Personalized Knowledge-based Graph Neural Networks and Regression Analysis for Computational Diagnosis of High-Risk Cardiovascular Disease Patients

Acute myocardial infarction (MI) is a major precursor to heart failure (HF), yet few biomarkers are routinely used to predict post-MI HF, and limited therapeutic options exist to prevent its development. Furthermore, identifying patients at extremely high risk of recurrent MI remains challenging. These gaps highlight the need for improved biomarkers, therapeutic targets, and computational approaches for risk assessment and treatment-response prediction. To address risk assessment, we developed a systems bioinformatics (SB), graph-based framework representing patient information as personalized networks and integrating omics, clinical, and molecular prior-knowledge data. Graph neural network (GNN) machine learning (ML) models were compared with conventional ML approaches. Two large-scale public plasma proteomic datasets were used to predict post-MI HF. To investigate treatment response, regression models were applied to longitudinal clinical data from >400 hospitalized patients enrolled in the EMMY trial evaluating empagliflozin. ML-driven feature selection identified proteins and clinical parameters with the greatest predictive value. The graph-based framework demonstrated strong and consistent performance across independent post-MI cohorts. GNN models outperformed conventional approaches, including generalized linear models and XGBoost, particularly when attention mechanisms were incorporated. Using biomarker panels alone, the best GNN achieved an external test AUC of 0.82, compared with 0.77 for the best conventional ML model. When biomarkers were combined with clinical and demographic variables, GNN and conventional ML models achieved AUCs of 0.80 and 0.77, respectively. Regression models also showed promise for predicting biomarker changes associated with treatment response, with the best model achieving a test RMSE of 0.56. Feature-importance analysis identified NT-proBNP (NPPB), cardiac troponins (TNNI3/TNNT2), and prior HF history as the most influential predictors, consistent with established clinical evidence. Overall, these findings support graph-based ML and regression analysis as promising approaches for improving post-MI HF risk prediction and therapeutic response and identifying clinically relevant markers.