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Machine learning for hydrologic sciences: An introductory overview

WILEY INTERDISCIPLINARY REVIEWS-WATER 2021年第5期8卷 e1533页

作者： Xu, Tianfang Liang, Feng Arizona State Univ Sch Sustainable Engn & Built Environm Tempe AZ 85281 USA Univ Illinois Dept Stat Champaign IL USA

The hydrologic community has experienced a surge in interest in machine learning in recent years. This interest is primarily driven by rapidly growing hydrologic data repositories, as well as success of machine learning in various academic and commercial applications, now possible due to increasing accessibility to enabling hardware and software. This overview is intended for readers new to the field of machine learning. It provides a non-technical introduction, placed within a historical context, to commonly used machine learning algorithms and deep learning architectures. Applications in hydrologic sciences are summarized next, with a focus on recent studies. They include the detection of patterns and events such as land use change, approximation of hydrologic variables and processes such as rainfall-runoff modeling, and mining relationships among variables for identifying controlling factors. The use of machine learning is also discussed in the context of integrated with process-based modeling for parameterization, surrogate modeling, and bias correction. Finally, the article highlights challenges of extrapolating robustness, physical interpretability, and small sample size in hydrologic applications.

关键词： data-driven modeling deep learning hydrology machine learning process-based modeling

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Validation of a coupled wave-flow model in a high-energy setting: The mouth of the Columbia River

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JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS 2012年第C9期117卷

作者： Elias, Edwin P. L. Gelfenbaum, Guy Van der Westhuysen, Andre J. Deltares NL-2600 MH Delft Netherlands US Geol Survey Pacific Coastal & Marine Sci Ctr Santa Cruz CA USA

A monthlong time series of wave, current, salinity, and suspended-sediment measurements was made at five sites on a transect across the Mouth of Columbia River (MCR). These data were used to calibrate and evaluate the performance of a coupled hydrodynamic and wave model for the MCR based on the Delft3D modeling system. The MCR is a dynamic estuary inlet in which tidal currents, river discharge, and wave-driven currents are all important. Model tuning consisted primarily of spatial adjustments to bottom drag coefficients. In combination with (near-) default parameter settings, the MCR model application is able to simulate the dominant features in the tidal flow, salinity and wavefields observed in field measurements. The wave-orbital averaged method for representing the current velocity profile in the wave model is considered the most realistic for the MCR. The hydrodynamic model is particularly effective in reproducing the observed vertical residual and temporal variations in current structure. Density gradients introduce the observed and modeled reversal of the mean flow at the bed and augment mean and peak flow in the upper half of the water column. This implies that sediment transport during calmer summer conditions is controlled by density stratification and is likely net landward due to the reversal of flow near the bed. The correspondence between observed and modeled hydrodynamics makes this application a tool to investigate hydrodynamics and associated sediment transport.

关键词： Columbia River Delft3D process-based modeling tidal inlet wave-current interaction

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Implementation and calibration of short-rotation eucalypt plantation module within the ECOSMOS land surface model

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AGRICULTURAL AND FOREST METEOROLOGY 2022年 323卷

作者： Colmanetti, Michel Anderson Almeida Cuadra, Santiago Vianna Lamparelli, Rubens Augusto Camargo Junior, Jair Bortolucci Cabral, Osvaldo Machado Rodrigues Campoe, Otavio Camargo Victoria, Daniel de Castro Barioni, Luis Gustavo Galdos, Marcelo Valadares Figueiredo, Gleyce Kelly Dantas Araujo le Maire, Guerric Univ Estadual Campinas Ctr Energy Planning 330 Cora Coralina St BR-13083896 Campinas SP Brazil EMBRAPA Agr Digital BR-13083886 Campinas SP Brazil EMBRAPA Meio Ambiente BR-13820000 Jaguariuna SP Brazil Univ Fed Lavras UFLA BR-37200000 Lavras MG Brazil Univ Leeds Inst Climate & Atmospher Sci Sch Earth & Environm Leeds LS2 9JT England Univ Estadual Campinas Sch Agr Engn FEAGRI Campinas Brazil UMR Eco&Sols CIRAD F-34398 Montpellier France Univ Montpellier Eco&Sols CIRAD INRAIRDMontpellier SupAgro Montpellier France

