Biomedical Informatics–  

The PhD Degree Requirements

This page is divided into several major sections. Click on the links in the Table of Contents to jump to each section.

Table of Contents

  1. The Qualifying Exam
  2. PhD Candidacy
  3. The Pre-Proposal
  4. The Reading Committee
  5. Alumni Photo
  6. The University Oral Defense
  7. Preparation of the Dissertation/Thesis

Qualifying Exam Process

Prior to being formally admitted to candidacy for the Ph.D. degree, the student must demonstrate knowledge of biomedical informatics fundamentals and a potential for research by passing a qualifying exam. The "quals" are taken after completing all of the BMI core curriculum, and no later than the October of the third year. MS students do not take the qualifying exam.

Purpose of the Exam: The PhD Qualifying Exam has several goals.

  1. To motivate students to review and synthesize course work and research material
  2. To determine the student's ability to understand and apply fundamental concepts
  3. To develop and test the student's ability to communicate orally and to respond to questions and comments
  4. To evaluate the student's potential to pursue doctoral research
  5. To identify areas that need to be strengthened for the student to be successful as a PhD student, independent scholar, and teacher.
  6. To provide a mechanism for a range of faculty to come to know the student's capabilities.

Procedure for the Exam

The procedure for the exam consists of six steps.

I) An Academic Council Member affiliated with the BMI program must be willing to supervise the student's PhD program and dissertation. The decision by the faculty member (Research Advisor) to supervise the student's program and dissertation is based on the potential of the student to become an independent scholar, and is based on many factors, such as the student's undergraduate and graduate course record, graduate record exam scores, and research, teaching and professional experience. The most important factor is the direct knowledge the faculty sponsor has obtained of the student's capabilities (e.g., as acquired through supervising the student in a project course, independent study, or as Research Assistant). The student must have a graduate Stanford GPA of 3.0 to be eligible for the exam. Students are encouraged to take the exam by October of their third year at the latest, and to work together to prepare for the exam. Students may ask to see examples of Quals folders from previous years. See the Student Services Officer.

2) Once the student has identified the time period in which he or she wishes to take the Quals Exam and has informed the Student Services Officer, the student must propose his/her 4 topic/depth areas, including an expanded syllabus for each topic area. The ontology of topic areas is accessible through the BMI student wiki. The student will submit the list of topic areas to the Student Services Officer, who will forward the list to the BMI Exec Committee for feedback. Once the student has worked with the BMI Exec to finalize the list of topic areas, the student may submit the Pre-Quals folder. The folder must be submitted in pdf format to the Student Services Officer and the Research Advisor no later than 2 weeks before the scheduled Pre-Quals meeting (see #3).

The folder should contain the following, in any order:

  1. Updated transcripts of all undergraduate and graduate course work
  2. Updated and completed BMI flowsheet
  3. Curriculum vitae
  4. Calculation showing the student's GPA for courses taken at Stanford.
  5. Research project abstract «300words). This abstract should be written by the student and represent the topic on which the student would lecture if asked (see below)
  6. Preliminary dissertation proposal (one page). Knowledge and work of the student, and/or others, should be synthesized to present a rationale for the proposed dissertation topic (e.g., theory to be developed, hypotheses to be tested) as well as proposed methodology to fulfill the dissertation objective.
  7. A list of four independent areas in which the student feels he/she has depth. One of these areas must come from a fundamental informatics topic (see Appendix B with listing). A second area should be from a biological or medical specialty (see appendix with listing). The other two areas may come from any medical, biological, informatics, biocomputation, bioengineering, or other topics that lead to a cohesive program of graduate study (see appendix with listing). Students should discuss these areas with their advisor in the process of planning their graduate program and prior to preparation of their application folder
  8. Include 4 faculty names likely to be on your committee, based on your current research topic. (They need not be invited to join your committee at this point, since Exec approval is needed before the committee is finalized around the 3rd year.)
  9. All completed TA evaluations, if applicable

3) The student's faculty advisor will be invited to a BMI Exec Meeting when the student's application for the quaIs is complete. The advisor will present the student's Quals Exam folder to the BMI exec and give a frank appraisal of the student's readiness for the exam. The Exec will evaluate the student's research progress, depth areas, coursework, etc. The student will not be present at the meeting.

