{ "id": 402802, "title": "CAFA 5 some relevant research papers", "url": "/competitions/cafa-5-protein-function-prediction/discussion/402802", "author_name": "", "post_date": "2023-04-19T18:49:39.547335700Z", "votes": 29, "comment_count": 3, "views": 0, "content": "

It is a regular challenge in bioinformatics and huge literature exists:
\nhttps://scholar.google.fr/scholar?start=0&q=cafa+protein+function+prediction&hl=en&as_sdt=0,5&as_vis=1

\n

Relevant Kaggle competition:
\nhttps://www.kaggle.com/competitions/novozymes-enzyme-stability-prediction

\n

Some papers and other links :

\n

Previous winner(?) :
\nIntegrating Self-Attention Transformer with Triplet Neural Networks for Protein Gene Ontology Prediction
\nY Zhu, C Zhang, DJ Yu, Y Zhang
\nhttps://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010793
\nbioRxiv, 2022.07. 07.499156 https://www.biorxiv.org/content/10.1101/2022.07.07.499156v1
\nhttps://scholar.google.com/citations?view_op=view_citation&hl=en&user=ainfZ1UAAAAJ&citation_for_view=ainfZ1UAAAAJ:WF5omc3nYNoC

\n

Review of CAFA 1-3: https://www.biorxiv.org/content/10.1101/653105v1
\nThe CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

\n

ProFAB – Open Protein Functional Annotation Benchmark
\nhttps://profab.kansil.org/
\nhttps://academic.oup.com/bib/article-abstract/24/2/bbac627/7025464

\n

Automatic Gene Function Prediction in the 2020’s
\nhttps://www.mdpi.com/2073-4425/11/11/1264

\n

CAFA site:
\nhttps://biofunctionprediction.org/cafa/

\n

CAFA4 Wiki:
\nhttps://www.synapse.org/#!Synapse:syn21035948/wiki/597156

\n

Ogranizer ( Iddo Friedberg ) twitter https://twitter.com/iddux

\n

PersGNN: Applying Topological Data Analysis and
\nGeometric Deep Learning to Structure-Based Protein Function Prediction
\nhttps://arxiv.org/abs/2010.16027

\n

A Review of Deep Learning Techniques for Protein Function Prediction
\nhttps://arxiv.org/abs/2211.09705

\n

Large language models generate functional protein sequences across diverse families
\nhttps://www.nature.com/articles/s41587-022-01618-2

\n

ProLanGO2: Protein Function Prediction with Ensemble of Encoder-Decoder Networks
\nhttps://dl.acm.org/doi/abs/10.1145/3388440.3414701

\n

with ESM:
\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8808544/

\n

NO ML:
\nhttps://onlinelibrary.wiley.com/doi/full/10.1002/pro.4193

\n

PPI + GCN
\nhttps://academic.oup.com/bib/article/23/5/bbac333/6659744

\n

Many more:
\nhttps://scholar.google.com/scholar?start=20&q=cafa+challenge&hl=en&as_sdt=0,5&as_ylo=2019

", "messages": [ { "id": "2227436", "postDate": "04/19/2023 18:49:39", "content": "

It is a regular challenge in bioinformatics and huge literature exists:
\nhttps://scholar.google.fr/scholar?start=0&q=cafa+protein+function+prediction&hl=en&as_sdt=0,5&as_vis=1

\n

Relevant Kaggle competition:
\nhttps://www.kaggle.com/competitions/novozymes-enzyme-stability-prediction

\n

Some papers and other links :

\n

Previous winner(?) :
\nIntegrating Self-Attention Transformer with Triplet Neural Networks for Protein Gene Ontology Prediction
\nY Zhu, C Zhang, DJ Yu, Y Zhang
\nhttps://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010793
\nbioRxiv, 2022.07. 07.499156 https://www.biorxiv.org/content/10.1101/2022.07.07.499156v1
\nhttps://scholar.google.com/citations?view_op=view_citation&hl=en&user=ainfZ1UAAAAJ&citation_for_view=ainfZ1UAAAAJ:WF5omc3nYNoC

\n

Review of CAFA 1-3: https://www.biorxiv.org/content/10.1101/653105v1
\nThe CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

\n

ProFAB – Open Protein Functional Annotation Benchmark
\nhttps://profab.kansil.org/
\nhttps://academic.oup.com/bib/article-abstract/24/2/bbac627/7025464

