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Token for unaligned amino acids #196

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VGPReys opened this issue Feb 12, 2025 · 1 comment
Open

Token for unaligned amino acids #196

VGPReys opened this issue Feb 12, 2025 · 1 comment

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@VGPReys
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VGPReys commented Feb 12, 2025 •
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Hi there,

I would like to generate embedding for a protein sequence that comes from a multiple sequence alignment (e.g: "AAA--AAA--A")

What kind of token should be used to describe the unaligned amino acids ?

My initial guess is that is could be one of these:

  • .
  • -
  • <pad>
  • <mask>

But which one ?

Thanks for your help
@thomas-a-neil
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Why not embed the unaligned sequence?

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@thomas-a-neil @VGPReys