Loading Tox21 through the dataloader.

[cmvcordova]

Hey guys,

I was trying to load the Tox21 dataset through the get_data_loaders() function with the following call:

Tox21_dataloader, _, _ = get_data_loaders(featurizer, batch_size=32, task_name='Tox', dataset_name ='Tox21')

Said call however, returned the following error:

ValueError: Please select a label name. You can use tdc.utils.retrieve_label_name_list('tox21') to retrieve all available label names.
In call to configurable 'data' (<function get_data_split at 0x7fb3f49b3e50>)

When adding the assay_name = 'nr-ar' parameter to the call, as hinted by tox21-nr-ar.gin, like this:

Tox21_dataloader, _, _ = get_data_loaders(featurizer, batch_size=32, task_name='Tox', dataset_name ='Tox21', assay_name = 'NR-AR')

I got the following error:

TypeError: get_data_loaders() got an unexpected keyword argument 'assay_name'

When I unpacked the get_data_loaders() function arguments using inspect.getfullargspec(get_data_loaders) with the inspect python package, I got:

FullArgSpec(args=['featurizer'], varargs=None, varkw=None, defaults=None, kwonlyargs=['batch_size', 'num_workers', 'cache_encodings', 'task_name', 'dataset_name'], kwonlydefaults={'num_workers': 0, 'cache_encodings': False, 'task_name': None, 'dataset_name': None}, annotations={'return': typing.Tuple[torch.utils.data.dataloader.DataLoader, torch.utils.data.dataloader.DataLoader, torch.utils.data.dataloader.DataLoader], 'featurizer': <class 'src.huggingmolecules.featurization.featurization_api.PretrainedFeaturizerMixin'>, 'batch_size': <class 'int'>, 'num_workers': <class 'int'>, 'cache_encodings': <class 'bool'>, 'task_name': <class 'str'>, 'dataset_name': <class 'str'>})

Which doesn't seem to have an option to specify additional parameters in the call.

Maybe I'm overthinking this. Could I get a few pointers on how to successfully load the NR-AR Tox21 dataset with a base get_data_loaders() call?

Regards,

César Miguel

[panpiort8]

Sorry for delay :) You are right: kwargs are missing. Adding them in the above MR.