Explicit representation of molecular shape of molecules is combined with neural network learning methods to provide models with high predictive ability that generalize to different chemical classes where structurally diverse molecules exhibiting similar surface characteristics are treated as similar. A new machine-learning methodology is disclosed that can accept multiple representations of objects and construct models that predict characteristics of those objects. An extension of this methodology can be applied in cases where the representations of the objects are determined by a set of adjustable parameters. An iterative process applies intermediate models to generate new representations of the objects by adjusting said parameters and repeatedly. retrains the models to obtain better predictive models. This method can be applied to molecules because each molecule can have many orientations and conformations (representations) that are determined by a set of translation, rotation and torsion angle parameters.