A spectral audit framework reveals task-dependent aperiodic reliance across EEG and ECG deep learning

Electroencephalograph (EEG) timeseries signals are characterized by significant noise and coarse spatial resolution, which complicates the classification of neurodegenerative diseases. Even SOTA deep learning architectures struggle to distinguish between healthy controls and diseased subjects, or between different disease types, due to high intergroup similarity. In this paper, we show that a spectrally selective approach to feature construction enhances class separability. By isolating signal strengths within the primary brainwave bands, we transform high dimensional raw data into high value spectral features. Our results demonstrate that in small datasets a) features derived from frequency and time frequency domain allow traditional machine learning models to match or exceed the performance of SOTA deep learning models, b) Attention mechanism is unable to distill the stable feature signatures that characterize healthy neural activity in both resting and task EEGs, and c) the limitations of attention based models in finding relevant spectral features appear to be robust in that providing frequency selective time domain input do not appreciably improve their performance. We validate our methodology across three open source resting EEG datasets and one task EEG dataset, providing robust empirical evidence for our claims.

Foundation models (FMs) promise to extract unified representations that generalize across downstream tasks. They have emerged across fields, including electroencephalography (EEG), but it is less clear how effective they are in this particular field. Published evaluations differ in datasets, in the EEG-specific preprocessing that might influence reported results, and in the reported metrics, frequently obscuring the clinical relevance in EEG. We introduce NeuroAtlas, the largest EEG benchmark to date: 42 datasets and 260k hours covering clinical EEG (epilepsy, sleep medicine, brain age estimation) and brain-computer interfaces, and include multiple datasets per task along with bespoke clinical evaluation metrics. Besides evaluating EEG-FMs with respect to supervised baselines, we present results from generic time-series FMs. We report three findings. First, EEG-specific FMs do not consistently outperform time-series FMs, which have neither EEG-focused architectures nor been pretrained on EEG. Second, standard machine learning metrics are insufficient to assess clinical utility: thus, we thoroughly evaluate more appropriate measures such as the quality of event-level decision-making, hypnogram-derived features, and the brain-age gap in the domains of epilepsy, sleep, and brain age, respectively. Third, model rankings and performance can vary substantially within domains. We conclude that pretrained models perform largely on par, with only narrow advantages for a few, and that current models do not yet deliver on the promise of an out-of-the-box unified EEG model. NeuroAtlas exposes this gap and provides the datasets and metrics for the next generation of unified EEG FMs.

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.