Problem with Embedding Gene Expression Profile Using scGPT

[LenisLin]

Dear @subercui @moritzschaefer,

First, I want to express my gratitude for the amazing work you've done with scGPT. It's truly insightful and has significantly contributed to my research.

However, I've encountered a challenge with installing the flash-attn module. Despite trying various solutions provided by other users, I have not been successful.

I would like to know if it is possible to use scGPT as a pre-trained embedding module without installing the flash-attn module, as I do not intend to train it in my workflow.

Thank you for your time and assistance. I look forward to your response.

Best regards,

[moritzschaefer]

Dear @LenisLin. Thanks you for your question. I think I am always running it with flash-attn so I cannot tell you for sure. I am sure the author's/package developers can help better with that, since I am just a user.

[LenisLin]

Dear @moritzschaefer,

Thank you for your prompt reply and for sharing your experience.

I will reach out to the package developers for further assistance

[subercui]

Thank you @LenisLin and @moritzschaefer for your help. Yes, it is possible to run without flash-attn especially if you are using pytorch>=2.1. Can you let me know your specific needs, such as the code piece you are trying to run?