BMI 5/625, Spring 2024

Course policies and grading

Grading Breakdown

Participation
20%		 Attendance at all sessions and labs; other participation.
Labs
40%		 Completion of all lab activities
Written Assignments (inc. KWLA essay)
20%		 As described
Final Project
20%		 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.

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, and that part of the point of this class is to develop your own practical abilities. 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 (though see the note below), 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. 🤘

Note: Regarding the use of ChatGPT or similar tools as informational resources, it is important to keep in mind that ChatGPTs output often contains “confabulations”: content that is not “real”, and that the language model has “made up”. I have personally seen ChaGPT suggest the use of R packages that do not exist, give incorrect information about how certain things work in ggplot, etc. In the context of a background section or literature review, this means that you will likely find yourself spending a great deal of time attempting to find non-existent articles and books; it is best to think of a ChatGPT-generated literature review as being closer to “fan-fiction” than an actual review. Remember, you are responsible for the veracity and accuracy of anything you turn in.

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 (which is 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.

A Note on Accessibility & Accomodation

Over the last year I have encountered multiple students and colleagues who have found resources such as ChatGPT to be helpful tools in their toolboxes for managing various aspects of their neurology in an academic setting, e.g. as a way to help them organize their thoughts in writing, or to overcome executive function challenges. As they have been described to me, many of these sorts of uses would ordinarily fall “out of bounds” according to the strictest interpretation of this policy. However, if you are in need of an accomodation involving the use of generative AI tools, please do not hesitate to reach out to me or the office of student access; we have robust and flexible policies on accomodation (see below) and I am very willing to discuss this issue.

Useful Readings about AI Tools

Here are a few (very) recent discussions on how to think about generative AI tools that you may find helpful and informative:

  1. Shanahan M. Talking about Large Language Models. Commun ACM. 2024 Feb;67(2):68–79.
  2. Fraser C. Generative AI is a hammer and no one knows what is and isn’t a nail. Medium.com [Internet] Posted Feb. 21 2024, cited Mar. 30 2024. (Wayback Machine Snapshot)

When I’m not teaching data visualization, language models are one of my core areas of academic research. As such, if you are interested in digging further into this space, please reach out and I can send you more pointers of things to read.

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.