Eucalypt is one of the most-planted broadleaf genera around the globe, exhibiting high yield, plasticity and growing capacity on a broad range of environments. The main objective of this study is to present the integration of a specific module for eucalypt short-rotation plantations into ECOSMOS (Ecosystem Model Simulator). Different calibrations and validations, from intensively monitored sites, experimental networks, and plots in commercial stands were performed. We calibrated all ECOSMOS model biophysical and physiological parameters for the Eucalyptus module using three micrometeorological experiments. A generic genotype was calibrated and applied to evaluate the model performance in response to contrasting environments and genotypes, on a dataset from an experimental network with high Genotype x Environment interactions. The model was applied over commercial eucalypt plantations sites, where re-calibration was necessary for four parameters of the ECOSMOSEucalyptus module related to leaf carbon allocation and specific leaf area, because of significant differences in genotypes and management among datasets. Results showed the consistency of the biophysical and physiological processes solved by the model, simulated energy and carbon fluxes, soil water dynamics, and growth of different plant components when compared with observations;Nash-Sutcliffe efficiency (NSE) of 0.93, 0.43 and 0.27 for net radiation, net ecosystem exchange and evapotranspiration, respectively were obtained for the validation dataset. The generic genotype calibration varied greatly in simulating the eucalypt stem growth of the 26 locations. The generic calibration can be used as reference for eucalypt plantation' areas in Brazil;however, a re calibration is recommended for operational applications to adjust the ECOSMOS-Eucalyptus module to the management conditions, management practices and genotypes used by companies.

关键词： Eucalypt process-based modeling ECOSMOS

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On the Influence of Antecedent Morphology on Development of Equilibrium Bathymetry in Estuaries Past and Future

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JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE 2022年第8期127卷 e2022JF006621-e2022JF006621页

作者： Rahdarian, Amin Bryan, Karin R. Van der Wegen, Mick Univ Waikato Fac Sci & Engn Sch Sci Hamilton New Zealand IHE Delft Inst Water Educ Delft Netherlands Deltares Delft Netherlands

Although analytical and numerical models have been widely used to explore evolution and equilibrium morphology in tidal environments, less attention has been paid to examining the impact of initial bathymetry on the model outcomes. Here we use two-dimensional idealized models with contrasting initial bathymetries to study how the interactions between antecedent morphology and tidal exchange processes determine the establishment of an estuarine equilibrium bathymetry, and how these interactions mediate the morphodynamic response to rising sea levels. In all model runs with sandy beds, inter-tidal zones reach the equilibrium condition first and equilibrium profiles are similar for points close to mean seal level. However, key aspects like channel formation, residence time and energy dissipation do not evolve to the same state and are inherited from the initial bathymetry. This implies that responses to sea-level rise (SLR) are different as well. Conversely, in cases with mud and sand input at the boundaries, equilibrium occurs more quickly and the equilibrium bathymetry and channel formation are dominated by the boundary mud concentration. General implications of the study are that predictions of coastal response to changes such as SLR depend on initial bathymetric conditions.

关键词： antecedent bathymetry equilibrium condition sea-level rise tidal environment physical services process-based modeling Delft3D drainage channel network

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Domain-specific model selection for structural identification of the Rab5-Rab7 dynamics in endocytosis

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BMC SYSTEMS BIOLOGY 2015年第1期9卷 31页

作者： Tanevski, Jovan Todorovski, Ljupco Kalaidzidis, Yannis Dzeroski, Saso Jozef Stefan Inst Ljubljana 1000 Slovenia Jozef Stefan Int Postgrad Sch Ljubljana 1000 Slovenia Univ Ljubljana Ljubljana 1000 Slovenia Max Planck Inst Mol Cell Biol & Genet D-01308 Dresden Germany

Background: Given its recent rapid development and the central role that modeling plays in the discipline, systems biology clearly needs methods for automated modeling of dynamical systems. process-based modeling focuses on explanatory models of dynamical systems;it constructs such models from measured time-course data and formalized modeling knowledge. In this paper, we apply process-based modeling to the practically relevant task of modeling the Rab5-Rab7 conversion switch in endocytosis. The task is difficult due to the limited observability of the system variables and the noisy measurements, which pose serious challenges to the process of model selection. To address these issues, we propose a domain-specific model selection criteria that take into account knowledge about the necessary properties of the simulated model behavior. Results: In a series of modeling experiments, we compare the results of process-based modeling obtained with different model selection criteria. The first is the standard maximum likelihood criterion based solely on least-squares model error. The second one is a parsimony-based criterion that also takes into account model complexity. We also introduce three domain-specific criteria based on domain expert expectations about the simulated behavior of an endocytosis model. According to the first criterion, 90 of the candidate models are indistinguishable. Furthermore, taking into account the complexity of the model does not lead to better model selection. However, the use of domain-specific criteria results in a remarkable improvement over the other two model selection criteria. Conclusions: We demonstrate the applicability of process-based modeling to the task of modeling the Rab5-Rab7 dynamics in endocytosis. Our experiments show that the domain-specific criteria outperform the standard domain-independent criteria for model selection. We also find that some of the model structures discarded as implausible in previous studies lead to the ex

