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xiangyue9607 / BioNEV

Graph Embedding Evaluation / Code and Datasets for "Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations" (Bioinformatics 2020)
MIT License
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Reproduction question: how were the datasets generated? #4

Open cthoyt opened 5 years ago

cthoyt commented 5 years ago

This repository includes five nice datasets which makes reproduction much easier, but it's missing whatever scripts (or instructions if manually done) were used to generate them. This would be helpful not only to ensure the correctness of the training data, but to enable periodic reproduction as the underlying databases are updated

xiangyue9607 commented 5 years ago

Thanks! We do not release the data pre-processing code since our focus is to develop a general package used to evaluate different graph embedding methods. The package can be used for various graph data, including but not limited to the 5 compiled datasets in this repo. Pre-processing these data is not a difficult thing and we also list the original data link in the README. Let me know if it sounds reasonable to you.