Interpretable EEG biomarkers with bag-of-waves: Spatial and temporal waveform dictionaries for low-data regimes

Abstract

Electroencephalography (EEG) is widely used to diagnose neurological conditions, but its analysis usually relies on either predefined spectral features or deep neural networks. Predefined features carry a strong bias, since they fix in advance what counts as informative, while deep neural networks and foundation models are hard to interpret and need large amounts of data and compute. We present bag-of-waves, an interpretable framework that learns a small dictionary of recurring EEG waveform templates, called atoms, using shift-invariant k-means without labels. The continuous EEG is then turned into a sequence of atom tokens, whose counts feed a simple downstream classifier or clustering step. We extend this representation in two ways: we add atom-to-atom transitions, which we call n- grams, to capture temporal structure, and we move from single-channel atoms to regional and cross-channel spatial atoms for the multichannel case. We test the method on three complementary datasets, each probing a different aspect: single-channel mouse genotype clustering with only sixteen animals (the low-data and temporal case), resting-state dementia classification (the spatial case), and the TUEV benchmark, a six-way classification of clinical EEG events (a high-data comparison against strong deep and foundation baselines). Across all three datasets, bag-of-waves achieves performance competitive with state-of-the-art deep and foundation models. Yet, it operates with a fraction of the parameter count and provides full interpretability: because every atom corresponds to an inspectable waveform, the method explicitly recovers known clinical morphologies that a neurophysiologist can directly validate. Its main advantage is that it works in the low-data regime where heavier models are a poor fit.