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LirongWu avatar LirongWu commented on June 11, 2024

The processing file is the correct version to run on my site. I noticed that this error may be due to the latest version of numpy discarding this usage.

As per the official instructions, "If you meant to do this, you must specify 'dtype=object' when creating the ndarray". Following this hint, we can solve this problem.

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SophieSarceau avatar SophieSarceau commented on June 11, 2024

Thanks, Lirong.
We can use the following code to pre-process the raw data.

r_edge_list = np.array(r_edge_list, dtype=object)
k_edge_list = np.array(k_edge_list, dtype=object)
np.save("../processed_data/protein.rball.edges.{}.npy".format(dataset), r_edge_list, allow_pickle=True)
np.save("../processed_data/protein.knn.edges.{}.npy".format(dataset), k_edge_list, allow_pickle=True)

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