A knowledge-guided pre-training framework for improving molecular representation learning

Han Li, Ruotian Zhang, Yaosen Min, Dacheng Ma, Dan Zhao () and Jianyang Zeng ()
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Han Li: Tsinghua University
Ruotian Zhang: Tsinghua University
Yaosen Min: Tsinghua University
Dacheng Ma: Zhejiang Laboratory
Dan Zhao: Tsinghua University
Jianyang Zeng: Tsinghua University

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract Learning effective molecular feature representation to facilitate molecular property prediction is of great significance for drug discovery. Recently, there has been a surge of interest in pre-training graph neural networks (GNNs) via self-supervised learning techniques to overcome the challenge of data scarcity in molecular property prediction. However, current self-supervised learning-based methods suffer from two main obstacles: the lack of a well-defined self-supervised learning strategy and the limited capacity of GNNs. Here, we propose Knowledge-guided Pre-training of Graph Transformer (KPGT), a self-supervised learning framework to alleviate the aforementioned issues and provide generalizable and robust molecular representations. The KPGT framework integrates a graph transformer specifically designed for molecular graphs and a knowledge-guided pre-training strategy, to fully capture both structural and semantic knowledge of molecules. Through extensive computational tests on 63 datasets, KPGT exhibits superior performance in predicting molecular properties across various domains. Moreover, the practical applicability of KPGT in drug discovery has been validated by identifying potential inhibitors of two antitumor targets: hematopoietic progenitor kinase 1 (HPK1) and fibroblast growth factor receptor 1 (FGFR1). Overall, KPGT can provide a powerful and useful tool for advancing the artificial intelligence (AI)-aided drug discovery process.

Date: 2023
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DOI: 10.1038/s41467-023-43214-1

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