the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
A machine learning approach targeting parameter estimation for plant functional type coexistence modeling using ELM-FATES (v2.0)
Abstract. Tropical forest dynamics play crucial roles in the global carbon, water, and energy cycles. Dynamic global vegetation models are the primary tools to simulate terrestrial ecosystem dynamics and their response to climate change. However, realistically simulating the dynamics of competition and coexistence of differing plant functional traits within tropical forests remains a significant challenge. This study aims to improve modeling of plant functional type (PFT) coexistence in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a vegetation demography model implemented in the Energy Exascale Earth System Model (E3SM) land model (ELM), ELM-FATES. Specifically, we explore: (1) whether plant trait relationships established from field measurements can constrain ELM-FATES simulations; and (2) whether machine learning based surrogate models can emulate the complex ELM-FATES model and optimize parameter selections to improve PFT coexistence modeling. We conducted ELM-FATES experiments for a tropical forest site near Manaus, Brazil. We first conducted two ensembles of ELM-FATES experiments, without (Exp-1) and with (Exp-2) consideration of observed trait relationships, respectively. Considering the observed trait relationships (Exp-2) slightly improves ELM-FATES simulations of water, energy, and carbon fluxes, but degrades the simulation of PFT coexistence. Using eXtreme Gradient Boosting (XGBoost) based surrogate models trained on Exp-1, we optimize the trait-related parameters in ELM-FATES to enable PFT coexistence and reduce model errors relative to the field observations. We used parameters selected by the surrogate model to conduct another ensemble of ELM-FATES experiments (Exp-3). The probability of experiments yielding PFT coexistence greatly increases from 21 % in Exp-1 to 73 % in Exp-3. Further filtering those experiments that allow for PFT coexistence to agree within 15 % of the observations, Exp-3 still has 33 % of experiments left, much higher than the 1.4 % in Exp-1. Exp-3 also better reproduces the annual means and seasonal variations of water, energy and carbon fluxes, and the field inventory of above ground biomass. Our study demonstrates the benefits of using machine learning models to improve PFT coexistence modeling in ELM-FATES, with important implications for modeling the response and feedback of ecosystem dynamics to climate change. Our results also suggest that new mechanisms are required for robust simulation of coexisting plants in FATES.
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The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
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The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
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Journal article(s) based on this preprint
Interactive discussion
Status: closed
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RC1: 'Comment on egusphere-2022-1286', Anonymous Referee #1, 01 Feb 2023
In this paper, the authors employ a machine-learning approach to optimize parameters from a vegetation demography model - FATES. Their approach clearly shows the bright application of ML as a tool to improve the next-generation Earth system models. The paper is very well written and the question being addressed is novel. I really enjoyed reading the manuscript and learned a lot from the authors. I would recommend accepting this paper in its current form.
Citation: https://doi.org/10.5194/egusphere-2022-1286-RC1 -
AC1: 'Reply on RC1', Lingcheng Li, 31 Mar 2023
RC: In this paper, the authors employ a machine-learning approach to optimize parameters from a vegetation demography model - FATES. Their approach clearly shows the bright application of ML as a tool to improve the next-generation Earth system models. The paper is very well written and the question being addressed is novel. I really enjoyed reading the manuscript and learned a lot from the authors. I would recommend accepting this paper in its current form.
AC: Thank you for your positive feedback and for suggesting acceptance of our submission for publication.
