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From [Algorithmic Simplicity](https://www.youtube.com/@algorithmicsimplicity):
- [x] [Why Does Diffusion Work Better than Auto-Regression? - YouTube](https://www.youtube.com/watch?v=zc5NTeJbk-k)
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> http://dx.doi.org/10.1371/journal.pone.0141287
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> **Motivation:** We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to…
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Dear Sir/Madam,
Thank you for such a great repo, but I am confused by the result for EC downstream task result. The result of multiview contrast in paper "PROTEIN REPRESENTATION LEARNING BY GEOMETR…
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https://doi.org/10.1101/137828
> Understanding the relationship between protein structure and function is a fundamental problem in protein science. Given a protein of unknown function, fast identif…
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https://doi.org/10.1101/099358 (http://biorxiv.org/content/early/2017/01/10/099358)
> Many biological processes are governed by protein-ligand interactions. Of such is the recognition of self and n…
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Hi! Thanks for your great work. I was wondering if this pre-trained network is state of the art or close? I am interested in doing some pre-training with biological sequences, and could use some guida…
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i.e. using multi-dimensional scaling (MDS), or could be a trained network. If a trained network, an interesting approach might be to map the representation (including redundant information) to the dir…
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Why the vectors for 3grams:
'HDU', 'USC', 'XLC', 'GUS', 'UKK', 'XNM', 'TGU', 'UAR', 'KBF', 'CUI', 'UGS', 'WXV', 'WCU', 'DUA', 'FXQ', 'SCU', 'XTC', 'URS', 'WRX', 'VWX', 'XGH', 'SSU', 'DKB'
are missin…
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Hi,
Thank you for the amazing work!
I am curious about the results in table 8. Why most models (other than GNN) perform dramatically worse in the 60% identity split than in the 30% identity split? I…
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ping: @Starnite!
Gonna leave a list here for you to consider. I have an inkling of the necessary tools to get these done. I've also ranked them (roughly) by what I think the difficulty would be. T…