关键词： process-based modeling Dynamical systems Structural identification Model selection Endocytosis

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Biochemical and steady-state kinetic analyses of arsenate reductases from an arsenic-tolerant strain of Citrobacter youngae IITK SM2

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BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2024年 739卷 150936页

作者： Verma, Akshat Chinnasamy, Hariharan Vedi Biswas, Bhumika Singh, Abhas Matheshwaran, Saravanan Indian Inst Technol Kanpur Dept Civil Engn Kanpur India Indian Inst Technol Kanpur Ctr Environm Sci & Engn Environm Geochem Lab Kanpur India Texas A&M Univ Zachry Dept Civil & Environm Engn College Stn TX USA Indian Inst Technol Kanpur Dept Biol Sci & Bioengn Microbial Adapdat & Chromatin Remodelling Lab Kanpur India Indian Inst Technol Kanpur Ctr Environm Sci & Engn Environm Microbiol Lab Kanpur India Indian Inst Technol Kanpur Kotak Sch Sustainabil Kanpur India

Arsenic (As) poisoning in aquifers is a serious problem worldwide, especially in the middle-Gangetic Plain (MGP) of India. Microbially-mediated As speciation in such aquifers is governed by the arsenate-reductase enzyme, ArsC, encoded by the arsC gene of As-metabolizing bacteria. In this study, ArsC1 (119 aa) and ArsC2 (141 aa) of a highly resistant strain to arsenic, Citrobacter youngae IITK SM2 (CyIITKSM2), isolated from a mixed-oxic MGP groundwater were biochemically characterized. Coupled-arsenate-reductase assay and IC-ICP-MS analysis confirmed that ArsC2 showed higher As(V) reduction than ArsC1 in the dissolved phase, which was consistent with the prominent structural changes in ArsC2 as identified through circular dichroism spectroscopy. Furthermore, the two ArsCs were able to mobilize arsenic from solid-bound arsenate [As(V)-loaded goethite, AsG] predominantly as As(III). However, the total arsenic released in the presence of ArsC2 was similar to 38 % and similar to 88 % higher, respectively, as compared to the ArsC1-containing and ArsC-free conditions. A process-based model that considered ArsC-mediated As(V) reduction to As(III) in the dissolved phase, and surface complexation of As (V) and As(III) on goethite, suggested that the extent of arsenate binding with ArsC was not affected by whether As(V) was dissolved or was sorbed. However, the catalytic reduction rate was at least an order of magnitude lower in sorbed As(V) than in dissolved As(V). Mutants of ArsC2 exhibited variable but reduced efficiencies compared to the wild-type ArsC2. This reduction may be attributed to the C-terminal loop observed in the AlphaFold predicted structure of ArsC2, which was absent in ArsC1. This comprehensive biochemical and biophysical analysis of the arsenate reductases in Citrobacter youngae could enhance our understanding of the role these microbes play in arsenic mobilization within MGP aquifers.

关键词： Arsenic Citrobacter youngae IITK SM2 (CyIITKSM2) Arsenate-reductase proteins (ArsC) Goethite Arsenate-loaded goethite Reduction efficiency process-based modeling

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Temperature and snowfall trigger alpine vegetation green-up on the world's roof

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GLOBAL CHANGE BIOLOGY 2015年第10期21卷 3635-3646页

作者： Chen, Xiaoqiu An, Shuai Inouye, David W. Schwartz, Mark D. Peking Univ Minist Educ Coll Urban & Environm Sci Lab Earth Surface Proc Beijing 100871 Peoples R China Univ Maryland Dept Biol College Pk MD 20742 USA Univ Wisconsin Dept Geog Milwaukee WI 53201 USA

