We introduce GlassMLP, a machine learning framework using physics-inspired structural input to predict the long-time dynamics in deeply supercooled liquids. We apply this deep neural network to atomistic models in 2D and 3D. Its performance is better than the state of the art while being more parsimonious in terms of training data and fitting parameters. GlassMLP quantitatively predicts four-point dynamic correlations and the geometry of dynamic heterogeneity. Transferability across system sizes allows us to efficiently probe the temperature evolution of spatial dynamic correlations, revealing a profound change with temperature in the geometry of rearranging regions.