Identifying Neural Signatures from fMRI using Hybrid Principal Components Regression

Abstract: Recent advances in neuroimaging analysis have enabled accurate decoding of mental state from brain activation patterns during functional magnetic resonance imaging scans. A commonly applied tool for this purpose is principal components regression regularized with the least absolute shrinkage and selection operator (LASSO PCR), a type of multi-voxel pattern analysis (MVPA). This model presumes that all components are equally likely to harbor relevant information, when in fact the task-related signal may be concentrated in specific components. In such cases, the model will fail to select the optimal set of principal components that maximizes the total signal relevant to the cognitive process under study. Here, we present modifications to LASSO PCR that allow for a regularization penalty tied directly to the index of the principal component, reflecting a prior belief that task-relevant signal is more likely to be concentrated in components explaining greater variance. Additionally, we propose a novel hybrid method, Joint Sparsity-Ranked LASSO (JSRL), which integrates component-level and voxel-level activity under an information parity framework and imposes ranked sparsity to guide component selection. We apply the models to brain activation during risk taking, monetary incentive, and emotion regulation tasks. Results demonstrate that incorporating sparsity ranking into LASSO PCR produces models with enhanced classification performance, with JSRL achieving up to 51.7\% improvement in cross-validated deviance $R^2$ and 7.3\% improvement in cross-validated AUC. Furthermore, sparsity-ranked models perform as well as or better than standard LASSO PCR approaches across all classification tasks and allocate predictive weight to brain regions consistent with their established functional roles, offering a robust alternative for MVPA.