Citation: https://doi.org/10.5194/egusphere-2022-1286-AC1
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AC1: 'Reply on RC1', Lingcheng Li, 31 Mar 2023
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RC2: 'Comment on egusphere-2022-1286', Gregory Duveiller, 15 Feb 2023
This is an interesting study making use of machine learning to improve modelling parametrization in a complicated set-up of tropical forests with competing PFTs adopting different strategies. The manuscripts reads well and is clear and exhaustive. The paper is well suited for GMD and should be published. But before, I have the following suggestions to make, hopefully to improve it ...L242: L_leaf is not defined yet in the text, and neither is WDL260: perhaps explain what the "ensemble" is before. Help readers understand what makes XGBoost different from a standard Random ForestThe following is a bit subjective, but I find the structure of the Methodology section slightly sub-optimal. I would have prefered to have an overall experimental design at the beginning, e.g. before talking about the SHAP values. This could be just an overview, not necessarily with all the details in section 2.4, but rather a general understanding of what will come up after. Furthermore, section 2.4 is very long compared to the other ones, so splitting it or rebalancing them would be good.Also, when you present the observational relaitonships (Eqn 1 to 3) it does not seem entirely clear why this is done. While after the difference between Exp 1 and Exp 2 is mentioned, that is clear. I this it would read better if these observatinal relationships are introduced when you explain the experimental design (around line 300).L313: why is this in bold?L348: why 15%?L349: why [0.3, 0.7]?L374: What does this incapacity of Exp2 (with the observational constraints) to reproduce realistic coexisting ratios tell us about the standard model itself (ELM-FATES without the ML)? Does it reveal some underlying biases/problems in the structure of ELM-FATES itself that makes it less adapted to this tropical context for some reason? It would nice to get some insights on this to guide model developement.L422: The main problem here is probably the paucity of ELM-FATES simulations that are available to train the XGBoost, rather than the ML algorithm itself. To get highly non-linear behaviour, these require many more training samples. These would typically be trainend with many 1000s of simulations. You could mention that other ML techniques work better for sparser data (even when highly non-linear). I believe Guassian Processes would be one good candidate to explore. (I am not saying this is needed in this paper, but it shoudl be discussed + acknowledged).L477: Why not place the orange coexistence above the green XGBoost, to increase clarity? or perhaps try some transparnecy?L525: Fig 9: There is something I am not following anymore... I must be missing something... why are there are both "early" and "late" boxes when the measure/index is precisely a difference between late and early? Not sure what I need to take home as a message from this plot.L549: Fig 10: Perhaps it would be wise to also add a bundle for the "standard" ELM-FATES without ML (ie. Exp 1? or also 2?) just to illustrate the improvements that the study proposes brings things closer to the observations.The discussion is quite nice and exhaustive. However, it stays very focused on this modelling experiment and context. This is nice, but it would be (in my opinion) better to also have a more general overview going beyond this specific case of ELM-FATES on tropical forests of Manaus. To increase the breadth of the paper, I think a more general discussion on how to incorporate ML with process-based models would be very welcome. Inspirations could come from the perspective paper of Reichstein et al (2019) [https://doi.org/10.1038/s41586-019-0912-1]. For instance, it would be interesting to know if here the present study could fit in this logic of "hybrid-modelling" . There are also there other strategies to combine ML with ELM-FATES (as discsussed in the perpective paper) that could be evoked to outline further perspectives of this GMD manuscript. Finally, I would also encourage some more words of how much the auhtors beleive their approach is transferable to other contexts beyond tropical forests.Citation: https://doi.org/
10.5194/egusphere-2022-1286-RC2 -
AC2: 'Reply on RC2', Lingcheng Li, 31 Mar 2023
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2022-1286/egusphere-2022-1286-AC2-supplement.pdf
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AC2: 'Reply on RC2', Lingcheng Li, 31 Mar 2023
Interactive discussion
Status: closed
-
RC1: 'Comment on egusphere-2022-1286', Anonymous Referee #1, 01 Feb 2023
In this paper, the authors employ a machine-learning approach to optimize parameters from a vegetation demography model - FATES. Their approach clearly shows the bright application of ML as a tool to improve the next-generation Earth system models. The paper is very well written and the question being addressed is novel. I really enjoyed reading the manuscript and learned a lot from the authors. I would recommend accepting this paper in its current form.
Citation: https://doi.org/10.5194/egusphere-2022-1286-RC1 -
AC1: 'Reply on RC1', Lingcheng Li, 31 Mar 2023
RC: In this paper, the authors employ a machine-learning approach to optimize parameters from a vegetation demography model - FATES. Their approach clearly shows the bright application of ML as a tool to improve the next-generation Earth system models. The paper is very well written and the question being addressed is novel. I really enjoyed reading the manuscript and learned a lot from the authors. I would recommend accepting this paper in its current form.
AC: Thank you for your positive feedback and for suggesting acceptance of our submission for publication.
