README.md

---
license: mit
language:
  - en
tags:
  - education
  - pytorch
  - flow-matching
  - diffusion
  - esm2
  - protein-generation
  - guidance
  - mnist
  - image-generation
---

# CIS 6270 Course Code



![CIS6270_Overview (1)](https://cdn-uploads.huggingface.co/production/uploads/64cd5b3f0494187a9e8b7c69/3v32uv04uEiPZktZnczFj.png)

This repository contains code examples for CIS 6270, organized by lecture.
We will develop the implementations alongside the course material, which connect
the mathematical definitions, training objectives, and sampling equations to
the executable PyTorch code herein. Each lecture directory contains its examples, data,
and implementation notes.

## Lecture index

| Lecture | Topics | Code and documentation |
| --- | --- | --- |
| 2 | Unconditional MNIST image generation with flow matching and a simple U-Net | [Guide](lecture_2/README.md) · [Script](lecture_2/flow_matching_unet_lecture.py) · [Saved checkpoint](https://huggingface.co/ChatterjeeLab/CIS6270/resolve/main/lecture_2/flow_unet_mnist.pt?download=true) |
| 3 | Flow matching, diffusion, and guidance for ESM-2 residue embeddings | [Guide](lecture_3/README.md) · [Flow matching](lecture_3/esm2_flow_guidance.py) · [Diffusion](lecture_3/esm2_diffusion_guidance.py) |
| 4 | Discrete diffusion, masked and uniform corruption, block generation, and guidance | [Guide](lecture_4/README.md) · [Training and generation](lecture_4/run.py) · [Slide code map](lecture_4/SLIDE_CODE_MAP.md) |
| 5 | Discrete flow matching, Dirichlet and Fisher paths, Gumbel-Softmax, rectification, and multi-objective generation | [Guide](lecture_5/README.md) · [Training and generation](lecture_5/run.py) · [Slide code map](lecture_5/SLIDE_CODE_MAP.md) |
| 6 | Continuous, latent, categorical, posterior, expanding, and strong stochastic flow maps | [Guide](lecture_6/README.md) · [Training and generation](lecture_6/run.py) · [Slide code map](lecture_6/SLIDE_CODE_MAP.md) |
| 7 | Optimal transport, Sinkhorn, continuous and discrete Schrödinger bridges, matching, reward tilting, branching, and interacting control | [Guide](lecture_7/README.md) · [Training and generation](lecture_7/run.py) · [Slide code map](lecture_7/SLIDE_CODE_MAP.md) |

## Installation

Use Python 3.11, or another compatible Python version at least 3.10, in a new
virtual environment. The shared `requirements.txt` pins PyTorch 2.9.1,
TorchVision 0.24.1, and Transformers 4.57.6. Lecture 2 uses PyTorch and
TorchVision; Lecture 3 also uses Transformers. Lectures 4 and 5 use PyTorch,
NumPy, and SciPy. Lecture 6 uses PyTorch and NumPy. Lecture 7 uses PyTorch, NumPy, and SciPy. These lecture folders also provide minimal requirements.

```bash
git clone https://huggingface.co/ChatterjeeLab/CIS6270
cd CIS6270
git lfs pull

python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install -r requirements.txt
```

On Windows PowerShell, create the environment with `python -m venv .venv`
and activate it with `.venv\Scripts\Activate.ps1`.

The saved checkpoint uses Git LFS. If Git LFS is unavailable, download
[flow_unet_mnist.pt](https://huggingface.co/ChatterjeeLab/CIS6270/resolve/main/lecture_2/flow_unet_mnist.pt?download=true)
directly and place it in `lecture_2/`. Training from scratch does not require
the saved checkpoint.

## Lecture 2: MNIST flow matching

Lecture 2 contains one self-contained, commented script. It downloads MNIST,
loads batches of normalized images, defines a small U-Net velocity network,
trains it with conditional flow matching, and generates images from Gaussian
noise using Euler integration.

From the repository root:

```bash
python lecture_2/flow_matching_unet_lecture.py
```

The default run trains for 20 epochs and writes `samples.png`, `trajectory.png`,
and a new `flow_unet_mnist.pt` to `flow_matching_outputs/`. The script selects
CUDA, Apple MPS, or CPU according to availability. Its numbered `# %%` sections
match the lecture walkthrough.

The bundled [checkpoint](lecture_2/flow_unet_mnist.pt) has **5 completed epochs**
on all 60,000 MNIST training images. The [Lecture 2 guide](lecture_2/README.md)
includes a short example for loading it and generating images without training,
along with selected generated digits and their noise-to-image trajectories.

## Lecture 3: Flow and diffusion guidance

From the repository root:

```bash
python lecture_3/esm2_flow_guidance.py --epochs 200 --samples 8
python lecture_3/esm2_diffusion_guidance.py --epochs 200 --samples 8
```

Both scripts train on ESM-2 residue embeddings and compare classifier-free
guidance, single-objective reward steering, and scalarized multi-objective
steering. We use the same property definitions, normalization, and final
constrained decoder to compare the flow and diffusion implementations.

The first run downloads the public ESM-2 checkpoint. Each script then writes
generated sequences and model parameters to its own output directory.
The [lecture guide](lecture_3/README.md) describes the data format, training
and sampling settings, property calculations, normalization, and residue-count
constraint, with commands for using a custom dataset.

