Spectral Considerations on Unsupervised Time-domain EEG Representation Learning with Deep Networks

Electroencephalography (EEG) is a non-invasive, scalable source of quantitative biomarkers for the early diagnosis of brain disorders, and deep representation learning has become a powerful paradigm for extracting information-rich latent features from raw signals. However, neural networks tend to under-represent high-frequency information, a concern that is especially acute for EEG given its oscillatory nature and characteristic 1/f^chi power decay, which risks masking disease-relevant high-frequency signatures. In this study, we systematically investigate the spectral constraints of unsupervised time-domain feature extraction across three autoencoder architectures (LSTMVAE, VAEEG, Transformer) and a state-of-the-art EEG foundation model. Using synthetic experiments and empirical validation, we show that while autoencoders capture macro-scale shifts such as alpha slowing, they remain biased against higher frequencies due to a magnitude-driven masking effect induced by the Mean Squared Error loss under 1/f-decaying spectra. Increasing latent dimensionality mitigates this attenuation but sacrifices latent compactness and generative stability. We argue that, as the field advances toward large-scale foundation-level feature extractors, it is imperative to move beyond simple time-domain reconstruction and to integrate spectral-domain loss terms and gradient-balancing techniques, so that the subtle high-frequency transients critical for diagnosing complex brain disorders are preserved in the latent representation.