# MedFlow: Class-Aware Multi-Scale Generation for Medical Time-Series Synthesis

arXiv: https://arxiv.org/abs/2609.04804 · HTML: https://mlsanity.com/paper/2609.04804/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 12 of its 21 references that are in the map.
- First posted on arXiv 4 Sep 2026.

## Placed in

- Diffusion models / [Flow matching, time series and science](https://mlsanity.com/diffusion/flow-matching-time-series-and-science/)

## Builds on (most cited first, 12 of 12)

- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Neural Discrete Representation Learning](https://mlsanity.com/paper/1711.00937/) (2017)
- [Autoregressive Image Generation using Residual Quantization](https://mlsanity.com/paper/2203.01941/) (2022)
- [Real-valued (Medical) Time Series Generation with Recurrent Conditional GANs](https://mlsanity.com/paper/1706.02633/) (2017)
- [Diffusion-TS: Interpretable Diffusion for General Time Series Generation](https://mlsanity.com/paper/2403.01742/) (2024)
- [Deep EHR: A Survey of Recent Advances in Deep Learning Techniques for Electronic Health Record (EHR) Analysis](https://mlsanity.com/paper/1706.03446/) (2017)
- [TimeVAE: A Variational Auto-Encoder for Multivariate Time Series Generation](https://mlsanity.com/paper/2111.08095/) (2021)
- [Membership Inference Attacks against Synthetic Data through Overfitting Detection](https://mlsanity.com/paper/2302.12580/) (2023)
- [Warpformer: A Multi-scale Modeling Approach for Irregular Clinical Time Series](https://mlsanity.com/paper/2306.09368/) (2023)
- [Vector Quantized Time Series Generation with a Bidirectional Prior Model](https://mlsanity.com/paper/2303.04743/) (2023)
- [Semi-supervised learning for medical image classification using imbalanced training data](https://mlsanity.com/paper/2108.08956/) (2021)
- [BioDiffusion: A Versatile Diffusion Model for Biomedical Signal Synthesis](https://mlsanity.com/paper/2401.10282/) (2024)

## Abstract (arXiv)

Synthetic medical time-series generation can alleviate data scarcity and support the development of reliable clinical prediction models. However, existing methods mainly focus on matching the overall distribution and temporal dynamics of real data, which does not necessarily ensure strong downstream utility on imbalanced medical datasets. Clinically informative patterns often occur at heterogeneous temporal scales, while rare minority-class characteristics can be obscured by dominant population patterns. To address these challenges, we propose MedFlow, a class-aware multi-scale flow matching framework for medical time-series synthesis. MedFlow employs a vector-quantized multi-scale tokenizer to represent medical sequences at complementary temporal resolutions, capturing both coarse clinical trends and fine-grained dynamics. We further introduce Token Marginal Guidance, which incorporates class-conditional token statistics directly into the flow matching process to steer generation toward class-specific regions of the learned tokens. This mechanism strengthens minority-class patterns, while preserving the global and tail distributions of real data. Experiments on four public datasets covering electronic health records, EEG, and ECG signals demonstrate that MedFlow consistently outperforms recent state-of-the-art diffusion-based baselines across downstream prediction tasks. On average, it improves AUPRC by 5.8%, reduces Context-FID by 88.6%, and achieves 3.8× higher sampling throughput.