# B[FM]2: Brain Foundation Model via Flow Matching with SplitUNet

arXiv: https://arxiv.org/abs/2606.20812 · HTML: https://mlsanity.com/paper/2606.20812/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical imaging and segmentation, one of 14 directions in Diffusion models.
- Builds on 39 of its 66 references that are in the map.
- First posted on arXiv 18 Jun 2026.

## Placed in

- Diffusion models / [Medical imaging and segmentation](https://mlsanity.com/diffusion/medical-imaging-and-segmentation/)

## Builds on (most cited first, 30 of 39)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Improved Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2102.09672/) (2021)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [Are Transformers Effective for Time Series Forecasting?](https://mlsanity.com/paper/2205.13504/) (2022)
- [DiffWave: A Versatile Diffusion Model for Audio Synthesis](https://mlsanity.com/paper/2009.09761/) (2020)
- [A Closer Look at Spatiotemporal Convolutions for Action Recognition](https://mlsanity.com/paper/1711.11248/) (2017)
- [Improving and generalizing flow-based generative models with minibatch optimal transport](https://mlsanity.com/paper/2302.00482/) (2023)
- [Chronos: Learning the Language of Time Series](https://mlsanity.com/paper/2403.07815/) (2024)
- [SiT: Exploring Flow and Diffusion-based Generative Models with Scalable Interpolant Transformers](https://mlsanity.com/paper/2401.08740/) (2024)
- [Time-LLM: Time Series Forecasting by Reprogramming Large Language Models](https://mlsanity.com/paper/2310.01728/) (2023)
- [A decoder-only foundation model for time-series forecasting](https://mlsanity.com/paper/2310.10688/) (2023)
- [EEGNet: A Compact Convolutional Network for EEG-based Brain-Computer Interfaces](https://mlsanity.com/paper/1611.08024/) (2016)
- [Unified Training of Universal Time Series Forecasting Transformers](https://mlsanity.com/paper/2402.02592/) (2024)
- [CSDI: Conditional Score-based Diffusion Models for Probabilistic Time Series Imputation](https://mlsanity.com/paper/2107.03502/) (2021)
- [Label-Efficient Semantic Segmentation with Diffusion Models](https://mlsanity.com/paper/2112.03126/) (2021)
- [Emergent Correspondence from Image Diffusion](https://mlsanity.com/paper/2306.03881/) (2023)
- [Open-Vocabulary Panoptic Segmentation with Text-to-Image Diffusion Models](https://mlsanity.com/paper/2303.04803/) (2023)
- [Efficient Attention: Attention with Linear Complexities](https://mlsanity.com/paper/1812.01243/) (2018)
- [Large Brain Model for Learning Generic Representations with Tremendous EEG Data in BCI](https://mlsanity.com/paper/2405.18765/) (2024)
- [BENDR: using transformers and a contrastive self-supervised learning task to learn from massive amounts of EEG data](https://mlsanity.com/paper/2101.12037/) (2021)
- [CBraMod: A Criss-Cross Brain Foundation Model for EEG Decoding](https://mlsanity.com/paper/2412.07236/) (2024)
- [SimMTM: A Simple Pre-Training Framework for Masked Time-Series Modeling](https://mlsanity.com/paper/2302.00861/) (2023)

## Abstract (arXiv)

EEG foundation models can learn generalizable representations from large-scale EEG corpora to enable single-backbone transfer across diverse clinical and brain-computer interface tasks. Existing models typically discretize the continuous multi-channel EEG waveform into patches or codebook tokens and train a transformer with masked self-supervision. Recognizing that this discretization fragments continuous brain rhythms and obscures fine-grained temporal dynamics, we present B[FM]2(Brain Foundation Model via Flow Matching), whose inductive bias aligns with the data by pretraining directly on the raw signal using continuous-time flow matching without patches, tokenization, or masking. However, multi-channel EEG signals pose an architectural challenge for flow matching: time is densely sampled and highly autocorrelated (thousands of timepoints), while the electrode axis is short (tens of channels) at distinct scalp positions. To address this time-electrode asymmetry, we introduce SplitUNet, a velocity network that factorizes each block into separate 1D temporal and 1D electrode convolutions and downsamples only along time, preserving electrode topology throughout the hierarchy. B[FM]2 sets a new state of the art on 7 of 9 standard downstream EEG classification tasks, using a pretraining budget of only 36,895 segments (≈ 307h), 1-2 orders of magnitude (≈ 30x) less than required by existing EEG foundation models. Further, it generates synthetic EEGs that two board-certified neurologists cannot distinguish from brain data (Cohen's kappa = -0.096). https://jd730.github.io/projects/BFM2