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)
  • Note: 601.496 is identical to 601.456, except students must be members of a 3 person team. This option is provided for CS undergrads seeking to satisfy the “team” degree requirement.
• Prerequisite: CIS I or permission of instructor.
• Teaching Assistant: Juan Barragan
  • Email: jbarrag3@jh.edu
  • Office Address: Hackerman 137
  • TA office Hours: By appointment
• * 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.
• Canvas link: https://jhu.instructure.com/courses/37966
  • 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.
• Piazza page (for communication): https://piazza.com/jhu/spring2023/cs601456496656/home
  • Self signup link: https://piazza.com/jhu/spring2023/cs601456496656

• Course kickoff slidescis_ii_kickoff_-_2023.pdf
• PDF copy of course syllabus. However, the key (and controlling) information is on this website.

• Follow this link for CIS II Projects for Spring 2023
  • Word file template and instructions for CIS II Project Mentors reports
• Follow this link for CIS II Spring 2023 class schedule

• Template for faculty and other mentors wanting to propose projects
• Nondisclosure agreement (NDA) to facilitate in-class discussions (2023 - Online form)
  • PDF of NDA for your reference
• Final Poster Template
• Final Presentation Poster Teaser Template

• Follow this link for CIS II Projects for Spring 2011
• Follow this link for CIS II Projects for Spring 2012
• Follow this link for CIS II Projects for Spring 2013
• Follow this link for CIS II Projects for Spring 2014
• Follow this link for CIS II Projects for Spring 2015
• Follow this link for CIS II Projects for Spring 2016
• Follow this link for CIS II Projects for Spring 2017
• Follow this link for CIS II Projects for Spring 2018
• Follow this link for CIS II Projects for Spring 2019
• Follow this link for CIS II Projects for Spring 2020
• Follow this link for CIS II Projects for Spring 2021
• Follow this link for CIS II Projects for Spring 2022

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.

• Students who are struggling with anxiety, stress, depression or other mental health related concerns, please consider connecting with resources through the JHU Counseling Center. The Counseling Center will be providing services remotely to protect the health of students, staff, and communities. Please reach out to get connected and learn about service options based on where you are living this fall at 410-516-8278 and online at http://studentaffairs.jhu.edu/counselingcenter/.
• Because of the ongoing COVID-19 pandemic special requirements may be in effect this term, and these may vary during the term. Please keep updated with these at the following sites:
  • University information: https://covidinfo.jhu.edu/
  • Whiting School of Engineering information: https://engineering.jhu.edu/covid-19/
  • COVID-19 vaccination is required unless an exception has been granted by the university for health or religious reasons.
• If you are sick please notify us by email and/or Piazza so that we can make appropriate accommodations should this affect your ability to attend class, complete assignments, or participate in assessments. The Student Health and Wellness Center is open and operational for primary care needs. If you would like to speak with a medical provider, please call 410-516-8270, and staff will determine an appropriate course of action. See also https://studentaffairs.jhu.edu/student-life/student-outreach-support/absences-from-class/illness-note-policy/
• If you are struggling with anxiety, stress, depression, or other mental health related concerns, please consider visiting the JHU Counseling Center. If you are concerned about a friend, please encourage that person to seek out their services. The Counseling Center is located at 3003 North Charles Street in Suite S-200 and can be reached at 410-516-8278 and online at http://studentaffairs.jhu.edu/counselingcenter/
• Johns Hopkins University values diversity and inclusion. We are committed to providing welcoming, equitable, and accessible educational experiences for all students. Students with disabilities (including those with psychological conditions, medical conditions, and temporary disabilities) can request accommodations for this course by providing an Accommodation Letter issued by Student Disability Services (SDS). Please request accommodations for this course as early as possible to provide time for effective communication and arrangements. For further information or to start the process of requesting accommodations, please contact Student Disability Services at Homewood Campus, Shaffer Hall #101, call: 410-516-4720 and email: studentdisabilityservices@jhu.edu or visit the website https://studentaffairs.jhu.edu/disabilities/

• Resources for Students from the JHU Office of Academic Support
• Whiting School of Engineering Responsible Conduct of Research Training Policy

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

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).

• 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.

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:

1. 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
2. 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
3. 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.