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code for "Self-supervised edge features for improved Graph Neural Network training",

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Deep Learning self-supervsed_edge_feats
Overview

Self-supervised edge features for improved Graph Neural Network training

Data availability: Here is a link to the raw data for the organoids dataset. The raw COVID-19 patients dataset can be found on GEO (GSE145926). The pre-processed data (with the train/test/val splits we used in the paper) can be found here as pickle files. Unfortunately, I made the inadvertent error of storing the feature names in the pkl files as numbers so you need attached names, which are ordered the same as the numbers in the data pkl files for the key 'feat_names' key, to go from numbers to gene names (see two attached files).

See dataset folder for feature names pkl

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Comments
  • Package versions

    Package versions

    Hello! Thank you for the cool software!

    I'm trying to use your tool in my research but failed to run the code. I suspect that it is because of the versions of the packages (pytorch, torch_geometric, etc) that I used are not compatible with the ones that you used. I noticed that some of your code for re-writing the models are similar to older versions of torch_geometric, yet there're some functions that I wasn't able to load successfully in those older versions.

    It would be great if you could share the package versions you used so I can use the exact same ones for the analysis. Thanks so much in advance!

    opened by hongyaz 0
  • hello

    hello

    Hello, I don't quite understand the notice you introduced. How can I modify the code? And it's being carried out main.py ，'replicate': sys.argv [1] Something went wrong. Look forward to your reply

    opened by wangzhengzhengkai 0
Owner
Neal Ravindra
Neal Ravindra
GitHub
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