4) The BMI faculty will then determine if the student should be offered the PhD Qualifying Examination. If the student is not offered the exam, a designated faculty member will convey to the student the reasons for the faculty's decision. If the student is offered the exam, the BMI executive committee will appoint a subcommittee with three or four members, to cover the depth areas and research area proposed by the student. The BMI executive committee will designate one member of the committee as chair. The student's research advisor will usually be included on this committee as well. The student will work with the BMI student services officer to schedule the date of the qualifying exam. Students should not schedule personal vacation until AFTER the Quals date has been set or the student could be asked to reschedule the vacation.

5) Beyond the quals folder, the subcommittee needs to obtain additional information regarding the student's potential to become an independent scholar. To accomplish this objective, the student will present to the subcommittee a 15-minute technical lecture on the topic contained in the abstract (see #2e).

  1. One week prior to the lecture, the student will give each subcommittee member a one page "reminder" containing the short abstract of the lecture, and the time and place of the lecture.
  2. The two-hour time-slot and the place of the lecture and questioning will be arranged by the Student Services Officer with consent of all subcommittee members.
  3. This lecture, followed by a short question/answer session, will be open to all faculty and students.
  4. Afterwards, in a closed session (up to 1.5 hrs.) the student will answer additional questions regarding the topic presented at the lecture, the four areas chosen by the student (see #2g), the preliminary dissertation proposal (see #2f), or other related topics.
  5. Generally, the research advisor is encouraged to allow the student to answer independently during the questioning by the other members of the committee, and not act as an advocate or interpreter. Of the four subcommittee members, the research advisor will be the final one to examine the student.
  6. At the conclusion of questioning, the subcommittee will deliberate on all the information it has acquired (from the preliminary evaluation by all faculty of the contents of the quals folder, from the 15 minute lecture and the question/answer session both open and closed) and will decide on a recommendation of pass, conditional pass, or fail (see #6 below).
  7. This recommendation will be communicated to the student. All members of the committee, including the advisor will participate in the deliberation and vote.
  8. The Quals Exam form should be completed during the Exam.

6) At the next meeting of the BMI executive committee, the Chair, after commenting on the additional information obtained at the student's technical lecture and during the closed-session question and answer period, will convey to the faculty their recommendation.

Academic council members of the BMI exec, after consideration of the subcommittee's recommendation, will decide if the student has passed the PhD qualifying examination. (A majority vote of the faculty is needed to carry any recommendation, with no less than three total votes).

Possible outcomes are that the student:

  1. passes unconditionally;
  2. passes conditionally; In this case, the faculty will outline the weaknesses and the conditions the student must fulfill before reconsideration (e.g., specific courses must be taken with performance at a specified level; communication skills need to be improved as evidenced by...). With the Chair's endorsement, the student will later request a change from "conditional pass" to "pass" after he/she believes that the conditions have been fulfilled. The student will outline in this request the reasons for this belief. The faculty will meet again to act on the request.
  3. fails, with or without option to retake.

7) The Chair will notify the student and the Student Services Office of the results of the examination.

PhD Candidacy

After passing the Qualifying Exam, students must submit the required PhD Candidacy form to Student Services Officer. Admission to candidacy signifies that the department considers the student capable of completing the requirements necessary for earning a Ph.D. degree. Candidacy is valid for five calendar years (through the end of the quarter in which candidacy expires), unless terminated by the department for unsatisfactory progress. An extension of candidacy may be obtained for a maximum of one additional year.

Pre-Proposal

The pre-proposal is a practice talk introducing research that may form the basis of the PhD work. The pre-proposal is generally scheduled during the Tuesday talk schedule about 6 months following the QuaIs Exam. The student should invite those faculty members who he or she is planning to have as readers of the dissertation. It is the student's responsibility to invite relevant and interested faculty members to the pre-proposal. The faculty in attendance will complete a feedback form which critiques the student's research proposal, presentation style, and provide suggestions. The Student Services Officer will provide the forms and the student should retain copies of the complete forms and return the originals to Student Services Officer.

Reading Committee

Each Ph.D. candidate is required to establish a reading committee for the doctoral dissertation late 3rd year/early 4th year. The student should consult frequently with all members of the committee about the direction and progress of the dissertation research and is required to meet annually with their committee. Students must have at least three faculty members: the principal dissertation advisor and two other readers serve on their Doctoral Dissertation Reading Committee who read and certify their dissertation. At least two members must be on the Stanford Academic Council. The Doctoral Dissertation Reading Committee Form is to be completed and filed with the Student Service Office before scheduling a University oral examination that is a defense of the dissertation. On occasion, the department chair, may in some cases, approve the appointment of a reader who is not on the Academic Council, if that person is particularly well qualified to consult on the dissertation topic and holds a Ph.D. or equivalent foreign degree. Request approval by filing a Petition for Doctoral Committee Form.

Alumni Photo

To avoid last minute pressure and scheduling difficulties. we request PhD students have their photograph taken (for the graduate photo wall in X275) before they hold the oral defense of their proposal. See Mary Jeanne Oliva for more information; the BMI program will pay for the photographs.

The University Orals Defense

Approximately, six months before the anticipated completion of your thesis/dissertation, you will need to schedule your oral defense. The six months allows you time to incorporate feedback from the Orals Examination Committee.

To schedule your Orals defense, you must complete these steps in this approximate order:

  1. Identify your Orals Examination Committee (at least 2-3 months before your Oral Exam)
  2. Schedule a time to hold the Orals (start 2 months before your Oral Exam)
  3. Identify the Chair of your Oral Examination Committee
  4. Submit the "University Orals Examination Schedule" to the Student Services Officer 3 weeks before the Exam
  5. 3 weeks or more before your Defense, your research advisor has given you comprehensive feedback about your thesis proposal
  6. Submit your written thesis proposal to the committee two weeks before the Defense
  7. Submit your title and abstract to the Student Services Officer at least two weeks before the Defense
  8. The Oral Defense (about 2.5-3 hours)

The Examination Committee

The Ph.D. Orals Examination Committee typically consists of the same 4 faculty members who will serve on the student's dissertation committee - plus 1 other member, who may be chosen by the student. At least two examiners must be members of the Stanford Academic Council. The Committee Chair must be a Stanford Academic Council member from a department not represented on the committee. A courtesy appointment in the same department is allowed. Together, the student and his or her research advisor need to consider the selection of the Committee Chair thoughtfully.

The thesis proposal is a written document that must submitted to the student's Ph.D. orals committee at least two weeks before the oral exam.

Submit the completed University Oral Examination Schedule form (available from the BMI administrator) to the BMI Student Services Officer at least 3 weeks before the scheduled exam date.

The oral exam will generally be scheduled when the University is in session (during an academic quarter) in accordance with University guidelines.

1. Because it is difficult to find times when all committee members can simultaneously set aside the time for an oral exam, the student should schedule the orals at least two months prior to the anticipated date. Plan on one hour for the public presentation, followed by a 30 minute open session for questions from the audience, followed by 30-90 minutes of closed session with your committee, leading to a vote. This means that committee members should set aside 2-1/2 to 3 hours if at all possible. If you plan on using the conference room (x-275) in MSOB, please confirm with Carol Maxwell that the room is available before committing to the date and time. If a student attempts to schedule the Orals less than 2 months in advance, the BMI Exec can ask the student to choose a new date that is at least 2 months into the future.

