Our observations were largely explained by a replicate model of the latent space based on perturbational updates that integrate neighborhood chemical compositions in layers. This perturbational model relates the structure of the latent space to chemical composition. We showed how such a model can explain the approximately constant reaction vectors. We then showed how linear analogies in the latent space carry over to chemical properties such as NMR and atomization energies. In other words, the integrity of linear analogies lies beyond just the latent space and can be used to explain quasi linear changes in chemical properties, such as constant NMR shifts, and near-constant changes in atomization energies.