The graduate program of a thesis route candidate is largely set by the supervisor upon admission, with the exception of Comp690A/B (Research Methods in Computer Science), which is required for all Master students in the thesis route.

The student will take a mix of courses from Computer Science and other disciplines closely related to the research program of the student. The program requires 15 credit-hours (or five courses of three credit-hours each). From those, nine credit-hours (or three three-credit-hour courses) are courses offered by the Computer Science department, and six credit hours (or two three-credi-hour courses) are either courses offered by the Computer Science department or courses selected from the list of CS-approved electives.