arXiv:2606.20329cs.LGphysics.geo-ph2026-06中稿 · ICML

用基因数据预测土壤微生物动力学,提升碳循环模型精度。

Constrained hybrid modelling to predict microbial dynamics and organic matter turnover in soil systems

论文配图:Constrained hybrid modelling to predict microbial dynamics and organic matter turnover in soil systems
图 1 · 摘自论文原文
  • 结合基因组功能特征与神经网络,推导过程模型参数。
  • 在小样本下仍能准确预测不可观测的微生物动态。
  • 融合生态理论约束,确保模型行为合理可信。

土壤微生物调控有机质循环,影响土壤应对气候变化的能力。准确建模微生物动态对预测土壤碳循环至关重要,但受限于数据难以实现。整合基因组数据是改进模型参数化的有效途径,然而微生物基因组与驱动过程间复杂未知的关系仍是难题。本文提出首个混合建模框架,基于宏基因组推断的功能特征(来自DNA测序),通过神经网络推导过程模型的生物动力学参数,并引入生态理论与文献约束,确保即使在未观测状态变量下模型行为仍合理。我们在合成数据和真实数据上评估该方法,结果表明其性能优于多个基线,在小样本训练下也能有效学习不可测量组分的动力学特征。

原文摘要 · Abstract (English)

Soil microorganisms control organic matter cycling and largely determine how soil systems can cope with and mitigate climate change and environmental threats. Representing microbial dynamics in process-based soil models is therefore critical to predict carbon cycling in soils, albeit highly challenging to inform from data. One promising approach to improve their parametrisation is the integration of genomic data, yet modelling the complex and unknown relationship between genomes and the processes the microbes are driving is an unsolved problem. In this work, we present the first hybrid modeling framework for deriving biokinetic parameter values of a process-based soil organic matter turnover model from metagenome-inferred functional traits based on DNA sequencing data. Our model predicts biokinetic parameters of the process-based model from genomic trait data with a neural network and integrates constraints from ecological theory and literature to ensure realistic behavior, even of non-observed state variables. We evaluate our method on synthetic genomic trait datasets of varying complexity and on real data, showing that our approach improves performance over multiple baselines and learns the dynamics of unmeasurable components of the process-based model effectively, even for small training datasets.

微生物模型碳循环基因组数据混合建模

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