Integrating across neuroimaging modalities boosts prediction accuracy of cognitive ability

Variation in cognitive ability arises from subtle differences in underlying neural architectural properties. Understanding and predicting individual variability in cognition from the differences in brain networks requires harnessing the unique variance captured by different neuroimaging modalities. Here we adopted a multi-level machine learning approach that combines diffusion, functional, and structural MRI data from the Human Connectome Project (N=1050) to provide unitary prediction models of various cognitive abilities: global cognitive function, fluid intelligence, crystallized intelligence, impulsivity, spatial orientation, verbal episodic memory and sustained attention. Out-of-sample predictions of each cognitive score were first generated using a sparsity-constrained principal component regression on individual neuroimaging modalities. These individual predictions were then aggregated and submitted to a LASSO estimator that removed redundant variability across channels. This stacked prediction led to a significant improvement in accuracy, relative to the best single modality predictions (approximately 1% to 4% boost in variance explained), across a majority of the cognitive abilities tested. Further analysis found that diffusion and brain surface properties contribute the most to the predictive power. Our findings establish a lower bound to predict individual differences in cognition using multiple neuroimaging measures of brain architecture, both structural and functional, quantify the relative predictive power of the different imaging modalities, and reveal how each modality provides unique and complementary information about individual differences in cognitive function. Author summary Cognition is a complex and interconnected process whose underlying mechanisms are still unclear. In order to unravel this question, studies usually look at one neuroimaging modality (e.g. functional MRI) and associate the observed brain properties with individual differences in cognitive performance. However, this approach is limiting because it fails to incorporate other sources of brain information and does not generalize well to new data. Here we tackled both problems by using out-of-sample testing and a multi-level learning approach that can efficiently integrate across simultaneous brain measurements. We tested this scenario by evaluating individual differences across several cognitive domains, using five measures that represent morphological, functional and structural aspects of the brain network architecture. We predicted individual cognitive differences using each brain property group separately and then stacked these predictions, forming a new matrix with as many columns as separate brain measurements, that was then fit using a regularized regression model that isolated unique information among modalities and substantially helped enhance prediction accuracy across most of the cognitive domains. This holistic approach provides a framework for capturing non-redundant variability across different imaging modalities, opening a window to easily incorporate more sources of brain information to further understand cognitive function.