Unsupervised Representation Learning of Brain Activity via Bridging Voxel Activity and Functional Connectivity

Effective brain representation learning is a key step toward revealing the understanding of cognitive processes and unlocking detecting and potential therapeutic interventions for neurological diseases/disorders. Existing studies have focused on either (1) voxel-level activity, where only a single beta weight for each voxel (i.e., aggregation of voxel activity over a time window) is considered, missing their temporal dynamics, or (2) functional connectivity of the brain in the level of region of interests, missing voxel-level activities. In this paper, we bridge this gap and design BrainMixer, an unsupervised learning framework that effectively utilizes both functional connectivity and associated time series of voxels to learn voxel-level representation in an unsupervised manner. BrainMixer employs two simple yet effective MLP-based encoders to simultaneously learn the dynamics of voxel-level signals and their functional correlations. To encode voxel activity, BrainMixer fuses information across both time and voxel dimensions via a dynamic self-attention mechanism. To learn the structure of the functional connectivity graph, BrainMixer presents a temporal graph patching and encodes each patch by combining its nodes' features via a new adaptive temporal pooling. Our experiments show that BrainMixer attains outstanding performance and outperforms 13 baselines in different downstream tasks and experimental setups.