SIGnature Model Files

This repository includes helper files to run the SIGnature package using multiple scRNA-seq foundation models:

1. scimilarity: includes all necessary files from SCimilarity and the published model's pretrained weights
2. scfoundation: includes helper function and gene lists from scFoundation that are necessary for calculating attributions
3. scvi: includes structure to run scVI model trained on CZI census data (version "2023-12-15-scvi-homo-sapiens") and ensembl to gene symbol mapping file
4. ssl: includes gene variables used to calculate attributions using self-supervised models trained on scTab data 

In order to utilize these models, appropriate model weights must be downloaded from the source:

1. SCimilarity: model weights are included in "model_files/scimilarity", but can also be found here
2. scFoundation: model weights can be downloaded from here (models.ckpt) and placed at "model_files/scfoundation/models.ckpt".
3. scVI (CZI): model weights can be downloaded from here (models.pt) and placed at "model_files/scvi/2023-12-15-scvi-homo-sapiens/scvi.model/model.pt"
4. scTab-SSL: model weights can be downloaded from here (e.g. RandomMask.ckpt) and placed at "model_files/ssl/RandomMask.ckpt"

After downloading the file, run "tar -xzf model_files.tar.gz" to extract the data. This will produce a folder titled "model_files" that contains the folder structure where pretrained weights can be downloaded and used with the SIGnature package.