Jaedong Hwang, Kathleen Zhang, Wei Dai, Konstantinos Kontras, Maarten Vanmarcke, Maarten De Vos, Ila Fiete, Paul Pu Liang
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 ($\approx$ 307h), 1-2 orders of magnitude ($\approx$ 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 $κ= -0.096$). https://jd730.github.io/projects/BFM2
Emma Andrews, Konstantinos Kontras, Keane Ong, Maarten De Vos, Gianmarco Mengaldo
When one time series informs another, the delay at which that information arrives determines if models can utilize this relationship effectively. A source may be strongly predictive at one delay but uninformative at neighboring lags. Therefore, fixed input windows may obscure this structure by bundling informative and irrelevant history together. Transfer entropy (TE) can recover these delays by measuring how much a source's past tells us about a target beyond the target's own history. However, existing TE estimators require separate fits across source and conditioning depths, with further estimation on local windows to track delays over time. We introduce ATEMPO, a diffusion-based transfer entropy estimator amortized over lags and time. ATEMPO samples source and conditioning depths during training and conditions explicitly on temporal position, allowing a single score network to estimate the full TE surface without refitting. Differencing this surface recovers when information arrives. Across synthetic datasets with ground-truth TE, ATEMPO achieves the lowest mean relative error among baselines, and on datasets with known lags, ATEMPO achieves $0.98\pm0.04$ lag-detection accuracy. ATEMPO requires a single fit across source depths $K=6$ and target depths $L=3$, whereas existing estimators require 18 separate fits to evaluate the same $K \times L$ grid. On three systems with time-varying lag, ATEMPO is the only estimator to maintain perfect lag-detection accuracy across all evaluated window lengths. These recovered delays improve downstream forecasting: ATEMPO-selected inputs reduce MSE on WEATHER-5K by 7.25%, while 120 selected inputs outperform the benchmark's 240-feature default by 4.6%. Across three brain-computer interface tasks, using ATEMPO-selected lags achieves the highest or equal-best $R^2$, improving mean $R^2$ by 4.1% relative to the strongest competing baseline.