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v0.2.0

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@konstin konstin released this 14 May 15:57
· 294 commits to develop since this release
  • Added the prottrans_t5_xl_u50/ProtTransT5XLU50Embedder embedder from the latest ProtTrans revision. You should use this over prottrans_t5_bfd and prottrans_t5_uniref50.
  • The projected_embeddings_file.csv of project stages has been renamed to projected_reduced_embeddings_file.h5. For backwards compatibility, projected_embeddings_file.csv is still written.
  • The projected_embeddings_file parameter of visualize stages has been renamed to projected_reduced_embeddings_file and takes an h5 file. For backwards compatibility, projected_embeddings_file and csv files are still accepted.
  • Added the pb_tucker model as project stage. Tucker is a contrastive learning model trained to distinguish CATH superfamilies. It consumes prottrans_bert_bfd embeddings and reduces the embedding dimensionality from 1024 to 128. See https://www.biorxiv.org/content/10.1101/2021.01.21.427551v1
  • Renamed half_model to half_precision_model