DyGraphTrans: A temporal graph representation learning framework for modeling disease progression from Electronic Health Records

Motivation Electronic Health Records (EHRs) contain vast amounts of longitudinal patient medical history data, making them highly informative for early disease prediction. Numerous computational methods have been developed to leverage EHR data; however, many process multiple patient records simultaneously, resulting in high memory consumption and computational cost. Moreover, these models also often lack interpretability, limiting insight into the factors driving their predictions. Efficiently handling large-scale EHR data while maintaining predictive accuracy and interpretability therefore remains a critical challenge. To address this gap, we propose DyGraphTrans, a dynamic graph representation learning framework that represents patient EHR data as a sequence of temporal graphs. In this representation, nodes correspond to patients, node features encode temporal clinical attributes, and edges capture patient similarity. DyGraphTrans models both local temporal dependencies and long-range global trends, while a sliding-window mechanism reduces memory consumption without sacrificing essential temporal context. Unlike existing dynamic graph models, DyGraphTrans jointly captures patient similarity and temporal evolution in a memory-efficient and interpretable manner.

We evaluated DyGraphTrans on Alzheimer’s Disease Neuroimaging Initiative (ADNI) and National Alzheimer’s Coordinating Center (NACC) for disease progression prediction, as well as on the Medical Information Mart for Intensive Care (MIMIC-IV) dataset for early mortality prediction. We further assessed the model on multiple benchmark dynamic graph datasets to evaluate its generalizability. DyGraphTrans achieved strong predictive performance across diverse datasets. We also demonstrated interpretability of DyGraphTrans aligned with known clinical risk factors. The source code and datasets are available at https://github.com/bozdaglab/DyGraphTrans. Contact Serdar.Bozdag{at}unt.edu Supplementary Uploaded as an attachment. Competing Interest Statement The authors have declared no competing interest. Footnotes Figure captions were missing in the previous version and have now been included in the revised manuscript.