# CodeBrain: Bridging Decoupled Tokenizer and Multi-Scale Architecture for EEG Foundation Model

arXiv: https://arxiv.org/abs/2506.09110 · HTML: https://mlsanity.com/paper/2506.09110/

## Key facts

- Cited by 28 papers in the map (data through 14 Oct 2026).
- Builds on 50 of its 96 references that are in the map.
- First posted on arXiv 10 Jun 2025.

## Builds on (most cited first, 30 of 50)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Neural Discrete Representation Learning](https://mlsanity.com/paper/1711.00937/) (2017)
- [Longformer: The Long-Document Transformer](https://mlsanity.com/paper/2004.05150/) (2020)
- [Neural Machine Translation of Rare Words with Subword Units](https://mlsanity.com/paper/1508.07909/) (2015)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [SentencePiece: A simple and language independent subword tokenizer and detokenizer for Neural Text Processing](https://mlsanity.com/paper/1808.06226/) (2018)
- [Root Mean Square Layer Normalization](https://mlsanity.com/paper/1910.07467/) (2019)
- [Simplified State Space Layers for Sequence Modeling](https://mlsanity.com/paper/2208.04933/) (2022)
- [Long Range Arena: A Benchmark for Efficient Transformers](https://mlsanity.com/paper/2011.04006/) (2020)
- [EEGNet: A Compact Convolutional Network for EEG-based Brain-Computer Interfaces](https://mlsanity.com/paper/1611.08024/) (2016)
- [HiPPO: Recurrent Memory with Optimal Polynomial Projections](https://mlsanity.com/paper/2008.07669/) (2020)
- [Hungry Hungry Hippos: Towards Language Modeling with State Space Models](https://mlsanity.com/paper/2212.14052/) (2022)
- [InternImage: Exploring Large-Scale Vision Foundation Models with Deformable Convolutions](https://mlsanity.com/paper/2211.05778/) (2022)
- [Finite Scalar Quantization: VQ-VAE Made Simple](https://mlsanity.com/paper/2309.15505/) (2023)
- [On the Parameterization and Initialization of Diagonal State Space Models](https://mlsanity.com/paper/2206.11893/) (2022)
- [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)
- [CLOCS: Contrastive Learning of Cardiac Signals Across Space, Time, and Patients](https://mlsanity.com/paper/2005.13249/) (2020)
- [Transformer-based Spatial-Temporal Feature Learning for EEG Decoding](https://mlsanity.com/paper/2106.11170/) (2021)
- [XSleepNet: Multi-View Sequential Model for Automatic Sleep Staging](https://mlsanity.com/paper/2007.05492/) (2020)
- [NeuroLM: A Universal Multi-task Foundation Model for Bridging the Gap between Language and EEG Signals](https://mlsanity.com/paper/2409.00101/) (2024)
- [What Makes Convolutional Models Great on Long Sequence Modeling?](https://mlsanity.com/paper/2210.09298/) (2022)
- [Simple Hardware-Efficient Long Convolutions for Sequence Modeling](https://mlsanity.com/paper/2302.06646/) (2023)
- [Online Clustered Codebook](https://mlsanity.com/paper/2307.15139/) (2023)

