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Molecular representation learning is vital for various downstream applications, including the analysis and prediction of molecular properties and side effects. While Graph Neural Networks (GNNs) have been a popular framework for modeling molecular data, they often struggle to capture the full complexity of molecular representations. In this paper, we introduce a novel method called Gode, which accounts for the dual-level structure inherent in molecules. Molecules possess an intrinsic graph structure and simultaneously function as nodes within a broader molecular knowledge graph. Gode integrates individual molecular graph representations with multi-domain biochemical data from knowledge graphs. By pre-training two GNNs on different graph structures and employing contrastive learning, Gode effectively fuses molecular structures with their corresponding knowledge graph substructures. This fusion yields a more robust and informative representation, enhancing molecular property predictions by leveraging both chemical and biological information. When fine-tuned across 11 chemical property tasks, our model significantly outperforms existing benchmarks, achieving an average ROC-AUC improvement of 12.7% for classification tasks and an average RMSE/MAE improvement of 34.4% for regression tasks. Notably, Gode surpasses the current leading model in property prediction, with advancements of 2.2% in classification and 7.2% in regression tasks.
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GraSeq: Graph and Sequence Fusion Learning for Molecular Property Prediction
With the recent advancement of deep learning, molecular representation learning -- automating the discovery of feature representation of molecular structure, has attracted significant attention from both chemists and machine learning researchers. Deep learning can facilitate a variety of downstream applications, including bio-property prediction, chemical reaction prediction, etc. Despite the fact that current SMILES string or molecular graph molecular representation learning algorithms (via sequence modeling and graph neural networks, respectively) have achieved promising results, there is no work to integrate the capabilities of both approaches in preserving molecular characteristics (e.g, atomic cluster, chemical bond) for further improvement. In this paper, we propose GraSeq, a joint graph and sequence representation learning model for molecular property prediction. Specifically, GraSeq makes a complementary combination of graph neural networks and recurrent neural networks for modeling two types of molecular inputs, respectively. In addition, it is trained by the multitask loss of unsupervised reconstruction and various downstream tasks, using limited size of labeled datasets. In a variety of chemical property prediction tests, we demonstrate that our GraSeq model achieves better performance than state-of-the-art approaches.
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- Award ID(s):
- 1925607
- PAR ID:
- 10231955
- Date Published:
- Journal Name:
- GraSeq: Graph and Sequence Fusion Learning for Molecular Property Prediction
- Page Range / eLocation ID:
- 435 to 443
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1145/3340531.3411981
