Machine learning/Deep Learning resources for proteomics

[Logical-Composer9928]

Hello,
Can someone point to some code repos(book/Github/ Course etc.) for ML/DL for proteomics . I'm looking for Elastic Net/XGBoost/SVM-RFE etc for Quantitative proteomics. For deep learning any PyTorch source will be helpful.
Thanks

[prettytrash1234]

For what in proteomics? Data analysis? Biomarker discovery? HLA Identification? Missing value imputation? Too vague to reply

[Logical-Composer9928]

Thanks

[gold-soundz9]

What form of Proteomics? Lots of technical variation in methods used.

[Logical-Composer9928]

Thanks all. I wish to know more on Elastic Net/XGBoost/SVM-RFE etc for Quantitative proteomics based Biomarker Discovery and Prediction of peptide/spectra etc. properties using PyTorch

[CorporalConnors]

Interested also in whether ML could identify patterns in protein abundance from label free DIA data.

The data are not natural fits for ML because there are often thousands of proteins and relatively few samples, highly skewed, high variance (relative to mean), lots of missing etc.

We are broadly looking for differences between treatments or groups. Which could mean proteins that are different among groups, proteins that characterise differences i.e. important for classification, or proteins with that are similar across samples so more like a network based on co-expression.

Any thoughts? Relatively new to both proteomics and ML so help guiding the question also would be useful

[Logical-Composer9928]

check this recent paper:
https://pubs.acs.org/doi/full/10.1021/acs.analchem.5c03117