metadata
license: bigscience-openrail-m
widget:
- text: O=C([C@@H](c1ccc(cc1)O)N)[MASK][C@@H]1C(=O)N2[C@@H]1SC([C@@H]2C(=O)O)(C)C
datasets:
- ChEMBL
pipeline_tag: fill-mask
tags:
- biology
- medical
BERT base for SMILES
This is bidirectional transformer pretrained on SMILES (simplified molecular-input line-entry system) strings.
Example: Amoxicillin
O=C([C@@H](c1ccc(cc1)O)N)N[C@@H]1C(=O)N2[C@@H]1SC([C@@H]2C(=O)O)(C)C
Two training objectives were used:
- masked language modeling
- molecular-formula validity prediction
Intended uses
This model is primarily aimed at being fine-tuned on the following tasks:
- molecule classification
- molecule-to-gene-expression mapping
- cell targeting
How to use in your code
from transformers import BertTokenizerFast, BertModel
checkpoint = 'unikei/bert-base-smiles'
tokenizer = BertTokenizerFast.from_pretrained(checkpoint)
model = BertModel.from_pretrained(checkpoint)
example = 'O=C([C@@H](c1ccc(cc1)O)N)N[C@@H]1C(=O)N2[C@@H]1SC([C@@H]2C(=O)O)(C)C'
tokens = tokenizer(example, return_tensors='pt')
predictions = model(**tokens)