\n

Automatic Gene Function Prediction in the 2020’s
\nhttps://www.mdpi.com/2073-4425/11/11/1264

\n

CAFA site:
\nhttps://biofunctionprediction.org/cafa/

\n

CAFA4 Wiki:
\nhttps://www.synapse.org/#!Synapse:syn21035948/wiki/597156

\n

Ogranizer ( Iddo Friedberg ) twitter https://twitter.com/iddux

\n

PersGNN: Applying Topological Data Analysis and
\nGeometric Deep Learning to Structure-Based Protein Function Prediction
\nhttps://arxiv.org/abs/2010.16027

\n

A Review of Deep Learning Techniques for Protein Function Prediction
\nhttps://arxiv.org/abs/2211.09705

\n

Large language models generate functional protein sequences across diverse families
\nhttps://www.nature.com/articles/s41587-022-01618-2

\n

ProLanGO2: Protein Function Prediction with Ensemble of Encoder-Decoder Networks
\nhttps://dl.acm.org/doi/abs/10.1145/3388440.3414701

\n

with ESM:
\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8808544/

\n

NO ML:
\nhttps://onlinelibrary.wiley.com/doi/full/10.1002/pro.4193

\n

PPI + GCN
\nhttps://academic.oup.com/bib/article/23/5/bbac333/6659744

\n

Many more:
\nhttps://scholar.google.com/scholar?start=20&q=cafa+challenge&hl=en&as_sdt=0,5&as_ylo=2019

", "rawMarkdown": "It is a regular challenge in bioinformatics and huge literature exists:\nhttps://scholar.google.fr/scholar?start=0&q=cafa+protein+function+prediction&hl=en&as_sdt=0,5&as_vis=1\n\nRelevant Kaggle competition:\nhttps://www.kaggle.com/competitions/novozymes-enzyme-stability-prediction\n\nSome papers and other links : \n\nPrevious winner(?) : \nIntegrating Self-Attention Transformer with Triplet Neural Networks for Protein Gene Ontology Prediction\nY Zhu, C Zhang, DJ Yu, Y Zhang\nhttps://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010793\nbioRxiv, 2022.07. 07.499156 https://www.biorxiv.org/content/10.1101/2022.07.07.499156v1\nhttps://scholar.google.com/citations?view_op=view_citation&hl=en&user=ainfZ1UAAAAJ&citation_for_view=ainfZ1UAAAAJ:WF5omc3nYNoC\n\nReview of CAFA 1-3: https://www.biorxiv.org/content/10.1101/653105v1\nThe CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens\n\nProFAB – Open Protein Functional Annotation Benchmark\nhttps://profab.kansil.org/\nhttps://academic.oup.com/bib/article-abstract/24/2/bbac627/7025464\n\nAutomatic Gene Function Prediction in the 2020’s\nhttps://www.mdpi.com/2073-4425/11/11/1264\n\nCAFA site:\nhttps://biofunctionprediction.org/cafa/\n\nCAFA4 Wiki:\nhttps://www.synapse.org/#!Synapse:syn21035948/wiki/597156\n\nOgranizer ( Iddo Friedberg ) twitter https://twitter.com/iddux\n\nPersGNN: Applying Topological Data Analysis and\nGeometric Deep Learning to Structure-Based Protein Function Prediction\nhttps://arxiv.org/abs/2010.16027\n\nA Review of Deep Learning Techniques for Protein Function Prediction\nhttps://arxiv.org/abs/2211.09705\n\nLarge language models generate functional protein sequences across diverse families\nhttps://www.nature.com/articles/s41587-022-01618-2\n\nProLanGO2: Protein Function Prediction with Ensemble of Encoder-Decoder Networks\nhttps://dl.acm.org/doi/abs/10.1145/3388440.3414701\n\nwith ESM:\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8808544/ \n\nNO ML:\nhttps://onlinelibrary.wiley.com/doi/full/10.1002/pro.4193 \n\nPPI + GCN\nhttps://academic.oup.com/bib/article/23/5/bbac333/6659744\n\nMany more: \nhttps://scholar.google.com/scholar?start=20&q=cafa+challenge&hl=en&as_sdt=0,5&as_ylo=2019", "votes": null }, { "id": "2342979", "postDate": "07/13/2023 10:04:10", "content": "

Nice you put Geometric Deep Learning ! I went through the Bronstein paper which is the basis of it and I am trying to implement it now ! Maybe it can be useful for that case

", "rawMarkdown": "Nice you put Geometric Deep Learning ! I went through the Bronstein paper which is the basis of it and I am trying to implement it now ! Maybe it can be useful for that case", "votes": null }, { "id": "2345405", "postDate": "07/15/2023 10:59:25", "content": "

Really thanks the good review list! I have just know about this field, but I can learn about the theme quickly by your good job.

