Necessary steps:
Constructing a PPIK network,
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Generating frequent subgraphs (up to 5 nodes): https://github.com/ehab-abdelhamid/GraMi
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Solving subgraph matching problem to match the existing nodes with the frequent subgraphs: http://www.yfang.site/data-and-tools/submatch
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Generating a feature matrix from the output of second step. Overall code is available as read_SubMatch_output.java.
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Also final representations (Metagraph representations), node/protein ids, test indices, i.e., all necessary files are provided to generate the final representations as well as the final representations themselves.
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Feature selection and oversampling codes are also available to be performed on final representations