Comments (10)
Where can I find the contribution guideline and looks like the input of the original model in that paper only has two graph data and different interaction types without context features, do I need to incorporate also the context features into the current framework? Or do I need to find a way to transform the context features into a specific interaction type? Sorry that this is my first time using such a cooperative mode of GitHub and there might be some silly questions.
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- Context features are unused in this model.
- There is a public reference implementation out.
from chemicalx.
- Context features are unused in this model.
- There is a public reference implementation out.
Thanks! Where can I find the public reference implementation out? Is it the documentation of this ChemicalX or just the original code associated with this paper?
from chemicalx.
https://github.com/kanz76/SSI-DDI/blob/master/models.py
Do not rely on PyTorch Geometric.
from chemicalx.
from chemicalx.
Torchdrug already has that layer.
from chemicalx.
The original paper defines different M learnable matrices for different interaction types in Equation (11), I guess here in our problem, can we assume only one interaction type is considered since the input is only the leftmolecules and rightmolecules.
from chemicalx.
Yes.
from chemicalx.
Just finished coding the model part, which is all based on torchdrug, pytorch and the current existing packages of chemicals, and currently working on testing the model. One question is that does the current pipeline support GPU training? If not, I guess I will just modify it a little bit on my end and try to train using GPU to test my implementation.
from chemicalx.
For testing whether our implementation is right, can I directly write a testing case following the previous script written in the test folder on github? But one thing is since it currently does not support GPU training, it will take me so long time to get the results. Can someone help me with that?
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Related Issues (20)
- KeyError: 'node_feature' from running deepdds_example.py HOT 7
- How are the methods implemented outside of the domain they are designed for? HOT 1
- Incorporate various dataset splits HOT 1
- Inconsistent labels in DrugCombDB
- Is this repo dead? Improve communication of its status HOT 2
- Performance bug of deepsynergy, deepdds and matchmaker on DrugBankDDI HOT 1
- How to retrieve the drug name?
- Data resolver tests HOT 2
- Add the AUDNNSynergy model HOT 1
- Add the TWOSIDES dataset with molecular features HOT 1
- Add the DrugComb and DrugCombDB data cleaning HOT 2
- Make dataset loaders on-the-fly
- GPU Transfer HOT 3
- DeepDDS Softmax bug
- BatchGenerator move back to name space HOT 2
- ChemicalX Tutorials are not working HOT 4
- 'LabeledTriples' object is not iterable HOT 2
- Pipeline - Unexpected Labels
- Tensor's device mismatch HOT 3
- Typo within documentation
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