FP-GNN: a versatile deep learning architecture for enhanced molecular property prediction

Deep learning is an important method for molecular design and exhibits considerable ability to predict molecular properties, including physicochemical, bioactive, and ADME/T (absorption, distribution, metabolism, excretion, and toxicity) properties. In this study, we advanced a novel deep learning a...

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Bibliographic Details
Published in:arXiv.org 2022-05
Main Authors: Cai, Hanxuan, Zhang, Huimin, Zhao, Duancheng, Wu, Jingxing, Wang, Ling
Format: Article
Language:English
Subjects:
Algorithms
Biocompatibility
Chemical fingerprinting
Datasets
Deep learning
Graphs
Machine learning
Molecular properties
Toxicity
Online Access:Get full text
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Summary:Deep learning is an important method for molecular design and exhibits considerable ability to predict molecular properties, including physicochemical, bioactive, and ADME/T (absorption, distribution, metabolism, excretion, and toxicity) properties. In this study, we advanced a novel deep learning architecture, termed FP-GNN, which combined and simultaneously learned information from molecular graphs and fingerprints. To evaluate the FP-GNN model, we conducted experiments on 13 public datasets, an unbiased LIT-PCBA dataset, and 14 phenotypic screening datasets for breast cell lines. Extensive evaluation results showed that compared to advanced deep learning and conventional machine learning algorithms, the FP-GNN algorithm achieved state-of-the-art performance on these datasets. In addition, we analyzed the influence of different molecular fingerprints, and the effects of molecular graphs and molecular fingerprints on the performance of the FP-GNN model. Analysis of the anti-noise ability and interpretation ability also indicated that FP-GNN was competitive in real-world situations.
ISSN:2331-8422