## Lecture 4 - Discrete diffusion

Train small DNA denoisers and generate sequences with MDLM, UDLM, block diffusion,
classifier-free guidance, exact and gradient-based classifier guidance, and a
PepTune-style search. The [guide](lecture_4/README.md) includes each method's
command and mathematical assumptions. The [code map](lecture_4/SLIDE_CODE_MAP.md)
links the slide walkthroughs to their functions.

From the repository root, run the complete MDLM example.

```bash
python lecture_4/run.py --method mdlm --data lecture_4/data/dna_train.tsv --out lecture_4/outputs/mdlm
python lecture_4/run.py --method mdlm --mode sample --out lecture_4/outputs/mdlm
```

The script trains, saves a checkpoint, and writes generated DNA and loss logs.
The bundled data are synthetic, and the guidance objectives are explicit toy
properties. No pretrained model or external dataset is required.

## Lecture 5 - Discrete flow matching

Start with Gat et al.'s discrete flow matching, then run Dirichlet, Fisher,
Gumbel-Softmax, rectified flow, ReDi, MOG-DFM, and AReUReDi examples. Each method
has a complete training and generation command in the [guide](lecture_5/README.md).

```bash
python lecture_5/run.py --method gat --data lecture_5/data/dna_train.tsv --out lecture_5/outputs/gat
python lecture_5/run.py --method gat --mode sample --out lecture_5/outputs/gat
```

Both folders include numerical examples, mathematical tests, and saved results
from seeded CPU runs. The guides explain finite endpoint approximations and
classroom simplifications for each method.

## Lecture 6 - Flow Maps

Learn finite-time motion after the local flows from Lecture 5. The new folder
contains 16 complete examples covering flow-map matching and self-distillation,
consistency, Shortcut, MeanFlow, learned latent representations, Flow Map
Language Models, Categorical and Discrete Flow Maps, Diamond Maps, Meta Flow
Maps, Expanding Flow Maps, and Strong Stochastic Flow Maps.

```bash
python lecture_6/run.py --method self-distill --out lecture_6/outputs/self-distill
python lecture_6/run.py --mode sample --out lecture_6/outputs/self-distill --sample-steps 1
python lecture_6/run_all.py --quick
```

The [Lecture 6 guide](lecture_6/README.md) includes all method commands,
training objectives, data formats, and numerical assumptions. The
[slide code map](lecture_6/SLIDE_CODE_MAP.md) links implementations to the
[Flow Maps presentation](https://docs.google.com/presentation/d/1wfLAazqYveMoyvdy0y5ILeionp7eUjcPgxu-5QFlWwI/edit).
[Source notes](lecture_6/SOURCES.md) identify the exact papers and inspected
author-code revisions, including differences between paper pseudocode and
released implementations. [Verified examples](lecture_6/verified_examples/README.md)
contain actual training logs, generated samples, and checkpoint-reload checks.

## Lecture 7 - Optimal Transport and Schrödinger Bridges

The final lecture includes 17 complete numerical and learned examples: OT,
Sinkhorn, finite and continuous-time bridges, DSB, DSBM, SF2M, DDSBM, CSBM,
TR2-D2, BranchSBM, and EntangledSBM. Each runner saves its solved distribution
or learned parameters and can reload them to generate samples.

```bash
python lecture_7/run.py --method sf2m --out lecture_7/outputs/sf2m
python lecture_7/run.py --mode sample --out lecture_7/outputs/sf2m
python lecture_7/run_all.py --quick
```

The [guide](lecture_7/README.md), [mathematical notes](lecture_7/MATHEMATICS.md),
[slide code map](lecture_7/SLIDE_CODE_MAP.md), and [verified examples](lecture_7/verified_examples/README.md)
follow the earlier lecture structure. The synthetic demonstrations distinguish
exact calculations, finite discretizations, and learned approximations.
Lectures [6](lecture_6/EQUATION_READINGS.md) and [7](lecture_7/EQUATION_READINGS.md)
also include spoken readings of their equations before the intuition.

## Repository organization

| Location | Contents |
| --- | --- |
| Repository root | Course index, installation requirements, and license |
| [`lecture_2/`](https://huggingface.co/ChatterjeeLab/CIS6270/tree/main/lecture_2) | One MNIST flow-matching script, guide, trained checkpoint, and selected example images |
| [`lecture_3/`](https://huggingface.co/ChatterjeeLab/CIS6270/tree/main/lecture_3) | ESM-2 flow and diffusion guidance scripts, sequence data, guide, and mathematical notes |
| [`lecture_4/`](https://huggingface.co/ChatterjeeLab/CIS6270/tree/main/lecture_4) | Seven discrete diffusion and guidance examples, synthetic DNA, slide code map, and verified outputs |
| [`lecture_5/`](https://huggingface.co/ChatterjeeLab/CIS6270/tree/main/lecture_5) | Eight discrete and simplex flow examples, synthetic DNA, slide code map, and verified outputs |
| [`lecture_6/`](https://huggingface.co/ChatterjeeLab/CIS6270/tree/main/lecture_6) | Sixteen flow-map implementations, text data, mathematical notes, slide links, and verified outputs |
| [`lecture_7/`](https://huggingface.co/ChatterjeeLab/CIS6270/tree/main/lecture_7) | Seventeen OT and bridge examples, derivations, equation readings, slide links, tests, and verified outputs |

Installation instructions and the lecture index are maintained at the
repository root. Lecture-specific commands, mathematical explanations, and
references accompany the corresponding code.

## License

The repository code is distributed under the
[MIT License](https://huggingface.co/ChatterjeeLab/CIS6270/blob/main/LICENSE).
ESM-2 weights are downloaded from their original repository under the
corresponding distribution terms.