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Journal of Chemical Information and Modeling
Article . 2025 . Peer-reviewed
License: CC BY
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https://doi.org/10.26434/chemr...
Article . 2025 . Peer-reviewed
License: CC BY
Data sources: Crossref
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KGG: Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions

Authors: Van-Thinh To; Phuoc-Chung Van-Nguyen; Gia-Bao Truong; Tuyet-Minh Phan; Tieu-Long Phan; Rolf Fagerberg; Peter Stadler; +1 Authors

KGG: Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions

Abstract

Molecular property prediction has become essential in accelerating advancements in drug discovery and materials science. Graph Neural Networks have recently demonstrated remarkable success in molecular representation learning; however, their broader adoption is impeded by two significant challenges: (1) data scarcity and constrained model generalization due to the expensive and timeconsuming task of acquiring labeled data, and (2) inadequate initial node and edge features that fail to incorporate comprehensive chemical domain knowledge, notably orbital information. To address these limitations, we introduce a Knowledge-Guided Graph (KGG) framework employing self-supervised learning to pre-train models using orbital-level features in order to mitigate reliance on extensive labeled datasets. In addition, we propose novel representations for atomic hybridization and bond types that explicitly consider orbital engagement. Our pre-training strategy is cost-efficient, utilizing approximately 250,000 molecules from the ZINC15 dataset, in contrast to contemporary approaches that typically require between two and ten million molecules, consequently reducing the risk of potential data contamination. Extensive evaluations on diverse downstream molecular property datasets demonstrate that our method significantly outperforms state-of-the-art baselines. Complementary analyses, including t-SNE visualizations and comparisons with traditional molecular fingerprints, further validate the effectiveness and robustness of our proposed KGG approach.

Keywords

104027 Computational chemistry, Computer, Neural Networks, 104022 Theoretical chemistry, 104022 Theoretische Chemie, Supervised Machine Learning, Drug Discovery/methods, 104027 Computational Chemistry

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
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