Inferring continuous cognitive traits from limited neuroimaging data using pairwise convolutional neural networks

Individual differences in cognitive abilities vary widely, yet the structural brain features supporting these differences remain poorly understood. Traditional brain-behavior analyses rely on predefined metrics such as volume or cortical thickness and typically assume linear relationships with behavior, limiting sensitivity in small datasets. Here, we introduce a pairwise convolutional ranking framework that learns directly from whole-brain T1-weighted MRI by making comparative rather than absolute predictions, which performs well even with small samples (N=108). We tested this method with four small-scale spatial abilities tasks. Regression analysis predicted performance with high accuracy across all tasks, achieving greater predictive power over standard regression and pointwise deep learning baselines. Iterative cortical-region removal (backward elimination) revealed brain regions supporting individual performance common to all four tasks, as well as task-specific regions. These results demonstrate that pairwise learning extracts meaningful behavioral information from structural MRI, providing prediction and interpretable insight into the neuroanatomy of individual differences.