A system for using a smartpen as a tool for automatically assessing student learning that is simple and accurate. The system has a computer with at least one processor, a memory, a storage, and communications through a protocol, one or more than one smartpen in communication with the computer and a plurality of software modules having non-transitory instructions executable on the processor for at least a characterization module, for characterizing spatial and temporal organization of a student's work, and a machine learning module utilizing the spatial and temporal organization to assess student learning.