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Possible supporting gpn series model? #1
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Tagging the relevant people: @frederikkemarin @fteufel |
Hi, yes, GPN-MSA is not supported. As indicated in the readme (https://github.com/MachineLearningLifeScience/BEND?tab=readme-ov-file#embedders-overview), the embedder is meant to be used with the A. thaliana/Brassicales models. My last status was that it's unclear whether GPN-MSA is useful as an embedding model (https://x.com/gsbenegas/status/1727746984055083075). Supporting it in our embedders would be a bit more complicated, as it operates on MSAs, rather than single sequences. |
@frederikkemarin can you replace the repo here with a fork from the main repo in your account, so that it points back correctly and can be synced? |
Hi thanks a lot, that makes sense to me. I notice that there is one paper custome trained a GPN for human genome, and I tried that model with BEND which worked for me. Thanks a lot. https://www.biorxiv.org/content/10.1101/2024.02.29.582810v1.full.pdf |
Hi, thanks for your great work. It seems that gpn model is not supported (gpn-msa, its new version supports human genome). Would you please consider including it? Thanks.
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