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v0.2.0: 2022-06-24 -- Integration of Topsy-Turvy

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@samsledje samsledje released this 25 Jun 00:42
v0.2.0
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Learn about vigilant mode.

Topsy-Turvy Integration

  • Integrate Topsy-Turvy to allow for top-down supervision
  • See the GitHub repository
  • See the landing page
  • To appear at ISMB 2022 and in Bioinformatics as Devkota*, Singh*, Sledzieski, Berger, Cowen, “Topsy-Turvy: integrating a global view into sequence-based PPI prediction”

Bug Fixes and Quality of Life

  • Use utils.log function across all commands
  • Speed up loading embeddings into memory using parallel processing
  • Update fasta.parse and fasta.write to use BioPython SeqIO (better error checking)
  • More comprehensive test suite for main commands
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