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jaydu1 / VITAE

Joint Trajectory Inference for Single-cell Genomics Using Deep Learning with a Mixture Prior
https://jaydu1.github.io/VITAE/
MIT License
26 stars 8 forks source link

Implement in scvi-tools #6

Open adamgayoso opened 1 year ago

adamgayoso commented 1 year ago

Hello,

I found your manuscript to be interesting and I'm wondering whether you have any interest in implementing a version that takes a pre-trained scvi-tools model as input (e.g., scVI) . I think this would get a lot of usage in our package!

jaydu1 commented 1 year ago

Hi,

Thanks for the great proposal!

We're currently finishing and revising the paper to include more real data applications. A few updates will also be made to the model, to make it more robust and stable. I expect to spend about one month on finishing this.

And yes, after we settle down on the model somehow, we would be very happy to implement a version with scvi-tools as well! Though I'm not sure if it is possible to use a pre-train model from scvi-tools, add new layers to the latent space, and continue training both of them? Or if you have any reference on similar usage of your package, that would be helpful.

adamgayoso commented 1 year ago

Though I'm not sure if it is possible to use a pre-train model from scvi-tools, add new layers to the latent space, and continue training both of them? Or if you have any reference on similar usage of your package, that would be helpful.

This is definitely possible, we do this for scANVI which is warm-started with a simpler scvi model (see here)

shahrozeabbas commented 2 months ago

Hi, just came across this tool and the preprint. Commenting to offer a vote in favor of a scvi-tools implementation. Looking forward to the final paper!