{ "id": 406658, "title": "Art gallery: Protein embeddings ", "url": "/competitions/cafa-5-protein-function-prediction/discussion/406658", "author_name": "", "post_date": "2023-05-03T08:43:54.052788Z", "votes": 17, "comment_count": 4, "views": 0, "content": "

Here are some curious visualizations of the proteins embedding spaces .
\nSee also more beautiful from Tilli : https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406336 , https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406573

\n

Links to the notebooks with collections of different dimensional-reduction methods: PCA,ICA, UMAP, PacMap, NCVis, TriMap, etc… also provided.

\n

Joke dialogue:
\nyoung protein: bro, where are we ?
\nwise protein: in the embedding space !
\n( Inspired by Svyatoslav Kovalev: https://habr.com/ru/companies/ods/articles/464715/
\n see also his telegram channel with lots beautiful visualizations and data science of https://t.me/sv9t_channel )

\n
\n

ICA for Levenshtein distance features: https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=13

\n

\"\"

\n
\n

Do these clusters have some biological sense ?

\n

https://www.kaggle.com/code/alexandervc/cafa5-sgt-embeddings-visualizations?scriptVersionId=127896762&cellId=11

\n

\"\"

\n

https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=15

\n

\"\"

\n
\n

https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=16

\n

\"\"

\n
\n

https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=25

\n

\"\"

\n
\n

https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=31

\n

\"\"

\n
\n

https://www.kaggle.com/code/alexandervc/cafa5-esm2-protein-embeddings-visualizations?scriptVersionId=128044650&cellId=15

\n

ESM2 model, thanks Andrey for sharing data: https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406168 (please uptove him)

\n

\"\"

\n
\n

ESM2 model, thanks Andrey for sharing data: https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406168 (please uptove him)

\n

Do these clusters make biological sense ?

\n

https://www.kaggle.com/code/alexandervc/cafa5-esm2-protein-embeddings-visualizations?scriptVersionId=128044650&cellId=18
\n\"\"

", "messages": [ { "id": "2243874", "postDate": "05/03/2023 08:43:54", "content": "

Here are some curious visualizations of the proteins embedding spaces .
\nSee also more beautiful from Tilli : https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406336 , https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406573

\n

Links to the notebooks with collections of different dimensional-reduction methods: PCA,ICA, UMAP, PacMap, NCVis, TriMap, etc… also provided.

\n

Joke dialogue:
\nyoung protein: bro, where are we ?
\nwise protein: in the embedding space !
\n( Inspired by Svyatoslav Kovalev: https://habr.com/ru/companies/ods/articles/464715/
\n see also his telegram channel with lots beautiful visualizations and data science of https://t.me/sv9t_channel )

\n
\n

ICA for Levenshtein distance features: https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=13

\n

\"\"

\n
\n

Do these clusters have some biological sense ?

\n

https://www.kaggle.com/code/alexandervc/cafa5-sgt-embeddings-visualizations?scriptVersionId=127896762&cellId=11

\n

\"\"

\n

https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=15

\n

\"\"

\n
\n

https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=16

\n

\"\"

\n
\n

https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=25

\n

\"\"

\n
\n

https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=31

\n

\"\"

\n
\n

https://www.kaggle.com/code/alexandervc/cafa5-esm2-protein-embeddings-visualizations?scriptVersionId=128044650&cellId=15

\n

ESM2 model, thanks Andrey for sharing data: https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406168 (please uptove him)

\n

\"\"

\n
\n

ESM2 model, thanks Andrey for sharing data: https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406168 (please uptove him)

\n

Do these clusters make biological sense ?

\n

https://www.kaggle.com/code/alexandervc/cafa5-esm2-protein-embeddings-visualizations?scriptVersionId=128044650&cellId=18
\n\"\"

