KeyError: 'node_feature' from running deepdds_example.py #100
Comments
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Hi, I just re-ran the example code with chemicalx 0.1.0 and had no such issue. Could you provide a bit more details? How are you running the example? |
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I copied and pasted the python script and ran the script like python deepdds_example.py
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Traceback (most recent call last):
File "deepdds_example.py", line 27, in <module>
main()
File "deepdds_example.py", line 14, in main
results = pipeline(
File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/chemicalx/pipeline.py", line 155, in pipeline
prediction = model(*model.unpack(batch))
File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1110, in _call_impl
return forward_call(*input, **kwargs)
File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/chemicalx/models/deepdds.py", line 176, in forward
features_left = self._forward_molecules(molecules_left)
File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/chemicalx/models/deepdds.py", line 158, in _forward_molecules
features = self.drug_conv(molecules, molecules.data_dict["node_feature"])["node_feature"]
KeyError: 'node_feature' |
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Thanks so much for the help! I added the following code block at the top of example script for DeepDDS: But still the same issue : running with device: Tesla V100S-PCIE-32GB
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Traceback (most recent call last):
File "deepdds_example.py", line 30, in <module>
main()
File "deepdds_example.py", line 17, in main
results = pipeline(
File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/chemicalx/pipeline.py", line 155, in pipeline
prediction = model(*model.unpack(batch))
File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1110, in _call_impl
return forward_call(*input, **kwargs)
File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/chemicalx/models/deepdds.py", line 176, in forward
features_left = self._forward_molecules(molecules_left)
File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/chemicalx/models/deepdds.py", line 158, in _forward_molecules
features = self.drug_conv(molecules, molecules.data_dict["node_feature"])["node_feature"]
KeyError: 'node_feature'But I can run the deepsynerg without this issue roc_auc 0.834909 |
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It's not surprising that deepsynergy worked for you given that it has a way simpler architecture and doesn't use the same layer as deepdds. Could add the details of your environment? What versions of packages do you have in your env? |
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Operating system : CENTOS_MANTISBT_PROJECT="CentOS-7" CentOS Linux release 7.9.2009 (Core)
Name Version Build Channel |
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I think I found the root of the problem. It seems that with torchdrug update from 0.1.2 to 0.1.3, there was a change in the key name mentioned here:
This would mean that for this model to work with torchdrug 0.1.3 we'd have to rename "node_feature" key to "atom_feature" or fix torchdrug to 0.1.2. @cthoyt @benedekrozemberczki opinions? |
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If AstraZeneca wants to pay for some consulting work done for this, I think the best strategy would be to divest from |
Please see the following log.
File "deepdds.py", line 27, in <module> main() File "deepdds.py", line 14, in main results = pipeline( File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/chemicalx/pipeline .py", line 155, in pipeline prediction = model(*model.unpack(batch)) File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/torch/nn/modules/m odule.py", line 1110, in _call_impl return forward_call(*input, **kwargs) File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/chemicalx/models/d eepdds.py", line 176, in forward features_left = self._forward_molecules(molecules_left) File "/storage/htc/nih-tcga/sc724/conda/synergy/lib/python3.8/site-packages/chemicalx/models/d eepdds.py", line 158, in _forward_molecules features = self.drug_conv(molecules, molecules.data_dict["node_feature"])["node_feature"] KeyError: 'node_feature'The text was updated successfully, but these errors were encountered: