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How can I use LoRA to fine tune ESMC model?

3

I want to use ESMC for getting the embedding of the protein and I also want to use LoRA to adapt the model to my specific task. How can I...

hassanzadehmahdi

Hi. I want to fine-tune the esm3 series model to fit my downstream task. Can I use the most basic version of your model? I just want the min size...

nullland1027

LogitsConfig.__init__() got an unexpected keyword argument 'ith_hidden_layer'

5

How can I extract ESMC_6B embedding of sequences? I tried to extract protein embedding, following the instructions in https://github.com/evolutionaryscale/esm/blob/main/cookbook/tutorials/2_embed.ipynb. ``` ESMC_6B_EMBEDDING_CONFIG = LogitsConfig(return_hidden_states=True, ith_hidden_layer=55) ``` --------------------------------------------------------------------------- TypeError Traceback (most recent...

zw-SIMM

Hello, I noticed that in the paper, during Stage 2 training of the structure tokenizer, full-atom modeling is performed. However, it seems that the provided repository code does not include...

lonelycrab888

Dear ESMC Developer, When I running the following snippet from the README to use ESMC 6B: ``` from esm.sdk.forge import ESM3ForgeInferenceClient from esm.sdk.api import ESMProtein, LogitsConfig # Apply for forge...

Ty9Sandra

Dear ESMC Developer, I am attempting to generate embeddings for a set of proteins, including a particularly large protein (>34,000 residues) — ENSMUSP00000097561.4 (mouse heart muscle gene titin). However, I...

soumitrakp

How does ESMC implement encoding proteins in a local computer, that is, converting sequences into arrays?

4

Dear all, is there any tutorial that can be provided, thanks a lot. According to the official documentation, I try to use the following code but it always gives me...

ht-234

Hello! Was the ESM3 structure encoder trained with all chains in a protein complex being jointly encoded or separately encoded (jointly meaning all coords for all chains in one complex...

williamberman

Reopen #7: pLDDT not writing to PDB

1

I am having the same issue as was previously reported in #7, where all pLDDT values are being stored as 1.00. Including print(protein.plddt) provides the per-residue tensor values for pLDDT...

LandonGetz

Any limit on the input protein length for ESM C?

1

Thank you for your great work. I am currently using the ESM C model to generate protein embeddings. I want to know if there is a maximum sequence length that...

jdcc2098