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--- |
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license: mit |
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task_categories: |
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- feature-extraction |
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tags: |
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- embeddings |
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size_categories: |
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- 100K<n<1M |
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--- |
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Want to analyze some proteins, but lack embeddings? Want to perform vector similarity search? Want a context of known proteins embeddings? Look no further! |
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This repository is a dataset of [Reviewed Swiss-Prot Proteins](https://www.uniprot.org/help/downloads). Each protein I compute the embeddings for [ESM2](https://github.com/facebookresearch/esm) (6 layer model) and [ProteinCLIP](https://github.com/wukevin/proteinclip). |
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## Specs |
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See the data viewer for all information. Most of the metadata on each protein and the sequences themself come from [Reviewed Swiss-Prot Proteins](https://www.uniprot.org/help/downloads). |
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**Important columns** |
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- `accession`: the Uniprot Accession Number that identifies each protein uniquely |
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- `embedding`: 128 dimensional vectors computed from the [ProteinCLIP](https://github.com/wukevin/proteinclip) models (first from ESM 6 layer model last layer). |
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## Examples |
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Yeah this dataset is easy to use! See some quick examples! |
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### Example 1 |
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Upload all the embeddings to Nomic Atlas to create https://atlas.nomic.ai/data/donnybertucci/swissprot-proteinclip/map |
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<video controls autoplay src="https://cdn-uploads.huggingface.co/production/uploads/6260e4e99c4c9dc0ed60e8ca/xyugJj612OtpsixQy2oio.qt"></video> |
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### Example 2 |
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Similarity search with cosine similarity https://github.com/xnought/DS569k-viewer (live site https://ocular.cc.gatech.edu/DS569k/) |
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<video controls autoplay src="https://cdn-uploads.huggingface.co/production/uploads/6260e4e99c4c9dc0ed60e8ca/gCdHAI7vSCOv_BHOCQqqc.qt"></video> |
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## Credit |
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All credit for the data goes to https://www.uniprot.org/ and https://www.expasy.org/resources/uniprotkb-swiss-prot and to the original authors of each protein. I directly took the data from them. |
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Large pieces of code were copied from https://github.com/wukevin/proteinclip to embed both ESM and ProteinCLIP. Without their pretrained models and code, I could not have produced the embeddings. |
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And credit to Fair ESM for the pretrained ESM2 models https://github.com/facebookresearch/esm. |