2. When a date and time for the oral exam is identified, THEN seek a chair for the exam committee. Chairs should be members of the academic council who are NOT from the same department as the thesis advisor. They CAN be from another department that is represented on the committee by one of the examiners other than the thesis advisor. Once the full committee is defined, including the chair, fill out the University-mandated paperwork and provide the forms to Student Services Officer at least 2 weeks prior to the Defense. The Student Services Officer will make sure that the talk is announced in the Stanford Report, etc. You should also send a title and abstract to Student Services Officer at least 2 weeks in advance so that the event can be announced to the colloquia-list.

3. Meet with all members of the committee (chair is optional; see below) as often as is possible in the months leading up to the exam. Be sure that they understand what you are doing, agree with your thesis statement and evaluation plan, and believe that what you are proposing is worthy of a Stanford PhD.

4. Work out an arrangement with your thesis advisor to assure that he or she has read all chapters of your proposal and has agreed that they are adequate no later than THREE WEEKS PRIOR TO YOUR EXAM. If your advisor has not seen drafts of all chapters by this time, and agreed that everything is on track, it is his or her responsibility to notify Student Services Officer that the scheduled exam should be cancelled; you will need to reschedule it at a time when the 3-week window is likely to be achievable

5. Incorporate comments from your advisor and generate a final thesis proposal for delivery to your committee no later than TWO WEEKS PRIOR TO YOUR EXAM. This provides your committee with enough time to have a reasonable chance of reading the document prior to your oral defense. Failure to meet this deadline will also trigger a cancellation of the oral exam by your thesis advisor so that the exam can be rescheduled for a time when the committee will have had adequate time to read the proposal.

6. It is a courtesy to provide your orals committee chair with a copy of the proposal and the Orals Guidelines, and to offer to meet with him/her before the event. They will generally not require that you do this, but make the offer. Also, be sure they understand that you will be defending a proposal and not a completed dissertation.

Tips for the Defense

  1. Develop your oral defense in consultation with your thesis advisor. Decide in advance what points you need to make, what background needs to be provided to the audience, and what you can leave out or save for questions (since you will always have more to say than is possible to include in an hour's talk).
  2. Practice the talk. Make sure it times out. Go over the slides with your advisor.
  3. Avoid glibness, or excessive informality; this is one time when a presentation needs to be rather formal - you are trying to demonstrate that you are already master of a field and are striking out to break new and important ground of some kind.
  4. Even though you will have shared your proposal with your committee and often with other members of the audience, do not assume that everyone will have digested it in detail. Be sure that your talk is accessible to someone who has a technical background but knows little about your precise topic and is thus starting out cold at the beginning of your presentation. State your goals clearly; make sure people understand the motivation for what you are doing, as well as the technical details. The defense should close with a summary of what remains to be done before your dissertation will be complete, including a detailed time line of tasks, milestones, and their anticipated completion dates.

Thesis/Dissertation Preparation

University regulations specify the composition and the format of the dissertation defense. Students should refer to the booklet "Directions for Preparing Doctoral Dissertations", available from the Registrar's Office, for specific information. Read these guidelines carefully before final preparation of the manuscript to avoid costly and time-consuming revisions. Previously published dissertations may not be a good guide as the directions may have changed. Published papers may be included in dissertations; however, they must meet the University's format guidelines. Retain manuscripts and figures submitted for publication for reformatting and inclusion in the dissertation. BMI will pay for the printing costs of up to 10 copies of the bound dissertation. Keep the receipt and submit to Student Services Officer for reimbursement. Give one red-bound copy to the research advisor and submit one copy to Student Services Officer for the BMI library. Additional (soft-cover) copies are printed and distributed by the BMI staff.

Dissertation Formatting

If you would like to have the format of your dissertation checked by the Registrars Office, you must schedule an appointment. Slots fill up early, so contact the Registrars by the first week of May. Check with the Registrars Office for more information.

Deadlines for Submission of the Dissertation

Stanford Medicine Resources:

Footer Links: