# Self-supervised Representation Learning on Electronic Health Records with Graph Kernel Infomax

arXiv: https://arxiv.org/abs/2209.00655 · HTML: https://mlsanity.com/paper/2209.00655/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 36 of its 55 references that are in the map.
- First posted on arXiv 1 Sep 2022.

## Builds on (most cited first, 30 of 36)

- [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)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Delving Deep into Rectifiers: Surpassing Human-Level Performance on ImageNet Classification](https://mlsanity.com/paper/1502.01852/) (2015)
- [Supervised Contrastive Learning](https://mlsanity.com/paper/2004.11362/) (2020)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [TUDataset: A collection of benchmark datasets for learning with graphs](https://mlsanity.com/paper/2007.08663/) (2020)
- [Contrastive Multi-View Representation Learning on Graphs](https://mlsanity.com/paper/2006.05582/) (2020)
- [GCC: Graph Contrastive Coding for Graph Neural Network Pre-Training](https://mlsanity.com/paper/2006.09963/) (2020)
- [InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization](https://mlsanity.com/paper/1908.01000/) (2019)
- [RETAIN: An Interpretable Predictive Model for Healthcare using Reverse Time Attention Mechanism](https://mlsanity.com/paper/1608.05745/) (2016)
- [From Softmax to Sparsemax: A Sparse Model of Attention and Multi-Label Classification](https://mlsanity.com/paper/1602.02068/) (2016)
- [BEHRT: Transformer for Electronic Health Records](https://mlsanity.com/paper/1907.09538/) (2019)
- [Towards K-means-friendly Spaces: Simultaneous Deep Learning and Clustering](https://mlsanity.com/paper/1610.04794/) (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)
- [Dipole: Diagnosis Prediction in Healthcare via Attention-based Bidirectional Recurrent Neural Networks](https://mlsanity.com/paper/1706.05764/) (2017)
- [Learning the Graphical Structure of Electronic Health Records with Graph Convolutional Transformer](https://mlsanity.com/paper/1906.04716/) (2019)
- [Geodesic Exponential Kernels: When Curvature and Linearity Conflict](https://mlsanity.com/paper/1411.0296/) (2014)
- [RAIM: Recurrent Attentive and Intensive Model of Multimodal Patient Monitoring Data](https://mlsanity.com/paper/1807.08820/) (2018)
- [Neighborhood Contrastive Learning Applied to Online Patient Monitoring](https://mlsanity.com/paper/2106.05142/) (2021)
- [Model Degradation Hinders Deep Graph Neural Networks](https://mlsanity.com/paper/2206.04361/) (2022)
- [Improving Clinical Predictions through Unsupervised Time Series Representation Learning](https://mlsanity.com/paper/1812.00490/) (2018)
- [Kernel Methods on the Riemannian Manifold of Symmetric Positive Definite Matrices](https://mlsanity.com/paper/1412.4172/) (2014)

## Built on by (most cited first, 2 of 2)

- [DiaLLMs: EHR Enhanced Clinical Conversational System for Clinical Test Recommendation and Diagnosis Prediction](https://mlsanity.com/paper/2506.20059/) (2025)
- [MiGHT-EHR: A Multi-task Graph Transformer for Heterogeneous Temporal Electronic Health Records](https://mlsanity.com/paper/2608.06430/) (2026)

## Abstract (arXiv)

Learning Electronic Health Records (EHRs) representation is a preeminent yet under-discovered research topic. It benefits various clinical decision support applications, e.g., medication outcome prediction or patient similarity search. Current approaches focus on task-specific label supervision on vectorized sequential EHR, which is not applicable to large-scale unsupervised scenarios. Recently, contrastive learning shows great success on self-supervised representation learning problems. However, complex temporality often degrades the performance. We propose Graph Kernel Infomax, a self-supervised graph kernel learning approach on the graphical representation of EHR, to overcome the previous problems. Unlike the state-of-the-art, we do not change the graph structure to construct augmented views. Instead, we use Kernel Subspace Augmentation to embed nodes into two geometrically different manifold views. The entire framework is trained by contrasting nodes and graph representations on those two manifold views through the commonly used contrastive objectives. Empirically, using publicly available benchmark EHR datasets, our approach yields performance on clinical downstream tasks that exceeds the state-of-the-art. Theoretically, the variation on distance metrics naturally creates different views as data augmentation without changing graph structures.