BMIN 5200 — Foundations of Artificial Intelligence in Health

Course materials for BMIN 5200, Perelman School of Medicine, University of Pennsylvania.

Fall 2026 moved this course off Canvas. Canvas is still used for assignment submission and grades, because Penn requires it; everything else — the schedule, the slides, the papers, the assignment specifications, and the in-class coding notebooks — lives here and on Penn Box.

Layout

new-course-site/       The public course site. One hand-written HTML file.
exercises/             13 Colab-ready notebooks; 12 are scheduled this year.
tools/                 extract_imscc.py, apply_links.py
old-canvas/            The Canvas export and a readable extraction of it.  [not committed]
links.tsv              Every Box URL in the project, in one table.
syllabus-2026.tex      Syllabus source. Run ./build-syllabus.sh, commit the PDF.
build-syllabus.sh      Compiles the syllabus into new-course-site/ (reproducibly).
journal-club-2026.md   Paper selection and format for the reduced journal club.
SETUP.md               Student-facing software setup: Colab, local Python, submission.
LICENSE                CC BY-NC-SA 4.0, covering the public course material.
NOTICE.md              What the licence does and does not cover. Read before reusing.
.github/workflows/     pages.yml — builds and deploys the site on push to main.

What is not in the repository

old-canvas/ is gitignored and stays in the Box folder only. It is 763 MB of copyrighted journal club PDFs, the 2025 decks, assignment archives, and two 228 MB cartridge files — GitHub rejects anything over 100 MB, and this repository is public because the Colab links require it. It is source material for the refactor, not part of the course site.

Everything else is committed. In particular exercises/ must be: the notebook links on the site are colab.research.google.com/github/RomanoLab/bmin5200/blob/main/exercises/weekNN.ipynb, which Colab resolves against the public repo. No notebooks in the repo means a page of dead links. tools/ and links.tsv must be there too — the deploy workflow runs apply_links.py from the repository root.

Publishing the site

The site is live at https://bmin5200.jdr.bio (GitHub Pages, custom domain).

Pushing to main publishes it. .github/workflows/pages.yml runs tools/apply_links.py — which fills the LINK:: placeholders from links.tsv into build/ — and deploys build/new-course-site/. build/ is generated and gitignored; nothing about the deploy needs doing by hand.

To see which Box URLs are still unfilled:

python3 tools/apply_links.py --check

Details, including how the custom domain is wired up, are in new-course-site/README.md.

What changed from Fall 2025

Journal club halved. 22 papers (two a week) became 11 (one a week). Students now present in pairs, so everyone still presents exactly once. See journal-club-2026.md.

Coding exercises added. The reclaimed ~25 minutes each week goes to a hands-on notebook. Previously the only code students wrote was in four take-home assignments; the first of those contains no code at all. See exercises/README.md.

Calendar rebuilt for 12 meetings. Penn's Fall 2026 breaks (Oct 1–4, Nov 26–29) take out two Thursdays, and Sep 24 was cancelled after the calendar was set. Twelve meetings, twelve lecture topics, one per week; the agentic AI lecture came out to absorb the lost week. No class time is spent on final presentations — those remain recorded videos, as in 2025.

Materials moved to Box. Slides and journal club PDFs are behind PennKey SSO. Nothing copyrighted is committed to this repository.

Lecture content itself is unchanged. The decks are the 2025 decks.

The Canvas export

old-canvas/ holds the original .imscc cartridge and extracted/, a readable copy produced by tools/extract_imscc.py. An .imscc is a plain ZIP of IMS Common Cartridge XML — the extractor walks the manifest and writes Markdown with the Canvas metadata preserved as YAML frontmatter.

To regenerate:

python3 tools/extract_imscc.py old-canvas/*.imscc -o old-canvas/extracted

Two things the export did not contain, worth knowing if you ever need to go back to it: the manifest's <organizations> block is empty, so the Canvas module structure did not survive, and wiki_content/ is empty, so there are no Pages. Student submissions and grades are never included in a cartridge.

Licence

The public course material here — notebooks, site, syllabus source, and the structure of the course — is under CC BY-NC-SA 4.0: share and adapt with attribution, non-commercially, under the same terms. Instructors elsewhere are welcome to it.

Material behind a PennKey login (slides, journal club papers, assignment files, class recordings on Canvas or Box) is not covered and must not be redistributed — much of it is publisher-copyrighted and not the course's to relicense. See NOTICE.md.