Haotian Cui
Haotian Cui
Hi, I am encountering the same issue and also need to backdrop. I wonder has this one been solved in any recent release, or is there a workaround so far?
Thank you all for bringing this up. I've also seen another report for similar reasons #288. I am working on this and hopefully provide new dependencies to solve these issues...
Hi, thanks and I am trying to understand your comment. > The UMAP is plotted with the single cell gene expression, UMAP embeddings and not leveraging the cell embeddings. I...
Hi, thank you for the question. The input to the model is actually the binned values, so actually these preprocessing including log1p should not matter.
Hi, can you let me know what new models you mean that didn't work?
You can find how the example faiss index of atlas was built in this file https://github.com/bowang-lab/scGPT/blob/main/tutorials/build_atlas_index_faiss.py . Also, new scGPT processed cell embeddings have been hoIsted at CELLxGENE [models](https://cellxgene.cziscience.com/census-models). Are...
@claude review
Hi, thanks for the suggestion. Working on it right now. Should be able to have it in one day