Time-Aware Tranformer-Based Prediction Model for AECOPD

Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) can worsen rapidly, making timely prediction a clinical priority. Most existing machine learning approaches rely on episodically collected clinical variables, introducing delays that limit their practical utility in home monitoring settings. Home ventilators offer a lower-latency alternative, producing a near-continuous record of respiratory status during daily use. However existing ventilator-based approaches either compress the waveform into handcrafted features or focus primarily on binary risk classification, leaving the timing of an impending event unresolved. In this paper, we present a two-stage framework that operates directly on raw pressure and flow waveforms from the most recent seven days of home ventilator use. The first-stage classification model identifies patients at high risk of a severe exacerbation. The second-stage regression model then estimates how many days remain before the event occurs. Our experimental results demonstrate that the two-stage model outperforms traditional baseline models on both risk classification and time-to-event estimation, with our selected Stage 1 classifier achieving F1 = 0.91 and our Stage 2 regression model achieving RMSE = 1.00 days and R^2 = 0.76, giving clinicians both an early warning and actionable lead time before a severe exacerbation occurs.

Electronic Health Record (EHR) prediction models in the intensive care unit must learn from sparse and irregular measurements while preserving the clinical meaning of time and supporting transparent decision-making. We present INTERVenE, a family of Transformer architectures whose input is an interval-based, knowledge-based temporal abstraction (KBTA), a token stream of named clinical concepts (states, trends, events, contexts) drawn from a curated medical ontology, rather than an unnamed bin index or a raw measurement triplet. This naming layer is what we ask KBTA to do: it makes the model's per-token attributions resolve to clinical concepts by construction. INTERVenE offers two complementary variants: an auto-regressive decoder that generates future abstraction trajectories with a per-step risk readout (localizing when and after which events risk rises), and a bidirectional encoder for single-pass joint risk and time-to-event prediction. On 57,078 MIMIC-IV admissions, INTERVenE-Enc outperformed GRU-D, STraTS, and KarmaLego, reaching a support-weighted AUPRC of 0.672 ($+0.046$ over the strongest neural baseline, with non-overlapping 95% bootstrap CIs), AUROC of 0.901, and length-of-stay MAE of 44.4,h. INTERVenE-Ar complements these predictions with generated abstraction trajectories and evolving risk scores, achieving AUROC of 0.854 and AUPRC of 0.588 under the harder generative readout. An alternative-discretization ablation preserved predictive performance, supporting KBTA's role as a clinically named attribution substrate rather than a prerequisite for accuracy.

Accurate disease trajectory prediction is critical for early intervention, resource allocation, and improving long-term outcomes. While electronic health records (EHRs) provide a rich longitudinal view of patient health in clinical environments, models trained on curated research cohorts may not reflect routine deployment settings, and those trained on single-hospital datasets capture only fragments of each patient's trajectory. This highlights the importance of leveraging large, multi-hospital health systems for training and validation to better reflect real-world clinical complexity. In this work, we develop DT-Transformer, a foundation model trained on 57.1M structured EHR entries over 1.7M patients from Mass General Brigham (MGB), spanning 11 hospitals and a broad network of outpatient clinics. DT-Transformer achieves strong discrimination in both held-out and prospective validation settings. Next-event prediction achieves a median age- and sex-stratified AUC of 0.871 across 896 disease categories, with all categories exceeding AUC 0.5. These results support health system-scale training as a path toward foundation models suited to real-world clinical forecasting.