Provide dataset to run an individual training round

theislab / chemCPA

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

https://arxiv.org/abs/2204.13545

MIT License

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Provide dataset to run an individual training round #115

Closed ggonzalezp closed 11 months ago

ggonzalezp commented 1 year ago

Hello, You mentioned you provide the file manual_seml_sweep.py to run experiments manually. This one uses the dataset simon/config_sciplex3_interactive.yaml, could you provide this dataset for me to be able to use the script, please? I tried with other datasets and it doesn't work out of the box Thank you

MxMstrmn commented 11 months ago

Hi @ggonzalezp, I provided a fix for your problem. It should work now! Thanks for your interest in our work :)

Note that you have to put the remit embeddings from here at embeddings/rdkit/data/embeddings/rdkit2D_embedding_lincs_trapnell.parquet

Hrovatin commented 9 months ago

The link can not be used without requesting access. I would need chemCPA/embeddings/rdkit/data/embeddings/rdkit2D_embedding_lincs_trapnell.parquet