# Brain-Token Learning: Microstate-Based Tokenization and Multi-Scale Interaction for Long-Horizon EEG Sequence Modeling

arXiv: https://arxiv.org/abs/2609.24324 · HTML: https://mlsanity.com/paper/2609.24324/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 35 of its 84 references that are in the map.
- First posted on arXiv 21 Sep 2026.

## Builds on (most cited first, 30 of 35)

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- [Autoformer: Decomposition Transformers with Auto-Correlation for Long-Term Series Forecasting](https://mlsanity.com/paper/2106.13008/) (2021)
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- [Deep CORAL: Correlation Alignment for Deep Domain Adaptation](https://mlsanity.com/paper/1607.01719/) (2016)
- [TimesNet: Temporal 2D-Variation Modeling for General Time Series Analysis](https://mlsanity.com/paper/2210.02186/) (2022)
- [iTransformer: Inverted Transformers Are Effective for Time Series Forecasting](https://mlsanity.com/paper/2310.06625/) (2023)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [SoundStream: An End-to-End Neural Audio Codec](https://mlsanity.com/paper/2107.03312/) (2021)
- [High Fidelity Neural Audio Compression](https://mlsanity.com/paper/2210.13438/) (2022)
- [EEGNet: A Compact Convolutional Network for EEG-based Brain-Computer Interfaces](https://mlsanity.com/paper/1611.08024/) (2016)
- [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)

## Abstract (arXiv)

Electroencephalography (EEG) provides a non-invasive window into dynamic brain activity, yet modeling long-horizon EEG sequences remains challenging due to their high temporal complexity, substantial variability across subjects, and the lack of biologically meaningful sequence representations. Existing tokenization strategies, such as fixed-window and patch-based representations, discretize EEG signals according to artificial temporal boundaries, which may disrupt intrinsic brain-state dynamics. In this work, we propose Brain-Token Learning, a neuroscience-inspired framework that introduces Brain Tokenization for long-horizon EEG sequence modeling. Instead of partitioning EEG signals into predefined temporal segments, Brain Tokenization represents EEG as sequences of recurrent microstate-derived brain tokens, where each token corresponds to a quasi-stable large-scale brain state with variable temporal duration. Based on these biologically grounded tokens, we further develop a multi-scale token interaction module consisting of Latent State Aggregation and State Transition Modeling to jointly capture global brain-state context and local microstate transitions. We evaluate Brain-Token on five heterogeneous EEG datasets, including the newly collected long-horizon NeuroLong dataset and four affective or clinical EEG datasets (SEED, DEAP, MDD, and NSSI). Extensive experiments demonstrate that Brain-Token consistently outperforms conventional CNN/LSTM architectures, Transformer-based models, and domain adaptation methods across diverse EEG scenarios. Further analysis verifies the effectiveness of microstate-based tokenization and multi-scale interaction for learning robust and interpretable EEG representations. These results establish Brain-Token as a biologically grounded tokenization paradigm for long-horizon EEG sequence modeling.