GraphBEAT: Graph-based Bucketized Event Aggregation Over Time for Early Risk Stratification of Gastrointestinal Cancers

Leo Y. Li-Han, Chris Varghese, Elizabeth B. Habermann, Mark J. Truty, William R. G. Perry +2

Longitudinal electronic health records (EHRs) contain complementary diagnostic and laboratory information about patient health. However, irregularity, sparsity, heterogeneity, and incompleteness in documentation complicate EHR modeling. To address the problem, we introduce GraphBEAT (Graph-based Bucketized Event Aggregation over Time), a temporal graph representation learning framework that groups clinical events into time buckets and transforms observed features into patient-specific, temporally directed graphs to enable early risk stratification for gastrointestinal cancers. Each node in an EHR graph encodes feature identity, observed value, and temporal position of clinical events. A context-aware, time-decay message-passing mechanism models transitions between successive buckets, followed by multi-head attention pooling to generate patient-level representations. GraphBEAT was trained and evaluated on multi-site longitudinal diagnosis codes and laboratory tests to predict pancreatic, liver, and intestinal cancer at 12-, 24-, and 36-month diagnostic lead times. In all experimental setups, GraphBEAT consistently outperformed baseline graph neural networks (GraphSAGE, GAT, and…