PathwayLLM: Explainable Clinical Trajectory Modeling with Structured Pathways for Sepsis Prediction

Patient-level sepsis prediction requires models that track clinical deterioration over time and integrate heterogeneous structured evidence from electronic health records. We present PathwayLLM, a trajectory-based framework that grounds prediction on temporal signals, graph-structured evidence, and pathway-level clinical information derived from statistical dependency discovery. PathwayLLM follows a three-stage design. First, each observation window is encoded from multiple structured views, including physiological measurements, temporal dynamics, a heterogeneous patient-diagnosis-medication graph, and dependency-derived pathway signals. Second, these representations are injected into a pretrained language model as auxiliary contextual embeddings so that risk prediction and evidence-conditioned explanations can be learned jointly. Third, a Clinical Trajectory LSTM with Deterioration Attention aggregates window-level representations to highlight critical deterioration points and produce patient-level risk scores. On MIMIC-IV (15,410 ICU patients; 8.45% sepsis prevalence), PathwayLLM achieves AUROC 0.891 and AUPRC 0.724, outperforming strong time-series and pretrained baselines. External validation on eICU achieves AUROC 0.842 zero-shot and 0.867 after light fine-tuning. Ablation studies indicate that trajectory aggregation and structured clinical signals are key contributors, and clinician review suggests coherent, interpretable, and clinically relevant explanations.