But it may well be semi-supervised.
For some time now I have thought that building a latent representation of protein sequence space is a really good idea, both because we have far more sequences than any form of labelled data, and because, once built, such a representation can inform a broad range of downstream tasks. This is why I jumped at the opportunity last year when Surge Biswas, from the Church Lab, approached me about collaborating on exactly such a project. Last week we posted a preprint on bioRxiv describing this effort. It was led by Ethan Alley, Grigory Khimulya, and Surge. All I did was to enthusiastically cheer them on, and so the bulk of the credit goes to them and George Church for his mentorship.Continue reading