This is the code for Marlene, presented at ISMB 2025 https://academic.oup.com/bioinformatics/article/41/Supplement_1/i628/8199402.

Config files used for training can be found under configs

Download the data following the instructions in the respective papers https://www.nature.com/articles/s41591-023-02327-2, https://www.nature.com/articles/s41590-023-01608-9 and https://www.nature.com/articles/s41467-020-17358-3. Convert the expression data to AnnData using the anndata package and place the files under the data folder.

First install Marlene from setup.py

pip install -e .

To run Marlene, use

python train.py --conf configs/pmbc.ini --runid your-run-id

or

python train.py --conf configs/hlca.ini --runid your-run-id

The main model class for Marlene is under marlene/models/marlene.py.