Citation: https://doi.org/10.5194/egusphere-2022-1286-AC1
-
AC1: 'Reply on RC1', Lingcheng Li, 31 Mar 2023
-
RC2: 'Comment on egusphere-2022-1286', Gregory Duveiller, 15 Feb 2023
This is an interesting study making use of machine learning to improve modelling parametrization in a complicated set-up of tropical forests with competing PFTs adopting different strategies. The manuscripts reads well and is clear and exhaustive. The paper is well suited for GMD and should be published. But before, I have the following suggestions to make, hopefully to improve it ...L242: L_leaf is not defined yet in the text, and neither is WDL260: perhaps explain what the "ensemble" is before. Help readers understand what makes XGBoost different from a standard Random ForestThe following is a bit subjective, but I find the structure of the Methodology section slightly sub-optimal. I would have prefered to have an overall experimental design at the beginning, e.g. before talking about the SHAP values. This could be just an overview, not necessarily with all the details in section 2.4, but rather a general understanding of what will come up after. Furthermore, section 2.4 is very long compared to the other ones, so splitting it or rebalancing them would be good.Also, when you present the observational relaitonships (Eqn 1 to 3) it does not seem entirely clear why this is done. While after the difference between Exp 1 and Exp 2 is mentioned, that is clear. I this it would read better if these observatinal relationships are introduced when you explain the experimental design (around line 300).L313: why is this in bold?L348: why 15%?L349: why [0.3, 0.7]?L374: What does this incapacity of Exp2 (with the observational constraints) to reproduce realistic coexisting ratios tell us about the standard model itself (ELM-FATES without the ML)? Does it reveal some underlying biases/problems in the structure of ELM-FATES itself that makes it less adapted to this tropical context for some reason? It would nice to get some insights on this to guide model developement.L422: The main problem here is probably the paucity of ELM-FATES simulations that are available to train the XGBoost, rather than the ML algorithm itself. To get highly non-linear behaviour, these require many more training samples. These would typically be trainend with many 1000s of simulations. You could mention that other ML techniques work better for sparser data (even when highly non-linear). I believe Guassian Processes would be one good candidate to explore. (I am not saying this is needed in this paper, but it shoudl be discussed + acknowledged).L477: Why not place the orange coexistence above the green XGBoost, to increase clarity? or perhaps try some transparnecy?L525: Fig 9: There is something I am not following anymore... I must be missing something... why are there are both "early" and "late" boxes when the measure/index is precisely a difference between late and early? Not sure what I need to take home as a message from this plot.L549: Fig 10: Perhaps it would be wise to also add a bundle for the "standard" ELM-FATES without ML (ie. Exp 1? or also 2?) just to illustrate the improvements that the study proposes brings things closer to the observations.The discussion is quite nice and exhaustive. However, it stays very focused on this modelling experiment and context. This is nice, but it would be (in my opinion) better to also have a more general overview going beyond this specific case of ELM-FATES on tropical forests of Manaus. To increase the breadth of the paper, I think a more general discussion on how to incorporate ML with process-based models would be very welcome. Inspirations could come from the perspective paper of Reichstein et al (2019) [https://doi.org/10.1038/s41586-019-0912-1]. For instance, it would be interesting to know if here the present study could fit in this logic of "hybrid-modelling" . There are also there other strategies to combine ML with ELM-FATES (as discsussed in the perpective paper) that could be evoked to outline further perspectives of this GMD manuscript. Finally, I would also encourage some more words of how much the auhtors beleive their approach is transferable to other contexts beyond tropical forests.Citation: https://doi.org/
10.5194/egusphere-2022-1286-RC2 -
AC2: 'Reply on RC2', Lingcheng Li, 31 Mar 2023
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2022-1286/egusphere-2022-1286-AC2-supplement.pdf
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AC2: 'Reply on RC2', Lingcheng Li, 31 Mar 2023
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Cited
Yilin Fang
Zhonghua Zheng
Mingjie Shi
Marcos Longo
Charles Koven
Jennifer Holm
Rosie Fisher
Nate McDowell
Jeffrey Chambers
Ruby Leung
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
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(8882 KB) - Metadata XML
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(10883 KB) - BibTeX
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- Final revised paper