Doctoral Degree in Biomedical Informatics Curriculum

To earn the PhD degree in Biomedical Informatics, a student must complete a program of study approved by a committee of biomedical informatics faculty. This program must include (a) the required coursework described below; (b) successful completion of a preliminary evaluation; (c) an MS-level research project involving significant research, design, or development work and a written report; (d) successful completion of a comprehensive examination composed by the doctoral committee; (e) 18 or more credits of research work leading to an acceptable dissertation; and (f) completion of accomplishments in the Requirements Prior to Admission to Doctoral Candidacy section. All required courses must be taken for a letter grade, with the exception of the Journal Clubs/Colloquiums and some Independent and/or Dissertation Studies (to be determined by faculty advisors). A minimum “B” grade is required in all graduate courses. The doctoral committee may waive course requirements that have been satisfied through prior university-level study, in accordance with the Committee on Graduate Studies guidelines. A student must comply with the regulations of the Committee on Graduate Studies, as well as those regulations established by the biomedical informatics faculty. As with the masters curriculum, the doctoral curriculum is designed to support studies across all domains that describe the program’s scope.

(Note: Up to 30 credits – “B” grade or better – from a master’s program in another institution or department within the University of Pittsburgh can be considered for transfer towards the Biomedical Informatics Doctoral degree. In recognition of graduate study beyond the Masters’ degree successfully completed elsewhere or within the University of Pittsburgh, no more than 12 additional credits may be accepted at the time of admission to meet the minimum credit requirement. (At least three terms, or 36 credits, of full-time doctoral study, or the equivalent in part-time study, must be successfully completed at the University of Pittsburgh.) Acceptance of transfer credit must be discussed between student and advisor, and approved by Chair of Curriculum Committee.)

The Doctoral degree in Biomedical Informatics requires at least 72 credits (54 credits of coursework and 18 dissertation credits following admission to candidacy).

Biomedical Informatics Core (4-7 credits)

BIOINF 2011: Introduction to Biomedical Informatics (3 credits)

BIOINF 2032: Journal Club (1 credit) Revised format will focus on seminal and new literature in the field w/ weekly preparation and critical analysis facilitated by an instructor; required of all students in first year. Biomedical Informatics Colloquium (0 credit) Revised format will showcase presentations from DBMI researchers and invited speakers from across campus and beyond. Will meet weekly for one hour. Required attendance (75% minimum) for all students.

BIOINF 2013: Clinical Environments in Biomedical Informatics (3 credits: OPTIONAL: for U.S. trained clinicians)

Computational Competency: Tools and Concepts (minimum 9 credits)

TOOLS (minimum 3 credits)

BIOINF 2012 Problem-Oriented Programming in Medical Informatics (3 credits) is strongly recommended. An alternative* programming language elective may be substituted, pending approval of advisor.[CG1] Only those students for whom prior experience or other approved forms of demonstrated programming competency proficiency (such as online courses or portfolio development) exist, may seek a waiver of the programming elective.

CONCEPTS (minimum 6 credits)

Database Management (3 credits): INFSCI 2710, HSR 2424, CS 2550 or alternative* approved by advisor.
Data Structures (3 credits): INFSCI 2500 or alternative* approved by advisor.
Algorithms (3 credits): CS 2150 or alternative* approved by advisor.
*Note: alternative courses must be graduate-level courses (having course numbers in the 2000 or 3000 series). Prerequisites may apply.

Biomedical Informatics Distribution (minimum 15 credits)

BIOINF 2014: Biomedical Informatics Project Course (3 credits)
BIOINF 2051: Introduction to Bioinformatics (3 credits)
BIOINF 2052: Introduction to Computational Structural Biology (2 credits)
BIOINF 2053: Sequence Analysis Laboratory (3 credits; includes Pittsburgh Supercomputing Center (PSC) Workshop in August)
BIOINF 2054: Statistical Foundations for Bioinformatics Data Mining (3 credits)
BIOINF 2055: Practical Analysis of High-Throughput Genomic and Proteomic Data Sources (3 Credits)
BIOINF 2056: Bioinformatics of Gene Regulation (3 credits)
BIOINF 2057: Elements of Statistical Learning (3 credits)
BIOINF 2101: Probabilistic Methods for Computer-based Decision Support (3 credits)
BIOINF 2104: Information Technology and Health Care Organizations (3 credits)
BIOINF 2109: The Internet and Health Informatics (3 credits)
BIOINF 2110: Concepts of Software Project Engineering in Health Care (3 credits)
BIOINF 2111: Cognitive Studies for Health Informatics (3 credits)
BIOINF 2112: Methods and Principles of User-Centered Design (3 credits)
BIOINF 2113: Realtime Outbreak and Disease Surveillance (3 credits)
BIOINF 2114: Introduction to Medical Language Processing (3 credits)
BIOINF 2115: Mathematical Modeling Techniques for Complex Biological Systems (3 credits)
BIOINF 2131: Practicum in Advanced Biomedical Information Technology (1-6 credits)
BIOINF 2134: Research Writing Practicum (2 credits)
BIOINF 2992: Information in Radiological Imaging (Directed Study) (3 credits)

