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Refactoring and releasing second coembedding algorithm under new name proteingps

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@dzoanka dzoanka released this 29 Jan 00:15
· 54 commits to main since this release
v1.0.0
1ef8250

  • Rename auto coembedding name and proteinGPS. --algorithm auto option is depreacted and --algorithm proteingps
    should be used. The coembedding implementation was moved to ProteinGPSCoEmbeddingGenerator class and
    AutoCoEmbeddingGenerator is deprecated and calls proteingps. The package name was renamed from autoembed_sc
    to proteingps.

  • Added mean_losses mean loses flag and argument in ProteinGPSCoEmbeddingGenerator. If set, uses mean of losses
    otherwise sum of losses.

  • Constants updated in ProteinGPSCoEmbeddingGenerator (triplet_margin=0.2) and in proteingps's fit_predict
    (triplet_margin=0.2, lambda_reconstruction=5.0, lambda_triplet=5.0)

  • Bug fix: add missing a .to(device) call to ensure tensors are correctly moved to the appropriate device.

  • Update version bounds of required packages

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