GCN with MolGraphConv Featurization on BACE

mufeili commented 3 years ago

@rbharath This PR is for a submission of GCN with MolGraphConv featurization on BACE. It includes:

An entry for the submission in the leaderboard
A script for training and hyperparameter search as well as a README file for the script. I want to reuse the script as much as possible across models and datasets.

It depends on PR #2328 in DeepChem for a bug fix.

We also need to fix a warning related to DGL in DeepChem.

/home/ubuntu/anaconda3/envs/deepchem/lib/python3.6/site-packages/dgl/base.py:45: DGLWarning: DGLGraph.__len__ is deprecated.Please directly call DGLGraph.number_of_nodes.
  return warnings.warn(message, category=category, stacklevel=1)

mufeili commented 3 years ago

@rbharath Thank you for the review. I think you can go ahead and merge it. For the follow-up PRs, do we now have an overview of all the datasets and their statistics, including the new ones in MoleculeNet v2?

Also copy @miaecle in case you have bandwidth to take a look.

rbharath commented 3 years ago

@mufeili The list of datasets on https://deepchem.readthedocs.io/en/latest/api_reference/moleculenet.html is probably pretty representative of MoleculeNet v2 (although we might have a few more datasets trickling in before we made the cut). We don't have a nice table with statistics though (which would be nice to have!)

Going to go ahead and merge this in (please still free to comment @miaecle if you have bandwidth!)

deepchem / moleculenet

GCN with MolGraphConv Featurization on BACE #16