Graduate Training Programs in Biostatistics

7. Graduate Training Programs in Biostatistics

This version of the biostatistics portion of the handbook applies to students who entered the program in the fall of 2016 or thereafter.  For students who matriculated prior to this, please refer to the previous version of the handbook that may be found here. Questions about the program for any cohort should be referred to the student’s academic advisor, the Program Chair, or the GGEB Chair.

The PhD program in biostatistics is designed to prepare students to be independent researchers in the development of statistical methodologies and in the appropriate and innovative application of these methodologies to biomedical research problems.  In the first five semesters of the program, students complete a series of courses in both theory and applied methodology, engage in individually mentored research experiences, explore statistical collaboration, and complete the qualifications examination.  Within this period, students also identify a dissertation research problem and an advisor and present a research proposal as part of the candidacy examination.  Students typically defend their dissertations and graduate within five years of matriculation.

The MS program is designed to prepare students to be practitioners of biostatistical methodologies.  Some MS students may move to enter the PhD program.  The MS program closely parallels the first two years of the PhD program and requires four full-time semesters of course work, exploration of practical aspects of collaboration, and an independent research project which serves as the MS thesis.

7.1 Elements Common to MS and PhD Programs
7.1.1 Academic Advisor

Each incoming student is assigned an academic advisor who serves as the student's primary mentor, advising in course selection and related academic matters.  The program attempts to match students to advisors who have similar backgrounds and interests.  A student may change advisors at any time by request to the Program Chair.  A PhD student’s dissertation advisor, once selected, assumes the role of academic advisor during the later years of study.  Furthermore, at any time a student may refer questions about his or her program to the chair of the Academic Advising Committee.

At the beginning of the academic year, each student, in collaboration with his/her advisor, prepares a proposed academic program, the Individual Development Plan (IDP), including courses to be taken, courses to be transferred, and timelines for examinations and dissertation preparation.

7.1.2 Non-Credit Requirements

The department hosts a weekly biostatistics research seminar that invites speakers from other universities, industry, and government.  All students are expected to attend at least six seminars per semester, provided there is no conflict with courses.  Other non-credit requirements include Responsible Conduct of Research, CITI, and HIPAA training.  These requirements are described in detail in Section 6.3.  Biostatistics in Practice I and II, as well as, for PhD students, serving as a teaching assistant, are also non-credit requirements (see Sections 7.3.9 and 7.5, respectively).

7.1.3 Transfer of Credit

Only courses considered at the graduate level may be transferred from previous training.  At least eight course units of the total program required for the MS degree must be completed while enrolled in a graduate program at UPenn.  Because the MS program requires only 12 total course units, no more than four may be satisfied by transfer credit.  A maximum of eight units may be transferred from previous training towards the PhD degree.  Courses proposed for transfer credit must be relevant to training in biostatistics and may include courses in theory, methods, or towards a minor (see Section 7.3.6 regarding minors).  Transfer of credit must be approved by the Program Chair and the GGEB Chair.

7.1.4 Auditing

Auditing a course is not allowed for any students in the PhD program. For MS students, auditing of a course is strongly discouraged.  If a MS student wishes to audit a course he/she must consult their academic advisor, the course director, and prepare a written request to the Program Chair explaining reasons for the proposed course audit. Final approval must be obtained from the GGEB Chair.

7.2 Master of Science (MS) in Biostatistics
7.2.1 Course Requirements

Candidates for the MS degree must complete 12.5 units of course credit and prepare a Master’s thesis.  Required courses cover probability, mathematical statistics, and statistical methods including categorical data analysis, linear models, survival analysis, and applied data analysis.  All students also take a course in epidemiology. MS students will have the option to take the written qualifying exam but it is not required to obtain a masters in biostatistics.

The MS in Biostatistics typically requires four semesters of formal course work.  Students must complete nine units of required courses, three units of electives, and the Biostatistics in Practice and project requirements (see Section 7.3.9). The required courses are described below.  The courses in bold type are the “core” courses for the MS degree that are covered on the written qualifications examination.


Theory:

BSTA 620: Probability (1 unit)
BSTA 621: Statistical Inference I (1 unit)

Methods:

BSTA 630: Methods I (1 unit)
BSTA 632: Statistical Methods for Categorical and Survival Data (Methods II) (1 unit)
BSTA 651: Introduction to Linear Models & Generalized Linear Models (1 unit)
BSTA 656: Longitudinal Data Analysis (1 unit) 
BSTA 660: Design of Observational Studies (1 unit) OR BSTA 661 Design of Interventional Studies I (1.0 unit) 
BSTA 670: Statistical Computing (1 unit)

Applications:

BSTA 509: Introductory Epidemiology (0.5 unit)
BSTA 511: Biostatistics in Practice (1 unit)

7.2.1.1 Electives

Students in the MS program choose three additional units from a list of advanced courses in biostatistics and related topics.  At least two of these courses must be quantitative; the third may be in a related scientific field subject to approval by the Program Chair and GGEB Chair.  A partial listing appears under the section on electives for the PhD program (Section 7.3.3).  In addition to these electives, BSTA 622 Inference II and BSTA 754 Advanced Survival Analysis, which are required courses for the PhD program, may be used as advanced electives for the MS program.  Courses not described here may be used as advanced electives for the MS program upon receiving approval from the Program Chair and GGEB Chair.

7.2.2 Biostatistics in Practice and the MS Thesis

All MS students must participate in Biostatistics in Practice and complete a Biostatistics in Practice project, which serves as the MS thesis.  The project may be completed in any semester.  See the description of the Biostatistics in Practice requirements in Section 7.3.9.

