You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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