", "rawMarkdown": "Here are some curious visualizations of the proteins embedding spaces .\nSee also more beautiful from Tilli : https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406336 , https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406573\n\n Links to the notebooks with collections of different dimensional-reduction methods: PCA,ICA, UMAP, PacMap, NCVis, TriMap, etc... also provided. \n\nJoke dialogue:\nyoung protein: bro, where are we ? \nwise protein: in the embedding space ! \n( Inspired by Svyatoslav Kovalev: https://habr.com/ru/companies/ods/articles/464715/\n see also his telegram channel with lots beautiful visualizations and data science of https://t.me/sv9t_channel ) \n\n-----------------------------------------------------------\n\n\nICA for Levenshtein distance features: https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=13\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Fced7af6bc7b8bb13e5644f9db99a3176%2FScreenshot%202023-05-03%20102752.png?generation=1683102504446699&alt=media)\n\n-----------------------------------------------------------\n\nDo these clusters have some biological sense ? \n\nhttps://www.kaggle.com/code/alexandervc/cafa5-sgt-embeddings-visualizations?scriptVersionId=127896762&cellId=11\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F94597551a04e854c0579b8f4fc1e13b3%2FScreenshot%202023-05-03%20104536.png?generation=1683103555124675&alt=media)\n-----------------------------------------------------------\n\nhttps://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=15\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F934a7d113b6e5e9c59ebb13f47c9f3f4%2FScreenshot%202023-05-03%20103717.png?generation=1683103072042505&alt=media)\n\n------------------------------------------------------------\nhttps://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=16\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F9ba55f05b145eaa61c51632f602a4fd7%2FScreenshot%202023-05-03%20103839.png?generation=1683103161306912&alt=media)\n\n------------------------------------------------------------\n\nhttps://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=25\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F9fb08fe71a40a7ae94faae51582fe9c0%2FScreenshot%202023-05-03%20104137.png?generation=1683103320530633&alt=media)\n\n------------------------------------------------------------\n\nhttps://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=31\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F1fe055319b8fb931c7da1e1464d0587f%2FScreenshot%202023-05-03%20104253.png?generation=1683103392248770&alt=media)\n\n--------------------------------------------------------------\n\nhttps://www.kaggle.com/code/alexandervc/cafa5-esm2-protein-embeddings-visualizations?scriptVersionId=128044650&cellId=15\n\nESM2 model, thanks Andrey for sharing data: https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406168 (please uptove him)\n\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F25bec1b3a482f993d72c9abfef6326eb%2FScreenshot%202023-05-03%20112700.png?generation=1683106079811540&alt=media)\n\n--------------------------------------------------------------\n\n\nESM2 model, thanks Andrey for sharing data: https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406168 (please uptove him)\n\nDo these clusters make biological sense ? \n\nhttps://www.kaggle.com/code/alexandervc/cafa5-esm2-protein-embeddings-visualizations?scriptVersionId=128044650&cellId=18\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F26921e73d0941fce3a79ceaede665efa%2FScreenshot%202023-05-03%20113106.png?generation=1683106284991157&alt=media)", "votes": null }, { "id": "2243879", "postDate": "05/03/2023 08:49:10", "content": "

@alexandervc amazing topic. Thanks! This subject very interesting and specific for usual data scientists.

", "rawMarkdown": "alexandervc amazing topic. Thanks! This subject very interesting and specific for usual data scientists.", "votes": null }, { "id": "2243912", "postDate": "05/03/2023 09:28:25", "content": "

@alexandervc The visuals are wonderful!

", "rawMarkdown": "alexandervc The visuals are wonderful!", "votes": null }, { "id": "2243961", "postDate": "05/03/2023 10:24:33", "content": "

Hi @alexandervc, So beautiful charts! Thanks for sharing them and also the links!

", "rawMarkdown": "Hi @alexandervc, So beautiful charts! Thanks for sharing them and also the links!", "votes": null }, { "id": "2248163", "postDate": "05/06/2023 14:48:25", "content": "

T5 embeddings:
\nhttps://www.kaggle.com/code/alexandervc/cafa5-t5-protein-embeddings-visualization?scriptVersionId=128515805&cellId=18
\n(Thanks to Sergei Fironov dataset -
\nhttps://www.kaggle.com/datasets/sergeifironov/t5embeds
\nplease upvote it )

\n

\"\"

\n

ProtBert embeddings
\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=16
\n(Thanks to @henriupton dataset - https://www.kaggle.com/datasets/henriupton/protbert-embeddings-for-cafa5 - please upvote it)
\n\"\"

\n

Same dataset
\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=30
\n\"\"

\n

Same dataset:
\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=24
\n\"\"

\n

Same dataset only the first 2000 samples
\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=36
\n\"\"

\n

Dataset created by Anton Kostin (please upvote - based on NLP (sentence Bert) embeddings of the textual description of the protein taken from the Uniprot: https://www.kaggle.com/datasets/visualcomments/uniprot-description-only )
\nhttps://www.kaggle.com/code/alexandervc/cafa5-nlp-description-protein-embeddings-visualiz?scriptVersionId=128545017&cellId=16

\n

\"\"

