scholarly journals Efficient global sensitivity analysis of biochemical networks using Gaussian process regression

Author(s):  
Tamara Kurdyaeva ◽  
Andreas Milias-Argeitis
2020 ◽  
Vol 34 (11) ◽  
pp. 1813-1830
Author(s):  
Daniel Erdal ◽  
Sinan Xiao ◽  
Wolfgang Nowak ◽  
Olaf A. Cirpka

Abstract Ensemble-based uncertainty quantification and global sensitivity analysis of environmental models requires generating large ensembles of parameter-sets. This can already be difficult when analyzing moderately complex models based on partial differential equations because many parameter combinations cause an implausible model behavior even though the individual parameters are within plausible ranges. In this work, we apply Gaussian Process Emulators (GPE) as surrogate models in a sampling scheme. In an active-training phase of the surrogate model, we target the behavioral boundary of the parameter space before sampling this behavioral part of the parameter space more evenly by passive sampling. Active learning increases the subsequent sampling efficiency, but its additional costs pay off only for a sufficiently large sample size. We exemplify our idea with a catchment-scale subsurface flow model with uncertain material properties, boundary conditions, and geometric descriptors of the geological structure. We then perform a global-sensitivity analysis of the resulting behavioral dataset using the active-subspace method, which requires approximating the local sensitivities of the target quantity with respect to all parameters at all sampled locations in parameter space. The Gaussian Process Emulator implicitly provides an analytical expression for this gradient, thus improving the accuracy of the active-subspace construction. When applying the GPE-based preselection, 70–90% of the samples were confirmed to be behavioral by running the full model, whereas only 0.5% of the samples were behavioral in standard Monte-Carlo sampling without preselection. The GPE method also provided local sensitivities at minimal additional costs.


Agronomy ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 984
Author(s):  
W. B. M. A. C. Bandara ◽  
Kazuhito Sakai ◽  
Tamotsu Nakandakari ◽  
Preecha Kapetch ◽  
R. H. K. Rathnappriya

Process-based crop models are advantageous for the identification of management strategies to cope with both temporal and spatial variability of sugarcane yield. However, global optimization of such models is often computationally expensive. Therefore, we performed global sensitivity analysis based on Gaussian process emulation to evaluate the sensitivity of cane dry weight to trait parameters implemented in the Agricultural Productions System Simulator (APSIM)-Sugar model under selected environmental and management conditions in Khon Kaen (KK), Thailand. Emulators modeled 30 years, three soil types and irrigated or rainfed conditions, and emulator performance was investigated. rue, green_leaf_no, transp_eff_cf, tt_emerg_to_begcane and cane_fraction were identified as the most influential parameters and together they explained more than 90% of total variance on the simulator output. Moreover, results indicate that the sensitivity of sugarcane yield to the most influential parameters is affected by water stress conditions and nitrogen stress. Our findings can be used to improve the efficiency and accuracy of modeling and to identify appropriate management strategies to address temporal and spatial variability of sugarcane yield in KK.


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