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.

SelfEEG is an open-source Python library developed to assist researchers in conducting Self-Supervised Learning (SSL) experiments on electroencephalography (EEG) data. Its primary objective is to offer a user-friendly but highly customizable environment, enabling users to efficiently design and execute self-supervised learning tasks on EEG data.

Objective. This work presents xEEGNet, a novel, compact, and explainable neural network for electroencephalography (EEG) data analysis. It is fully interpretable and reduces overfitting through a major parameter reduction. Approach. As an applicative use case to develop our model, we focused on the classification of common dementia conditions, Alzheimer’s and frontotemporal dementia, versus controls. xEEGNet, however, is broadly applicable to other neurological conditions involving spectral alterations. We used ShallowNet, a simple and popular model in the EEGNet family, as a starting point. Its structure was analyzed and gradually modified to move from a ‘black box’ model to a more transparent one, without compromising performance. The learned kernels and weights were analyzed from a clinical standpoint to assess their medical significance. Model variants, including ShallowNet and the final xEEGNet, were evaluated using a robust nested-leave-n-subjects out cross-validation for unbiased performance estimates. Variability across data splits was explained using the embedded EEG representations, grouped by class and set, with pairwise separability to quantify group distinction. Overfitting was measured through training-validation loss correlation and training speed. Main results. xEEGNet uses only 168 parameters, 200 times fewer than ShallowNet, yet retains interpretability, resists overfitting, achieves comparable median performance (−1.5%), and reduces performance variability across splits. This variability is explained by the embedded EEG representations: higher accuracy correlates with greater separation between test-set controls and Alzheimer’s cases, without significant influence from the training data. Significance. The capability of xEEGNet to filter specific EEG bands, learns band specific topographies and use the right EEG spectral bands for disease classification demonstrates its interpretability. While big deep learning models are typically prioritized for performance, this study shows that smaller architectures like xEEGNet can be equally effective in pathology classification, using EEG data.

Objective. This study aims to address the challenges associated with data-driven electroencephalography (EEG) data analysis by introducing a standardised library called BIDSAlign. This library efficiently processes and merges heterogeneous EEG datasets from different sources into a common standard template. The goal of this work is to create an environment that allows to preprocess public datasets in order to provide data for the effective training of deep learning (DL) architectures. Approach. The library can handle both Brain Imaging Data Structure (BIDS) and non-BIDS datasets, allowing the user to easily preprocess multiple public datasets. It unifies the EEG recordings acquired with different settings by defining a common pipeline and a specified channel template. An array of visualisation functions is provided inside the library, together with a user-friendly graphical user interface to assist non-expert users throughout the workflow. Main results. BIDSAlign enables the effective use of public EEG datasets, providing valuable medical insights, even for non-experts in the field. Results from applying the library to datasets from OpenNeuro demonstrate its ability to extract significant medical knowledge through an end-to-end workflow, facilitating group analysis, visual comparison and statistical testing. Significance. BIDSAlign solves the lack of large EEG datasets by aligning multiple datasets to a standard template. This unlocks the potential of public EEG data for training DL models. It paves the way to promising contributions based on DL to clinical and non-clinical EEG research, offering insights that can inform neurological disease diagnosis and treatment strategies.

Electroencephalography (EEG) is an important noninvasive diagnostic tool for detecting neurodegenerative disorders. In this context, EEG-based deep learning models show promise due to their ability to capture nonlinear brain dynamics but often suffer from poor generalizability caused by high inter-subject variability. Self-supervised learning (SSL) offers a promising solution by enabling models to learn robust representations from large unlabeled datasets. This study introduces a double-masking representation learning framework for EEG analysis. Using data aggregated from eight multi-center datasets (3156 subjects; 439 h of EEG recordings), a hybrid convolutional-transformer model (TransformEEG) is pretrained to enhance generalization in neurodegenerative disease classification, focusing on Parkinson’s and Alzheimer’s diseases. This approach combines phase-swap data augmentation, designed to facilitate the learning of EEG phase-amplitude coupling, with a double-masking function that operates at both the signal and the transformer’s token levels. The pretrained model was evaluated against a fully supervised baseline using Monte Carlo cross-validation with 100 splits across three public pathology detection datasets. Pretraining led to consistent improvements in both median balanced accuracy and Inter-Quartile Range (IQR) across all fine-tuning datasets. Compared to the fully supervised baseline, the proposed approach increases median balanced accuracy by 2.8% for Parkinson’s disease detection and by 4.2% for Alzheimer’s disease detection, while also reducing performance variability across 100 Monte Carlo splits. These results demonstrate that SSL can enhance EEG deep learning performance, though achieving robust generalization in clinical applications remains an open research challenge.