7.2.3 Typical Course Sequence for Full-Time Students in the MS Program

 

   

Semester


Required Credit Courses (units)

 

 

 

Year 1

Fall

BSTA 620: Probability (1)
BSTA 630: Statistical Methods and Data Analysis I (1) 
BSTA 509: Introductory Epidemiology (0.5)
BSTA 511: Biostatistics in Practice (0.5)

Spring

BSTA 621: Statistical Inference I (1) 
BSTA 632: Statistical Methods for Categorical and Survival Data (Methods II) (1)
BSTA 651: Introduction to Linear Models & GLM (1)
BSTA 511: Biostatistics in Practice (0.5 continued)


Summer


Written Qualifications Examination (Optional for MS students)

 

 

 

Year 2

Fall

BSTA 670: Statistical Computing (1)
Advanced Electives (2)

Biostatistics in Practice project / MS Thesis

Spring

BSTA 656: Longitudinal Data Analysis (1) 
BSTA 660: Design of Observational Studies (1) or BSTA 661: Design of Interventional Studies (1)
Advanced Elective (1)

Biostatistics in Practice / MS Thesis Presentation

 

7.3 Doctor of Philosophy (PhD) in Biostatistics
7.3.1 Funding Policies

Full-time PhD students are eligible for funding in the form of traineeships, fellowships, and research and teaching assistantships.  The work associated with these sources of support is an essential part of the graduate training program.

At the beginning of the academic year, each funded student receives a letter describing sources of support and associated obligations.  All doctoral students admitted to the program receive support from BGS for up to 21 months. During this time students take courses and explore research opportunities with faculty in the department.  Once students decide on a dissertation advisor, the advisor, the student and the Program chair will work to develop a sustained funding plan that will cover the student’s time during the remainder of their graduate program. A number of funding opportunities are available including federally funded research and training grants, partial TAships and funding through partnerships with industry. The typical length of time in the program is five years.  Students in good academic standing have occasionally received funding for up to six years in the program.

7.3.2 Course Requirements

The PhD in Biostatistics typically requires five to six semesters of coursework and additional semesters devoted to dissertation research.  This is usually accomplished in four to five years of full-time study.  The standard course sequence for PhD students consists of 3 units in theory, 7 units in statistical methods, 0.5 unit of epidemiology, 1.0 unit of Biostatistics in Practice, 2 units toward a minor and 4 units of electives in advanced theory and methods. In addition, a minimum of three units of credit including one unit of independent study (BSTA 999), two units of guided research (BSTA 920 and BSTA 995) and three semesters of lab rotations (BSTA 699) are required.  In general, students are expected to have completed all required courses by the end of their 4th year (or equivalent for those who enter with a Masters degree).  In rare cases substitutions may be made.  Such alternatives must be pre-approved by the chair of the Curriculum Committee, the Program Chair, GGEB Chair and the director of the course being waived, who is in the best position to evaluate whether the necessary skills are met by the substitution.

Below are the required core courses; the courses in bold type are PhD “core” courses that are covered on the written qualifying examination.

Theory:

BSTA 620: Probability (1 unit)
BSTA 621: Statistical Inference I (1 unit)
BSTA 622: Statistical Inference II (1 unit)

Methods:

BSTA 630: Statistical Methods and Data Analysis I (1 unit)
BSTA 632: Statistical Methods for Categorical and Survival Data (Methods II) (1 unit)
BSTA 651: Introduction to Linear Models & Generalized Linear Models (1 unit)
BSTA 656: Longitudinal Data Analysis (1 unit)
BSTA 660: Design of Observational Studies (1 unit) OR BSTA 661: Design of Interventional Studies I (1.0 unit) 
BSTA 670: Statistical Computing (1 unit)
BSTA 754: Advanced Survival Analysis (1 unit)

Applications:

BSTA 509: Introductory Epidemiology (0.5 unit)
BSTA 511: Biostatistics in Practice I (1.0)

7.3.3 Electives and Independent Study

Students are required to take 4 additional advanced electives; a partial listing of such courses is given below.  In addition to this list, other courses offered by departments outside of Biostatistics and Epidemiology may be appropriate advanced electives and may be used as an advanced elective for the PhD program upon receiving approval from the student’s academic advisor and the Program Chair.  Independent study or reading courses (BSTA 999) are reserved for doctoral students who have passed the written qualifications examination and are either choosing a dissertation topic or undertaking the early stages of dissertation research.  At most one of the four required advanced electives may be a reading course, and only on a topic not offered as a formal course with a year.
 

STAT 530: Probability (1 unit)
STAT 531: Stochastic Processes (1 unit)
STAT 921: Observational Studies (1 unit)
STAT 925: Multivariate Analysis: Theory (1 unit) 
OPIM 930: Stochastic Models II (1 unit)
BSTA 751: Statistical Methods for Neuroimaging (1 unit)
BSTA 771: Applied Bayesian Analysis (1 unit)
BSTA 774: Statistical Methods for Evaluating Diagnostic Tests (0.5/1 unit) 
BSTA 775/STAT 920: Sample Survey Methods (1 unit)
BSTA 782: Statistical Methods for Incomplete Data (1 unit)
BSTA 783: Multivariate and Functional Data Analysis (1 unit) 
BSTA 785: Statistical Methods for Genomic Data Analysis (1 unit) 
BSTA 786: Advanced Topics in Clinical Trials (1 unit)
BSTA 787: Methods for Statistical Genetics in Complex Human Disease (1 unit) 
BSTA 788: Functional Data Analysis (1)
BSTA 789: Big Data (1)
BSTA 790: Causal Inference in Biomedical Research (1 unit)
BSTA 820/STAT 552: Statistical Inference III (1 unit)
BSTA 852/STAT 910: Forecasting and Time Series (1 unit)
BSTA 854/STAT 927: Bayesian Statistical Theory and Methods (1 unit)

7.3.4 Applied Research Requirement, Equivalent of MS Thesis

All PhD students must participate in Biostatistics in Practice and complete a Biostatistics in Practice project, a requirement that students typically satisfy during the first or second year.  See Section 7.3.9 for further details.

