how to extract the embeddings for each Protein Sequence about openfold HOT 8 CLOSED

I'm not familiar with this 1280-element embedding. Could you elaborate? Are you talking about what DeepMind calls the "single" embedding?

from openfold.

I'm not familiar with this 1280-element embedding. Could you elaborate? Are you talking about what DeepMind calls the "single" embedding?

Thanks for your quick response. I'm talking about the Evolutionary Scale Modeling(ESM) from FACEBOOK. for each protein sequence they output just one single embedding that represents the whole protein sequence in tabular form #aminoacids*1280. this embedding has information about the protein sequence and I want to extract this from the inner layers of Openfold. I'm looking for sth like this embedding in the Openfold. could you give me the details about this single embedding from DeepMind? maybe this is the one that I'm looking for.

from openfold.

It's one of the outputs of the model (I think it's called "single" in the output dictionary), and is derived from the first row of the MSA embedding that comes out of the evoformer. It has shape [N, 384].

from openfold.

Whoops---didn't mean to close. If you want the single sequence embedding from different points in the model, you could look at its value during different recycling iterations, for example.

from openfold.

could you elaborate on the "different points in the model". also I have this question, if I just run the code from the Colab version that you provide, is this information available in the zip file that it generates?

from openfold.

No, it's not in the output zip by default. You'll have to slightly modify the Colab to extract more stuff from the output dictionary.

As for "different points in the model:" you asked about viewing the single embedding in the "inner layers" of OpenFold. I assumed that meant you want to observe how the single embedding evolves over time. One way to do that would be to inspect its value after each recycling iteration.

from openfold.

No, it's not in the output zip by default. You'll have to slightly modify the Colab to extract more stuff from the output dictionary.

As for "different points in the model:" you asked about viewing the single embedding in the "inner layers" of OpenFold. I assumed that meant you want to observe how the single embedding evolves over time. One way to do that would be to inspect its value after each recycling iteration.

Thanks for the explanation. could you please also give me some instructions on how to extract these single embeddings from the Colab version or even from the original code that I could follow?

That would be a great help and I really appreciate it.

from openfold.

The model outputs a dictionary. In the Colab, only the structure and pLDDT scores are currently retrieved from it. Getting the single embedding is as simple as retrieving "single" from the dictionary.

from openfold.