A Hierarchical Tokenization Framework for Voxel-Level fMRI Representation Learning

Karanpartap Singh, Yue Zhao, Mohammad H. Abbasi, Ehsan Adeli

We introduce HBAR (Hierarchical Brain Activity Representation), a hierarchical tokenization framework for learning compact, multi-scale representations of neuroimaging data. HBAR organizes voxel-level resting-state fMRI into a hierarchy spanning sub-parcel voxel groups, parcels, and large-scale functional networks, enabling up to 415x compression while preserving fine-grained spatial information beyond conventional parcellation. The framework supports fixed atlas-based, fully learned, and softly prior-guided hierarchies, allowing us to systematically study the role of structured priors in brain representation learning. On HCP-YA, at approximately 415x compression, HBAR achieves higher parcel and network correlations than rate-matched flat tokenizers, while at a lower 52x compression rate, shuffling the anatomical grouping reduces parcel correlation from 0.920 to 0.886. Demographic readouts with autoregressive training also reveal potential gains from the hierarchical structure. By combining sub-parcel inputs, compact discrete tokens, and multiscale brain structure, HBAR offers a practical framework for representation learning in high-dimensional neuroimaging data.