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mims-harvard / SubGNN

Subgraph Neural Networks (NeurIPS 2020)
https://zitniklab.hms.harvard.edu/projects/SubGNN
MIT License
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Empty files in dataset: HP-NEURO #8

Closed dongkwan-kim closed 3 years ago

dongkwan-kim commented 3 years ago

Hi, I really appreciate the detailed description and instruction in running codes and datasets.

I found that there are multiple empty files in the HP-NEURO folder you provided.

https://www.dropbox.com/sh/zv7gw2bqzqev9yn/AABa4J3UlMDkbbcksYKKHrgKa/hpo_neuro?dl=0&subfolder_nav_tracking=1

Would you please check this?

Thanks in advance.

EmilyAlsentzer commented 3 years ago

Hi @dongkwan-kim, Are you referring to the similarities folder? All of the files in that folder are generated by running the code if they do not already exist. You should still be able to run everything without the files there, but I just added the similarity pre-computations for HPO-NEURO so that you don't need to recalculate them. If there's something else missing from the folder, please let me know.

dongkwan-kim commented 3 years ago

Thank you for adding similarities files.

But empty files I am saying are degree_sequence.txt, edge_list.txt. ego_graphs.txt, gin_embeddings.pth, graphsaint_gcn_embedddings.pth, and shortest_path_matrix.npy in hpo_neuro/.

These files are 0-bytes files to me on the dropbox preview and my filesystem after download.

I think there seems to be an error when uploading hpo_neuro/ to the dropbox. (There is no error for other datasets as far as I can see..)

Here is a screenshot for 0-bytes ego_graphs.txt as an example.

image

Or..., am I missing something?

EmilyAlsentzer commented 3 years ago

I see, I think this occurred because the HPO-NEURO files were symbolic links to HPO-METAB (the datasets share the same base underlying graph). I have updated the dropbox so that these files are no longer empty. Let me know if you have any more trouble.

dongkwan-kim commented 3 years ago

Oh, I see. Thank you for your effort. I will close this issue.