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Metabolomics‑driven, data‑augmented machine learning for predicting toxicity of microplastic mixtures

Ecotoxicology and Environmental Safety 2026
Beilei Yuan, Chengzhi Liu, Shuang Chen, Jiangliang Chu, Yifan Yang, Yifan Yang, Yong Pan, Huazhong Zhang

Summary

Scientists developed a computer model that can predict how harmful mixtures of microplastics (tiny plastic particles) might be to our cells without testing each combination individually. The model works by analyzing how these plastic particles change the way cells produce energy, which helps explain why microplastics can be toxic. This breakthrough could help researchers quickly assess health risks from the complex mix of microplastics we're exposed to in real life through food, water, and air.

Microplastics (MPs) occur as heterogeneous mixtures in real‑world environments, making one‑by‑one toxicity testing impractical. This study aims to use predictive models to quickly and effectively evaluate the toxicity of MPs. We explored three model frameworks: a quantitative structure-activity relationship (QSAR) model based on physicochemical descriptors; a quantitative bioactivity relationship (QBAR) model with biodescriptors screened by metabolomics data; and a quantitative structure-bioactivity relationship (QSBAR) model combining both physicochemical and biodescriptors. Under a simplex centroid design, six machine learning algorithms were trained using data augmentation strategies to predict the cytotoxicity of microplastic mixtures. The results showed that the QBAR-based eXtreme Gradient Boosting (XGB-qbar) model performed best (R2tra = 0.9322, R2test = 0.8923), outperforming the QSAR and the QSBAR frameworks. The three descriptor importance methods consistently identified key biological descriptors helpful for toxicity prediction. Moreover, metabolomics analysis indicated that mixed exposure to MPs may mediate toxic responses by reprogramming cellular energy metabolism pathways. The metabolomics-driven and data-augmented machine learning approach proposed in this study can efficiently predict toxicity and provide mechanistic clues in small sample and complex mixture scenarios, providing a feasible path for environmental exposure risk assessment.

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