Articles | Volume 20, issue 13
https://doi.org/10.5194/bg-20-2671-2023
© Author(s) 2023. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-20-2671-2023
© Author(s) 2023. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
06 Jul 2023
Research article |
| 06 Jul 2023
| 06 Jul 2023
A differentiable, physics-informed ecosystem modeling and learning framework for large-scale inverse problems: demonstration with photosynthesis simulations
Doaa Aboelyazeed
Civil and Environmental Engineering, The Pennsylvania State
University, University Park, PA 16802, USA
Chonggang Xu
Earth and Environmental Sciences Division, Los Alamos National
Laboratory, Los Alamos, NM 87544, USA
Forrest M. Hoffman
Computational Sciences & Engineering Division and the Climate
Change Science Institute, Oak Ridge National Laboratory, Oak Ridge,
TN 37830, USA
Department of Civil and Environmental Engineering, University of
Tennessee, Knoxville, TN 37996, USA
Jiangtao Liu
Civil and Environmental Engineering, The Pennsylvania State
University, University Park, PA 16802, USA
Alex W. Jones
SciML, Open Source Software Organization, Cambridge, MA, USA
Chris Rackauckas
Computer Science and Artificial Intelligence Laboratory (CSAIL),
Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Kathryn Lawson
Civil and Environmental Engineering, The Pennsylvania State
University, University Park, PA 16802, USA
Civil and Environmental Engineering, The Pennsylvania State
University, University Park, PA 16802, USA
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Forrest M. Hoffman, Birgit Hassler, Ranjini Swaminathan, Jared Lewis, Bouwe Andela, Nathaniel Collier, Dóra Hegedűs, Jiwoo Lee, Charlotte Pascoe, Mika Pflüger, Martina Stockhause, Paul Ullrich, Min Xu, Lisa Bock, Felicity Chun, Bettina K. Gier, Douglas I. Kelley, Axel Lauer, Julien Lenhardt, Manuel Schlund, Mohanan G. Sreeush, Katja Weigel, Ed Blockley, Rebecca Beadling, Romain Beucher, Demiso D. Dugassa, Valerio Lembo, Jianhua Lu, Swen Brands, Jerry Tjiputra, Elizaveta Malinina, Brian Mederios, Enrico Scoccimarro, Jeremy Walton, Philip Kershaw, André L. Marquez, Malcolm J. Roberts, Eleanor O’Rourke, Elisabeth Dingley, Briony Turner, Helene Hewitt, and John P. Dunne
EGUsphere, https://doi.org/10.5194/egusphere-2025-2685, https://doi.org/10.5194/egusphere-2025-2685, 2025
This preprint is open for discussion and under review for Geoscientific Model Development (GMD).
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As Earth system models become more complex, rapid and comprehensive evaluation through comparison with observational data is necessary. The upcoming Assessment Fast Track for the Seventh Phase of the Coupled Model Intercomparison Project (CMIP7) will require fast analysis. This paper describes a new Rapid Evaluation Framework (REF) that was developed for the Assessment Fast Track that will be run at the Earth System Grid Federation (ESGF) to inform the community about the performance of models.
Wouter J. M. Knoben, Ashwin Raman, Gaby J. Gründemann, Mukesh Kumar, Alain Pietroniro, Chaopeng Shen, Yalan Song, Cyril Thébault, Katie van Werkhoven, Andrew W. Wood, and Martyn P. Clark
Hydrol. Earth Syst. Sci., 29, 2361–2375, https://doi.org/10.5194/hess-29-2361-2025, https://doi.org/10.5194/hess-29-2361-2025, 2025
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Hydrologic models are needed to provide simulations of water availability, floods, and droughts. The accuracy of these simulations is often quantified with so-called performance scores. A common thought is that different models are more or less applicable to different landscapes, depending on how the model works. We show that performance scores are not helpful in distinguishing between different models and thus cannot easily be used to select an appropriate model for a specific place.
