The More, the Better? Evaluating the Role of EEG Preprocessing for Deep Learning Applications

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.