PORTER: Language-Grounded Event Representations for Portable Structured EHR Foundation Models
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Computer Science > Computation and Language
arXiv:2606.24102 (cs)
[Submitted on 23 Jun 2026]
Title:PORTER: Language-Grounded Event Representations for Portable Structured EHR Foundation Models
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Abstract:Most electronic health record (EHR) foundation models encode clinical events as discrete event tokens from a fixed vocabulary and therefore cannot directly represent events containing unseen concepts or new combinations of concepts and attributes such as numeric values. This limits transfer across institutions and even across deployment pipelines within the same institution. We introduce PORTER, a language-grounded structured EHR foundation model that decouples event representation from this fixed vocabulary. PORTER represents events through their descriptions using a frozen text encoder, integrates numeric values through a dedicated pathway, and learns clinical dynamics over patient timelines with an autoregressively pretrained temporal backbone. Across 74 clinical prediction tasks at a pediatric hospital, PORTER matched the mean AUROC of a fixed-vocabulary model with the same temporal backbone and pretraining objective. When the same patient timelines were rendered using event descriptions not seen during pretraining, PORTER transferred without retraining or vocabulary mapping, recovering 97.1% of the mean AUROC of a model trained directly on the target vocabulary. When transferred to MIMIC, PORTER outperformed the fixed-vocabulary model, which dropped 69% of events because their tokens were unseen. Mechanistic analyses showed cross-vocabulary transfer tracked preservation of patient-level representation geometry rather than the scale of the text encoder, and the numeric pathway improved sensitivity to magnitude without disrupting clinical concept identity. PORTER also achieved higher AUROC than a task-specific text serialization comparator, at 329-fold lower amortized compute. PORTER is a step toward vocabulary-independent EHR foundation models that reduce the need for vocabulary harmonization while preserving in-domain performance and enabling efficient cross-task reuse.
| Subjects: | Computation and Language (cs.CL); Machine Learning (cs.LG) |
| Cite as: | arXiv:2606.24102 [cs.CL] |
| (or arXiv:2606.24102v1 [cs.CL] for this version) | |
| https://doi.org/10.48550/arXiv.2606.24102
arXiv-issued DOI via DataCite (pending registration)
|
Submission history
From: Lin Lawrence Guo [view email][v1] Tue, 23 Jun 2026 03:33:25 UTC (1,665 KB)
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