7.3.5 Teaching Practicum

All students in the PhD program must provide teaching support for a course or courses offered by the Department of Biostatistics and Epidemiology or related programs.  This is discussed in detail in Section 7.5.

7.3.6 Minor

Students must complete a two-unit minor sequence in one or more areas of science relevant to biomedical research. Some possible subject areas for minor courses include epidemiology, genetics, biology, psychology, economics, computer science, and bioengineering. Minor courses are typically taken outside of the GGEB, with the exception of advanced epidemiology courses (beyond BSTA 509) which may also be counted toward the minor. The two-unit minor sequence must be approved by the curriculum committee chair and the program chair.

7.3.7 Examinations

The PhD program requires the successful passing of three examinations: the written Qualifications Evaluation, the oral Candidacy Examination, and the Dissertation Examination.  Later sections outline the procedures for each of these.

7.3.8 Lab Rotations
Goals and Objectives

The overall goal of the rotations is to expose students to biomedical research, and in particular research related to statistical methodology early in their training.  In addition, students will rotate through a number of different labs, in order to get a broad perspective on research and faculty.   This will also assist the students in identifying their research interests and dissertation topic earlier in their educational process.  In addition, both the students and faculty can assess whether they are a good match for possible dissertation advisor/advisee relationships. By the end of 21 months of training (summer of year 2) students who were initially funded by BGS will identify their dissertation advisor, have a foundation for the first topic in their dissertation work, and move off of BGS funding and onto funding that is related to their dissertation work. Students will normally identify their PhD mentor through working with them on a lab rotation.  Students who are funded by a training grant during their first 21 months in the program will remain on the training grant throughout their program.  Students who are currently funded or who have interests in receiving funding during their dissertation research from a training grant should discuss how to structure their lab rotations with the training grant director. Lab rotations that offer research experience in areas relevant to our training grants will be available each year.

Lab Rotation Content

Laboratory rotations should focus on statistical research as opposed to simple data analysis or service/project work.  Ideas include implementation of a method from the literature, literature review of methods, running and summarizing simulations, or the analysis of a complicated dataset.  It is recognized that, depending upon the background of the students matriculating into the program, the first lab rotation may need to be a lighter introduction to the methodological area such as focusing on literature review, study design, logistics, and data management and/or data analysis.

Duration and Number of Individual Rotations and Dissertation Advisor Choice

Students are expected to participate in 3-5 rotations in total with a minimum of 2 different mentors.  First year students will have 3 rotations: fall, spring, and summer.  Students can expect to spend 20+ hours per week during the fall/spring semesters and full time 40+ hours during the summer.  In the second year it is expected that students will settle into a relationship with a potential PhD dissertation advisor with the goal of focusing their research in an area of research related to that of the advisor.  Nevertheless, if needed, a fourth or even fifth lab rotation may occur in the second year to help the student decide on a research topic and mentor.  In many cases the MS thesis (Biostatistics in Practice project) will be related to the dissertation for a PhD student.  In addition to determining an area of research interest, the dissertation advisor must show willingness to, at least partially, support the student.

Laboratory Rotation Assignments

Prior to the arrival of the new students, interested faculty mentors will submit a short summary describing their proposed laboratory rotation (similar to a course description).  During new student orientation and the first week of classes, faculty who are interested in serving as a mentor for the upcoming semester will make a brief presentation of their projects.  Faculty mentors can also distribute a handout with a more detailed project description to interested students.  Next, the students will rank their choice of projects and the rankings will be reviewed by members of the Academic Advising Committee.  Each student will be encouraged by the committee to meet with individual faculty of 2 or 3 potential collaborations.  This should occur within a short period of time so that assignments can be made and begin in a timely fashion for the Fall semester.  After those meetings, participating biostatistics faculty will also rank their student preferences.  The Academic Advising Committee will take this information and facilitate matching students to faculty.  It is important to note that each student will be working in three labs during their first year, so students and faculty will have ample opportunity to work with each other over the course of the program and initial matches do not preclude options for other collaborations.  It is the responsibility of faculty mentors to make sure any required IRB approvals are obtained, and that students have the requisite CITI training to work with any data related to their laboratory rotation project.

Evaluation

At  the initiation of each new lab rotation, the advisor and mentee will write a short summary of the goals and expectations for the particular laboratory rotation.  This document will be submitted to the Academic Advising Committee for review.  Laboratory rotations are taken for credit (1 unit, BSTA 699) and students receive both a written evaluation and a letter grade.  Summer rotations also receive a letter grade; however, these will not appear on the formal transcript.  In addition, each student will present a 15-minute (shorter for 1st rotation) oral presentation of their laboratory rotation work annually during a brown bag format “chalk talk”.  Attendance will be required for all students participating in various lab rotations and encouraged for upper class students as well as faculty.

Laboratory Rotation Lab Notebook

PhD students are required to keep a formal record/notebook of work being conducted during mentored laboratory rotations as part of the first 21 months in the PhD programs. The lab notebook should be a shared document between the mentor and mentee.  This document should be stored in a location that both mentor and mentee can access such as a project directory or a shared PENN Box folder. Both mentor and mentee should continue to have access to the shared folder once the lab rotation has been completed.

The lab notebook should contain dated entries including a list of the goal(s) for each week, and a summary of progress towards those goals.  The notebook progress should be reviewed at weekly meetings between the mentee and mentor with new goals set for the following week. A copy of the lab notebook along with all work products should be retained by the mentor at the end of each rotation.

