AstraZeneca/chemicalx

Add the GCNBMP model

cthoyt opened this issue · 2 comments

  • Please read the paper first. It is here.
  • There is also code-release with the paper here.
  • After that read the contributing guidelines.
  • If there is an existing open-source version of the model please take a look.
  • ChemicalX is built on top of PyTorch 1.10. and torchdrug.
  • The library heavily builds on top on torchdrug and molecules in batches are PackedGraphs.
  • There is already a model class under ./chemicalx/models/
  • Context features, drug level features, and labels are all FloatTensors.
  • Look at the examples and tests under ./examples/ and ./tests/.
  • Add auxiliary layers as you see fit - please document these, add tests, and add these layers to the main readme.md if needed.
  • Add typing to the initialization and forward pass.
  • Non-data-dependent hyperparameters should have default values.
  • Please add tests under ./tests/ and make sure that your model/layer is tested with real data.
  • Write an example under ./examples/. What is the AUC on the test set? Is it reasonable?

Hey @cthoyt

I discussed with @benedekrozemberczki and I'm gonna implement this one. I've had a look at the original code and the paper and I think the architecture is pretty clear for me now. Will let you know how it goes.

Excellent!