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# Replacing the current Hugging Face repository
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This tree is a rebuild of `ChatterjeeLab/CIS6270` from the final lecture notes. Everything in it is
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new except the four files listed under "keep" below.
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## Keep from the current repository
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| File | Why |
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| --- | --- |
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| `lecture_2/flow_unet_mnist.pt` | The published five-epoch checkpoint. `lecture_2/flow_matching_mnist.py` still defines `FlowUNet` with the same state-dict keys, so the file loads unchanged. Move it to `lecture_2/`. |
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| `lecture_2/mnist_selected_examples.png` | The selected generations in the Lecture 2 guide. |
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| `lecture_2/mnist_selected_trajectories.png` | The noise-to-image trajectories in the same guide. |
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| `LICENSE` | Unchanged, MIT. |
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The overview figure at the top of the README is hosted on the Hugging Face CDN and is linked, not
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stored, so it carries over on its own.
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## Delete
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Everything else. The old tree held 67 files per lecture folder of which most were generated:
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- `run.py`, `run_all.py`, `lecture_core.py`, `common.py`, `diffusion.py`, `flows.py`, `examples/`.
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One file per framework replaces the dispatcher, so a method is read in one place.
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- `verified_examples/` in lectures 4 to 7, about 300 JSON files, several over 200 KB. A seeded run
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is now reproduced by running the script, and the numbers a default run gives are in each
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lecture's README.
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- `lecture_6/EQUATION_READINGS.md` (138 KB) and `lecture_7/lecture7_ot_sbm_notes.md` (148 KB). The
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book carries both.
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- `MATHEMATICS.md`, `SOURCES.md`, `SLIDE_CODE_MAP.md`, `source_manifest.json`,
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`paper_manifest.json`, `lecture7_examples.ipynb`. The slide maps pointed at the decks as they
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were before the October rewrites.
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- `lecture_4/data/dna_train.tsv` and `lecture_5/data/dna_train.tsv`, which were byte-identical
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copies of each other. `cis6270.data.synthetic_dna` generates the same data in one place, and
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`cis6270.data.write_dna_tsv` writes it out in the old format for anyone who wants the file.
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- `lecture_3/esm2_example.csv`, `GUIDANCE_NOTES.md`, and the per-lecture `requirements.txt` files.
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## What changed for a reader
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- There is a Lecture 1 now, covering the mathematical foundations chapter.
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- `pip install -e .` puts `cis6270` on the path; otherwise run from the repository root with
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`PYTHONPATH=.`.
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- The shared flags are the same everywhere: `--steps`, `--batch-size`, `--lr`, `--width`,
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`--length`, `--samples`, `--sample-steps`, `--seed`, `--device`, `--out`, `--quiet`.
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- `python -m pytest tests -q` runs 484 tests, which assert the numbers the notes work by hand.
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