@inproceedings{liu-etal-2023-molxpt,
    title = "{M}ol{XPT}: Wrapping Molecules with Text for Generative Pre-training",
    author = "Liu, Zequn  and
      Zhang, Wei  and
      Xia, Yingce  and
      Wu, Lijun  and
      Xie, Shufang  and
      Qin, Tao  and
      Zhang, Ming  and
      Liu, Tie-Yan",
    editor = "Rogers, Anna  and
      Boyd-Graber, Jordan  and
      Okazaki, Naoaki",
    booktitle = "Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers)",
    month = jul,
    year = "2023",
    address = "Toronto, Canada",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2023.acl-short.138",
    doi = "10.18653/v1/2023.acl-short.138",
    pages = "1606--1616",
    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.",
}

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