occurring concepts may have few…

Transformers-based models, such as BERT, have dramatically improved the performance for various natural language processing tasks. The clinical knowledge enriched model, namely ClinicalBERT, also achieved state-of-the-art results when…

Processing information locked within clinical health records is a challenging task that remains an active area of research in biomedical NLP. In this work, we evaluate a broad set of machine learning techniques ranging from simple RNNs to…

Large language models (LLMs) show promise for supporting clinical decision-making in complex fields such as rheumatology. Our evaluation shows that smaller language models (SLMs), combined with retrieval-augmented generation (RAG), achieve…

Large language models (LLMs) demonstrate remarkable medical expertise, but data privacy concerns impede their direct use in healthcare environments. Although offering improved data privacy protection, domain-specific small language models…

Large Language Models (LLMs), known for their versatility in textual data, are increasingly being explored for their potential to enhance medical image segmentation, a crucial task for accurate diagnostic imaging. This study explores…

The growth rate in the amount of biomedical documents is staggering. Unlocking information trapped in these documents can enable researchers and practitioners to operate confidently in the information world. Biomedical NER, the task of…

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…

Large Language Models (LLMs) have revolutionized various sectors, including healthcare where they are employed in diverse applications. Their utility is particularly significant in the context of rare diseases, where data scarcity,…

Large Language Models (LLMs) are increasingly being explored for clinical question answering and decision support, yet safe deployment critically requires reliable handling of patient measurements in heterogeneous clinical notes. Existing…

Large language models (LLMs) can potentially democratize access to medical knowledge. While many efforts have been made to harness and improve LLMs' medical knowledge and reasoning capacities, the resulting models are either closed-source…

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…

Effective patient-provider communication is crucial in clinical care, directly impacting patient outcomes and quality of life. Traditional evaluation methods, such as human ratings, patient feedback, and provider self-assessments, are often…

In this study, we uncover the unexpected efficacy of residual-based large language models (LLMs) as part of encoders for biomedical imaging tasks, a domain traditionally devoid of language or textual data. The approach diverges from…

Large pre-trained language models (LMs) have been widely adopted in biomedical and clinical domains, introducing many powerful LMs such as bio-lm and BioELECTRA. However, the applicability of these methods to real clinical use cases is…

Proprietary Large Language Models (LLMs) such as GPT-4 and Gemini have demonstrated promising capabilities in clinical text summarization tasks. However, due to patient data privacy concerns and computational costs, many healthcare…

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…

Mental health challenges pose considerable global burdens on individuals and communities. Recent data indicates that more than 20% of adults may encounter at least one mental disorder in their lifetime. On the one hand, the advancements in…