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Welcome to CS793!


The Basics

Location and Time (Winter 2013)

  • DC2585 (note change - was originally DC3313)
  • Tuesdays 14:30-17:20 (2:30pm-5:20pm)


  • Jesse Hoey
  • Any queries about the course should be directed to the Piazza discussion board
  • Private questions can be emailed directly to the instructor - email him jhoey <at> cs.uwaterloo.ca



(these texts are for reference only in the course, you do not need to purchase them)

  • Edward H. Shortliffe and James J. Cimino "Biomedical Informatics: Computer Applications in Health Care and Biomedecine". Third Edition, Springer, 2006

(parts are avaialable online)

  • The Handbook of Biomedical Informatics is all free and can be downloaded as a single (800 page!) PDF.
  • Ira J. Kalet "Principles of Biomedical Informatics". Academic Press, 2009.

Important Dates

  • First Class: Jan 8th, 2013 at 2:30pm (DC2585)
  • Wiki updates: Jan 22nd, 2013 at 12:00pm (noon), and every Tuesday at noon thereafter
  • Project proposals (PDF ONLY by email): Feb 1st, 2013 at 5pm
  • Final projects (PDF ONLY by email): April 8th, 2013 at 5pm

The Details

The course is structured around a set of "topics" in health informatics. The topics are a developing set (so new topics can be added, old topics can be split, merged, etc).

Lecture time will be a mixture of

  • Invited lecture by an expert in the field (see the Schedule) covering one of the topics of interest
  • Student-led presentation of their research on a topic, followed by in-class discussion

Students are responsible for the following:

  1. A final course project (40%)
  2. A project proposal (10%)
  3. Weekly edits to the wiki (30%)
  4. In-class presentations (20%)
  5. Participation in class and online Piazza/Wiki (as measured by the EAF)

Student responsibilities

Each week, each student should:

  • attend class,
  • choose some content (paper, book, webpage, software or hardware), usually of relevance to their project topic, but not necessarily so. The content can be research questions posed by the invited speaker from the previous weeks,
  • study the content and make an update to the wiki, with proper citations to materials,
  • engage in discussion about their updates, either on Piazza or in the Discussion pages of the wiki. Start these discussions by posing a Piazza question to the class about what you are working on. Engage in the discussions by reading other student's questions and posting replies. The posting student can integrate the discussions into his/her wiki update.

Additionally, each week, four students will:

  • present their content study (each student will give two presentations during the term, each lasting 10 minutes including discussion). Students can also choose to present an update on their course project work, provided this is also added to the wiki as above.

Finally, in the last two weeks of class, all students will:

  • present their project in class (20 minutes per presentation including discussion).

Wiki Updates

Wiki updates should take the form of a paragraph describing a paper, software, hardware, newsworthy advance, etc., and must:

  • be written in proper English
  • have at least one reference, and this be proper (see Citations Help)
  • make relevance to computational health informatics clear

Wiki updates can also be edits to previous updates, so long as the edit is sufficiently involved (i.e. not just typographical)

Wiki updates will be scored each week at 12pm on Tuesdays. Each student will receive marks only if they have added at least 500 characters of text: 0.5 for doing at least this much, and another 0.5 unless one of their edits is randomly sampled and shows no relevance to the wiki topic in any way (i.e. is spam). Each week, 5% of the wiki updates for the week will be randomly sampled and checked by the instructor. Furthermore, all wiki deletions will be checked. The total grade for the term will be the average of all weekly grades.


Students should prepare a brief presentation (maximum 10 minutes), to be delivered to the class. Presentations must be

  • clear and concise
  • make some kind of point
  • be responsive and engaging with the audience

The presentation can be based around the wiki update made, but could be done using separate slides or other visuals. Presenters should try to make the presentations engaging for the audience (make it fun!) and so can include audience participation, etc. Presentations will be graded as pass or fail, and this will be communicated to the student by email after the presentation. An 8 minute talk that does a reasonable job of communicating an idea, and includes any discussion from the class will be deemed a pass.


Students also must complete an individual course project. Group projects will be considered only in exceptional cases where a significant amount of work in different areas is required (e.g. if a user study is planned, requiring ethical aprpoval). More details on projects can be found here. A written project proposal must be submitted early in the term, and a written report must be submitted in the last week of class. The final classes will include short presentations of each project. The entire project is worth 50% of the final mark: (proposal=10%, final report=40%).

The project reports will be evaluated on three main criteria, with weights as shown. These are used as guidelines for the instructor when evaluating the work. For some types of project (e.g. literature reviews), these are modified slightly (e.g. it is hard to cover assumptions in literature reviews, so this will not be expected).

