BMI 5/625, Spring 2023

Course policies and grading

Grading Breakdown

Attendance at all sessions and labs; other participation.
Completion of all lab activities
Written Assignments (inc. KWLA essay)
As described
Final Project
As described

Attendance & Participation

Attendance is required. If you need to miss a class, I will need advance notice except in cases of emergencies.

In addition to attending each class session, I expect all students to actively participate in the discussions. This can be in the form of asking a question, responding to another student’s question (or one from the instructor!), raising an issue, etc.

While the class will be in-person this year, I will be setting up Webex streaming for those who are unable to make it up to campus. That said, the room we are teaching in is not set up optimally for hybrid education, and the experience may be less than ideal- please stay in communication with me about this aspect of the class.

Plagiarism & Attribution

We expect and require that all submissions be the student’s own, original work. Any and all text, code, figures, etc. that you include from any other source must be properly cited, including quotation and paraphrasing. The Purdue University Online Writing Lab has an excellent set of online resources regarding citation and attribution, as well as a useful resource specifically on avoiding plagiarism. If you are unsure about whether something must be cited, the answer is probably “yes”; when in doubt, please ask.

Note that the School of Medicine has a policy regarding ethical and professional conduct for graduate students that specifically addresses plagiarism (sections 4.b and 4.c). We expect all students to be aware of and familiar with this policy. If you have any questions about this policy, please ask.

On a more personal note: in my experience, students who engage in plagiarism typically do so because they feel that they have no other choice. A deadline is looming, they are overwhelmed by some aspect of the assignment, a personal crisis comes up that keeps them from being able to finish, etc., and they feel like using somebody else’s work, or reusing some of their own work from another class, is the best option available. I can 100% guarantee that this is not the case: you have other options, and choosing plagiarism will not result in a good outcome.

When we catch you, the consequences will depend on the precise circumstances, but will at a minimum involve a score of zero points for the assignment in question, and often involve a failing grade on the course.

So: don’t wait for me to catch you: ask for help early and often.

Code Snippets and AI Tools

Automated code- or text-generation tools such as GitHub’s Copilot or OpenAI’s ChatGPT, and image-generation tools like Midjourney and DALL-E, pose a particular challenge to both students and instructors. As a guiding principle, recall that we expect and require that all submissions be your own, original work. When considering using such a tool, ask yourself: will the tool’s output be something I will be turning in directly? In general, you may use such tools as a source of information, but not to produce output that you intend to turn in or as a replacement for a traditional cited reference.

Here are examples of appropriate, in-bounds uses of AI text-generation tools:

Here are examples of inappropriate, out-of-bounds uses:

Out-of-bounds uses of AI tools will be screened for and treated in the same manner as other forms of plagiarism; if you are uncertain about whether your use is in- or out-of-bounds, please ask. And if you think up an interesting or helpful (in-bounds) use case for these technologies, please feel free to share it on the class Sakai forum!

This technology is very new and is also developing rapidly, so there may be situations and use cases that this policy does not address- we are figuring this out together, in real-time!

Some Notes on Citing AI Tools

One might ask, “why can’t I just cite ChatGPT’s output like I would any other source?” There are several reasons:

  1. The output of tools like ChatGPT is not deterministic, so a citation would not necessarily allow your reader to see the same “original” information as you saw at the time of writing (i.e., one of the more important reasons to cite something in the first place).
  2. Part of the point of citing a source is to allow your reader to see where you got your information, so as to be able to learn more about the subject or understand the context of your quotation. ChatGPT (and other such tools, such as Google’s Bard and Microsoft’s Bing)) are designed in such a way that they are not able to provide documentation or any other factual basis for their output, and as such a citation would not be helpful in this way.
    • Note that while Bing often appears to be providing sources for its information, this is not actually the case from a technical standpoint. Because of how the model works, those sources are often incorrect or even entirely confabulated (see point 5 below) and should not be relied on as evidence of its output’s veracity.
  3. Another, closely related, reason for citing sources is that it allows the reader to critically evaluate the veracity, quality, credibility, and perspective of your source (“do they know what they are talking about?”, “what sort of biases and context might they have that would affect their opinion?”). ChatGPT and related tools do not provide us with any way to make this assessment, so a citation is not helpful for this purpose.
  4. One of the main purposes for citing a source is to give credit to the source’s author for their work and expertise; ChatGPT is not a person (as it will be the first to point out), and as such, cannot be so credited.
  5. ChatGPT (and other such tools) frequently produce output that is confabulated - “made up”, in other words. This is different from information that is merely inaccurate, outdated, or otherwise “wrong”; sources providing such information may be mistaken, but they are mistaken for a knowable reason, and in a scholarly context it is usually safe to assume that their author believed their contents to be true at the time that they wrote it. This is qualitatively different from the way that ChatGPT and its cousins work: they are not “wrong” for any predictable, consistent, or ontologically grounded reasons. Citing their output is meaningless, as the output does not reflect an actual claim about the state of reality. Citing confabulated information is not helpful; if you have verified the accuracy of ChatGPT’s output (by cross-referencing it with a more authoritative source), you should cite that source, instead.
  6. Finally, ChatGPT (and similar tools) are built by incorporating the creative and scholarly work of countless actual humans, and the output of these tools often includes verbatim or paraphrased portions of that database- in other words, ChatGPT’s output often includes plagiarized text. Citing this and crediting it to ChatGPT would be mis-allocating credit that is owed to the actual people who made the content that ChatGPT is regurgitating.

Additional Policies

See the syllabus page on Sakai for a full list of university policies, etc.

Accessibility & Accomodations

I would like to make an additional note regarding accessibility and accommodations. The syllabus link above will include the University’s official language about accessibility, and will list the various resources that you have available to you. While comprehensive, the official verbiage is pretty dense; in the past, some have found its “legalese” language to be off-putting or unclear. I am committed to helping each of you succeed to the best of my ability, and I fully support the University’s Office of Student Access.

If you anticipate needing any kind of accommodation, I encourage you to reach out to the Office of Student Access or to myself as early as possible in the term. I will be able to help you more effectively if we begin our discussions around your needs earlier rather than later. If you have a need that is not covered by the OHSU accessibility and accommodation policies, or if you have questions or concerns about anything along these lines, please do not hesitate to ask me for information or help.