Abstract: Example molecular embedding systems and methods are described. In one implementation, a system includes a molecular embedder configured to receive structural and chemical information associated with a single-molecule ingredient from a plurality of single-molecule ingredients. The molecular embedder also generates a representation of the single-molecule ingredient. A preparation modeler receives multiple representations of single-molecule ingredients and preparation instructions. The molecular embedder generates a representation of the prepared ingredients. A predictor receives a representation of the prepared ingredients and generates predicted characteristics of the prepared ingredients.