Yuan-Bin She

Transfer Learning across Different Chemical Domains: Virtual Screening of Organic Materials with Deep Learning Models Pretrained on Small Molecule and Chemical Reaction Data

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Machine learning prediction of organic materials properties is an efficient virtual screening method ahead of more expensive screening methods. However, this approach has suffered from insufficient labeled data on organic materials to train state-of-the-art machine learning models. In this study, we demonstrate that drug-like small molecule and chemical reaction databases can be used to pretrain the BERT model for the virtual screening of organic materials. Among the BERT models fine-tuned by five virtual screening tasks on organic materials, the USPTO-SMILES pretrained BERT model had R2 > 0.90 for two tasks and R2 > 0.82 for one, which was generally superior to the same models pretrained by the small molecule or organic materials databases, as well as to the other three traditional machine learning models trained directly on the virtual screening task data. The superior performance of the USPTO-SMILES pretrained BERT model is due to the greater variety of organic building blocks in the USPTO database and the broader coverage of the chemical space. The even better performance of the BERT model pretrained externally from a chemical reaction database with additional sources of chemical reactions strengthens our proof of concept that transfer learning across different chemical domains is practical for the virtual screening of organic materials.

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