BCB Qualifying Exam

The Bioinformatics and Computational Biology (BCB) Group at UIUC Computer Science is led by Professors Mohammed El-Kebir, Ge Liu, and Tandy Warnow, who comprise the Core Faculty. The group also includes other faculty (e.g., Nancy Amato, Jiawei Han, Olgica Milenkovic, and ChengXiang Zhai) with primary or affiliate positions in Computer Science who have active research in bioinformatics and computational biology. The area chair is Tandy Warnow.

The BCB qualifying exam supports the research of students whose advisors are BCB faculty, which includes the primary and secondary faculty. The BCB qualifying exam has a coursework requirement (see bottom of page) and otherwise consists of two components: (1) a written research paper suitable for submission to a journal or conference (written entirely by the student) and (2) a 90-minute oral exam, in which the student presents his or her own research and one assigned paper to a committee of three professors. The student’s presentation serves as a starting point for questions from the committee, which generally will focus on the presented material but could range more broadly. The exam is structured to ensure that students are evaluated in a consistent manner and serves multiple purposes:

  • Learning: Encourage students to study fundamental background topics. Time spent in preparation should be a good investment for research success.
  • Diagnostic: Identify deficiencies in a student’s knowledge or abilities that can be corrected to improve chances for a successful dissertation and career. The student receives clear and actionable feedback, including areas to focus development and, if applicable, the main reason(s) for failure.
  • Qualification: Identify students that are unlikely to succeed in the program. This is mainly a consideration if there is a retake of the exam, in which a pass is required.

Formation of Committee

  • The student’s advisor will not be a member of the committee, but will be a member of the BCB faculty.
  • The default committee will contain three BCB faculty, at least one of whom is core BCB faculty. However, the objective is that at least one faculty member is familiar enough with the candidate’s general research area to ask in-depth questions about the research. If no one meeting that criterion (other than the advisor) is a member of the BCB faculty then a CS department faculty member from outside the BCB faculty should be recruited, with the help of the student’s advisor.
  • Committee selection must be approved by the BCB area chair.

Selection of Paper for Oral Exam

Each student must pick one paper from a short list of 3–5 papers sent in advance by the qualifying exam committee chair. The papers in the list are chosen to so as to satisfy one or both of the following criteria: (a) to be understandable by a student who has completed CS 581 and CS 582 and (b) to be in or close to the research field of the candidate (e.g., protein function prediction methods for someone who studies systems biology) and accessible to examiners from other research areas. The paper list is  created in consultation with the advisor and other faculty in the BCB area.

Process

  • At least 60 days before the exam: The student sends a 1-2 page abstract of their research paper to the area chair, along with the student’s CV. The C.V. will provide academic background and publications to date, including papers in submission and in preparation. We note that this could be done at the same time as the submission of the qual statement to the department (i.e., much earlier).
  • At least 42 days before the exam: The committee is assembled by the area chair and communicated to the student. The committee will include a designated chair.
  • At least 28 days before the exam: The student sends the research paper (at least 6 pages, not counting figures and bibliography) to the committee chair. The research can be collaborative, but the student is required to write this paper on their own.
  • At least 21 days before the exam: The committee chair sends a list of 3–5 papers to the student, for the student to select from.
  • At least 14 days before the exam: The student communicates the choice of paper for the qualifying exam to the committee chair, who then communicates this to the rest of the committee.

Exam Format

The following is the recommended timeline for the exam. Examiners should do their best to adhere to the time guidelines to prevent the exam from getting off track. The student should bring slides on his or her own laptop. Note that the student has the option of the order of the presentations (i.e., their research paper can be presented before or after the committee-selected paper).

  1. Introduce self and background (5 min)
  2. Presentation of student’s research paper (20 min prepared, 20-30 minutes Q&A, 40 -50 min total). Include motivation for research, summary of state of the art, major challenges, key ideas of proposed or in-progress work, and method for evaluation. During this portion of the exam, the committee should aim to evaluate whether the candidate understands and can explain the motivation, significance, and technical background of his or her research ideas. This portion of the exam should end 45 to 55 minutes after the start of the exam.
  3. Presentation of committee-selected paper (10 min prepared, 10-20 minutes Q&A, 20 -30 min total). The presentation should explain the significance of the paper’s contributions (considering prior art), walk through key technical components and experiments, and critically evaluate the paper. During this portion of the exam, the committee should aim to evaluate the candidate’s analytical ability and technical understanding. This portion of the exam should end 65 to 85 minutes after the start of the exam.
  4. Further questions (15 min). Examiners can ask general knowledge questions, or re-examine topics from the research or paper presentation. Generally the questions should be at a level that one would expect most 2nd year PhD students in BCB to know the answer. Any single line of questions should be curtailed if the student is stuck.

Evaluation

The committee will determine the outcome (pass, conditional pass, or failure), and provide detailed feedback on the following aspects:

  • Knowledge of the topic of presentation
  • Knowledge of areas closely related to the primary area of interest
  • Oral communication
  • Written communication (based on the research paper sent to committee ahead of exam)

Coursework requirement

The student must have met the following coursework-related requirements to pass the BCB qualifying exam. (Concurrent enrollment is permitted during the qualifying exam, in which case the student may receive a conditional pass with the requirement to complete the course requirement.)

  1. The student must take CS 581 and CS 582 (previously CS 598-Advance Bioinformatics), with a minimum grade of B+ in each. If 581 or 582 is not taught in the academic year that the qualifying exam is taken, then a substitution may be proposed. Specifically, CS 581 can be replaced by a 500-level course taught by either Professors El-Kebir or Warnow, and CS 582 can be replaced by a 500-level course in machine learning or statistics (taught within the CS department or the Statistics department). A proposal for a substitution of 581 or 582 by another course must be made by the end of the semester preceding the qualifying exam, and will be considered by the BCB core faculty, with a decision communicated within two weeks. If the substitution is not permitted, alternatives will be presented, including delaying taking the required course until the following year.
  2. The student must take one 400- or 500-level course in probability, statistics, machine learning, algorithms, or any topic directly relevant to their research, approved as such by their program of study committee. The should earn a minimum grade of B+ in this course.