MolXPT: Wrapping Molecules with Text for Generative Pre-training
Authors: name: Zequn Liu, name: Wei Zhang, name: Yingce Xia, name: Lijun Wu, name: Shufang Xie, name: Tao Qin, name: Ming Zhang, name: Tie-Yan Liu

Generative pre-trained Transformer (GPT) has demonstrates its great success
in natural language processing and related techniques have been adapted into
molecular modeling. Considering that text is the most important record for
scientific discovery, in this paper, we propose MolXPT, a unified language
model of text and molecules pre-trained on SMILES (a sequence representation of
molecules) wrapped by text. Briefly, we detect the molecule names in each
sequence and replace them to the corresponding SMILES. In this way, the SMILES
could leverage the information from surrounding text, and vice versa. The above
wrapped sequences, text sequences from PubMed and SMILES sequences from PubChem
are all fed into a language model for pre-training. Experimental results
demonstrate that MolXPT outperforms strong baselines of molecular property
prediction on MoleculeNet, performs comparably to the best model in
text-molecule translation while using less than half of its parameters, and
enables zero-shot molecular generation without finetuning.