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

arXiv: https://arxiv.org/abs/2606.20329 · HTML: https://mlsanity.com/paper/2606.20329/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 5 of its 38 references that are in the map.
- First posted on arXiv 18 Jun 2026.

## Builds on (most cited first, 5 of 5)

- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [Delving Deep into Rectifiers: Surpassing Human-Level Performance on ImageNet Classification](https://mlsanity.com/paper/1502.01852/) (2015)
- [Multi-Task Learning Using Uncertainty to Weigh Losses for Scene Geometry and Semantics](https://mlsanity.com/paper/1705.07115/) (2017)
- [Auxiliary Tasks in Multi-task Learning](https://mlsanity.com/paper/1805.06334/) (2018)
- [From calibration to parameter learning: Harnessing the scaling effects of big data in geoscientific modeling](https://mlsanity.com/paper/2007.15751/) (2020)

## Abstract (arXiv)

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.