  • Completeness (60%): does the report state contributions, claims, assumptions, strengths and weaknesses? Does the report have an abstract that clearly defines the work and results? Does the report give a complete overview of the methods used? Does the report provide a discussion that appropriately summarises the work? Are there experimental or theoretical results to back up the claims?
  • Clarity (30%): is the critique clear, readable, and free of spelling and grammar errors, and presented using the required format?
  • Originality (10%): does the report uncover something novel? You do not need to invent time-travel to get this extra 10%! An original take on an old problem, or an original problem statement can be sufficient. Clearly state in your report what is novel about your work!

Late reports will not be accepted.

Effort Adjustment Factor

Final marks will be multiplied by an Effort Adjustment Factor between 0.95 and 1.05, contingent on the participation and effort students put into the class. The vast majority of students will have an EAF of 1.0 and should not be concerned by this.

However, success of the course as a useful learning experience hinges on active participation and effort of the students. Students are expected to attend all classes and are expected to actively participate in both in-class and online discussion and presentation sessions. The EAF of a student may be adjusted to reflect their level of participation if it falls outside what is expected. Students demonstrating an effort that goes above and beyond the class requirements in other ways may have their EAF adjusted to reflect their effort.

Remember: always edit as yourself (so the history shows your contributions)

Academic Integrity

All submitted work (wiki updates and project reports) should be the submitting student's own work, and should bear his/her name as author (for wiki edits this means editing as yourself and you must have a username that can be used to uniquely and easily identify you - e.g. your name). Any evidence of writing from a different person or source will be considered plagiarism and will be dealt with as such (see University policy below). A few simple rules may help you here:

  1. ALWAYS write your own submitted work.
  2. CLEARLY indicate contributions from anyone else: enclose the text in "quotations" and CLEARLY indicate the source right next to the text. Just citing the work that you are quoting from at the end in the bibliography is NOT sufficient. Rule 2 must be applied IMMEDIATELY upon putting any text or image that is not your own into your document. Don't wait, you'll regret it later when you submit your work but have forgotten to go back and put in the citation.
  3. DON'T cut and paste.
  4. If you do cut and paste (remember: don't cut and paste - see rule 3), then apply rule 2 IMMEDIATELY.
  5. DON'T cite Wikipedia or other publicly generated web content. Read about citing Wikipedia or other web content.

University of Waterloo Academic Integrity Policy

The University of Waterloo Senate Undergraduate Council has also approved the following message outlining University of Waterloo policy on academic integrity and associated policies.

Academic Integrity

In order to maintain a culture of academic integrity, members of the University of Waterloo community are expected to promote honesty, trust, fairness, respect and responsibility. Check the Office of Academic Integrity's website for more information. All members of the UW community are expected to hold to the highest standard of academic integrity in their studies, teaching, and research. This site explains why academic integrity is important and how students can avoid academic misconduct. It also identifies resources available on campus for students and faculty to help achieve academic integrity in — and out — of the classroom.


A student who believes that a decision affecting some aspect of his/her university life has been unfair or unreasonable may have grounds for initiating a grievance. Read Policy 70 — Student Petitions and Grievances, Section 4. When in doubt please be certain to contact the department's administrative assistant who will provide further assistance.


A student is expected to know what constitutes academic integrity, to avoid committing academic offenses, and to take responsibility for his/her actions. A student who is unsure whether an action constitutes an offense, or who needs help in learning how to avoid offenses (e.g., plagiarism, cheating) or about "rules" for group work/collaboration should seek guidance from the course professor, academic advisor, or the Undergraduate Associate Dean. For information on categories of offenses and types of penalties, students should refer to Policy 71 — Student Discipline. For typical penalties, check Guidelines for the Assessment of Penalties.

Avoiding Academic Offenses

Most students are unaware of the line between acceptable and unacceptable academic behaviour, especially when discussing assignments with classmates and using the work of other students. For information on commonly misunderstood academic offenses and how to avoid them, students should refer to the Faculty of Mathematics Cheating and Student Academic Discipline Policy.


A decision made or a penalty imposed under Policy 70, Student Petitions and Grievances (other than a petition) or Policy 71, Student Discipline may be appealed if there is a ground. A student who believes he/she has a ground for an appeal should refer to Policy 72 — Student Appeals.

Note for students with disabilities

The Office for Persons with Disabilities (OPD), located in Needles Hall, Room 1132, collaborates with all academic departments to arrange appropriate accommodations for students with disabilities without compromising the academic integrity of the curriculum. If you require academic accommodations to lessen the impact of your disability, please register with the OPD at the beginning of each academic term.

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