7.3.9 Biostatistics in Practice

Participation in Biostatistics in Practice is required for both the MS and PhD degrees.  This year-long 1-unit course covers practical aspects of utilizing biostatistics in multi-disciplinary research teams.  Didactic lectures address both the substantive and communications aspects of consulting, with student participation in class discussions considered critical.  In addition, each student attends 2-3 consulting sessions between a biostatistics faculty member and his/her collaborators.  For PhD candidates, Biostatistics in Practice may be waived if the student 1) has previously achieved an MS in Biostatistics or Applied Statistics and 2) can demonstrate exposure to an equivalent curriculum in their previous degree program.  Such a waiver requires the approval of the Program Chair and GGEB Chair.

Biostatistics in Practice Project

The Biostatistics in Practice project offers the student an opportunity to acquire and demonstrate proficiency in statistical collaboration and data analysis.  The project is defined by several elements:  A scientific question or hypothesis arising in medical research; the statistical methodology needed to address the question; the development of a study design and/or analysis of a relevant data set; and a summary of the results of these analysis. In most cases, a collaborating medical scientist provides the research question and the data.  The student, under the supervision of a biostatistics faculty member, identifies the appropriate statistical methods and conducts the analysis.  The analysis should be sufficiently extensive and detailed to support a manuscript publishable in the medical literature.

The project consists of two parts.  The first is a written report including:  a description of the research question; background and significance; a description of the statistical methods applied; the results of the analysis; and summary of the major findings and conclusions.  The written report should describe the study in a format suitable for publication in a scientific journal. Students may use this Biostatistics in Practice project write-up as their MS thesis.The second part is a short (15 minute) oral presentation of the project to the biostatistics faculty and students. 

The project must be completed by the end of the second semester of Biostatistics in Practice (end of April).

Al ll data analyses done as part of the Biostatistics in Practice project must have IRB approval.  In most cases this requirement is satisfied if the research objectives are part of an existing protocol of the participating medical research collaborator, as long as the student is added to the protocol according to the standard modification procedures required by the IRB.

7.3.10 Typical Course Sequence for Full-Time Students in the PhD Program:

 

Semester 1

Funds

Plans

 

 

 

 

Year 1

Fall

BGS

FT Courses:

  • BSTA 620: Probability (1)
  • BSTA 630: Statistical Methods and Data Analysis I (1)
  • BSTA 509: Introduction to Epidemiology (0.5)
  • BSTA 511: Biostatistics in Practice (0.5)
  • BSTA 699: Lab Rotation

Spring

BGS

FT Courses:

  • BSTA 621: Statistical Inference I (1)
  • BSTA 632: Statistical Methods for Categorical and Survival Data (Methods II) (1)
  • BSTA 651: Linear Models and Generalized Linear Models (1)
  • BSTA 511: Biostatistics in Practice (0.5 continued)
  • BSTA 699: Lab Rotation

Summer

BGS

Written Qualifications Examination

  • BSTA 699: Lab Rotation

 

 

 

 

Year 2

Fall

BGS

FT Courses:

  • BSTA 622: Statistical Inference II (1)
  • BSTA 670: Statistical Computing (1)
  • BSTA 754: Advanced Survival Analysis (1)
  • BSTA 699: Lab Rotation or BSTA 899: Pre Dissertation Lab Rotation (if a dissertation advisor has been chosen)
Biostatistics in Practice Project / MS Thesis

Spring

BGS

FT Courses:

  • BSTA 660: Design of Observational Studies or BSTA 661: Design of Interventional Studies (1)
  • BSTA 656: Longitudinal Data Analysis (1)
  • Advanced Electives (1)
  • BSTA 699: Lab Rotation or BSTA 899: Pre Dissertation Lab Rotation (if a dissertation advisor has been chosen)
Biostatistics in Practice Project / MS Thesis Presentation

Summer

BSTA

Oral Candidacy Examination
PhD Thesis*

 

 

 

 

Year 3

Fall

BSTA

FT Courses:

  • BSTA 999: Independent Study (1)
  • Advanced Electives (1)
  • Minor (1)

Oral Candidacy Examination (if not completed in summer)
F31 Grant Proposal
PhD Dissertation

Spring

BSTA

FT Courses:

  • BSTA 920: Guided Dissertation Research (1)
  • Advanced Electives (1)
  • Minor (1)
  • F31 Grant Proposal (if not completed in fall)
  • PhD Dissertation

Summer

BSTA

PhD Dissertation

 

Years 4-5

Fall

BSTA

FT Courses:

  • BSTA 995: Dissertation Research (1)
  • Advanced Electives (1)
PhD Dissertation

 

7.4 Evaluation and Examinations

Evaluation for the MS degree is based on performance in the required and elective courses, and completion of the MS thesis/Biostatistics in Practice project.  Evaluation for the PhD degree is based on these criteria plus ongoing interactions with the faculty advisor(s), laboratory rotations, successful performance on the written Qualifications Examination, Candidacy and Dissertation Examinations, and the dissertation itself.

7.4.1 The Written Qualifying Examination (MS and PhD)

The following guidelines refer to the written Qualifications Examination required for all PhD students and optional for MS students in Biostatistics.  The Qualifying Examination Committee develops and administers the examination each year and presents the results to the full faculty.

Passing of the written Qualifications Examination is required for continuation in the PhD program.  This examination also satisfies the UPenn examination requirements as outlined below. 

7.4.2 MS Program Examination Requirements

Students in the MS program in Biostatistics are not required to take and pass the written qualifying examination. In order to obtain the degree, students will need to write and deposit an MS thesis and conduct an oral presentation of their work on one of the designated Biostatistics in Practice presentation days. MS candidates will have the option to take the exam if they are considering PhD work but it is not required. If the MS student passes the QE at the PhD level and is subsequently admitted to our PhD program, he/she will not need to take the exam again (if they pass one part and not the other and are subsequently admitted to the PhD program, they will need to retake the part of the exam that they did not pass).

