# Foundation models for electronic health records: representation dynamics and transferability

arXiv: https://arxiv.org/abs/2504.10422 · HTML: https://mlsanity.com/paper/2504.10422/

## Key facts

- Cited by 11 papers in the map (data through 14 Oct 2026).
- Builds on 19 of its 40 references that are in the map.
- First posted on arXiv 14 Apr 2025.

## Builds on (most cited first, 19 of 19)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Optuna: A Next-generation Hyperparameter Optimization Framework](https://mlsanity.com/paper/1907.10902/) (2019)
- [Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction](https://mlsanity.com/paper/2005.12833/) (2020)
- [Scalable and accurate deep learning for electronic health records](https://mlsanity.com/paper/1801.07860/) (2018)
- [BEHRT: Transformer for Electronic Health Records](https://mlsanity.com/paper/1907.09538/) (2019)
- [Doctor AI: Predicting Clinical Events via Recurrent Neural Networks](https://mlsanity.com/paper/1511.05942/) (2015)
- [EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Models](https://mlsanity.com/paper/2307.02028/) (2023)
- [Learning to Diagnose with LSTM Recurrent Neural Networks](https://mlsanity.com/paper/1511.03677/) (2015)
- [Language Models Are An Effective Patient Representation Learning Technique For Electronic Health Record Data](https://mlsanity.com/paper/2001.05295/) (2020)
- [MOTOR: A Time-To-Event Foundation Model For Structured Medical Records](https://mlsanity.com/paper/2301.03150/) (2023)
- [Zero Shot Health Trajectory Prediction Using Transformer](https://mlsanity.com/paper/2407.21124/) (2024)
- [Event Stream GPT: A Data Pre-processing and Modeling Library for Generative, Pre-trained Transformers over Continuous-time Sequences of Complex Events](https://mlsanity.com/paper/2306.11547/) (2023)
- [Context Clues: Evaluating Long Context Models for Clinical Prediction Tasks on EHRs](https://mlsanity.com/paper/2412.16178/) (2024)
- [EHRMamba: Towards Generalizable and Scalable Foundation Models for Electronic Health Records](https://mlsanity.com/paper/2405.14567/) (2024)
- [A Multi-Center Study on the Adaptability of a Shared Foundation Model for Electronic Health Records](https://mlsanity.com/paper/2311.11483/) (2023)
- [ClinicalMamba: A Generative Clinical Language Model on Longitudinal Clinical Notes](https://mlsanity.com/paper/2403.05795/) (2024)
- [Foundation Model of Electronic Medical Records for Adaptive Risk Estimation](https://mlsanity.com/paper/2502.06124/) (2025)

## Built on by (most cited first, 11 of 11)

- [One Loss to Rule Them All: Marked Time-to-Event for Structured EHR Foundation Models](https://mlsanity.com/paper/2602.00541/) (2026)
- [Quantifying surprise in clinical care: Detecting highly informative events in electronic health records with foundation models](https://mlsanity.com/paper/2507.22798/) (2025)
- [Learning Clinical Representations Under Systematic Distribution Shift](https://mlsanity.com/paper/2603.07348/) (2026)
- [Discriminative Representation Learning for Clinical Prediction](https://mlsanity.com/paper/2603.20921/) (2026)
- [Clin-JEPA: A Multi-Phase Co-Training Framework for Joint-Embedding Predictive Pretraining on EHR Patient Trajectories](https://mlsanity.com/paper/2605.10840/) (2026)
- [Uncertainty-Aware Foundation Models for Clinical Data](https://mlsanity.com/paper/2604.04175/) (2026)
- [Event Fields: Learning Latent Event Structure for Waveform Foundation Models](https://mlsanity.com/paper/2605.08685/) (2026)
- [WISTERIA: Learning Clinical Representations from Noisy Supervision via Multi-View Consistency in Electronic Health Records](https://mlsanity.com/paper/2605.09765/) (2026)
- [AURORA: Contextual Orthogonalization for Geometric Representation Learning in Healthcare Foundation Models](https://mlsanity.com/paper/2605.17765/) (2026)
- [MorphologyFM: A Foundation Model for Morphology-Aware Representation Learning from ECG and Pulse Oximetry Waveforms](https://mlsanity.com/paper/2607.09749/) (2026)
- [Federated generative event models for tokenized electronic health records](https://mlsanity.com/paper/2608.02939/) (2026)

## Abstract (arXiv)

Foundation models (FMs) trained on electronic health records (EHRs) have shown strong performance on a range of clinical prediction tasks. However, adapting these models to local health systems remains challenging due to limited data availability and resource constraints. In this study, we investigated what these models learn and evaluated the transferability of an FM trained on MIMIC-IV to an institutional EHR dataset at the University of Chicago Medical Center. We assessed their ability to identify outlier patients and examined representation-space patient trajectories in relation to future clinical outcomes. We also evaluated the performance of supervised fine-tuned classifiers on both source and target datasets. Our findings offer insights into the adaptability of FMs across different healthcare systems, highlight considerations for their effective implementation, and provide an empirical analysis of the underlying factors that contribute to their predictive performance.