chemicalx

chemicalx copied to clipboard

Tensor's device mismatch

3

Hi! I have found a bug during the training of the caster model. It was caused by the `torch.eye` manipulation, simply it did not specify the device. When the Cuda...

hzcheney

How are the methods implemented outside of the domain they are designed for?

1

For example, `DeepSynergy` and `MatchMaker` are requiring cell line information, and they are both implemented in the DrugBankDDI & TWOSIDES benchmarks where no cell line information is available at all...

jasperhyp

KeyError: 'node_feature' from running deepdds_example.py

7

Please see the following log. ```python-traceback File "deepdds.py", line 27, in 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 =...

cshukai

Incorporate various dataset splits

1

I also have one suggestion for future updates of this library perhaps. The current dataloaders, if I'm not mistaken, are not considering the different dataset split strategies. Recent works have...

jasperhyp

Simplify installation

1

This PR updates the pyproject.toml to tell build systems that torch needs to be available _before_ installation so there's no issues with the torch_scatter. It switches from setup.py to a...

cthoyt

I think it would be better to have the dataset download and processing happen client-side, then use `pystow` to store the results in a reliable place. This would also allow...

cthoyt

Add the DrugComb and DrugCombDB data cleaning

2

benedekrozemberczki

It seems deepsynergy, deepdds and matchmaker use the groundtruth (which is called context in the dataset) as model input. So the models performance are extremely high.

wjxts

Is this repo dead? Improve communication of its status

2

I'm under the impression that AstraZeneca isn't allocating resources to maintaining this repository or answering questions. Is this correct? I don't feel comfortable answering questions or maintaining this as long...

cthoyt