Electives (9 or more credits)

Student choice which must be approved by the student’s advisor of 2xxx or higher level courses that address student’s educational and career goals. Six (6) elective credits must be taken in a single Cognate Area, to be chosen by the student – with advisor approval – from 2000 or higher level courses. Suggested Cognate Areas include sub-areas of computer science, artificial intelligence, bioinformatics, decision science, cognitive science, telecommunications, human-computer interfaces, education, and modeling. The electives can be met through additional courses chosen from the biomedical informatics distribution list. Students who are allowed to waive one or more required credits will use additional electives to earn the required 72 total credits for the doctoral degree.

Research Methods (8 credits)

Introductory Statistics/Biostatistics (3 credits) The statistics core requirement can be met in a variety of ways. Many of our current students take one or more of the following: Intro to Statistical Methods I (BIOST 2041: 3 credits), Intro to Biostatistics II (BIOST 2042: 2 credits), Statistics in Information Sciences (INFSCI 2060: 3 credits), Statistical Methods I (PSYED 2014: 3 credits), Statistical Methods 2 (PSYED 2015: 3 credits), or Statistical Methods 3 (PSYED 2016: 3 credits). (A waive of this requirement can be requested based on previous coursework in statistics (send e-mail request to tls18@pitt.edu; however, a biostatistics course taken in medical school is typically too brief an experience to justify a waiver.) Those students who must take a course to fulfill this requirement will be strongly urged to do so early in their plan of study.

BIOINF 2033: Introduction to Research in Biomedical Informatics (2 credits)
New course being developed as an early structured research experience to be mentored by the student’s research advisor with oversight by Course Coordinator; required of all masters and doctoral students in their first year.

BIOINF 2480: Master’s Level Research Project (3 or more credits).
Students pursuing a doctoral degree should have completed the masters-level research project/thesis by the end of the summer term of the second year of full-time study. The doctoral student should register to receive 3 credits under Master’s Thesis/Project Research (BIOINF 2480). The research project is intended to provide doctoral students with an early research experience and to identify content and methodology deficiencies for remediation prior to the doctoral comprehensive examination. The research project has two key deliverables: (1) the writing and submission (to the Training Program, via their advisor) of a paper of publishable quality based upon the research and (2) the completion of an oral examination on its contents. The research project is required of masters and PhD students. The research paper is expected to be 20-30 pages double spaced type, inclusive of abstract, figures, tables and references, and to include Objective, Background, Design, Measurements, Results, and Conclusion (or the equivalent, dependent on the specific research focus). There is the strong expectation that students will submit their projects for publication to appropriate journals and conferences, such as JAMIA, AMIA, or other respected academic publications in their field of study. All students should refer to Master’s Research Project Requirements for detailed description of this requirement, including committee, timeline, and deliverables.

Doctoral students pursing a masters on their way to a doctoral degree have the option of developing their project into a formal master’s thesis. It is expected that those students who choose the thesis option will additionally satisfy all University requirements, including format and submission of copies, for the Master’s thesis. For more information, see http://www.pitt.edu/~graduate/regmasters.html and http://www.pitt.edu/~graduate/dissertation.html

Advanced Statistics or Research Design (minimum 6 credits)

Students may draw from a wide range of advanced courses offered at the University, including Applied Statistical Methods 2 (STAT 2132: 3 credits), Advances in Applied Statistics 1 (STAT 2391: 3 credits), Advanced Modern Statistical Computing (STAT 3341: 3 credits), Research Design (INFSCI 2100: 3 credits), Intro to Research Methods (EDU 2201: 3 credits), and Elements of Statistical Learning (BIONF 2057). Approval by advisor is required.

Teaching Practicum (3 credits)

As part of the training for the PhD, each student is required to complete 3 credits (8 hours per week for one semester) of teaching assistant service in biomedical informatics courses – in consultation with biomedical informatics faculty. Register for BIOINF 3998.

