Advanced Computer-Integrated Surgery (CIS II)
CIS II (601.456/496/656/356) is a projects course for graduate students and upper-level undergrads, in which students work in teams of 1-3 on semester-long projects broadly related to computer-integrated interventions, AI in medicine, medical image analysis, or related topics. In addition to material covered in lectures/seminars by the instructor and other faculty, students are expected to read and provide critical analysis/presentations of selected papers in recitation sessions. Students taking this course are required to undertake and report on a significant term project under the supervision of the instructor and clinical end users. Grades are based both on the project and on classroom recitations. The only difference between the undergraduate versions (601.456/496) and the graduate version (601.656) of this course is the level of project undertaken. Typically, 601.656 projects require a greater degree of mathematical, image processing, or modeling background. Students wishing to attend the weekly lectures as a 1-credit seminar should sign up for 601.356.
Instructor: Russell H. Taylor (rht@jhu.edu)
Course number: 601.456/601.496/601.656/601.356 (formerly 600.446/646/346)
Prerequisite: CIS I or permission of instructor.
Teaching Assistant: Juan Barragan
* Meeting times and place: Tuesdays and Thursdays 1:30-2:45 in Hackerman Hall Room B17 (basement auditorium)
Note: This class is intended to be in-person. However, we will provide a
Zoom link for people who have a legitimate reason (e.g., illness) for missing a class or for guests. After the first couple weeks, this link will have a passcode, which can be obtained from the TA or the Instructor.
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Note: We will use Canvas only in a very limited way. This Wiki site is the main web site for CIS II. We will use
Piazza for most routine communication.
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Projects in 2023
Projects in Prior Years
Some of the projects may involve potentially patentable or otherwise confidential material
Premature disclosure can compromise patentability
Student inventors can get patents and licensing income
Some projects (e.g., those using ISI
API data) may require students to sign a separate non-disclosure agreement with a company.
Students need to close the loop with the Instructor on projects involving 3rd party confidential data, to be sure that something is publishable. Usually, this has not been a problem, but should be addressed early.
Web sites for these projects will be only accessible by Instructor, the TA, the students involved, and the mentors. Access will remain restricted for about a year, unless other arrangements are made between the Instructor, the students, and the project mentors.
The whole class will sign a non-disclosure agreement to cover in-class presentations and discussion (JHTV has provided a template). This year, we will use this
online form for the agreement.
Students who are uncomfortable with this should contact the Instructor immediately to see if an accommodation is possible.
CIS II Resources
Personal Well-Being
Academic Resources
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Human Subjects Research:
Many projects involve some sort of user study or (less commonly) access to clinical data or clinical research at the School of Medicine. For these projects, a research protocol approved by an Institutional Review Board (IRB) is required.
You should note that an approved protocol is a project dependency in your planning process if you plan a human subjects protocol.You should consult with your project mentors on what sort of protocol is needed and start the process of obtaining approval early in the semester, since the process can take a long time.
For most user studies conducted on the Academic Campus, the
Homewood IRB (HIRB) is appropriate. The
investigators page on the HIRB web site has useful information. Note that all team members on HIRB protocols must have completed human subjects research training. You can refer to the web page
Steps for Creating a CITI Account and Completing Human Subjects Research Training to learn how to get this training. Note that you should contact the HIRB via email at email hirb@jhu.edu or call 410-516-6580 to be sure that you sign up for the correct training. The HIRB can also provide other useful advice.
Ethics
The strength of the university depends on academic and personal integrity. In this course, you must be honest and truthful. Ethical violations include cheating on exams, plagiarism, reuse of assignments, improper use of the Internet and electronic devices, unauthorized collaboration, alteration of graded assignments, forgery and falsification, lying, facilitating academic dishonesty, and unfair competition.
You should be aware of (and follow) the JHU's policies for responsible conduct of research. Training is available at http://eng.jhu.edu/wse/page/conduct-of-research-training.
Report any violations you witness to the instructor. You can also contact:
For undergraduates: the director of student conduct (or designee) by calling the Office of Student Conduct at 410-516-2509 or via email at studentconduct@jhu.edu
For KSAS Graduate Students; rseitz5@jh.edu
For WSE Graduate Students: christinekavanagh@jhu.edu
Classroom Climate
I am committed to creating a classroom environment that values the diversity of experiences and perspectives that all students bring. Everyone here has the right to be treated with dignity and respect. I believe fostering an inclusive climate is important because research and my experience show that students who interact with peers who are different from themselves learn new things and experience tangible educational outcomes. Please join me in creating a welcoming and vibrant classroom climate. Note that you should expect to be challenged intellectually by me, the TAs, and your peers, and at times this may feel uncomfortable. Indeed, it can be helpful to be pushed sometimes in order to learn and grow. But at no time in this learning process should someone be singled out or treated unequally on the basis of any seen or unseen part of their identity.
If you ever have concerns in this course about harassment, discrimination, or any unequal treatment, or if you seek accommodations or resources, I invite you to share directly with me or the TAs. I promise that we will take your communication seriously and seek mutually acceptable resolutions and accommodations. Reporting will never impact your course grade. You may also share concerns with the department chair ([Chair’s Name and Email]), the Director of Undergraduate Studies ([DUS Name and Email]), the WSE Assistant Dean for Diversity and Inclusion (Darlene Saporu, dsaporu@jhu.edu), the KSAS Assistant Dean for Diversity and Inclusion (Araceli Frias, afrias3@jhu.edu) or the Office of Institutional Equity (oie@jhu.edu). In handling reports, people will protect your privacy as much as possible, but faculty and staff are required to officially report information for some cases (e.g., sexual harassment).
Guests and Family Members
Occasionally students may wish to have a guest attend class. You should discuss this with me before the class, in order to be sure that we can accommodate request in a manner consistent with non-disclosure agreement. Generally, this will require that anyone presenting potentially confidential material on the day in question agree to the visitor seeing the material presented and that the presence of the guest be known to the entire class. It may also require the guest to sign the non-disclosure agreement. Similarly, one should not share the video link with any third party or permit any third party to view the “live” video or video recording without my explicit permission in writing.
Family accommodations policy: Occasionally, you may need to bring a family member to class when your responsibilities require it (for instance, if emergency child care is unavailable, or for health needs of a relative). In these cases, it usually will be better to view participate using the video link. However, if this is not possible, then discuss the situation with us beforehand and we will work with you to find a suitable accommodation. Please be sensitive to the classroom environment, and if your family member becomes uncomfortably disruptive, you may leave the classroom and return as needed.
Incompletes
There are important revisions to the Incomplete Grade policy in effect for the 2022-2023 academic year. The following text is an excerpt from the full policy:
A request for an Incomplete grade must be initiated by the student no later than the last day of classes via the Incomplete Grade Contract available in SIS
The required elements on the Incomplete Grade Contract are listed below; all of these topics should be included in the conversation between the student and the instructor:
The reason for the request for an incomplete grade
A description of all outstanding work that must be completed
Date the work is due from the student
The reversion grade if the student does not complete any of the outstanding work
Instructors are required to submit the new grade to the Office of the Homewood Registrar no later than 45 calendar days after the last day of classes. If the Incomplete grade is not resolved within 45 calendar days after the last day of classes, the Incomplete grade is automatically converted to the reversion grade.
