# EEG-JEPA: Structured Latent Prediction for EEG Foundation Models

arXiv: https://arxiv.org/abs/2608.00114 · HTML: https://mlsanity.com/paper/2608.00114/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 17 of its 33 references that are in the map.
- First posted on arXiv 31 Jul 2026.

## Builds on (most cited first, 17 of 17)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Similarity of Neural Network Representations Revisited](https://mlsanity.com/paper/1905.00414/) (2019)
- [data2vec: A General Framework for Self-supervised Learning in Speech, Vision and Language](https://mlsanity.com/paper/2202.03555/) (2022)
- [EEGNet: A Compact Convolutional Network for EEG-based Brain-Computer Interfaces](https://mlsanity.com/paper/1611.08024/) (2016)
- [TS2Vec: Towards Universal Representation of Time Series](https://mlsanity.com/paper/2106.10466/) (2021)
- [Time-Series Representation Learning via Temporal and Contextual Contrasting](https://mlsanity.com/paper/2106.14112/) (2021)
- [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)
- [Uncovering the structure of clinical EEG signals with self-supervised learning](https://mlsanity.com/paper/2007.16104/) (2020)
- [NeuroLM: A Universal Multi-task Foundation Model for Bridging the Gap between Language and EEG Signals](https://mlsanity.com/paper/2409.00101/) (2024)
- [REVE: A Foundation Model for EEG -- Adapting to Any Setup with Large-Scale Pretraining on 25,000 Subjects](https://mlsanity.com/paper/2510.21585/) (2025)
- [EEG2Rep: Enhancing Self-supervised EEG Representation Through Informative Masked Inputs](https://mlsanity.com/paper/2402.17772/) (2024)
- [What Do EEG Foundation Models Capture from Human Brain Signals?](https://mlsanity.com/paper/2605.11410/) (2026)
- [DSAINet: An Efficient Dual-Scale Attentive Interaction Network for General EEG Decoding](https://mlsanity.com/paper/2604.18095/) (2026)

## Abstract (arXiv)

Electroencephalography (EEG) foundation models aim to learn reusable representations from large-scale unlabeled recordings. A common pretraining strategy is masked waveform reconstruction, but applying supervision directly to noisy EEG may encourage models to recover predictable background activity, acquisition effects, and artifacts rather than neural structure that transfers across tasks. This raises a central question: what should an EEG foundation model predict to learn transferable representations? We introduce EEG-JEPA a structured latent-prediction framework for EEG foundation modeling. Rather than reconstructing masked voltage samples, a masked context encoder and predictor infer contextual latent states produced by an exponential-moving-average target encoder that observes the complete input. EEG-JEPA organizes target design along three complementary dimensions: target content specifies what representation is predicted, target support specifies where prediction occurs over structured electrode--time regions through Neurotopology-Aware Multi-scale Electrode-Temporal Masking (N-MET), and target depth specifies at which encoder layers supervision is applied. Together, these designs shift EEG pretraining from recovering missing measurements to inferring latent states from structured electrode--time context. We evaluate EEG-JEPA through controlled objective comparisons, frozen multitask transfer, and full fine-tuning. Under the same backbone, pretraining corpus, and training duration, EEG-JEPA improves the 14-task frozen macro balanced accuracy from 40.49% to 50.42% over CBraMod-style masked waveform reconstruction. Multi-source continuation further raises this result to 52.94%, the highest average among the EEG foundation models evaluated on EEG-FM-Bench. Under protocol-matched full fine-tuning, EEG-JEPA also improves the nine-task average balanced accuracy from 68.98% to 70.65%.