Yuan Yang, Ming Pan, Dapeng Feng, Mu Xiao, Taylor Dixon, Robert Hartman, Chaopeng Shen, Yalan Song, Agniv Sengupta, Luca Delle Monache, and F. Martin Ralph
EGUsphere, https://doi.org/10.5194/egusphere-2025-1708, https://doi.org/10.5194/egusphere-2025-1708, 2025
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We explore a machine learning-based data integration method that integrates streamflow (Q) and snow water equivalent (SWE) to improve streamflow estimates at various lag times (1–10 days, 1–6 months) and timescales (daily and monthly) over Western U.S. basins. Benefits rank as: integrating Q at the daily scale > Q at the monthly scale > SWE at the monthly scale > SWE at the daily scale. Results highlight the method’s potential for short- and long-term streamflow forecasting in the Western U.S.
Jiangtao Liu, Chaopeng Shen, Fearghal O'Donncha, Yalan Song, Wei Zhi, Hylke E. Beck, Tadd Bindas, Nicholas Kraabel, and Kathryn Lawson
EGUsphere, https://doi.org/10.5194/egusphere-2025-1706, https://doi.org/10.5194/egusphere-2025-1706, 2025
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Using global and regional datasets, we compared attention-based models and Long Short-Term Memory (LSTM) models to predict hydrologic variables. Our results show LSTM models perform better in simpler tasks, whereas attention-based models perform better in complex scenarios, offering insights for improved water resource management.
Mohammad Sina Jahangir, John Quilty, Chaopeng Shen, Andrea Scott, Scott Steinschneider, and Jan Adamowski
EGUsphere, https://doi.org/10.5194/egusphere-2025-846, https://doi.org/10.5194/egusphere-2025-846, 2025
This preprint is open for discussion and under review for Hydrology and Earth System Sciences (HESS).
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This study presents a novel hybrid approach to streamflow prediction, significantly improving the efficiency and accuracy of fine-tuning deep learning models for hydrological prediction. Tested across numerous catchments in the U.S. and Europe, this method accelerates the fine-tuning process and improves prediction accuracy in locations beyond the training data. This innovative approach sets the stage for future hydrological models leveraging transfer learning.
Peijun Li, Yalan Song, Ming Pan, Kathryn Lawson, and Chaopeng Shen
EGUsphere, https://doi.org/10.5194/egusphere-2025-483, https://doi.org/10.5194/egusphere-2025-483, 2025
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This study explores how combining different model types improves streamflow predictions, especially in data-sparse scenarios. By integrating two highly accurate models with distinct mechanisms and leveraging multiple meteorological datasets, we highlight their unique strengths and set new accuracy benchmarks across spatiotemporal conditions. Our findings enhance the understanding of how diverse models and multi-source data can be effectively used to improve hydrological predictions.
Ather Abbas, Yuan Yang, Ming Pan, Yves Tramblay, Chaopeng Shen, Haoyu Ji, Solomon H. Gebrechorkos, Florian Pappenberger, Jong Cheol Pyo, Dapeng Feng, George Huffman, Phu Nguyen, Christian Massari, Luca Brocca, Tan Jackson, and Hylke E. Beck
EGUsphere, https://doi.org/10.5194/egusphere-2024-4194, https://doi.org/10.5194/egusphere-2024-4194, 2025
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Our study evaluated 23 precipitation datasets using a hydrological model at global scale to assess their suitability and accuracy. We found that MSWEP V2.8 excels due to its ability to integrate data from multiple sources, while others, such as IMERG and JRA-3Q, demonstrated strong regional performances. This research assists in selecting the appropriate dataset for applications in water resource management, hazard assessment, agriculture, and environmental monitoring.
Kamal Nyaupane, Umakant Mishra, Feng Tao, Kyongmin Yeo, William J. Riley, Forrest M. Hoffman, and Sagar Gautam
Biogeosciences, 21, 5173–5183, https://doi.org/10.5194/bg-21-5173-2024, https://doi.org/10.5194/bg-21-5173-2024, 2024
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Representing soil organic carbon (SOC) dynamics in Earth system models (ESMs) is a key source of uncertainty in predicting carbon–climate feedbacks. Using machine learning, we develop and compare predictive relationships in observations (Obs) and ESMs. We find different relationships between environmental factors and SOC stocks in Obs and ESMs. SOC prediction in ESMs may be improved by representing the functional relationships of environmental controllers in a way consistent with observations.
