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

Effective brain representation learning is a key step toward the understanding of cognitive processes and diagnosis of neurological diseases/disorders. Existing studies have focused on either (1) voxel-level activity, where only a single weight relating the voxel activity to the task (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. 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 attention mechanism. To learn the structure of the functional connectivity, 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 14 baselines in different downstream tasks and setups.