deepFPlearn+: Enhancing toxicity prediction across the chemical universe using 
graph neural networks

Soulios, Kyriakos; Scheibe, Patrick; Bernt, Matthias; Hackermüller, Jörg; Schor, Jana

doi:10.1093/bioinformatics/btad713

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deepFPlearn+: Enhancing toxicity prediction across the chemical universe using graph neural networks

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Scheibe, Patrick
Department Neurophysics (Weiskopf), MPI for Human Cognitive and Brain Sciences, Max Planck Society;

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引用

Soulios, K., Scheibe, P., Bernt, M., Hackermüller, J., & Schor, J. (2023). deepFPlearn+: Enhancing toxicity prediction across the chemical universe using graph neural networks. Bioinformatics, 39(12):. doi:10.1093/bioinformatics/btad713.

引用: https://hdl.handle.net/21.11116/0000-000D-FDC4-9

要旨

Summary: Sophisticated approaches for the in-silico prediction of toxicity are required to support the risk assessment of chemicals. The number of chemicals on the global chemical market and the speed of chemical innovation stand in massive contrast to the capacity for regularizing chemical use. We recently proved our ready-to-use application deepFPlearn as a suitable approach for this task. Here, we present its extension deepFPlearn+ incorporating i) a graph neural network to feed our AI with a more sophisticated molecular structure representation and ii) alternative train-test splitting strategies that involve scaffold structures and the molecular weights of chemicals. We show that the GNNs outperform the previous model substantially and that our models can generalize on unseen data even with a more robust and challenging test set. Therefore, we highly recommend the application of deepFPlearn+ on the chemical inventory to prioritize chemicals for experimental testing or any chemical subset of interest in monitoring studies.

Availability and implementation: The software is compatible with python 3.6 or higher, and the source code can be found on our GitHub repository: https://github.com/yigbt/deepFPlearn. A complete data and models archive is also available on Zenodo: https://zenodo.org/record/8146252. Detailed installation guides via Docker, Singularity, and Conda are provided within the repository for operability across all operating systems.