DNA-T: Deformable Neighborhood Attention Transformer for Irregular Medical Time Series

Jianxuan Huang, Baoyao Yang*, Kejing Yin, Jingwen Xu

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review


The real-world Electronic Health Records (EHRs) present irregularities due to changes in the patient's health status, resulting in various time intervals between observations and different physiological variables examined at each observation point. There have been recent applications of Transformer-based models in the field of irregular time series. However, the full attention mechanism in Transformer overly focuses on distant information, ignoring the short-term correlations of the condition. Thereby, the model is not able to capture localized changes or short-term fluctuations in patients' conditions. Therefore, we propose a novel end-to-end Deformable Neighborhood Attention Transformer (DNA-T) for irregular medical time series. The DNA-T captures local features by dynamically adjusting the receptive field of attention and aggregating relevant deformable neighborhoods in irregular time series. Specifically, we design a Deformable Neighborhood Attention (DNA) module that enables the network to attend to relevant neighborhoods by drifting the receiving field of neighborhood attention. The DNA enhances the model's sensitivity to local information and representation of local features, thereby capturing the correlation of localized changes in patients' conditions. We conduct extensive experiments to validate the effectiveness of DNA-T, outperforming existing state-of-the-art methods in predicting the mortality risk of patients. Moreover, we visualize an example to validate the effectiveness of the proposed DNA. Our code is available at https://github.com/Nekumiya-x/DNA-T.
Original languageEnglish
Pages (from-to)1-14
Number of pages14
JournalIEEE Journal of Biomedical and Health Informatics
Publication statusE-pub ahead of print - 30 Apr 2024

Scopus Subject Areas

  • Health Information Management
  • Health Informatics
  • Electrical and Electronic Engineering
  • Computer Science Applications

User-Defined Keywords

  • Transformer
  • Medical Time Series
  • Deformable Neighborhood Attention


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