DAPNet: multi-view graph contrastive network incorporating disease clinical and molecular associations for disease progression prediction.

Abstract

Background: Timely and accurate prediction of disease progress is crucial for facilitating early intervention and treatment for various chronic diseases. However, due to the complicated and longitudinal nature of disease progression, the capacity and completeness of clinical data required for training deep learning models remains a significant challenge. This study aims to explore a new method that reduces data dependency and achieves predictive performance comparable to existing research.

Methods: This study proposed DAPNet, a deep learning-based disease progression prediction model that solely utilizes the comorbidity duration (without relying on multi-modal data or comprehensive medical records) and disease associations from biomedical knowledge graphs to deliver high-performance prediction. DAPNet is the first to apply multi-view graph contrastive learning to disease progression prediction tasks. Compared with other studies on comorbidities, DAPNet innovatively integrates molecular-level disease association information, combines disease co-occurrence and ICD10, and fully explores the associations between diseases; RESULTS: This study validated DAPNet using a de-identified clinical dataset derived from medical claims, which includes 2,714 patients and 10,856 visits. Meanwhile, a kidney dataset (606 patients) based on MIMIC-IV has also been constructed to fully validate its performance. The results showed that DAPNet achieved state-of-the-art performance on the severe pneumonia dataset (F1=0.84, with an improvement of 8.7%), and outperformed the six baseline models on the kidney disease dataset (F1=0.80, with an improvement of 21.3%). Through case analysis, we elucidated the clinical and molecular associations identified by the DAPNet model, which facilitated a better understanding and explanation of potential disease association, thereby providing interpretability for the model.

Conclusions: The proposed DAPNet, for the first time, utilizes comorbidity duration and disease associations network, enabling more accurate disease progression prediction based on a multi-view graph contrastive learning, which provides valuable insights for early diagnosis and treatment of patients. Based on disease association networks, our research has enhanced the interpretability of disease progression predictions.