Add the DeepDDS model
cthoyt opened this issue · comments
Charles Tapley Hoyt commented
- 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 hyper-ammeters 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?
Benedek Rozemberczki commented
Gavin?
Charles Tapley Hoyt commented
Benedek Rozemberczki commented
Assigned him the GCN BMP paper, we can switch around.
Benedek Rozemberczki commented
This paper is easier - what do you think @cthoyt ?
Charles Tapley Hoyt commented
I think it would be better to give Klas the easier one :)
Benedek Rozemberczki commented
Okay, let me switch around in a moment.