KG-FGNN: Knowledge-guided GNN Foundation Model for Fertilisation-oriented Soil GHG Flux Prediction

Precision soil greenhouse gas (GHG) flux prediction is essential in agricultural systems for assessing environmental impacts, developing emission mitigation strategies and promoting sustainable agriculture. Due to the lack of advanced sensor and network technologies on majority of farms, there are challenges in obtaining comprehensive and diverse agricultural data. As a result, the scarcity of agricultural data seriously obstructs the application of machine learning approaches in precision soil GHG flux prediction. This research proposes a knowledge-guided graph neural network framework that addresses the above challenges by integrating knowledge embedded in an agricultural process-based model and graph neural network techniques. Specifically, we utilise the agricultural process-based model to simulate and generate multi-dimensional agricultural datasets for 47 countries that cover a wide range of agricultural variables. To extract key agricultural features and integrate correlations among agricultural features in the prediction process, we propose a machine learning framework that integrates the autoencoder and multi-target multi-graph based graph neural networks, which utilises the autoencoder to selectively extract significant agricultural features from the agricultural process-based model simulation data and the graph neural network to integrate correlations among agricultural features for accurately predict fertilisation-oriented soil GHG fluxes. Comprehensive experiments were conducted with both the agricultural simulation dataset and real-world agricultural dataset to evaluate the proposed approach in comparison with well-known baseline and state-of-the-art regression methods. The results demonstrate that our proposed approach provides superior accuracy and stability in fertilisation-oriented soil GHG prediction.

@article{zhang2025_2506.15896,
  title={ KG-FGNN: Knowledge-guided GNN Foundation Model for Fertilisation-oriented Soil GHG Flux Prediction },
  author={ Yu Zhang and Gaoshan Bi and Simon Jeffery and Max Davis and Yang Li and Qing Xue and Po Yang },
  journal={arXiv preprint arXiv:2506.15896},
  year={ 2025 }
}