Information about the Ph.D. Program

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

The Ph.D. program is for students interested in obtaining academic or research positions in colleges and universities or in government or industrial research laboratories. The program gives students a rigorous and thorough knowledge of a broad range of theoretical and practical research subject areas and develops the ability to recognize and pursue significant research in computer science.

The first two years of graduate study are devoted to coursework. By the end of the second year the research phase of the student’s graduate career should be underway, with participation in advanced study and preliminary research work. The final years of graduate study are devoted to dissertation research. Upon entrance to the program, each student is assigned an academic advisor. Each graduate student seeks a faculty member to serve as a research or dissertation advisor within the first two semesters in the program.



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. The Ph.D. qualifier is based on taking graduate courses from the following four areas – three core areas and one elective area.

Core Area: Theory:

  • CSE 548: Analysis of Algorithms
  • CSE 540: Theory of Computation
  • CSE 541: Logic in Computer Science
  • CSE 547: Discrete Mathematics

Core Area: Software:

  • CSE 504: Compiler Design
  • CSE 526: Principles Programming Languages
  • CSE 532: Theory of Database Systems
  • CSE 537: Artificial Intelligence

Core Area: Systems:

  • CSE 502: Computer Architecture
  • CSE 506: Operating Systems
  • CSE 534: Fundamentals of Computer Networks
  • CSE 528: Computer Graphics 

Elective Area:

  • CSE 527: Introduction to Computer Vision
  • CSE 505: Computing with Logic
  • CSE 535: Asynchronous Systems
  • CSE 508: Network Security
  • CSE 509: Computer System Security
  • CSE 549: Computational Biology
  • CSE 564: Visualization
  • CSE 512: Machine Learning

Ph.D. students must take a total of at least five courses from the above areas. At most one course can be included from the Elective area. At least four courses must be from the Core areas and there must be at least one course from each of the three Core areas. Minimum passing grade for a qualifier course is A-. A student who fails to secure a passing grade will have to take another course not taken before, in the following semester. All qualifier courses must be completed within the first three semesters. We recommend students take at least two courses per semester, because most graduate courses are offered only once a year. No course substitutions, exchanges, or pleas for better grades will be accepted.

The makeup of the qualifier course groups and courses has been carefully chosen to balance breadth and depth.


To further ensure the breadth preparation, the Ph.D. students must satisfy a set of proficiency requirements.

This requirement must be satisfied before the student takes the RPE. See the Graduate Program Handbook for more details.


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 GPAs.
  • Progress in proficiency requirements.
  • Performance as Teaching Assistant.
  • Research productivity: publications, talks, software, systems, etc.
  • Faculty input, especially from advisers.
  • 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. program for one more semester.
  • 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 wish to get into the Ph.D. program may take the same qual courses as Ph.D. students take, and are expected to get a qual passing grade of A- or better in those. MS students are also expected to secure an adviser who will fund them if they get admitted into the Ph.D. program.

However, admission to the Ph.D. program is no longer automatic: MS students must apply formally through the graduate school. 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.