Dissertation Study (18 credits)

Eighteen additional credits of dissertation study must be completed after completion of required coursework (BIOINF 3999).
NOTE: Regarding Registration for Dissertation Credit All doctoral students who are still accruing required dissertation credits must register under BIOINF 3999 (1-9 credits). Doctoral students who have acquired all of their required credits yet must still register as a student in the University (e.g., according to the regulations of the University of Pittsburgh, you must be registered in the term in which you graduate; or for Graduate Student Researchers (GSRs) who must be registered as full-time students) can register under a discounted tuition rate full-time dissertation study, FTDS 0000 (0 credits).

Additional Requirements

Instruction in the Responsible Conduct of Research: See specific information on Research Practice Fundamentals. This requirement must be satisfied within the first month of beginning any academic program at DBMI. Attendance at and participation in the Department of Biomedical Informatics’ invited lectures, symposia, conferences, etc., e.g. the Annual Training Program Retreat. Such lectures are considered to be important educational experiences, as well as introducing students to primary researchers and their work in the field of biomedical informatics.

Doctoral students are required to produce one first-author, peer-reviewed conference paper or journal per year beginning in their second year of doctoral study.

All students are required to follow the Biomedical Informatics Training Program’s Academic Integrity Policy [PDF], which is in accordance with the rules and regulations of the University of Pittsburgh.

Preliminary Evaluation

At approximately the end of the first year of full-time graduate study, a preliminary evaluation designed to assess the breadth of the student’s knowledge of the discipline, achievement to date, and potential to apply research methods independently will be conducted. The evaluation results will be reported to the Office of Graduate Studies of the School of Medicine. The Preliminary Evaluation consists of an oral presentation in the form of a poster presentation at the Annual Training Program Retreat in late-August or a fall Biomedical Informatics Colloquium presentation, together with the regular evaluation that is done on all students in the program by the Evaluation Committee at least twice each year.

Doctoral Comprehensive Examination

See specific Doctoral Degree Comprehensive Examination Guidelines.

Candidacy for the PhD Degree, Doctoral Committee, and the Doctoral Dissertation

To qualify for admission to candidacy for the PhD degree, a doctoral student must have completed formal coursework with a 3.3 QPA or higher, successfully completed the masters level project, passed the doctoral comprehensive examination, and received approval of the proposed subject and plan for the dissertation from his/her dissertation committee following a Dissertation Overview/Prospectus Meeting. (Note: In this program, 18 credits of dissertation study must be completed after completion of coursework.)

The dissertation committee usually includes the principal dissertation advisor (responsible for oversight of the student’s dissertation research; also referred to as the “major advisor”) and three additional members. The role of the committee Chair (responsible for administrative oversight and the final oral examination) may be filled by the dissertation advisor or another committee member. The majority of the committee, including those members filling the roles of the dissertation advisor and the committee Chair, must have Graduate Faculty status. A majority of the committee must be Biomedical Informatics Core Faculty. A minimum of one Graduate Faculty member from the University community who is not a member of the student’s training program must participate on the committee. The dissertation committee must be approved by the Director of the training program prior to seeking approval from the Graduate Dean (signed nomination of a doctoral dissertation committee form). Only upon this approval may the student meet with his/her committee at their Overview/Prospectus meeting and proceed with Admission to Candidacy. This doctoral committee has the responsibility to advise the student during the progress of the candidate’s research and has the authority to require high quality research and/or the rewriting of any portion or the entire dissertation. It conducts the final oral examination and determines whether the dissertation meets acceptable standards.

The Dissertation Advisor has the responsibility for primary oversight of the progress of the candidate’s research. The Dissertation Committee Chair will arrange the dates of the prospectus, annual, and final oral examination meetings of the committee well in advance, will oversee submission of all documents and forms requiring committee approval and signatures, and will coordinate and communicate all other matters related to the process of the dissertation in accordance to these guidelines. The Training Program Coordinator is available to assist the Chair in this process. An appropriate dissertation project involves a substantive piece of original and independent biomedical informatics research, grounded in an appropriate body of literature and providing a significant contribution to the field. The dissertation must be successfully defended in a public oral defense.

The dissertation process will follow the applicable regulations and procedures of the University and the School of Medicine, as described in the Regulations Governing Graduate Study at the University of Pittsburgh (see http://www.pitt.edu/~graduate/reg.html).

University policy requires submission of dissertations in electronic form for the doctoral degree. See http://www.pitt.edu/~graduate/regphd.html#dissertation and specifically http://www.pitt.edu/AFShome/g/r/graduate/public/html/etd/.

Requirements Prior to Admission to Doctoral Candidacy

The following skills must be demonstrated in the course of graduate study and prior to being admitted to doctoral candidacy.

• Writing accomplishment: This is satisfied by submitting a journal article or peer-reviewed conference paper with approval by his/her advisor.
• Literature Search: This is satisfied by completing RPF Module 11.