MolXPT: Wrapping Molecules with Text for Generative Pre-training

Zequn Liu, Wei Zhang, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Ming Zhang, Tie-Yan Liu

Main: NLP Applications Main-poster Paper

Session 7: NLP Applications (Virtual Poster)
Conference Room: Pier 7&8
Conference Time: July 12, 11:00-12:30 (EDT) (America/Toronto)
Global Time: July 12, Session 7 (15:00-16:30 UTC)
Keywords: healthcare applications, clincial nlp
TLDR: 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 langua...
You can open the #paper-P5167 channel in a separate window.
Abstract: 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.