# Serialized EHR make for good text representations

arXiv: https://arxiv.org/abs/2510.13843 · HTML: https://mlsanity.com/paper/2510.13843/

## Key facts

- Cited by 7 papers in the map (data through 14 Oct 2026).
- Builds on 43 of its 73 references that are in the map.
- First posted on arXiv 11 Oct 2025.

## Builds on (most cited first, 30 of 43)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [DistilBERT, a distilled version of BERT: smaller, faster, cheaper and lighter](https://mlsanity.com/paper/1910.01108/) (2019)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [SentencePiece: A simple and language independent subword tokenizer and detokenizer for Neural Text Processing](https://mlsanity.com/paper/1808.06226/) (2018)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Diffusion Models: A Comprehensive Survey of Methods and Applications](https://mlsanity.com/paper/2209.00796/) (2022)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [TabPFN: A Transformer That Solves Small Tabular Classification Problems in a Second](https://mlsanity.com/paper/2207.01848/) (2022)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission](https://mlsanity.com/paper/1904.05342/) (2019)
- [TaBERT: Pretraining for Joint Understanding of Textual and Tabular Data](https://mlsanity.com/paper/2005.08314/) (2020)
- [Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction](https://mlsanity.com/paper/2005.12833/) (2020)
- [TabLLM: Few-shot Classification of Tabular Data with Large Language Models](https://mlsanity.com/paper/2210.10723/) (2022)
- [BEHRT: Transformer for Electronic Health Records](https://mlsanity.com/paper/1907.09538/) (2019)
- [A Survey on Generative Diffusion Model](https://mlsanity.com/paper/2209.02646/) (2022)
- [GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records](https://mlsanity.com/paper/2203.03540/) (2022)
- [BERT Post-Training for Review Reading Comprehension and Aspect-based Sentiment Analysis](https://mlsanity.com/paper/1904.02232/) (2019)
- [Self-Supervised Representation Learning: Introduction, Advances and Challenges](https://mlsanity.com/paper/2110.09327/) (2021)
- [LIFT: Language-Interfaced Fine-Tuning for Non-Language Machine Learning Tasks](https://mlsanity.com/paper/2206.06565/) (2022)
- [Construction of the Literature Graph in Semantic Scholar](https://mlsanity.com/paper/1805.02262/) (2018)
- [Why Tabular Foundation Models Should Be a Research Priority](https://mlsanity.com/paper/2405.01147/) (2024)
- [EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Models](https://mlsanity.com/paper/2307.02028/) (2023)
- [A Comprehensive Survey on Process-Oriented Automatic Text Summarization with Exploration of LLM-Based Methods](https://mlsanity.com/paper/2403.02901/) (2024)
- [Multi-passage BERT: A Globally Normalized BERT Model for Open-domain Question Answering](https://mlsanity.com/paper/1908.08167/) (2019)
- [Fast WordPiece Tokenization](https://mlsanity.com/paper/2012.15524/) (2020)

## Built on by (most cited first, 7 of 7)

- [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)
- [Learning Longitudinal Health Representations from EHR and Wearable Data](https://mlsanity.com/paper/2601.12227/) (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)

## Abstract (arXiv)

The emergence of foundation models in healthcare has opened new avenues for learning generalizable representations from large scale clinical data. Yet, existing approaches often struggle to reconcile the tabular and event based nature of Electronic Health Records (EHRs) with the sequential priors of natural language models. This structural mismatch limits their ability to capture longitudinal dependencies across patient encounters. We introduce SerialBEHRT, a domain aligned foundation model that extends SciBERT through additional pretraining on structured EHR sequences. SerialBEHRT is designed to encode temporal and contextual relationships among clinical events, thereby producing richer patient representations. We evaluate its effectiveness on the task of antibiotic susceptibility prediction, a clinically meaningful problem in antibiotic stewardship. Through extensive benchmarking against state of the art EHR representation strategies, we demonstrate that SerialBEHRT achieves superior and more consistent performance, highlighting the importance of temporal serialization in foundation model pretraining for healthcare.