monsoon-nlp/protein-pairs-uniprot-swissprot
Protein Pairs and Similarity Selected protein similarities within training, test, and validation sets. Each protein gets two similarities selected at random and (usually) proteins within the top and bottom quintiles for similarity. The protein is represented by its UniProt ID and its amino acid sequence (using IUPAC-IUB codes where each amino acid maps to a letter of the alphabet, see: https://en.wikipedia.org/wiki/FASTA_format ). The distance column is cosine distance… See the full description on the dataset page: https://huggingface.co/datasets/monsoon-nlp/protein-pairs-uniprot-swissprot.
Protein Pairs and Similarity
Selected protein similarities within training, test, and validation sets. Each protein gets two similarities selected at random and (usually) proteins within the top and bottom quintiles for similarity.
The protein is represented by its UniProt ID and its amino acid sequence (using IUPAC-IUB codes where each amino acid maps to a letter of the alphabet, see: https://en.wikipedia.org/wiki/FASTA_format ).
The distance column is cosine distance (identical = 0) on UniProt / SwissProt 1,024-dimension embeddings, downloaded in March 2024, based on the https://huggingface.co/Rostlab/prott5xl_uniref50 model.
For models and training scripts optimizing for similarity, you should use (1 - distance).
Train / test / validation splits are from khairi/uniprot-swissprot
Code notebook: https://colab.research.google.com/drive/1rhoF0pAauHbiaNHdZkOI5O7A3mMcvS6G?usp=sharing
Source of proteins: UniProt-SwissProt
Download 1,024-dim embeddings from UniProt: https://www.uniprot.org/help/downloads#embeddings