1. A system configured to identify outliers in multiple instances of a pattern of interest on a specimen, comprising: an imaging subsystem comprising at least an energy source and a detector, wherein the energy source is configured to generate energy that is directed to a specimen, and wherein the detector is configured to detect energy from the specimen and to generate images responsive to the detected energy; and one or more computer subsystems configured for: acquiring images generated by the imaging subsystem at multiple instances of a pattern of interest within a die formed on the specimen, wherein the multiple instances comprise two or more instances that are located at aperiodic locations within the die; determining a feature of each of the images generated at the multiple instances of the pattern of interest; and identifying one or more outliers in the multiple instances of the pattern of interest based on the determined features.