Closed yuanqidu closed 3 years ago
Ah sorry this isn't well explained in the docs. The Kaggle, UV, Kinase datasets are from a paper with Merck I wrote several years ago where they only provided disguised descriptors. So we don't actually have the structures and can't apply models that need molecular structure
Thanks for your comments. Got it!
It seems the dataset loader has some issues. I tried to load the data and run the GCN model in moleculenet (dc.models.GCNModel). The following is the error message:
Traceback (most recent call last): File "gnn.py", line 235, in
val_metrics, test_metrics = bayesian_optimization(args)
File "gnn.py", line 160, in bayesian_optimization
max_evals=args['num_trials'])
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 553, in fmin
rval.exhaust()
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 356, in exhaust
self.run(self.max_evals - n_done, block_until_done=self.asynchronous)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 292, in run
self.serial_evaluate()
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/fmin.py", line 170, in serial_evaluate
result = self.domain.evaluate(spec, ctrl)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/hyperopt/base.py", line 907, in evaluate
rval = self.fn(pyll_rval)
File "gnn.py", line 143, in objective
val_metrics, test_metrics = main(save_path, configure, hyperparams)
File "gnn.py", line 78, in main
restore=epoch > 0)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/models/torch_models/torch_model.py", line 286, in fit
checkpoint_interval, restore, variables, loss, callbacks, all_losses)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/models/torch_models/torch_model.py", line 363, in fit_generator
inputs, labels, weights = self._prepare_batch(batch)
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/models/torch_models/gcn.py", line 349, in _prepare_batch
graph.to_dgl_graph(self_loop=self._self_loop) for graph in inputs[0]
File "/home/v-yuanqidu/.conda/envs/deepchem/lib/python3.7/site-packages/deepchem/models/torch_models/gcn.py", line 349, in
graph.to_dgl_graph(self_loop=self._self_loop) for graph in inputs[0]
AttributeError: 'numpy.ndarray' object has no attribute 'to_dgl_graph'