Deep learning-based embedding of functional connectivity profiles for precision functional mapping

Spatial similarity of functional connectivity profiles across matching anatomical locations in individuals is often calculated to delineate individual differences in functional networks. Likewise, spatial similarity is assessed across average functional connectivity profiles of groups to evaluate the maturity of functional networks during development. Despite its widespread use, spatial similarity is limited to comparing two samples at a time. In this study, we employed a variational autoencoder to embed functional connectivity profiles from various anatomical locations, individuals, and group averages for simultaneous comparison. We demonstrate that our variational autoencoder, with pre-trained weights, can project new functional connectivity profiles from the vertex space to a latent space with as few as two dimensions, yet still retain meaningful global and local structures in the data. Functional connectivity profiles from various functional networks occupy distinct compartments of the latent space. Moreover, the variability of functional connectivity profiles from the same anatomical location is readily captured in the latent space. We believe that this approach could be useful for visualization and exploratory analyses in precision functional mapping.