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.

The last decade has witnessed a notable surge in deep learning applications for electroencephalography (EEG) data analysis, showing promising improvements over conventional statistical techniques. However, deep learning models can underperform if trained with bad processed data. Preprocessing is crucial for EEG data analysis, yet there is no consensus on the optimal strategies in deep learning scenarios, leading to uncertainty about the extent of preprocessing required for optimal results. This study is the first to thoroughly investigate the effects of EEG preprocessing in deep learning applications, drafting guidelines for future research. It evaluates the effects of varying preprocessing levels, from raw and minimally filtered data to complex pipelines with automated artifact removal algorithms. Six classification tasks (eye blinking, motor imagery, Parkinson’s, Alzheimer’s disease, sleep deprivation, and first episode psychosis) and four established EEG architectures were considered for the evaluation. The analysis of 4800 trained models revealed statistical differences between preprocessing pipelines at the intra-task level for each model and at the inter-task level for the largest model. Models trained on raw data consistently performed poorly, always ranking last in average scores. In addition, models seem to benefit more from minimal pipelines without artifact handling methods. These findings suggest that EEG artifacts may affect the performance and generalizability of deep neural networks.

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.

In recent years, deep learning has revolutionized machine learning and its applications, producing results comparable to human experts in several domains, including neuroscience. Each year, hundreds of scientific publications present applications of deep neural networks for biomedical data analysis. Due to the fast growth of the domain, it could be a complicated and extremely time-consuming task for worldwide researchers to have a clear perspective of the most recent and advanced software libraries. This work contributes to clarifying the current situation in the domain, outlining the most useful libraries that implement and facilitate deep learning applications for neuroscience, allowing scientists to identify the most suitable options for their research or clinical projects. This paper summarizes the main developments in deep learning and their relevance to neuroscience; it then reviews neuroinformatic toolboxes and libraries collected from the literature and from specific hubs of software projects oriented to neuroscience research. The selected tools are presented in tables detailing key features grouped by the domain of application (e.g., data type, neuroscience area, task), model engineering (e.g., programming language, model customization), and technological aspect (e.g., interface, code source). The results show that, among a high number of available software tools, several libraries stand out in terms of functionalities for neuroscience applications. The aggregation and discussion of this information can help the neuroscience community to develop their research projects more efficiently and quickly, both by means of readily available tools and by knowing which modules may be improved, connected, or added.