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Leveraging Large Language Models for Clinical Abbreviation Disambiguation

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Abstract

Clinical abbreviation disambiguation is a crucial task in the biomedical domain, as the accurate identification of the intended meanings or expansions of abbreviations in clinical texts is vital for medical information retrieval and analysis. Existing approaches have shown promising results, but challenges such as limited instances and ambiguous interpretations persist. In this paper, we propose an approach to address these challenges and enhance the performance of clinical abbreviation disambiguation. Our objective is to leverage the power of Large Language Models (LLMs) and employ a Generative Model (GM) to augment the dataset with contextually relevant instances, enabling more accurate disambiguation across diverse clinical contexts. We integrate the contextual understanding of LLMs, represented by BlueBERT and Transformers, with data augmentation using a Generative Model, called Biomedical Generative Pre-trained Transformer (BIOGPT), that is pretrained on an extensive corpus of biomedical literature to capture the intricacies of medical terminology and context. By providing the BIOGPT with relevant medical terms and sense information, we generate diverse instances of clinical text that accurately represent the intended meanings of abbreviations. We evaluate our approach on the widely recognized CASI dataset, carefully partitioned into training, validation, and test sets. The incorporation of data augmentation with the GM improves the model’s performance, particularly for senses with limited instances, effectively addressing dataset imbalance and challenges posed by similar concepts. The results demonstrate the efficacy of our proposed method, showcasing the significance of LLMs and generative techniques in clinical abbreviation disambiguation. Our model achieves a good accuracy on the test set, outperforming previous methods.

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Data Availability

The datasets analyzed during the current study are available in the Clinical Abbreviation Sense Inventory repository, https://conservancy.umn.edu/handle/11299/137703.

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Authors and Affiliations

  1. Department of Computer Engineering, Zand Institute of Higher Education, Shiraz, Iran

    Manda Hosseini

  2. Department of Computer Engineering and IT, Shiraz University of Technology, Shiraz, Iran

    Mandana Hosseini & Reza Javidan

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  1. Manda Hosseini
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all authors contributed equally to this work.

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Correspondence to Manda Hosseini.

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Hosseini, M., Hosseini, M. & Javidan, R. Leveraging Large Language Models for Clinical Abbreviation Disambiguation. J Med Syst 48, 27 (2024). https://doi.org/10.1007/s10916-024-02049-z

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