Longitudinal electronic health records (EHRs) can reveal disease-progression structure, while useful forecasting requires leakage-controlled discovery, censor-aware outcomes, and inspectable trajectory evidence. We developed a graph-enhanced framework in MIMIC-IV v3.1 that splits patients before graph construction, learns train-only consecutive-admission transitions, and freezes endpoint-specific branching-motif policies selected on validation data. The final catalog contained 99,527 motifs, and a time-aware Transformer retrieved at most 24 patient-compatible motifs per endpoint through endpoint-specific cross-attention. Across five training seeds, micro-AUPRC increased from 0.9330 to 0.9357, while event-time MAE decreased from 676.9 to 657.7 days (reduction 19.2 days; 95% paired patient-cluster bootstrap CI, 13.8-24.8). Timing effects were heterogeneous: MAE worsened for events within 730 days but improved by 58.9 days for events occurring after 730 days. In an exploratory internal temporal split, branch conditioning reduced conditional event-time MAE by 26.9 days (95% CI, 23.0-30.8) without evidence of better micro-AUPRC. Corrected survival evaluation over the supported 0-2,555-day interval did not establish macro C-index or integrated Brier score superiority over a matched history-only discrete-hazard model. A directed, degree-matched GNN repair substantially improved unseen-edge discovery, yet replacing GNN-derived scores within fixed motif identities did not improve downstream forecasting. These results position branching motifs as structured trajectory context whose main value is long-range timing support rather than uniformly stronger endpoint discrimination, survival prediction, or causal explanation.

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