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VQ-VAE of your model #20

Closed fulacse closed 4 days ago

fulacse commented 4 days ago

Hi!

Thank you for your great work. I would like to ask if your model can be used solely for encoder and decoder of VQ-VAE. Because my model work into latent space for my project.

If so, do you have an example script that I can refer to?

Thank you!

ebetica commented 4 days ago

Code pointers for pretrained model: https://github.com/evolutionaryscale/esm/blob/e9f060214d19a6420a69cd1187fdaf81978791fc/esm/pretrained.py#L59-L76

pointer on how to run the encoder: https://github.com/evolutionaryscale/esm/blob/main/esm/utils/encoding.py#L89-L91

pointer on how to run the decoder: https://github.com/evolutionaryscale/esm/blob/e9f060214d19a6420a69cd1187fdaf81978791fc/esm/utils/decoding.py#L154

fulacse commented 3 days ago

Code pointers for pretrained model:

https://github.com/evolutionaryscale/esm/blob/e9f060214d19a6420a69cd1187fdaf81978791fc/esm/pretrained.py#L59-L76

pointer on how to run the encoder: https://github.com/evolutionaryscale/esm/blob/main/esm/utils/encoding.py#L89-L91

pointer on how to run the decoder:

https://github.com/evolutionaryscale/esm/blob/e9f060214d19a6420a69cd1187fdaf81978791fc/esm/utils/decoding.py#L154

I confirm one thing, the VQ_VAE process 3D structure but not amino acid sequence