7.4.3 PhD Program Examination Requirements

The written Qualifications Examination serves as the university-required “Qualifications Evaluation” as defined in the Graduate Studies catalog.  PhD students must pass the written Qualifications Examination as the first step toward full PhD candidacy.  The examination is offered each summer, in June, to allow for grading and faculty review such that students will have results before the July 4th holiday each year.  All full-time PhD students are expected to sit for the examination after their first year of study, with the option to retake the exam the following year if needed.  No student is allowed to take either part of the exam more than twice.

The exam consists of two parts: theory (“Part A”) and methods (“Part B”).  Students are given a grade on each part, and have up to two opportunities to take each part.  A student must receive a passing score at the PhD level on both parts of the exam to be considered to have passed.  Because the exam is offered only once a year, PhD students who do not pass one or both parts of the exam and elect to take it a second time have the opportunity to take two additional semesters of course work between examinations.  A PhD student who passes one part of the exam at the PhD level is not required to take that part a second time.

7.4.4 Examination Results and Notification

All matters pertaining to grading and review of the written qualifications examination by the faculty are confidential, but some general procedures are outlined here.

Once grading is complete (typically two weeks after the exam), the faculty of the Biostatistics program meet to review the examination.  The meeting also provides an opportunity to review the progress of all students in the program; grades, performance in lab rotations, and related materials may also be discussed in addition to the exam scores.  Because the difficulty of the examination may vary from year to year, there are no absolute cut-offs for passing.

For a PhD student, the examination has four possible outcomes:

1.    Pass at the PhD level.
2.    Pass only Part A (Theory) or only Part B (Methods) at the PhD level.
3.    Fail.

A PhD student who achieves outcome 1 is eligible to continue working to complete other PhD program requirements and, in particular, should begin the process of selecting a dissertation topic and advisor.  As described below, the oral Candidacy Exam is required within 18 months of the successful completion of the written qualifications examination.  Students will be strongly encouraged to take it the summer or early fall of the year after passing the written Qualifications Examination, especially if they have identified a topic/advisor through their lab rotations.  Students who do not meet this deadline will be on "academic probation".

A PhD student who achieves outcome 2 must re-take and pass the failed part at the next opportunity in order to continue in the PhD program.  A PhD student who has outcome 3 must re-take the entire exam, and pass both parts, at the next opportunity in order to continue in the PhD program. 

Each student who takes the exam receives written notification of his or her outcome as soon as possible after the faculty grading meeting.  No other information is made available before that time.  The letter notifies the student of the outcome of the exam, recommendations for continued study, and the process for discussion of the exam with the Examinations Committee.

Supplementary Oral Examination for Students Seeking an MS Who Fail at the MS Level

This oral examination is administered by a committee made up of three faculty members selected by the Chair of the Qualifying Examination Committee in consultation with the student’s academic advisor.  This supplementary oral exam should take place no later than the end of the fall semester following the distribution of the results of the written qualifying exam.  This examination is separate from the required presentation of MS thesis work (Biostatistics in Practice project) that is open to all students and faculty.

This oral examination is closed.  In order to provide focus for both the student and the exam committee, the examination begins with a brief presentation (no more than 20 minutes) by the student of the MS thesis.  The examination then focuses on methodology and applications related to the MS thesis. 

The faculty examination committee makes one of three recommendations for each student:  pass, conditional pass, or fail.  A student who successfully passes is eligible to continue in the MS program.  A conditional pass may be selected if the committee believes that there are specific weaknesses that can be addressed in a short time by the student.  For this option, the committee members must identify the area(s) of weakness, as well as specific remedies and a time frame for satisfying the conditions.  Possible remedies include, but are not limited to, repeat of the oral exam at a later date, writing a paper on a topic in statistics, or writing a paper on a data analysis covering the specific area(s) identified as requiring improvement.  The committee evaluates this work and makes a recommendation of pass or fail.  The student must satisfy the conditions of the pass within three (3) months of the oral exam.  A student who fails the oral examination is not eligible to receive the MS degree.

7.4.5 MS Students Applying to the PhD Program

Students enrolled in the MS program who wish to apply to the PhD program must submit a formal application.  As the written qualifications examination is typically administered in the summer after the first year of study, it is likely that the results will be known to the Admissions Committee.  The Admissions Committee determines how to use the results of the written examination in the admissions process.

MS students who pass both parts of the written qualifying examination at the PhD level on the first attempt and are admitted to the PhD program are not required to take a second examination.  MS students who pass only one part of the exam and are admitted to the PhD program are required to take the deficient part of the examination a second time and pass in order to continue in the PhD program.

7.4.6 Review of the Examination

A student who does not pass one or both parts of the examination at the intended level may request to review his/her exam paper with the Qualifying Examination Committee (QEC) chair and, optionally, his/her academic advisor.  The purpose of such a review is to help the student evaluate the types of mistakes made, identify areas where further study is needed, etc.  The QEC retains the graded exam papers and does not return them to the students.

A student may appeal the outcome of the qualifying examination to the QEC Chair, who together with the QEC membership evaluates the appeal and judges whether it has merit.  A grade can only be changed in cases of a specific error in scoring.  The QEC refers any grade change that could affect the student’s exam outcome to the full Biostatistics faculty, who decide whether to revise the exam outcome.

Because a minor revision of the score is unlikely to change the exam outcome, a student should only initiate a formal appeal if there were one or more egregious errors in the problem or in its grading, the correction of which would likely lead to a substantial increase in the score.  The QEC Chair can advise the student on the prospects for success of a proposed appeal.  A student who seeks a formal review must request it, in writing, from the QEC Chair within one week of the issuance of the letter notifying the student of the exam result.

