Git Product home page Git Product logo

Comments (4)

mheinzinger avatar mheinzinger commented on July 17, 2024

Hi Sam,

thanks a lot for the heads-up. I have replaced the '.full()' by '.to(torch.float32)' which solves the issue on my end.

from prostt5.

szimmerman92 avatar szimmerman92 commented on July 17, 2024

Thank you very much. That worked perfectly.

While I am here, can I ask you if there is any difference in accuracy in creating 3DI sequences from amino acids when running predict_3DI_encoderOnly.py compared to translate.py?

Thanks again!

Sam

from prostt5.

mheinzinger avatar mheinzinger commented on July 17, 2024

Yes, indeed there will be a difference. Unfortunately, I still did not manage to update the bioRxiv version of the paper to have a proper description of the difference but in a nutshell:

  • predict_3DI_encoderOnly.py only runs the encoder part of ProstT5 and predicts 3Di using an encoder trained on top of those embeddings.
  • translate.py will run the full ProstT5 encoder/decoder for generating 3Di.
    On the sets we compared, there is there is only a small (and even inconsistent - sometimes one is better sometimes the other) difference. So performance is nearly the same but running the encoder-only is MUCH faster, so I would clearly recommend that one.
    Only use-case for translate.py is if you want to generate a distribution over different 3Di-possibilities. Sampling from the encoder-decoder model is much easier than sampling from the probability distribution output by the CNN in predict_3Di_encoderOnly.py.

from prostt5.

szimmerman92 avatar szimmerman92 commented on July 17, 2024

Very interesting. Thank you for the detailed response!

from prostt5.

Related Issues (16)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.