Hi,
I tried to fine tune the model100 with a dataset with the following code:
python molbert/apps/finetune.py \
--train_file train.csv \
--valid_file valid.csv \
--test_file test.csv \
--mode regression \
--output_size 1 \
--pretrained_model_path molbert_100epochs/checkpoints/last.ckpt \
--label_column mylabel \
--default_root_dir output/ \
--num_workers 4 &> out.txt
When I try to use the finetune model, I have this error:
from molbert.utils.featurizer.molbert_featurizer import MolBertFeaturizer
mycheckpoint='MolBERT/output/lightning_logs/version_0/checkpoints/last.ckpt'
molbert = MolBertFeaturizer(mycheckpoint)
--------------------------------------------------------------------------
KeyError Traceback (most recent call last)
/Users/cecilepereira/opt/anaconda3/envs/molbert/lib/python3.7/site-packages/pytorch_lightning/utilities/parsing.py in __getattr__(self, key)
113 try:
--> 114 return self[key]
115 except KeyError:
KeyError: 'named_descriptor_set'
During handling of the above exception, another exception occurred:
AttributeError Traceback (most recent call last)
<ipython-input-64-046163d76401> in <module>()
1 from molbert.utils.featurizer.molbert_featurizer import MolBertFeaturizer
----> 2 molbert = MolBertFeaturizer(mycheckpoint)
molbert/utils/featurizer/molbert_featurizer.py in __init__(self, checkpoint_path, device, embedding_type, max_seq_len, permute)
63 # load model
64 self.config = Namespace(**config_dict)
---> 65 self.model = SmilesMolbertModel(self.config)
66 self.model.load_from_checkpoint(self.checkpoint_path, hparam_overrides=self.model.__dict__)
67
molbert/models/base.py in __init__(self, args)
125 self._datasets = None
126
--> 127 self.config = self.get_config()
128 self.tasks = self.get_tasks(self.config)
129 if len(self.tasks) == 0:
molbert/models/smiles.py in get_config(self)
38 max_position_embeddings=self.hparams.max_position_embeddings,
39 num_physchem_properties=self.hparams.num_physchem_properties,
---> 40 named_descriptor_set=self.hparams.named_descriptor_set,
41 is_same_smiles=self.hparams.is_same_smiles,
42 )
/Users/username/opt/anaconda3/envs/molbert/lib/python3.7/site-packages/pytorch_lightning/utilities/parsing.py in __getattr__(self, key)
114 return self[key]
115 except KeyError:
--> 116 raise AttributeError(f'Missing attribute "{key}"')
117
118 def __setattr__(self, key, val):
AttributeError: Missing attribute "named_descriptor_set"
Could you help?
Hi,
I tried to fine tune the model100 with a dataset with the following code:
When I try to use the finetune model, I have this error:
Could you help?