7.4.7 Sickness Policy

A student who has declared an intention to sit for the exam, but at the time of the exam is too ill to attend, may request a deferment by contacting both his/her academic advisor and the Chair of the QEC.  A deferment can be granted only if the student provides a note from a medical doctor excusing him or her from the exam as a result of the illness.  The student may then be allowed to take the exam on or before the first business day when the note indicates that the student may return to work.  The decision to request a deferment must be made before taking the exam.  A student who takes any part of a day’s exam will be considered a complete exam and graded accordingly.

7.4.8 The PhD Candidacy Examination

In order to advance to candidacy for the PhD degree in Biostatistics, a student must successfully pass a candidacy examination.  This examination satisfies the requirements of the University’s required “Candidacy Examination” defined in the Academic Rules on the Provost website: https://catalog.upenn.edu/pennbook/academic-rules-phd/

The purpose of the candidacy examination is to evaluate whether the student is qualified to proceed to dissertation research.  Although the examination is structured around the dissertation proposal, it may also cover any material in the student’s course work.  This includes the core courses and other requirements, as well as the minor courses.  The examination should emphasize the student’s qualification to continue as well as the content of the dissertation proposal.  Committee members are encouraged to communicate to both the student and the dissertation advisor suggestions regarding the proposed research, as well as the feasibility of completing the project in a reasonable time

Candidacy Examination Committee Membership

The committee will consist of a minimum of three members, not counting the advisor(s), of whom two must be faculty members of the GGEB, and one must be an external (non GGEB) member. A GGEB faculty member will be appointed as the Chair of the committee by the student’s advisor. The role of the Chair is to run committee meetings and to oversee the candidacy examination and final defense. Committee members will be collectively responsible for administering and evaluating the oral Candidacy Examination, reading the dissertation, and evaluating the final defense. Additional content experts from within or outside the GGEB may be added to the committee as needed. The initial constituency and any changes in the membership must be approved by the Program Chair and the Graduate Group Chair. This Committee will be in place at all times during the dissertation phase. If for some reason, a student changes to a different area of research, a new Dissertation Committee must be appointed immediately and must meet within three months to discuss new plans for the dissertation research

Candidacy Examination Scheduling

To maintain good academic standing, students must advance to candidacy by 18 months after passing their written qualifications examination.  In typical cases this will occur no later than the beginning of the student’s fifth (spring) semester, although students are encouraged to complete their candidacy examination within one year of passing the written qualifications examination.  It is the responsibility of the dissertation advisor to work with the student to schedule the candidacy exam once the dissertation research has been clearly outlined.  The Program Chair will schedule the candidacy examination for any student who has not met this deadline.

Content of the Dissertation Proposal

The student should provide a written dissertation proposal to the committee at least two weeks prior to the scheduled examination date.  The members review the proposal and prepare questions for the exam.

The dissertation proposal should include a review of the literature relevant to the topic to be studied.  The proposal may, but need not, include preliminary research results.  The paper should be primarily a true proposal and should typically not exceed twenty pages.

The examination lasts up to two hours and typically includes three parts:  First, the student gives a formal presentation of the proposal, generally not to exceed 45 minutes (which may be extended if there are questions during the talk).  Next, committee members question the student on the proposal or on topics in biostatistics or the minor.  Once all committee members are satisfied that the questioning is complete, the student is asked to leave the room.  The committee then discusses the examination, votes the outcome (see below), and makes recommendations (if any) for future research and study.  The student is then readmitted and informed of the outcome.  The committee chair ensures that necessary forms are signed and returned to the graduate program office.

Candidacy Examination Outcomes

The candidacy exam has four potential outcomes:

  • Pass.  The student has sufficiently mastered the material and advances to PhD candidacy.
  • Conditional pass.  Additional evidence of mastery of the material is required, the nature of this evidence to be determined by the committee.  An example would be a revised dissertation proposal that better represents the nature of the problem to be studied.  Once all committee members agree that the additional requirements have been met, the outcome of the examination is changed to a “Pass”.  The student is not required to retake the candidacy exam.
  • Fail with possibility of retaking the examination.  The student has not mastered the required material and must retake the examination within 6 months in order to progress to PhD candidacy.
  • Fail without possibility of retaking the examination.  The student has not mastered the required material and the committee determines that the student should not continue in the program.
Retaking the Candidacy Examination

A student who fails the candidacy exam after taking it a second time, or who does not make a second attempt within six months of the first (unsuccessful) attempt, is automatically withdrawn from the program.

A student who has passed the candidacy exam but wishes to change dissertation topics must prepare a new proposal and submit it to his or her committee.  A discussion of the new proposal should be scheduled within three months of its submission.  If there is no substantial change in the statistical content area, the candidacy exam need not be retaken, and the committee need not be reconstituted.  If there is a substantial change in the statistical content area, the full committee determines whether an additional candidacy exam is required.  The student, the advisor for the new proposal, and the other members of the committee also decide on any changes in the composition of the committee.

7.4.9 Review of “Lab Notebook”

BGS mandates that the student’s dissertation committee review the student’s “lab notebook” at each of its meetings.  The Biostatistics PhD program interprets this to mean that the student should make available for faculty review, upon request, primary documentation of any substantial element of the dissertation.  Such a review takes place at the candidacy exam and any subsequent meetings of the committee, and following the closed session of the dissertation defense.  Examples of materials subject to review include the statement and formal proof of a key theorem; the code and results of a simulation study; or the data, code and results of a data analysis.  Prior to the meeting, the student’s advisor, in consultation with the dissertation committee, designates a short list of such items that the student makes available in electronic or hard-copy format. The committee chair sets aside time at the meeting for the review of this material. In keeping with the BGS policy, there is no expectation that the committee should scrutinize all such documents “in their entirety”; rather, the review should be sufficient to satisfy the committee that the student’s research records are “complete and well managed”.

7.4.10 Frequency of Dissertation Committee Meetings

Once a student has advanced to candidacy, his/her dissertation committee must meet at least once every six months to review goals and progress.  A review of the “lab notebook” (see above) must accompany each such meeting.  The advisor, working with the chair of the committee, schedules the meetings.  The student is responsible for providing any review materials needed by the committee in a timely fashion, typically at least two weeks before a meeting.

7.4.11 PhD Dissertation Examination

T his section provides guidelines for the content of the dissertation and the format of the defense. The Biostatistics Program follows the regulations described by BGS. The final steps toward the PhD degree are the preparation of an acceptable dissertation and the dissertation defense.  Refer to the Academic Rules on the Provost website: https://catalog.upenn.edu/pennbook/academic-rules-phd/

Permission to Write and Defend the Dissertation

The dissertation committee must formally grant permission to write the dissertation.  Students must submit the dissertation to the graduate group within six months of receiving permission to write.

If the student will not meet the six-month deadline, s/he must meet with the committee again before the end of the six months.  The committee will review the student’s progress and set a new deadline for the submission of the dissertation.  Under normal circumstances, no more than one additional month will be granted.  If the student does not submit the dissertation or meet with the committee during the six-month period, the graduate group will put the student on academic probation.  The graduate group’s academic review committee will determine whether the student should be given permission to defend the dissertation, and under what circumstances, or whether the student should be withdrawn from the program or offered a terminal Masters degree.

After the student submits the dissertation, the committee has up to one month to review it.  If the committee determines that the student must revise the dissertation prior to defending it, the student will have one month to make the revisions.

Once the committee approves the dissertation, the student will have one month in which to finalize the defense arrangements.  It is expected that the student will make tentative arrangements for the defense before this point.
Students Leaving the Department Prior to Defending the Dissertation

Refer to http://www.med.upenn.edu/bgs/dissertation_policies.shtml

Dissertation Level Students Changing Mentors

Refer to http://www.med.upenn.edu/bgs/dissertation_policies.shtml

Scheduling

The dissertation defense should be scheduled when the candidate and the dissertation advisor agree that the research is near completion and the draft dissertation is in a format suitable for distribution to the committee.  As soon as a date and time are fixed, the graduate program coordinator reserves a room (for at least two hours) and prepares the necessary public announcements.  In order to accommodate space and scheduling constraints, the date of the exam should be set at least one month before it will take place.  All dissertation committee members must attend the exam in person.

Content and Format of the Dissertation

A typical dissertation consists of five chapters: The first is an introduction and brief literature review; in many cases, this is similar to the dissertation proposal. The next three cover the three main topics of the dissertation; these may be written in a format suitable for submission as individual articles to peer-reviewed journals. The final chapter summarizes the dissertation findings and indicates possible future research directions. There are no upper or lower limits on the length of the document. It is the expectation that at least two of the three middle chapters will be methodological and have been submitted to peer-reviewed journals at least two weeks prior to the dissertation defense. Exceptions to this submitted paper requirement would need prior approval from the dissertation committee and the Chair of the Graduate Program.

Content and Format of the Defense

At least four weeks prior to the exam, the student should provide each committee member with a copy of the full dissertation.  The committee members review the dissertation and prepare exam questions based on it.  The defense consists of two parts:

  1. Open session.  The chair describes the process to all attendees and introduces the candidate. The candidate then presents his/her research in the style of a departmental colloquium. Typically, the candidate presents one chapter in depth, with a very brief overview of the others. This presentation should not exceed 45 minutes.  At the close of the formal presentation the candidate takes questions from the audience.  To leave sufficient time for the closed portion of the exam, the chair has the right to terminate the open session if it goes on beyond one hour.
     
  2. Closed session.  In this part of the exam, attended only by the student and the committee, committee members ask specific questions related to the dissertation.  Because the committee members have read the entire dissertation, this is their opportunity to ask questions about any part of it, including chapters not presented in detail in the open session.  Once all committee members are satisfied that the questioning is complete, the student is asked to leave the room. The committee then discusses the exam and votes an outcome (see below).  The student is then readmitted and informed of the outcome.  The committee chair sees that necessary forms are signed and returned to the graduate program office.
Dissertation Examination Outcomes

The dissertation exam has three potential outcomes:

  1. Pass.  The student has completed the dissertation requirements for a PhD in biostatistics.  The student then works with the graduate program coordinator to ensure that all other requirements are met prior to deadlines for the proposed graduation date.
  2. Conditional pass.  The defense was satisfactory but additional requirements must be met.  Commonly, the student is asked to address specific questions raised at the defense, or to incorporate edits proposed by committee members.  The dissertation advisor typically oversees these changes, but other committee members may also review changes at their discretion.  Once the additional requirements are met, the student is considered to have completed the dissertation.  The student is not required to defend the dissertation again.
  3. Fail.  The student must defend the dissertation again.
7.5 Teaching Assistants
7.5.1 Courses That Receive Teaching Assistants

The program assigns TAs to courses in the biostatistics graduate program, the Masters of Science in Clinical Epidemiology, and programs outside of the department such as the Biomedical Graduate Studies program, the Masters of Public Health, or the Masters of Science in Health Policy.  The Program Chair assigns TAs to courses based on course needs and student qualifications.

7.5.2 Students Who Serve as Teaching Assistants

All doctoral students are required to spend the equivalent of six hours per week for one semester serving as a TA (1 course unit). Some students serve as full-time TAs during a single half-semester, full semester, or the entire academic year as part of their financial support. In this case the expected workload is 14 to 20 hours per week during the semester. Other students are assigned to serve as part-time TAs or graders, in addition to their RAship, for a lesser number of hours.  Full-time doctoral students may be asked to teach in additional semesters to meet the needs of the department’s educational programs. Students who are fully supported on research assistantships or traineeships are eligible to receive supplementary compensation for additional teaching. Teaching must be completed outside of the hours required for a student’s research assistantship, and must be approved by the Director of Biomedical Graduate Studies.

