FourierMask: Explain EEG-based End-to-end Deep Learning Models in the Frequency Domain

The rise of EEG-based end-to-end deep learning models has underscored the need to elucidate how these models process time-series raw EEG signals to generate predictions. The frequency domain provides a more suitable perspective for this task due to two key advantages: the strong correlation with cognitive states and the inherent capacity to model long-range temporal dependencies. However, this perspective remains underexplored in existing research. To bridge this gap, we propose FourierMask, the first mask perturbation framework specifically designed for frequency-domain explanation of EEG-based end-to-end models. Our method introduces three key innovations. First, the Fourier-based domain transformation enables direct manipulation of spectral components. Second, A learnable mask mechanism jointly models the spectral-spatial couplings relationship for EEG explanation. Third, a perturbation generator constrained by a target alignment loss ensures natural perturbations by minimizing distribution shift via cluster-aware regularization. We validate our method through experiments on an EEG benchmark dataset across EEGNet, TSCeption, and DeepConvNet models. Our method reaches a 36.0% average accuracy drop gap (vs. 8.6% for LIME and 6.6% for easyPEASI) at the group-level. And, it reaches a 17.8% average accuracy drop gap (vs. 8.9% for LIME and 9.9% for easyPEASI) at the instance-level. Our model-agnostic framework provides a plug-and-play solution for enhancing transparency of EEG-based end-to-end deep learning models. It links model decisions to frequency biomarkers, with potential applications in neuromedicine and brain-computer interfaces.