History

1.0.0 (2025-01-28)

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

0.4.0 (2024-12-02)

Added README generation.
Refactor code.

0.3.1 (2024-09-13)

Bug fix: raise more informative error when no embeddings overlap.

0.3.0 (2024-09-06)

Added --provenance flag to pass a path to json file with provenance information. This removes the necessity of input directory to be an RO-Crate.

0.2.0 (2024-07-17)

Added a new coembedding algorithm accessible via flag --algorithm auto. This algorithm utilizes neural networks to generate latent embeddings, optimizing both reconstruction and triplet losses to improve embedding accuracy by learning intra- and inter-modality relationships.

0.1.0 (2024-02-12)

First release on PyPI.