Benefits and duties of Serving as a Teaching Assistant

In addition to being a degree requirement for all doctoral students, the teaching experience is an opportunity to work closely with a faculty member in the department, review and deepen understanding of the material being taught, and acquire and sharpen teaching skills.

TA duties typically include some or all of the following:
  • Attend regular meetings with the course instructor
  • Attend lectures
  • Hold office hours
  • Assist in or teach lab sessions
  • Assist in the preparation of written course materials, exams and solution sets
  • Grade assignments or exams and record the grades
  • Coordinate access to computing facilities, online data sets, and web applications

Timeliness in the completion of these duties is essential.  The course instructor and TA should communicate regularly to discuss duties, to share feedback from the students, and to ensure that the TA’s time is being used efficiently.  A student who feels s/he is spending on average more than the designated number of hours on teaching activities should speak to the instructor or, if concerns remain, with the Program Chair.  Both instructors and TAs should recognize that time pressures can vary greatly over the course of a semester. Open communication is the key to a successful teaching experience.

In cases where TA duties include assisting in the grading of exams, course instructors should provide the TA with clear guidance on how to assign points.  Instructors should also recognize that some students may feel awkward evaluating their peers.

TAs should share their e-mail addresses and mailbox locations with their students.  TAs are not on call for their students; nevertheless, students should expect reasonable access to TAs, particularly in the days leading up to exams and project due dates.

TAs are encouraged to speak with the instructor, their academic advisor and the Program Chair about their teaching experiences, particularly if difficulties arise. A potential conflict can often be avoided if its warning signs are recognized early and the situation is handled thoughtfully.

7.6 Other Policies
7.6.1 Student Travel

BGS allows doctoral students to apply for partial reimbursement (currently, up to $500/year) for travel to professional meetings if they are making a presentation.  Applicants must justify the expenses prior to attending the meetings.  Dissertation advisors sometimes are able to augment these travel funds.  In addition, some training grants provide funds for student travel.

7.6.2 International Students Travelling Abroad

Students are entitled to two weeks of vacation per year.  Unfortunately it is sometimes difficult for international students leaving the US to re-enter in a timely fashion, often due to visa issues.  While the program understands that these issues are largely out of the control of our international students, it also puts a strain on financial sponsors when students are unavailable to carry out the obligations of their research assistantships in person.  International students who leave the country for vacation must make a plan with their sponsor in advance to address the possibility of delayed re-entry.  The written plan must be approved by both the research sponsor and the Program Chair.  Sponsors are not required to allow students to work remotely and, in particular, are not expected to fund students to work remotely for indefinite periods of time.  International students should expect that funding will be suspended if suitable arrangements are not made and/or if students are absent for more than two weeks.

7.6.3 Registration in Biostatistics Courses

Any student who does not have dissertation status and who wishes to take a course in Biostatistics must formally register for the course.  The University reserves the term “auditor” for a student who registers for a course without the intention of receiving a grade and academic credit.  BGS PhD students are not allowed to audit a course. MS students may request a waiver of this policy from the Chair of the GGEB.

A student with dissertation status (i.e., who is paying dissertation fees and therefore does not pay for course units) may sit in on a course without registering for it.  Students who intend to participate in a course in this way must agree to participate in the course in a manner defined by the instructor, and must obtain the instructor’s prior approval.
7.7 Committees

Six committees provide governance and administrative leadership to the Biostatistics graduate programs. Membership is subject to change annually.

The Admissions Committee is responsible for the application and admission process.  Responsibilities include developing admission policies; identifying qualified students; reviewing applications; selecting students interviews; ranking students for admission; and reviewing applications from students in other BGS programs who seek to transfer into Biostatistics.  Admission decisions are subject to approval by the GGEB Executive Committee (a committee of the whole) and the BGS Admission Committee.  The chair of the Admission Committee, together with a designated representative from the Epidemiology PhD program, represents the GGEB in the BGS Admission Committee.

The Curriculum Committee is responsible for all rules and policies related to courses, MS theses and doctoral dissertations.  Responsibilities include developing policies related to course content; reviewing requirements for MS theses and PhD dissertations; approving proposals for the creation of new courses; and reviewing student course evaluations.

The Academic Advising Committee was created to facilitate the assignment of academic advisors, lab rotation mentors and to insure that each student is meeting program requirements in a timely fashion. This committee works closely with the curriculum committee to insure that all faculty mentors are up-to-date on curriculum and requirement

The Qualifying Examination Committee conducts the Program’s written qualifications exam. Responsibilities include developing guidelines, policies and procedures for the exam; soliciting questions for the exam; reviewing and selecting questions; creating the exam itself; managing its grading; presenting results to the faculty; and evaluating the merits of appeals of exam results.  Decisions on the outcome of the exam are made by the Biostatistics faculty assembled as a committee of the whole.

The Student Recruitment Committee conducts outreach to establish and maintain a pipeline of talented undergraduate students to apply to the GGEB MS and PhD programs in biostatistics. Activities include informational presentations to undergraduate departments of mathematics and statistics in Greater Philadelphia and additional targeted areas, attendance and recruitment at national undergraduate research conferences, creation and national circulation of program announcements, and communication with prospective applicants. The Student Recruitment Committee also aims to increase awareness and enrollment in Penn's summer undergraduate research opportunities in biostatistics.

The Student Awards Committee explores opportunities and supports applications for student awards. The Committee chooses the award winner for the Saul Winegrad Award for Best Dissertation. In addition, along with students in the program, the Committee nominates an outstanding faculty member for the Jane M. Glick Graduate Student Teaching Award.