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Add Enformer and Borzoi models #91

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Add Enformer and Borzoi models #91

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casblaauw
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@casblaauw casblaauw commented Jan 16, 2025

To-do:

  • Code review
  • Finetuning tutorial notebook
  • Host pre-trained weights on server + add to get_model()
  • Add docs pages for pre-trained models for Enformer and Borzoi
  • Add model porting scripts

@LukasMahieu LukasMahieu self-requested a review January 22, 2025 13:35
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Excellent work, Cas. Can't find a thing to change. Docs also look good.
I see you also had the idea of moving the locus_scoring plotting to another module instead of the hist (and then undid those changes). I agree with those, let's add those changes in another PR later.

@casblaauw
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Yes, they'd conceptually fit very well with plotting functions for the Enformer/Borzoi output tracks, but I didn't get around to adding the plotting functions for those so I reversed the changes. I'll try to add those in another PR soon. For now, I'll clean up and add the finetuning notebook and this should be good to merge. Thanks for looking over everything!

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3 participants