", "rawMarkdown": "Really thanks the good review list! I have just know about this field, but I can learn about the theme quickly by your good job.", "votes": null }, { "id": "2361162", "postDate": "07/27/2023 08:27:07", "content": "

Thank you for compiling this up!

", "rawMarkdown": "Thank you for compiling this up!", "votes": null } ], "comments": [ { "id": 2342979, "author_name": "hamedjoorati", "author_url": "", "post_date": "07/13/2023 10:04:10", "content": "

Nice you put Geometric Deep Learning ! I went through the Bronstein paper which is the basis of it and I am trying to implement it now ! Maybe it can be useful for that case

", "votes": null, "replies": [] }, { "id": 2345405, "author_name": "ryumdra", "author_url": "", "post_date": "07/15/2023 10:59:25", "content": "

Really thanks the good review list! I have just know about this field, but I can learn about the theme quickly by your good job.

", "votes": null, "replies": [] }, { "id": 2361162, "author_name": "ridamahmood005", "author_url": "", "post_date": "07/27/2023 08:27:07", "content": "

Thank you for compiling this up!

", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "2227436": "It is a regular challenge in bioinformatics and huge literature exists:\nhttps://scholar.google.fr/scholar?start=0&q=cafa+protein+function+prediction&hl=en&as_sdt=0,5&as_vis=1\n\nRelevant Kaggle competition:\nhttps://www.kaggle.com/competitions/novozymes-enzyme-stability-prediction\n\nSome papers and other links : \n\nPrevious winner(?) : \nIntegrating Self-Attention Transformer with Triplet Neural Networks for Protein Gene Ontology Prediction\nY Zhu, C Zhang, DJ Yu, Y Zhang\nhttps://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010793\nbioRxiv, 2022.07. 07.499156 https://www.biorxiv.org/content/10.1101/2022.07.07.499156v1\nhttps://scholar.google.com/citations?view_op=view_citation&hl=en&user=ainfZ1UAAAAJ&citation_for_view=ainfZ1UAAAAJ:WF5omc3nYNoC\n\nReview of CAFA 1-3: https://www.biorxiv.org/content/10.1101/653105v1\nThe CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens\n\nProFAB – Open Protein Functional Annotation Benchmark\nhttps://profab.kansil.org/\nhttps://academic.oup.com/bib/article-abstract/24/2/bbac627/7025464\n\nAutomatic Gene Function Prediction in the 2020’s\nhttps://www.mdpi.com/2073-4425/11/11/1264\n\nCAFA site:\nhttps://biofunctionprediction.org/cafa/\n\nCAFA4 Wiki:\nhttps://www.synapse.org/#!Synapse:syn21035948/wiki/597156\n\nOgranizer ( Iddo Friedberg ) twitter https://twitter.com/iddux\n\nPersGNN: Applying Topological Data Analysis and\nGeometric Deep Learning to Structure-Based Protein Function Prediction\nhttps://arxiv.org/abs/2010.16027\n\nA Review of Deep Learning Techniques for Protein Function Prediction\nhttps://arxiv.org/abs/2211.09705\n\nLarge language models generate functional protein sequences across diverse families\nhttps://www.nature.com/articles/s41587-022-01618-2\n\nProLanGO2: Protein Function Prediction with Ensemble of Encoder-Decoder Networks\nhttps://dl.acm.org/doi/abs/10.1145/3388440.3414701\n\nwith ESM:\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8808544/ \n\nNO ML:\nhttps://onlinelibrary.wiley.com/doi/full/10.1002/pro.4193 \n\nPPI + GCN\nhttps://academic.oup.com/bib/article/23/5/bbac333/6659744\n\nMany more: \nhttps://scholar.google.com/scholar?start=20&q=cafa+challenge&hl=en&as_sdt=0,5&as_ylo=2019", "2342979": "Nice you put Geometric Deep Learning ! I went through the Bronstein paper which is the basis of it and I am trying to implement it now ! Maybe it can be useful for that case", "2345405": "Really thanks the good review list! I have just know about this field, but I can learn about the theme quickly by your good job.", "2361162": "Thank you for compiling this up!" }, "source": "meta" }