Rapid temperature increase and its impacts on alpine ecosystems in the Qinghai-Tibetan Plateau, the world's highest and largest plateau, are a matter of global concern. Satellite observations have revealed distinctly different trend changes and contradicting temperature responses of vegetation green-up dates, leading to broad debate about the Plateau's spring phenology and its climatic attribution. Large uncertainties in remote-sensing estimates of phenology significantly limit efforts to predict the impacts of climate change on vegetation growth and carbon balance in the Qinghai-Tibetan Plateau, which are further exacerbated by a lack of detailed ground observation calibration. Here, we revealed the spatiotemporal variations and climate drivers of ground-based herbaceous plant green-up dates using 72 green-up datasets for 22 herbaceous plant species at 23 phenological stations, and corresponding daily mean air temperature and daily precipitation data from 19 climate stations across eastern and southern parts of the Qinghai-Tibetan Plateau from 1981 to 2011. Results show that neither the continuously advancing trend from 1982 to 2011, nor a turning point in the mid to late 1990s as reported by remote-sensing studies can be verified by most of the green-up time series, and no robust evidence for a warmer winter-induced later green-up dates can be detected. Thus, chilling requirements may not be an important driver influencing green-up responses to spring warming. Moreover, temperature-only control of green-up dates appears mainly at stations with relatively scarce preseason snowfall and lower elevation, while coupled temperature and precipitation controls of green-up dates occur mostly at stations with relatively abundant preseason snowfall and higher elevation. The diversified interactions between snowfall and temperature during late winter to early spring likely determine the spatiotemporal variations of green-up dates. Therefore, prediction of vegetation growth an

关键词： alpine ecosystems coupled air temperature and precipitation controls green-up date herbaceous plant phenology preseason snowfall process-based modeling spatiotemporal variations the Qinghai-Tibetan Plateau

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modeling the Morphodynamic Response of Estuarine Intertidal Shoals to Sea-Level Rise

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JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE 2022年第1期127卷 e2021JF006152-e2021JF006152页

作者： Elmilady, H. van der Wegen, M. Roelvink, D. van der Spek, A. IHE Delft Dept Coastal & Urban Risk & Resilience Delft Netherlands Deltares Dept Appl Morphodynam Delft Netherlands Delft Univ Technol Fac Civil Engn & Geosci Delft Netherlands Univ Utrecht Fac Geosci Utrecht Netherlands

Intertidal shoals are key features of estuarine environments worldwide. Climate change poses questions regarding the sustainability of intertidal areas under sea-level rise (SLR). Our work investigates the SLR impact on the long-term morphological evolution of unvegetated intertidal sandy shoals in a constrained channel-shoal system. Utilizing a process-based model (Delft3D), we schematize a short tidal system in a rectangular (2.5 x 20 km) basin with a high-resolution grid. An initial, mildly sloping, bathymetry is subjected to constant semidiurnal tidal forcing, sediment supply, and small wind-generated waves modeled by SWAN. A positive morphodynamic feedback between hydrodynamics, sediment transport, and morphology causes the emergence of large-scale channel-shoal patterns. Over centuries, tide-residual sediment transport gradually decreases leading to a state of low morphological activity balanced by tides, waves, and sediment supply. Tidal currents are the main driver of the SLR morphodynamic adaptation. Wave action leads to wider and lower shoals but does not fundamentally change the long-term morphological evolution. SLR causes increased flood dominance which triggers sediment import into the system. Shoals accrete in response to SLR with a lag that increases as SLR accelerates, eventually causing intertidal shoals to drown. Seaward shoals near the open boundary sediment source have higher accretion rates compared to landward shoals. Similarly, on a shoal-scale, the highest accretion rates occur at the shoal edges bounding the sediment suppling channels. A larger sediment supply enhances the SLR adaptation. Waves help distribute sediment supplied from channels across shoals. Adding mud fractions leads to faster, more uniform, accretion and muddier shoals under SLR.

关键词： Sea-level rise Long-term morphological evolution Intertidal shoals Waves process-based modeling Delft3D

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modeling the Genesis of Sand-Starved Dunes in Steady Currents

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JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE 2023年第1期128卷 e2022JF006796-e2022JF006796页

作者： Porcile, Gaetano Damveld, Johan H. Roos, Pieter C. Blondeaux, Paolo Colombini, Marco Univ Caen Normandy Coastal & Continental Morphodynam Lab Caen France Univ Twente Water Engn & Management Enschede Netherlands Univ Genoa Dept Civil Chem & Environm Engn Genoa Italy

