A method including: obtaining a characteristic of a portion of a design layout; determining a characteristic of M3D of a patterning device including or forming the portion; and training, by a computer, a neural network using training data including a sample whose feature vector includes the characteristic of the portion and whose supervisory signal includes the characteristic of the M3D. Also disclosed is a method including: obtaining a characteristic of a portion of a design layout; obtaining a characteristic of a lithographic process that uses a patterning device including or forming the portion; determining a characteristic of a result of the lithographic process; training, by a computer, a neural network using training data including a sample whose feature vector includes the characteristic of the portion and the characteristic of the lithographic process, and whose supervisory signal includes the characteristic of the result.