Dapeng Feng, Hylke Beck, Jens de Bruijn, Reetik Kumar Sahu, Yusuke Satoh, Yoshihide Wada, Jiangtao Liu, Ming Pan, Kathryn Lawson, and Chaopeng Shen
Geosci. Model Dev., 17, 7181–7198, https://doi.org/10.5194/gmd-17-7181-2024, https://doi.org/10.5194/gmd-17-7181-2024, 2024
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Accurate hydrologic modeling is vital to characterizing water cycle responses to climate change. For the first time at this scale, we use differentiable physics-informed machine learning hydrologic models to simulate rainfall–runoff processes for 3753 basins around the world and compare them with purely data-driven and traditional modeling approaches. This sets a benchmark for hydrologic estimates around the world and builds foundations for improving global hydrologic simulations.
Yalan Song, Wouter J. M. Knoben, Martyn P. Clark, Dapeng Feng, Kathryn Lawson, Kamlesh Sawadekar, and Chaopeng Shen
Hydrol. Earth Syst. Sci., 28, 3051–3077, https://doi.org/10.5194/hess-28-3051-2024, https://doi.org/10.5194/hess-28-3051-2024, 2024
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Differentiable models (DMs) integrate neural networks and physical equations for accuracy, interpretability, and knowledge discovery. We developed an adjoint-based DM for ordinary differential equations (ODEs) for hydrological modeling, reducing distorted fluxes and physical parameters from errors in models that use explicit and operation-splitting schemes. With a better numerical scheme and improved structure, the adjoint-based DM matches or surpasses long short-term memory (LSTM) performance.
Peter Reichert, Kai Ma, Marvin Höge, Fabrizio Fenicia, Marco Baity-Jesi, Dapeng Feng, and Chaopeng Shen
Hydrol. Earth Syst. Sci., 28, 2505–2529, https://doi.org/10.5194/hess-28-2505-2024, https://doi.org/10.5194/hess-28-2505-2024, 2024
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We compared the predicted change in catchment outlet discharge to precipitation and temperature change for conceptual and machine learning hydrological models. We found that machine learning models, despite providing excellent fit and prediction capabilities, can be unreliable regarding the prediction of the effect of temperature change for low-elevation catchments. This indicates the need for caution when applying them for the prediction of the effect of climate change.
Jacquelyn K. Shuman, Rosie A. Fisher, Charles Koven, Ryan Knox, Lara Kueppers, and Chonggang Xu
Geosci. Model Dev., 17, 4643–4671, https://doi.org/10.5194/gmd-17-4643-2024, https://doi.org/10.5194/gmd-17-4643-2024, 2024
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We adapt a fire behavior and effects module for use in a size-structured vegetation demographic model to test how climate, fire regime, and fire-tolerance plant traits interact to determine the distribution of tropical forests and grasslands. Our model captures the connection between fire disturbance and plant fire-tolerance strategies in determining plant distribution and provides a useful tool for understanding the vulnerability of these areas under changing conditions across the tropics.
Junyan Ding, Polly Buotte, Roger Bales, Bradley Christoffersen, Rosie A. Fisher, Michael Goulden, Ryan Knox, Lara Kueppers, Jacquelyn Shuman, Chonggang Xu, and Charles D. Koven
Biogeosciences, 20, 4491–4510, https://doi.org/10.5194/bg-20-4491-2023, https://doi.org/10.5194/bg-20-4491-2023, 2023
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We used a vegetation model to investigate how the different combinations of plant rooting depths and the sensitivity of leaves and stems to drying lead to differential responses of a pine forest to drought conditions in California, USA. We found that rooting depths are the strongest control in that ecosystem. Deep roots allow trees to fully utilize the soil water during a normal year but result in prolonged depletion of soil moisture during a severe drought and hence a high tree mortality risk.
Chonggang Xu, Bradley Christoffersen, Zachary Robbins, Ryan Knox, Rosie A. Fisher, Rutuja Chitra-Tarak, Martijn Slot, Kurt Solander, Lara Kueppers, Charles Koven, and Nate McDowell
Geosci. Model Dev., 16, 6267–6283, https://doi.org/10.5194/gmd-16-6267-2023, https://doi.org/10.5194/gmd-16-6267-2023, 2023
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We introduce a plant hydrodynamic model for the U.S. Department of Energy (DOE)-sponsored model, the Functionally Assembled Terrestrial Ecosystem Simulator (FATES). To better understand this new model system and its functionality in tropical forest ecosystems, we conducted a global parameter sensitivity analysis at Barro Colorado Island, Panama. We identified the key parameters that affect the simulated plant hydrodynamics to guide both modeling and field campaign studies.
