Haotian Cui

Hi, thank you for the question. We only have a bit dependency to scvi, I will try to remove that package dependency today or tomorrow. In the meantime, try to...

Thank you @sklarz-bgu for providing the solution. I think that's some api mismatch bettween dependency versions. That solution does what it intended to do.

Hi thank you for the question! I think you mean the code around here: https://github.com/bowang-lab/scGPT/blob/4068d67caaac1e28d56964da68e0214817e38428/scgpt/data_collator.py#L348-L355 In the pretraining, these "gen_genes" can be considered unknown to the model. Their expression, as...

Are you using python 3.11? I have relaxed the python version dependency. Please update to the new release `v0.2.4`, may use `pip install -U scgpt` if you are using pip....

Thank you for the questions! 1. You are right both "reference mapping and fine-tuning require reference data with known cell types". The difference is reference mapping uses the pretrained model...

Hi, to explain, the workflow doesn't really need annotations from the "query data". It is merely because in the tutorial, we wanted to measure how well the model's predictions align...

Hi, sorry for the incovinience. The poetry lock file is indeed outdated. Will pip install work for your case?

It looks like an issue with scvi. Can you just try `import scvi` and see what happens? Also, the version of scvi-tools we used before was around 0.16. You may...

Thanks a lot for sharing the experience. Do you suggest modifying the notebooks to include `map_location=device`?