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This is a temporal graph neural network for predicting gastrointestinal cancer risk from sparse, irregular EHR data. It reports gains over GNN and sequence baselines (GraphSAGE, GAT, GCN, Transformer, LSTM) with far lower compute and parameter counts. For ML readers, the useful questions are how it generalizes across sites and whether those efficiency gains hold up under clinical validation.
GraphBEAT: Graph-based Bucketized Event Aggregation Over Time for Early Risk Stratification of Gastrointestinal Cancers
arXiv:2610.22014v1 Announce Type: cross Abstract: 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 GCN) and sequence modeling approaches (Transformer and long short-term memory [LSTM]). GraphBEAT also required over 250x fewer floating-point operations per patient and over 20x fewer parameters than the Transformer and LSTM baselines. These results support GraphBEAT as an accurate and computationally efficient approach for cancer risk stratification from sparse, heterogeneous longitudinal health records.
Abstract: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 GCN) and sequence modeling approaches (Transformer and long short-term memory [LSTM]). GraphBEAT also required over 250x fewer floating-point operations per patient and over 20x fewer parameters than the Transformer and LSTM baselines. These results support GraphBEAT as an accurate and computationally efficient approach for cancer risk stratification from sparse, heterogeneous longitudinal health records.
Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Signal Processing (eess.SP)
arXiv:2610.22014 [cs.LG]
(or arXiv:2610.22014v1 [cs.LG] for this version)
https://doi.org/10.48550/arXiv.2610.22014 Focus to learn more arXiv-issued DOI via DataCite (pending registration)
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