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Updated: Sep 17, 2025
Mapping Cortical Dynamics Using Simultaneous MEG/EEG and Anatomically-constrained Minimum-norm Estimates: an Auditory Attention Example
Published on: October 24, 2012
The role of data partitioning on the performance of EEG-based deep learning models in supervised cross-subject
Federico Del Pup1, Andrea Zanola2, Louis Fabrice Tshimanga2
1Department of Information Engineering, University of Padua, Padua, 35131, Italy; Department of Neuroscience, University of Padua, Padua, 35121, Italy; Padova Neuroscience Center, University of Padua, Padua, 35129, Italy.
Abstract:
Deep learning is significantly advancing the analysis of electroencephalography (EEG) data by effectively discovering highly nonlinear patterns within the signals. Data partitioning and cross-validation are crucial for assessing model performance and ensuring study comparability, as they can produce varied results and data leakage due to specific signal properties (e.g., biometric). Such variability in model evaluation leads to incomparable studies and, increasingly, overestimated performance claims, which are detrimental to the field. Nevertheless, no comprehensive guidelines for proper data partitioning and cross-validation exist in the domain, nor is there a quantitative evaluation of the impact of different approaches on model accuracy, reliability, and generalizability. To assist researchers in identifying optimal experimental strategies, this paper thoroughly investigates the role of data partitioning and cross-validation in evaluating EEG deep learning models. Five cross-validation settings are compared across three supervised cross-subject classification tasks (brain-computer interfaces, Parkinson's, and Alzheimer's disease classification) and four established architectures of increasing complexity (ShallowConvNet, EEGNet, DeepConvNet, and Temporal-based ResNet). The comparison of over 100,000 trained models underscores, first, the importance of using subject-based cross-validation strategies for evaluating EEG deep learning architectures, except when within-subject analyses are acceptable (e.g., BCI). Second, it highlights the greater reliability of nested approaches (e.g., N-LNSO) compared to non-nested counterparts, which are prone to data leakage and favor larger models overfitting to validation data. In conclusion, this work provides EEG deep learning researchers with an analysis of data partitioning and cross-validation and offers guidelines to avoid data leakage, currently undermining the domain with potentially overestimated performance claims.