", "rawMarkdown": "T5 embeddings:\nhttps://www.kaggle.com/code/alexandervc/cafa5-t5-protein-embeddings-visualization?scriptVersionId=128515805&cellId=18\n(Thanks to Sergei Fironov dataset -\nhttps://www.kaggle.com/datasets/sergeifironov/t5embeds\nplease upvote it )\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Ff95cc4ac07cfdb81adbd72f7aefcec0c%2FScreenshot%202023-05-06%20164147.png?generation=1683384152124227&alt=media)\n\nProtBert embeddings\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=16\n(Thanks to @henriupton dataset - https://www.kaggle.com/datasets/henriupton/protbert-embeddings-for-cafa5 - please upvote it)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Fbe64283c53f7bfd5914f5529c6bdae42%2FScreenshot%202023-05-06%20164332.png?generation=1683384298473304&alt=media)\n\nSame dataset\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=30\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F32af60c891fd72a3eed1c8a7b361c04e%2FScreenshot%202023-05-06%20164739.png?generation=1683384498761629&alt=media)\n\nSame dataset:\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=24\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F6d255119be4c1d8dcb7ae6ecaeb26360%2FScreenshot%202023-05-06%20165022.png?generation=1683384691514187&alt=media)\n\nSame dataset only the first 2000 samples\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=36\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F76533bfa22999cf26bcd897900f2fa42%2FScreenshot%202023-05-06%20164552.png?generation=1683384376061007&alt=media)\n\nDataset created by Anton Kostin (please upvote - based on NLP (sentence Bert) embeddings of the textual description of the protein taken from the Uniprot: https://www.kaggle.com/datasets/visualcomments/uniprot-description-only )\nhttps://www.kaggle.com/code/alexandervc/cafa5-nlp-description-protein-embeddings-visualiz?scriptVersionId=128545017&cellId=16\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F7f9c8b0f8019e4a1e56aeb46dec6fb02%2FScreenshot%202023-05-06%20201119.png?generation=1683396831923664&alt=media)", "votes": null } ], "comments": [ { "id": 2243879, "author_name": "serangu", "author_url": "", "post_date": "05/03/2023 08:49:10", "content": "

@alexandervc amazing topic. Thanks! This subject very interesting and specific for usual data scientists.

", "votes": null, "replies": [] }, { "id": 2243912, "author_name": "abishussainsyed", "author_url": "", "post_date": "05/03/2023 09:28:25", "content": "

@alexandervc The visuals are wonderful!

", "votes": null, "replies": [] }, { "id": 2243961, "author_name": "chemaplana", "author_url": "", "post_date": "05/03/2023 10:24:33", "content": "

Hi @alexandervc, So beautiful charts! Thanks for sharing them and also the links!

", "votes": null, "replies": [] }, { "id": 2248163, "author_name": "alexandervc", "author_url": "", "post_date": "05/06/2023 14:48:25", "content": "

T5 embeddings:
\nhttps://www.kaggle.com/code/alexandervc/cafa5-t5-protein-embeddings-visualization?scriptVersionId=128515805&cellId=18
\n(Thanks to Sergei Fironov dataset -
\nhttps://www.kaggle.com/datasets/sergeifironov/t5embeds
\nplease upvote it )

\n

\"\"

\n

ProtBert embeddings
\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=16
\n(Thanks to @henriupton dataset - https://www.kaggle.com/datasets/henriupton/protbert-embeddings-for-cafa5 - please upvote it)
\n\"\"

\n

Same dataset
\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=30
\n\"\"

\n

Same dataset:
\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=24
\n\"\"

\n

Same dataset only the first 2000 samples
\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=36
\n\"\"

\n

Dataset created by Anton Kostin (please upvote - based on NLP (sentence Bert) embeddings of the textual description of the protein taken from the Uniprot: https://www.kaggle.com/datasets/visualcomments/uniprot-description-only )
\nhttps://www.kaggle.com/code/alexandervc/cafa5-nlp-description-protein-embeddings-visualiz?scriptVersionId=128545017&cellId=16

\n

\"\"

", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "2243874": "Here are some curious visualizations of the proteins embedding spaces .\nSee also more beautiful from Tilli : https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406336 , https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406573\n\n Links to the notebooks with collections of different dimensional-reduction methods: PCA,ICA, UMAP, PacMap, NCVis, TriMap, etc... also provided. \n\nJoke dialogue:\nyoung protein: bro, where are we ? \nwise protein: in the embedding space ! \n( Inspired by Svyatoslav Kovalev: https://habr.com/ru/companies/ods/articles/464715/\n see also his telegram channel with lots beautiful visualizations and data science of https://t.me/sv9t_channel ) \n\n-----------------------------------------------------------\n\n\nICA for Levenshtein distance features: https://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=13\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Fced7af6bc7b8bb13e5644f9db99a3176%2FScreenshot%202023-05-03%20102752.png?generation=1683102504446699&alt=media)\n\n-----------------------------------------------------------\n\nDo these clusters have some biological sense ? \n\nhttps://www.kaggle.com/code/alexandervc/cafa5-sgt-embeddings-visualizations?scriptVersionId=127896762&cellId=11\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F94597551a04e854c0579b8f4fc1e13b3%2FScreenshot%202023-05-03%20104536.png?generation=1683103555124675&alt=media)\n-----------------------------------------------------------\n\nhttps://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=15\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F934a7d113b6e5e9c59ebb13f47c9f3f4%2FScreenshot%202023-05-03%20103717.png?generation=1683103072042505&alt=media)\n\n------------------------------------------------------------\nhttps://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=16\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F9ba55f05b145eaa61c51632f602a4fd7%2FScreenshot%202023-05-03%20103839.png?generation=1683103161306912&alt=media)\n\n------------------------------------------------------------\n\nhttps://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=25\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F9fb08fe71a40a7ae94faae51582fe9c0%2FScreenshot%202023-05-03%20104137.png?generation=1683103320530633&alt=media)\n\n------------------------------------------------------------\n\nhttps://www.kaggle.com/code/alexandervc/cafa5-levenshtein-distances-feature-visualizations?scriptVersionId=127921968&cellId=31\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F1fe055319b8fb931c7da1e1464d0587f%2FScreenshot%202023-05-03%20104253.png?generation=1683103392248770&alt=media)\n\n--------------------------------------------------------------\n\nhttps://www.kaggle.com/code/alexandervc/cafa5-esm2-protein-embeddings-visualizations?scriptVersionId=128044650&cellId=15\n\nESM2 model, thanks Andrey for sharing data: https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406168 (please uptove him)\n\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F25bec1b3a482f993d72c9abfef6326eb%2FScreenshot%202023-05-03%20112700.png?generation=1683106079811540&alt=media)\n\n--------------------------------------------------------------\n\n\nESM2 model, thanks Andrey for sharing data: https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/406168 (please uptove him)\n\nDo these clusters make biological sense ? \n\nhttps://www.kaggle.com/code/alexandervc/cafa5-esm2-protein-embeddings-visualizations?scriptVersionId=128044650&cellId=18\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F26921e73d0941fce3a79ceaede665efa%2FScreenshot%202023-05-03%20113106.png?generation=1683106284991157&alt=media)", "2243879": "alexandervc amazing topic. Thanks! This subject very interesting and specific for usual data scientists.", "2243912": "alexandervc The visuals are wonderful!", "2243961": "Hi @alexandervc, So beautiful charts! Thanks for sharing them and also the links!", "2248163": "T5 embeddings:\nhttps://www.kaggle.com/code/alexandervc/cafa5-t5-protein-embeddings-visualization?scriptVersionId=128515805&cellId=18\n(Thanks to Sergei Fironov dataset -\nhttps://www.kaggle.com/datasets/sergeifironov/t5embeds\nplease upvote it )\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Ff95cc4ac07cfdb81adbd72f7aefcec0c%2FScreenshot%202023-05-06%20164147.png?generation=1683384152124227&alt=media)\n\nProtBert embeddings\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=16\n(Thanks to @henriupton dataset - https://www.kaggle.com/datasets/henriupton/protbert-embeddings-for-cafa5 - please upvote it)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2Fbe64283c53f7bfd5914f5529c6bdae42%2FScreenshot%202023-05-06%20164332.png?generation=1683384298473304&alt=media)\n\nSame dataset\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=30\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F32af60c891fd72a3eed1c8a7b361c04e%2FScreenshot%202023-05-06%20164739.png?generation=1683384498761629&alt=media)\n\nSame dataset:\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=24\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F6d255119be4c1d8dcb7ae6ecaeb26360%2FScreenshot%202023-05-06%20165022.png?generation=1683384691514187&alt=media)\n\nSame dataset only the first 2000 samples\nhttps://www.kaggle.com/code/alexandervc/cafa5-protbert-protein-embeddings-visualization?scriptVersionId=128516411&cellId=36\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F76533bfa22999cf26bcd897900f2fa42%2FScreenshot%202023-05-06%20164552.png?generation=1683384376061007&alt=media)\n\nDataset created by Anton Kostin (please upvote - based on NLP (sentence Bert) embeddings of the textual description of the protein taken from the Uniprot: https://www.kaggle.com/datasets/visualcomments/uniprot-description-only )\nhttps://www.kaggle.com/code/alexandervc/cafa5-nlp-description-protein-embeddings-visualiz?scriptVersionId=128545017&cellId=16\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F2262596%2F7f9c8b0f8019e4a1e56aeb46dec6fb02%2FScreenshot%202023-05-06%20201119.png?generation=1683396831923664&alt=media)" }, "source": "meta" }