The formation of fluvial dunes is usually studied by investigating the time development of a small amplitude bottom perturbation of a uniform stream and considering that the dunes originate by the growth of the bottom mode characterized by the largest amplification rate under the assumption of an infinite availability of the mobile sediment (linear stability analysis). Here we undertake the stability analysis investigating the formation of sand dunes in steady currents by accounting for the nonlinear effects of sediment starvation on the formative mechanisms of the bedforms and comparing the theoretical results with laboratory experiments, and an application of a fully nonlinear commercial model of finite amplitude dunes, thus enabling an improved understanding of the genesis of starved fluvial dunes. As the growth of the dunes progressively exposes the motionless substratum, both the stability-based and the numerical models predict starved dunes characterized by increasing crest-to-crest distances. The increase of the crest-to-crest distance corresponds to a decrease of the length of individual dunes as well as a growing irregularity in their spacing and morphology. These findings conform with the outcome of physical experiments performed earlier in a laboratory flume and existing measurements of starved fluvial dunes in the field. Plain Language Summary The genesis of fluvial dunes is a topic of considerable interest to river engineering as dunes are a primary source of flow resistance, regulating water levels and transport processes. The modeling of fluvial dunes is usually performed assuming an infinite availability of the sediment that can be eroded and deposited by the water flow. Field observations and laboratory experiments nevertheless indicate that the supply of sediment affects dune growth and the resulting morphology of the river bed. Here we present a new theoretical model able to reproduce the effects that the lack of sediment has on the growth of dune

关键词： stability analysis process-based modeling fluvial dunes sediment starvation nonlinear effects morphodynamics

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Assessing the impacts of pre-growing-season weather conditions on soil nitrogen dynamics and corn productivity in the US Midwest

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FIELD CROPS RESEARCH 2022年 284卷

作者： Li, Ziyi Guan, Kaiyu Zhou, Wang Peng, Bin Jin, Zhenong Tang, Jinyun Grant, Robert F. Nafziger, Emerson D. Margenot, Andrew J. Gentry, Lowell E. DeLucia, Evan H. Yang, Wendy H. Cai, Yaping Qin, Ziqi Archontoulis, Sotirios, V Fernandez, Fabian G. Yu, Zhongjie Lee, DoKyoung Yang, Yufeng Univ Illinois Agroecosyst Sustainabil Ctr Inst Sustainabil Energy & Environm Urbana IL 61801 USA Univ Illinois Coll Agr Consumer & Environm Sci Urbana IL 61801 USA Univ Illinois Natl Ctr Supercomp Applicat Urbana IL 61801 USA Univ Minnesota Twin Cities Dept Bioprod & Biosyst Engn St Paul MN 55108 USA Lawrence Berkeley Natl Lab Climate & Ecosyst Sci Div Climate Sci Dept Berkeley CA 94720 USA Univ Alberta Dept Renewable Resources Edmonton AB T6G 2R3 Canada Univ Illinois Carl R Woese Inst Genom Biol Urbana IL USA Univ Illinois Dept Plant Biol Urbana IL 61801 USA Univ Illinois Ctr Adv Bioenergy & Bioprod Innovat Urbana IL USA Univ Illinois Dept Geol Urbana IL 61801 USA Iowa State Univ Dept Agron Ames IA 50011 USA Univ Minnesota Twin Cities Dept Soil Water & Climate St Paul MN 55108 USA

Improving nitrogen (N) use efficiency is urgently needed to achieve co-sustainability of agricultural productivity and environmental quality. Environmental conditions and farming management practices affect the N cycle in agroecosystems. Particularly, weather conditions during the pre-growing-season (e.g. winter and early spring for the U.S. Corn Belt) can influence the dynamics of soil inorganic N (SIN) content and have implications for the end-of-season crop yield. Here, we used an advanced agroecosystem model, ecosys, to assess the consequences of different pre-growing-season weather scenarios in terms of both SIN dynamics and crop productivity. We first benchmarked ecosys using extensive N trial data collected across the U.S. Midwest, and found that ecosys captured the N fertilizer-yield responses and field-scale N cycle dynamics. We then used ecosys to conduct multiple experiments by changing the pre-growing-season precipitation and temperature, and assessed how these changes affected soil N dynamics and crop yield. We found that: (1) wetter pre-growing-seasons reduced SIN content through increasing leaching, leading to a reduction in corn grain yield of 0.54-0.86 Mg/ha (5-14%) under no fertilizer and of 0.21-0.33 Mg/ha (1-3%) under the normal N fertilizer rate (167 kg N/ha;Illinois average N fertilizer rate in 2018);yield loss induced by higher pre-growing-season precipitation can be eliminated by applying more N fertilizer in spring;and (2) colder pre-growing-seasons can reduce SIN content through decreased N mineralization and enhanced leaching. Both factors further contribute to corn yield loss of 0.10-0.68 Mg/ha (2-8%) under no fertilizer and of 0.12-0.48 Mg/ha (1-4%) under the normal fertilizer rate;however, in this case adding more fertilizer does not necessarily eliminate the yield loss caused by the colder pre-growingseason, because the lower temperature not only causes SIN deficiency but also reduces early-growing-season active root nutrients uptake a

关键词： Corn agroecosystem nitrogen cycle process-based modeling Ecosys

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