https://github.com/genentech/pascient
https://github.com/genentech/pascient
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/genentech/pascient
- Owner: Genentech
- License: other
- Created: 2024-10-24T01:39:20.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-10-25T04:00:11.000Z (over 1 year ago)
- Last Synced: 2024-10-26T18:47:35.765Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 3.24 MB
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# PaSCient: Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states
## Setup environment
```
conda create -n pascient python=3.11
```
## Install
```
pip install -r requirements.txt
```
## Train a PaSCient model
`cd /pascient/scripts/`
```
HYDRA_FULL_ERROR=1 python train.py data.persistent_workers=True data.multiprocessing_context=null data.num_workers=12 experiment=pascient_multilabel paths.tiledb_dir=YOUR_PATH_TO_YOUR_TILEDB
```
You will need to provide the path to your tiledb.
## PaSCient inference
We provide a notebook with examples on how to run PaSCient on your data in `pascient/notebooks/paper_figures/model_inference_example.ipynb`
## Request model weights
Model weights are available upon request to `debroue1@gene.com`
## Figures reproduction
Figures were generated using the notebooks in `pascient/notebooks/paper_figures/`
- `UMAP.ipynb` reproduces Figure 3 of the paper
- `IG.ipynb` reproduces Figure 4 of the paper
- `severity.ipynb` reproduces Figure 5 of the paper
## Contact
If you have any questions, please contact Tianyu Liu (tianyu.liu@yale.edu) or Edward De Brouwer (debroue1@gene.com).