deepfindr/gnn-project

Error in f.to_pyg_graph(): TypeError: type object got multiple values for keyword argument 'pos'

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claudiofernandez commented

Hello, I am trying to run your code, but I am facing a problem when creating the dataset. Particularly on line 54 of the dataset_featurizer.py, where we are transforming to a Pytorch Geometric graph using:
data = f.to_pyg_graph()
I run into this error:
TypeError: type object got multiple values for keyword argument 'pos'

The f in this case looks like this:
GraphData(node_features=[46, 30], edge_index=[2, 108], edge_features=[108, 11], pos=[0])

This has been created from row = ('level_0', 0) ('Unnamed: 0', 3999) ('index', 3999) ('smiles', 'CSc1cc2[n+]3c(c1)-c1cccc[n+]1[Zn-4]314([n+]3ccccc3-2)[n+]2ccccc2-c2cc(SC)cc([n+]21)-c1cccc[n+]14.[O-]Cl+3([O-])[O-]') ('activity', 'CI') ('HIV_active', 0)

I don't really know what to do or how to solve it.
Maybe you could also upload the content in /data/processed, so that this issue is solved.

Help please, I am very stuck with this issue and I cannot run your code.

Thank you for your time.

deepfindr commented

Hi!

Here are a couple of propositions to get around your issue:

  • Use the dataset.py instead of the featurizer, then you don't have to do the conversion from deepchem
  • The issue you describe is known on the deepchem side (see here: deepchem/deepchem#3090), so maybe try to update to the version of their fix
  • Manually remove "pos" from the attributes to remove the error in a hacky way

Hope this helps

  • 👍1