Spatial Predictive Patterns of Cause-Specific Mortality: Evidence from East Africa

(1) Background: Whether spatial predictive patterns in non-communicable disease mortality persist after accounting for socio-demographic development and biomarkers remains understudied in East Africa. (2) Methods: This study used heterogeneous graph transformer (HGT) models and other techniques to model spatial patterns in cause- and sex/age-specific mortality (hypertensive heart disease [HHD], ischaemic heart disease [IHD], stroke, and diabetes), incorporating risk factors and socio-demographic development (SDI), using data from the Global Burden of Disease (GBD) study, 1990–2023, across Burundi, Kenya, Rwanda, Tanzania, and Uganda. (3) Results: HGT achieved higher performance than OLS spatial lag benchmarks (R2 0.948–0.970 vs. 0.194–0.376). Spatial predictive patterns were disease-specific. Stroke was the only disease with consistent positive spatial structure (SDI-only: 0.645%, 95% CI [0.380, 0.907]), with spatial structure strengthening after 2015. HHD exhibited severe and stable degradation (Risk-only: −137.892%, 95% CI [−181.908, −96.380]), driven by the interaction between metabolic risk covariates and geographic adjacency. Diabetes showed consistently severe degradation (SDI + Risk: −201.941%, 95% CI [−257.349, −150.082]). IHD patterns were weak and unstable. Sex disaggregation revealed stronger stroke spatial signals, indicating latent sex-specific patterns masked by aggregation. GBD measurement uncertainty contributed less than 0.025% of result variance, with model randomness dominating. (4) Conclusions: Spatial predictive patterns in NCD mortality in East Africa are disease-specific. Stroke shows emerging cross-border spatial structure after 2015, while HHD and diabetes reflect country-specific determinants. Sex-disaggregated graph construction reveals latent spatial heterogeneity invisible to aggregate models, supporting disease-specific, sex-stratified regional health strategies.