Information about the Ph.D. Program

This page provides detailed information regarding the Ph.D. Qualifier System and Research Proficiency Exam at Stony Brook University's Department of Computer Science. The information here is intended to be read in conjunction with the Graduate Program Handbook.



The purpose of Ph.D. qualifier is to ensure that the student has acquired an appropriate breadth in major computer science areas relevant to his/her research interest. To meet the qualifier requirement, Ph.D. students must pass a total of five graduate courses with a grade of A- or better, with the following two conditions:

1. At least 4 courses from the list below, covering at least 3 areas:


  • CSE 512: Machine Learning
  • CSE 526: Principles of Programming Languages
  • CSE 540: Theory of Computation
  • CSE 541: Logic in Computer Science
  • CSE 547: Discrete Mathematics
  • CSE 548: Analysis of Algorithms
  • CSE 549: Computational Biology


  • CSE 502: Computer Architecture
  • CSE 504: Compiler Design
  • CSE 506: Operating Systems
  • CSE 508: Network Security
  • CSE 509: Computer System Security
  • CSE 532: Theory of Database Systems
  • CSE 534: Fundamentals of Computer Networks
  • CSE 535: Distributed Systems

Information and Intelligent Systems:

  • CSE 505: Computing with Logic
  • CSE 519: Data Science Fundamentals
  • CSE 527: Introduction to Computer Vision
  • CSE 528: Computer Graphics
  • CSE 537: Artificial Intelligence
  • CSE 564: Visualization
  • CSE 628: Natural Language Processing

2. One non-generic graduate lecture course, more specifically:

  • Any CSE 5xx course except: CSE 500, 522, 523, 524, 587, 590--599.
  • Any course from the set CSE 601--638 
    All qualifier courses must be completed within two years after joining the program as a full-time Ph.D. student. We recommend students take at least two courses per semester because many graduate courses are offered only once a year. 


All Ph.D. students who have not yet met qualifier requirements and passed their RPEs, or who do not have an advisor, will be reviewed each semester, in periodic Research Assessment Meetings. This review is conducted by the entire faculty, who votes on the future status of each student. This review is comprehensive, and includes at least the following items (in no particular order):

  • Qualifier courses taken and passed with A- or better.
  • All other courses taken, grades received, and GPA.
  • Performance as Teaching Assistant.
  • Research productivity: publications, talks, software, systems, etc.
  • Faculty input, especially from advisors.
  • Student´s own input.
  • Cumulative history of the student's progress.

The outcome of the review will be a formal letter given to the student and placed in the student´s folder. A student can be placed in one of two categories:

  • In Good Standing: The student has performed well in the previous semester and may continue in the Ph.D. progra.
  • Not in Good Standing: The student had not performed sufficiently well in the previous semester. The student may be placed under probation for one more semester, may lose RA/GA/TA funding, may lose an advisor, or may even be dismissed from the program immediately. Being under probation for two consecutive semesters will likely lead to dismissal.

In addition to the outcome, the assessment letter may also make specific recommendations to the student, as to what will be expected of the student in the following semester (e.g., pass 2 more qualifier courses, pass the RPE, etc.).


Upon entrance to the program, each student is assigned an academic advisor. Each Ph.D. student should seek a faculty member to serve as a research or dissertation advisor within the first two semesters in the program. The choice may be changed. However, each change of advisor may delay a student´s progress. A research advisor is invaluable when it comes to issues such as financial support and progress through various examinations. Most faculty members have research groups, meetings and seminars by which a new student can become acquainted with the research being conducted in the Department. Please refer to the Graduate Program Handbook for the specific rules on choosing or changing an advisor.


MS students who want to be considered for admission to the Ph.D. program should contact CS Graduate Admissions for the application process.  They will be usually required to submit a new Personal Statement and update their resume and recommendation letters.  The Graduate Admissions Committee will endeavor to process such special MS-to-PhD requests very quickly. Generally speaking, MS students who passed their Ph.D. qualifying courses and have a strong letter from a funding adviser will have good chances of getting admitted into the Ph.D. program.