Nathan Alec Conroy, Jeffrey M. Heikoop, Emma Lathrop, Dea Musa, Brent D. Newman, Chonggang Xu, Rachael E. McCaully, Carli A. Arendt, Verity G. Salmon, Amy Breen, Vladimir Romanovsky, Katrina E. Bennett, Cathy J. Wilson, and Stan D. Wullschleger
The Cryosphere, 17, 3987–4006, https://doi.org/10.5194/tc-17-3987-2023, https://doi.org/10.5194/tc-17-3987-2023, 2023
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This study combines field observations, non-parametric statistical analyses, and thermodynamic modeling to characterize the environmental causes of the spatial variability in soil pore water solute concentrations across two Arctic catchments with varying extents of permafrost. Vegetation type, soil moisture and redox conditions, weathering and hydrologic transport, and mineral solubility were all found to be the primary drivers of the existing spatial variability of some soil pore water solutes.
Xiaojuan Yang, Peter Thornton, Daniel Ricciuto, Yilong Wang, and Forrest Hoffman
Biogeosciences, 20, 2813–2836, https://doi.org/10.5194/bg-20-2813-2023, https://doi.org/10.5194/bg-20-2813-2023, 2023
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We evaluated the performance of a land surface model (ELMv1-CNP) that includes both nitrogen (N) and phosphorus (P) limitation on carbon cycle processes. We show that ELMv1-CNP produces realistic estimates of present-day carbon pools and fluxes. We show that global C sources and sinks are significantly affected by P limitation. Our study suggests that introduction of P limitation in land surface models is likely to have substantial consequences for projections of future carbon uptake.
Dapeng Feng, Hylke Beck, Kathryn Lawson, and Chaopeng Shen
Hydrol. Earth Syst. Sci., 27, 2357–2373, https://doi.org/10.5194/hess-27-2357-2023, https://doi.org/10.5194/hess-27-2357-2023, 2023
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Powerful hybrid models (called δ or delta models) embrace the fundamental learning capability of AI and can also explain the physical processes. Here we test their performance when applied to regions not in the training data. δ models rivaled the accuracy of state-of-the-art AI models under the data-dense scenario and even surpassed them for the data-sparse one. They generalize well due to the physical structure included. δ models could be ideal candidates for global hydrologic assessment.
Bharat Sharma, Jitendra Kumar, Auroop R. Ganguly, and Forrest M. Hoffman
Biogeosciences, 20, 1829–1841, https://doi.org/10.5194/bg-20-1829-2023, https://doi.org/10.5194/bg-20-1829-2023, 2023
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Rising atmospheric carbon dioxide increases vegetation growth and causes more heatwaves and droughts. The impact of such climate extremes is detrimental to terrestrial carbon uptake capacity. We found that due to overall climate warming, about 88 % of the world's regions towards the end of 2100 will show anomalous losses in net biospheric productivity (NBP) rather than gains. More than 50 % of all negative NBP extremes were driven by the compound effect of dry, hot, and fire conditions.
Louise J. Slater, Louise Arnal, Marie-Amélie Boucher, Annie Y.-Y. Chang, Simon Moulds, Conor Murphy, Grey Nearing, Guy Shalev, Chaopeng Shen, Linda Speight, Gabriele Villarini, Robert L. Wilby, Andrew Wood, and Massimiliano Zappa
Hydrol. Earth Syst. Sci., 27, 1865–1889, https://doi.org/10.5194/hess-27-1865-2023, https://doi.org/10.5194/hess-27-1865-2023, 2023
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Hybrid forecasting systems combine data-driven methods with physics-based weather and climate models to improve the accuracy of predictions for meteorological and hydroclimatic events such as rainfall, temperature, streamflow, floods, droughts, tropical cyclones, or atmospheric rivers. We review recent developments in hybrid forecasting and outline key challenges and opportunities in the field.
