Workplace for diffusion regulatory element design models

This repository contains code related to running diffusion models for regulatory element design on single cell data. This is a show repo of my work, original is private and belongs to mkarikomi

Currently, the repo has 4 different models

All models reference and import original repos in the folder re_design located in the root folder of this repo

For reproduction, clone this repo and create re_design folder with the repo of interest.

The links and versions of original repos you can find below

Directories

• benchmarks (readme): scripts to run predictive and generative benchmarks on competing diffusion and supervised models on multiple single-cell datasets.
• classifier_diffusion : scripts run Classifier guided diffusion on single-cell data.
• data_preprocessing : notebooks and scripts to create .csv files for training on ATAC or tCRE data
• dirichlet_diffusion (readme): scripts to run Dirichlet diffusion models on single-cell data.
• dna_diffusion (readme): scripts to run DNA diffusion on single-cell data.
• train_utils : scripts to preprocess csv files for training and validation
• universal_guidance : scripts to run Universal Guidance diffusion on single-cell data. Currently under construction

Referenced repos

• Classifier Guided Diffusion , commit 22e0df8 on Jul 15, 2022
• Dirichlet Diffusion Score Model , commit 4a58839 on May 1, 2024
• DNA Diffusion , commit 74dc742 on Jun 6, 2024
• Universal Guidance for Diffusion Models, commit ff82f88 on Jul 11, 2023