Bayesian inference in plant growth models for prediction and uncertainty assessment

Abstract : Plant growth models aim to describe plant development and functional processes in interaction with the environment. They offer promising perspectives for many applications, such as yield prediction for decision support or virtual experimentation inthe context of breeding. This PhD focuses on the solutions to enhance plant growth model predictive capacity with an emphasis on advanced statistical methods. Our contributions can be summarized in four parts. Firstly, from a model design perspective, the Log-Normal Allocation and Senescence (LNAS) crop model is proposed. It describes only the essential ecophysiological processes for biomass budget in a probabilistic framework, so as to avoid identification problems and to accentuate uncertainty assessment in model prediction. Secondly, a thorough research is conducted regarding model parameterization. In a Bayesian framework, both Sequential Monte Carlo (SMC) methods and Markov chain Monte Carlo (MCMC) based methods are investigated to address the parameterization issues in the context of plant growth models, which are frequently characterized by nonlinear dynamics, scarce data and a large number of parameters. Particularly, whenthe prior distribution is non-informative, with the objective to put more emphasis on the observation data while preserving the robustness of Bayesian methods, an iterative version of the SMC and MCMC methods is introduced. It can be regarded as a stochastic variant of an EM type algorithm. Thirdly, a three-step data assimilation approach is proposed to address model prediction issues. The most influential parameters are first identified by global sensitivity analysis and chosen by model selection. Subsequently, the model calibration is performed with special attention paid to the uncertainty assessment. The posterior distribution obtained from this estimation step is consequently considered as prior information for the prediction step, in which a SMC-based on-line estimation method such as Convolution Particle Filtering (CPF) is employed to perform data assimilation. Both state and parameter estimates are updated with the purpose of improving theprediction accuracy and reducing the associated uncertainty. Finally, from an application point of view, the proposed methodology is implemented and evaluated with two crop models, the LNAS model for sugar beet and the STICS model for winter wheat. Some indications are also given on the experimental design to optimize the quality of predictions. The applications to real case scenarios show encouraging predictive performances and open the way to potential tools for yield prediction in agriculture.
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Yuting Chen. Bayesian inference in plant growth models for prediction and uncertainty assessment. Engineering Sciences [physics]. Ecole Centrale Paris, 2014. English. ⟨NNT : 2014ECAP0040⟩. ⟨tel-01165038⟩

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