# Multimodal data matters: language model pre-training over structured and unstructured electronic health records

arXiv: https://arxiv.org/abs/2201.10113 · HTML: https://mlsanity.com/paper/2201.10113/

## Key facts

- Cited by 13 papers in the map (data through 13 Oct 2026).
- Builds on 45 of its 107 references that are in the map.
- First posted on arXiv 25 Jan 2022.

## Builds on (most cited first, 30 of 45)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation](https://mlsanity.com/paper/1406.1078/) (2014)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Align before Fuse: Vision and Language Representation Learning with Momentum Distillation](https://mlsanity.com/paper/2107.07651/) (2021)
- [Convolutional Neural Networks for Sentence Classification](https://mlsanity.com/paper/1408.5882/) (2014)
- [Multimodal Machine Learning: A Survey and Taxonomy](https://mlsanity.com/paper/1705.09406/) (2017)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Multimodal Transformer for Unaligned Multimodal Language Sequences](https://mlsanity.com/paper/1906.00295/) (2019)
- [ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission](https://mlsanity.com/paper/1904.05342/) (2019)
- [VATT: Transformers for Multimodal Self-Supervised Learning from Raw Video, Audio and Text](https://mlsanity.com/paper/2104.11178/) (2021)
- [Stacked Cross Attention for Image-Text Matching](https://mlsanity.com/paper/1803.08024/) (2018)
- [Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction](https://mlsanity.com/paper/2005.12833/) (2020)
- [RETAIN: An Interpretable Predictive Model for Healthcare using Reverse Time Attention Mechanism](https://mlsanity.com/paper/1608.05745/) (2016)
- [Multitask learning and benchmarking with clinical time series data](https://mlsanity.com/paper/1703.07771/) (2017)
- [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)
- [Explainable Prediction of Medical Codes from Clinical Text](https://mlsanity.com/paper/1802.05695/) (2018)
- [Doctor AI: Predicting Clinical Events via Recurrent Neural Networks](https://mlsanity.com/paper/1511.05942/) (2015)
- [UniT: Multimodal Multitask Learning with a Unified Transformer](https://mlsanity.com/paper/2102.10772/) (2021)
- [GRAM: Graph-based Attention Model for Healthcare Representation Learning](https://mlsanity.com/paper/1611.07012/) (2016)
- [Deep EHR: A Survey of Recent Advances in Deep Learning Techniques for Electronic Health Record (EHR) Analysis](https://mlsanity.com/paper/1706.03446/) (2017)
- [Pre-training of Graph Augmented Transformers for Medication Recommendation](https://mlsanity.com/paper/1906.00346/) (2019)
- [Learning the Graphical Structure of Electronic Health Records with Graph Convolutional Transformer](https://mlsanity.com/paper/1906.04716/) (2019)
- [MiME: Multilevel Medical Embedding of Electronic Health Records for Predictive Healthcare](https://mlsanity.com/paper/1810.09593/) (2018)
- [A Review of Challenges and Opportunities in Machine Learning for Health](https://mlsanity.com/paper/1806.00388/) (2018)
- [RetainVis: Visual Analytics with Interpretable and Interactive Recurrent Neural Networks on Electronic Medical Records](https://mlsanity.com/paper/1805.10724/) (2018)

## Built on by (most cited first, 13 of 13)

- [Self-eXplainable AI for Medical Image Analysis: A Survey and New Outlooks](https://mlsanity.com/paper/2410.02331/) (2024)
- [Hierarchical Pretraining on Multimodal Electronic Health Records](https://mlsanity.com/paper/2310.07871/) (2023)
- [SimSUM: Simulated Benchmark with Structured and Unstructured Medical Records](https://mlsanity.com/paper/2409.08936/) (2024)
- [Memorize and Rank: Elevating Large Language Models for Clinical Diagnosis Prediction](https://mlsanity.com/paper/2501.17326/) (2025)
- [Unsupervised Discovery of Clinical Disease Signatures Using Probabilistic Independence](https://mlsanity.com/paper/2402.05802/) (2024)
- [Contrastive Learning on Multimodal Analysis of Electronic Health Records](https://mlsanity.com/paper/2403.14926/) (2024)
- [Text Knows What, Tables Know When: Clinical Timeline Reconstruction via Retrieval-Augmented Multimodal Alignment](https://mlsanity.com/paper/2605.15168/) (2026)
- [Improving ARDS Diagnosis Through Context-Aware Concept Bottleneck Models](https://mlsanity.com/paper/2508.09719/) (2025)
- [Learning to Route: Per-Sample Adaptive Routing for Multimodal Multitask Prediction](https://mlsanity.com/paper/2509.12227/) (2025)
- [Patient-level Information Extraction by Consistent Integration of Textual and Tabular Evidence with Bayesian Networks](https://mlsanity.com/paper/2511.17056/) (2025)
- [Temporal Fusion Nexus: A task-agnostic multi-modal embedding model for clinical narratives and irregular time series in post-kidney transplant care](https://mlsanity.com/paper/2601.08503/) (2026)
- [Augmenting representations with scientific papers](https://mlsanity.com/paper/2603.04516/) (2026)
- [A General Multimodal Probing Framework for Data Fusion and Prediction with Frozen Large Language Models: Evidence from Multimodal EHR Data](https://mlsanity.com/paper/2606.28798/) (2026)

## Abstract (arXiv)

As two important textual modalities in electronic health records (EHR), both structured data (clinical codes) and unstructured data (clinical narratives) have recently been increasingly applied to the healthcare domain. Most existing EHR-oriented studies, however, either focus on a particular modality or integrate data from different modalities in a straightforward manner, which usually treats structured and unstructured data as two independent sources of information about patient admission and ignore the intrinsic interactions between them. In fact, the two modalities are documented during the same encounter where structured data inform the documentation of unstructured data and vice versa. In this paper, we proposed a Medical Multimodal Pre-trained Language Model, named MedM-PLM, to learn enhanced EHR representations over structured and unstructured data and explore the interaction of two modalities. In MedM-PLM, two Transformer-based neural network components are firstly adopted to learn representative characteristics from each modality. A cross-modal module is then introduced to model their interactions. We pre-trained MedM-PLM on the MIMIC-III dataset and verified the effectiveness of the model on three downstream clinical tasks, i.e., medication recommendation, 30-day readmission prediction and ICD coding. Extensive experiments demonstrate the power of MedM-PLM compared with state-of-the-art methods. Further analyses and visualizations show the robustness of our model, which could potentially provide more comprehensive interpretations for clinical decision-making.