Jiangtao Liu, David Hughes, Farshid Rahmani, Kathryn Lawson, and Chaopeng Shen
Geosci. Model Dev., 16, 1553–1567, https://doi.org/10.5194/gmd-16-1553-2023, https://doi.org/10.5194/gmd-16-1553-2023, 2023
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Under-monitored regions like Africa need high-quality soil moisture predictions to help with food production, but it is not clear if soil moisture processes are similar enough around the world for data-driven models to maintain accuracy. We present a deep-learning-based soil moisture model that learns from both in situ data and satellite data and performs better than satellite products at the global scale. These results help us apply our model globally while better understanding its limitations.
Martijn M. T. A. Pallandt, Jitendra Kumar, Marguerite Mauritz, Edward A. G. Schuur, Anna-Maria Virkkala, Gerardo Celis, Forrest M. Hoffman, and Mathias Göckede
Biogeosciences, 19, 559–583, https://doi.org/10.5194/bg-19-559-2022, https://doi.org/10.5194/bg-19-559-2022, 2022
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Thawing of Arctic permafrost soils could trigger the release of vast amounts of carbon to the atmosphere, thus enhancing climate change. Our study investigated how well the current network of eddy covariance sites to monitor greenhouse gas exchange at local scales captures pan-Arctic flux patterns. We identified large coverage gaps, e.g., in Siberia, but also demonstrated that a targeted addition of relatively few sites can significantly improve network performance.
Yaoping Wang, Jiafu Mao, Mingzhou Jin, Forrest M. Hoffman, Xiaoying Shi, Stan D. Wullschleger, and Yongjiu Dai
Earth Syst. Sci. Data, 13, 4385–4405, https://doi.org/10.5194/essd-13-4385-2021, https://doi.org/10.5194/essd-13-4385-2021, 2021
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We developed seven global soil moisture datasets (1970–2016, monthly, half-degree, and multilayer) by merging a wide range of data sources, including in situ and satellite observations, reanalysis, offline land surface model simulations, and Earth system model simulations. Given the great value of long-term, multilayer, gap-free soil moisture products to climate research and applications, we believe this paper and the presented datasets would be of interest to many different communities.
Polly C. Buotte, Charles D. Koven, Chonggang Xu, Jacquelyn K. Shuman, Michael L. Goulden, Samuel Levis, Jessica Katz, Junyan Ding, Wu Ma, Zachary Robbins, and Lara M. Kueppers
Biogeosciences, 18, 4473–4490, https://doi.org/10.5194/bg-18-4473-2021, https://doi.org/10.5194/bg-18-4473-2021, 2021
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We present an approach for ensuring the definitions of plant types in dynamic vegetation models are connected to the underlying ecological processes controlling community composition. Our approach can be applied regionally or globally. Robust resolution of community composition will allow us to use these models to address important questions related to future climate and management effects on plant community composition, structure, carbon storage, and feedbacks within the Earth system.
Wu Ma, Lu Zhai, Alexandria Pivovaroff, Jacquelyn Shuman, Polly Buotte, Junyan Ding, Bradley Christoffersen, Ryan Knox, Max Moritz, Rosie A. Fisher, Charles D. Koven, Lara Kueppers, and Chonggang Xu
Biogeosciences, 18, 4005–4020, https://doi.org/10.5194/bg-18-4005-2021, https://doi.org/10.5194/bg-18-4005-2021, 2021
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We use a hydrodynamic demographic vegetation model to estimate live fuel moisture dynamics of chaparral shrubs, a dominant vegetation type in fire-prone southern California. Our results suggest that multivariate climate change could cause a significant net reduction in live fuel moisture and thus exacerbate future wildfire danger in chaparral shrub systems.
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Short summary
Photosynthesis is critical for life and has been affected by the changing climate. Many parameters come into play while modeling, but traditional calibration approaches face many issues. Our framework trains coupled neural networks to provide parameters to a photosynthesis model. Using big data, we independently found parameter values that were correlated with those in the literature while giving higher correlation and reduced biases in photosynthesis rates.
Photosynthesis is critical for life and has been affected by the changing climate. Many...
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