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license: cc |
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task_categories: |
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- sentence-similarity |
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tags: |
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- biology |
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- protein |
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--- |
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# Protein Pairs and Similarity |
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Selected protein similarities within training, test, and validation sets. |
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Each protein gets two similarities selected at random and (usually) proteins within the top and bottom quintiles for similarity. |
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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 ). |
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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/prot_t5_xl_uniref50 model. |
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For models and training scripts optimizing for similarity, you should use `(1 - distance)`. |
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Train / test / validation splits are from [khairi/uniprot-swissprot](https://huggingface.co/datasets/khairi/uniprot-swissprot/tree/39d2f9010ceb2599a12397b79babc902f8c440e6) |
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Code notebook: https://colab.research.google.com/drive/1rhoF0pAauHbiaNHdZkOI5O7A3mMcvS6G?usp=sharing |
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Source of proteins: UniProt-SwissProt |
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Download 1,024-dim embeddings from UniProt: https://www.uniprot.org/help/downloads#embeddings |
