# MUSE-Net: Missingness-aware mUlti-branching Self-attention Encoder for Irregular Longitudinal Electronic Health Records

arXiv: https://arxiv.org/abs/2407.00840 · HTML: https://mlsanity.com/paper/2407.00840/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 28 of its 94 references that are in the map.
- First posted on arXiv 30 Jun 2024.

## Builds on (most cited first, 28 of 28)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [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)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling](https://mlsanity.com/paper/1412.3555/) (2014)
- [An Empirical Evaluation of Generic Convolutional and Recurrent Networks for Sequence Modeling](https://mlsanity.com/paper/1803.01271/) (2018)
- [Temporal Fusion Transformers for Interpretable Multi-horizon Time Series Forecasting](https://mlsanity.com/paper/1912.09363/) (2019)
- [GPyTorch: Blackbox Matrix-Matrix Gaussian Process Inference with GPU Acceleration](https://mlsanity.com/paper/1809.11165/) (2018)
- [CSDI: Conditional Score-based Diffusion Models for Probabilistic Time Series Imputation](https://mlsanity.com/paper/2107.03502/) (2021)
- [Recurrent Neural Networks for Multivariate Time Series with Missing Values](https://mlsanity.com/paper/1606.01865/) (2016)
- [BBN: Bilateral-Branch Network with Cumulative Learning for Long-Tailed Visual Recognition](https://mlsanity.com/paper/1912.02413/) (2019)
- [GAIN: Missing Data Imputation using Generative Adversarial Nets](https://mlsanity.com/paper/1806.02920/) (2018)
- [Scalable and accurate deep learning for electronic health records](https://mlsanity.com/paper/1801.07860/) (2018)
- [Deep EHR: A Survey of Recent Advances in Deep Learning Techniques for Electronic Health Record (EHR) Analysis](https://mlsanity.com/paper/1706.03446/) (2017)
- [Exact Gaussian Processes on a Million Data Points](https://mlsanity.com/paper/1903.08114/) (2019)
- [Self-Supervised Transformer for Sparse and Irregularly Sampled Multivariate Clinical Time-Series](https://mlsanity.com/paper/2107.14293/) (2021)
- [Time Series as Images: Vision Transformer for Irregularly Sampled Time Series](https://mlsanity.com/paper/2303.12799/) (2023)
- [Learning to Detect Sepsis with a Multitask Gaussian Process RNN Classifier](https://mlsanity.com/paper/1706.04152/) (2017)
- [Deep Representation Learning of Electronic Health Records to Unlock Patient Stratification at Scale](https://mlsanity.com/paper/2003.06516/) (2020)
- [A Review of Deep Learning Methods for Irregularly Sampled Medical Time Series Data](https://mlsanity.com/paper/2010.12493/) (2020)
- [EVA: Generating Longitudinal Electronic Health Records Using Conditional Variational Autoencoders](https://mlsanity.com/paper/2012.10020/) (2020)
- [An Introductory Study on Time Series Modeling and Forecasting](https://mlsanity.com/paper/1302.6613/) (2013)
- [Hierarchical Deep Learning with Generative Adversarial Network for Automatic Cardiac Diagnosis from ECG Signals](https://mlsanity.com/paper/2210.11408/) (2022)
- [Physics-constrained Deep Learning for Robust Inverse ECG Modeling](https://mlsanity.com/paper/2107.12780/) (2021)
- [Automated Identication of Atrial Fibrillation from Single-lead ECGs Using Multi-branching ResNet](https://mlsanity.com/paper/2306.15096/) (2023)
- [MGP-AttTCN: An Interpretable Machine Learning Model for the Prediction of Sepsis](https://mlsanity.com/paper/1909.12637/) (2019)

## Built on by (most cited first, 4 of 4)

- [Transformer with Koopman-Enhanced Graph Convolutional Network for Spatiotemporal Dynamics Forecasting](https://mlsanity.com/paper/2507.03855/) (2025)
- [Physics-augmented Multi-task Gaussian Process for Modeling Spatiotemporal Dynamics](https://mlsanity.com/paper/2510.13601/) (2025)
- [Multi-Task LLM with LoRA Fine-Tuning for Automated Cancer Staging and Biomarker Extraction](https://mlsanity.com/paper/2604.13328/) (2026)
- [Multi-Modal Machine Learning for Breast Cancer Recurrence Prediction](https://mlsanity.com/paper/2606.02892/) (2026)

## Abstract (arXiv)

The era of big data has made vast amounts of clinical data readily available, particularly in the form of electronic health records (EHRs), which provides unprecedented opportunities for developing data-driven diagnostic tools to enhance clinical decision making. However, the application of EHRs in data-driven modeling faces challenges such as irregularly spaced multi-variate time series, issues of incompleteness, and data imbalance. Realizing the full data potential of EHRs hinges on the development of advanced analytical models. In this paper, we propose a novel Missingness-aware mUlti-branching Self-Attention Encoder (MUSE-Net) to cope with the challenges in modeling longitudinal EHRs for data-driven disease prediction. The proposed MUSE-Net is composed by four novel modules including: (1) a multi-task Gaussian process (MGP) with missing value masks for data imputation; (2) a multi-branching architecture to address the data imbalance problem; (3) a time-aware self-attention encoder to account for the irregularly spaced time interval in longitudinal EHRs; (4) interpretable multi-head attention mechanism that provides insights into the importance of different time points in disease prediction, allowing clinicians to trace model decisions. We evaluate the proposed MUSE-Net using both synthetic and real-world datasets. Experimental results show that our MUSE-Net outperforms existing methods that are widely used to investigate longitudinal signals.