Deep Learning Inductive Biases for fMRI Time Series Classification during Resting-state and Movie-watching

Deep learning has advanced fMRI analysis, yet it remains unclear which architectural inductive biases are most effective at capturing functional patterns in human brain activity. This issue is particularly important in small-sample settings, as most datasets fall into this category. We compare models with three major inductive biases in deep learning including convolutional neural networks (CNNs), long short-term memory networks (LSTMs), and Transformers for the task of biological sex classification. These models are evaluated within a unified pipeline using parcellated multivariate fMRI time series from the Human Connectome Project (HCP) 7-Tesla cohort, which includes four resting-state runs and four movie-watching task runs. We assess performance on Whole-brain, subcortex, and 12 functional networks. CNNs consistently achieved the highest discrimination for sex classification in both resting-state and movie-watching, while LSTM and Transformer models underperformed. Network-resolved analyses indicated that the Whole-brain, Default Mode, Cingulo-Opercular, Dorsal Attention, and Frontoparietal networks were the most discriminative. These results were largely similar between resting-state and movie-watching. Our findings indicate that, at this dataset size, discriminative information is carried by local spatial patterns and inter-regional dependencies, favoring convolutional inductive bias. Our study provides insights for selecting deep learning architectures for fMRI time series classification.