## Built on by (most cited first, 28 of 28)

- [Uni-NTFM: A Unified Foundation Model for EEG Signal Representation Learning](https://mlsanity.com/paper/2509.24222/) (2025)
- [DeeperBrain: A Neuro-Grounded EEG Foundation Model Towards Universal BCI](https://mlsanity.com/paper/2601.06134/) (2026)
- [ECHO: Toward Contextual Seq2Seq Paradigms in Large EEG Models](https://mlsanity.com/paper/2509.22556/) (2025)
- [Brain4FMs: A Benchmark of Foundation Models for Electrical Brain Signal](https://mlsanity.com/paper/2602.11558/) (2026)
- [DPsurv: Dual-Prototype Evidential Fusion for Uncertainty-Aware and Interpretable Whole-Slide Image Survival Prediction](https://mlsanity.com/paper/2510.00053/) (2025)
- [BrainRVQ: A High-Fidelity EEG Foundation Model via Dual-Domain Residual Quantization and Hierarchical Autoregression](https://mlsanity.com/paper/2602.16951/) (2026)
- [EEGDM: EEG Representation Learning via Generative Diffusion Model](https://mlsanity.com/paper/2508.14086/) (2025)
- [NeuroWeaver: An Autonomous Evolutionary Agent for Exploring the Programmatic Space of EEG Analysis Pipelines](https://mlsanity.com/paper/2602.13473/) (2026)
- [SingLEM: Single-Channel Large EEG Model](https://mlsanity.com/paper/2509.17920/) (2025)
- [SCOPE: Structured Prototype-Guided Adaptation for EEG Foundation Models with Limited Labels](https://mlsanity.com/paper/2602.17251/) (2026)
- [LERD: Latent Event-Relational Dynamics for Neurodegenerative Classification](https://mlsanity.com/paper/2602.18195/) (2026)
- [TRACE: Temporal Routing with Autoregressive Cross-channel Experts for EEG Representation Learning](https://mlsanity.com/paper/2605.11380/) (2026)
- [DLink: Distilling Layer-wise and Dominant Knowledge from EEG Foundation Models](https://mlsanity.com/paper/2604.15016/) (2026)
- [Context-aware tokenization for Cross-subject Emotion Decoding from EEG](https://mlsanity.com/paper/2606.00884/) (2026)
- [EvoBrain: Continual Learning of EEG Foundation Models Across Heterogeneous BCI Tasks](https://mlsanity.com/paper/2606.01767/) (2026)
- [Channel-Preserving Representation Alignment for EEG-to-Music Reconstruction](https://mlsanity.com/paper/2606.04040/) (2026)
- [SL-S4Wave: Self-Supervised Learning of Physiological Waveforms with Structured State Space Models](https://mlsanity.com/paper/2606.19888/) (2026)
- [B[FM]2: Brain Foundation Model via Flow Matching with SplitUNet](https://mlsanity.com/paper/2606.20812/) (2026)
- [ZIPBrain: Can EEG Foundation Models Be Faster, Locally Deployable, but Accurate?](https://mlsanity.com/paper/2608.07033/) (2026)
- [Continuous-Latent Predictive Modeling with Semantic Alignment for EEG-Language Foundation Models](https://mlsanity.com/paper/2608.11656/) (2026)
- [Taming foundation model with invariance-oriented pre-training for broad-spectrum EEG analysis across signal-level, brain-state, and brain-health tasks](https://mlsanity.com/paper/2608.24597/) (2026)
- [Neural State Prediction: Obstructing Shortcut Learning in EEG Foundation Models](https://mlsanity.com/paper/2609.31167/) (2026)
- [Representational and Functional Robustness to Electrode Montages in EEG Foundation Models](https://mlsanity.com/paper/2609.36288/) (2026)
- [ZeroMAG: Zero-Shot Multimodal Adapter Generation for Plug-and-Play EEG Foundation Models](https://mlsanity.com/paper/2610.03546/) (2026)
- [SPERA: Spherical Prior EEG Foundation Model with Geometry- and Frequency-Aware Latent Prediction](https://mlsanity.com/paper/2610.10571/) (2026)
- [DEFT: Disentanglement-Enhanced Fine-Tuning for EEG Foundation Models](https://mlsanity.com/paper/2610.14497/) (2026)
- [Brain2Face: A Study on the Relation of EEG Signals and Spatio-temporal Head Avatars](https://mlsanity.com/paper/2610.17356/) (2026)
- [NeuroDETR: Multiscale Discrete Spatiotemporal Tokenization for Asynchronous EEG Event Detection](https://mlsanity.com/paper/2610.20349/) (2026)

## Abstract (arXiv)

Electroencephalography (EEG) provides real-time insights into brain activity and supports diverse applications in neuroscience. While EEG foundation models (EFMs) have emerged to address the scalability issues of task-specific models, current approaches still yield clinically uninterpretable and weakly discriminative representations, inefficiently capturing global dependencies and neglecting important local neural events. We present CodeBrain, a two-stage EFM designed to fill this gap. In the first stage, we introduce the TFDual-Tokenizer, which decouples heterogeneous temporal and frequency EEG signals into discrete tokens, quadratically expanding the representation space to enhance discriminative power and offering domain-specific representation-level interpretability by suggesting potential links to neural events and spectral rhythms. In the second stage, we propose the multi-scale EEGSSM architecture, which combines structured global convolution with sliding window attention to efficiently capture both sparse long-range and local dependencies, reflecting the brain's small-world topology. Pretrained on the largest public EEG corpus, CodeBrain achieves strong generalization across eight downstream tasks and ten datasets under distribution shifts, supported by comprehensive ablations, scaling-law analyzes, and interpretability evaluations. The code and the pretrained weights are available at https://github.com/jingyingma01/CodeBrain.