Traditionally, chemistry problems are solved by means of a deductive approach. The question to be addressed is typically related to the value of a property that is either measured experimentally, computed using quantum-chemistry software, or (more recently) predicted using a machine-learned model. In this paper, we demonstrate that an inductive approach can be adopted using End-to-End (E2E) machine learning. This approach is illustrated for tackling the following chemistry problems: (i) determine the fully coordinated (FC) and undercoordinated (UC) atoms in a molecule with one missing atom, (ii) identify the type of atom that is missing in such an incomplete molecule, and (iii) predict the direction of a reaction between two molecules according to an existing dataset. The E2E approach leads to accuracies higher than 99%, 98%, and 93% for these three problems, respectively. Finally, in order to achieve such accuracies, a descriptor for the molecules, called bag of clusters, is introduced and compared with a series previously proposed descriptors, highlighting a series of advantages.