Alison Appling, PhD
Alison Appling, Ph.D., is a data scientist and ecologist who applies machine learning and other data-driven methods to predict and understand water resources dynamics.
Current Roles
- Project Manager: Nutrient Prediction Innovation and Evaluation (NPIE)
- Project Manager: Predictive Understanding of Multiscale Processes (PUMP)
- Task Lead: Advancing Machine Learning and Data Assimilation, within the PUMP Project
Alison studies the movement of energy, carbon, and nutrients through rivers, lakes, and floodplains to better predict and understand variations in water quality over space and time.
As a machine learning modeler and biogeochemist, Alison seeks modeling advances that bring together scientific knowledge and data-driven models, using approaches including process-guided deep learning and differentiable hydrology.
As a data scientist, Alison conducts analyses in ways that are reproducible, efficient, and transparent, and Alison has developed tools and workflows to support others in these goals.
In leadership roles, Alison plans projects and organizes teams to deliver relevant, timely, high-quality products; challenges individuals to excel in their projects and careers; and coordinates across projects to realize the Water Mission Area’s vision of fit-for-purpose, integrated tools for modeling water quantity and quality across the nation.
Alison is a member of the Analysis and Prediction Branch in the Integrated Modeling and Prediction Division in the Water Resources Mission Area. Alison is on the USGS career track called Equipment Development Grade Evaluation (EDGE).
Professional Experience
Development Ecologist and Data Scientist, U.S. Geological Survey, 2019-Present
Ecologist, U.S. Geological Survey, 2016-2019
Postdoctoral Fellow, USGS Powell Center and University of Wisconsin-Madison. Mentors: E. H. Stanley, J. S. Read, E. G. Stets, and R. O. Hall, 2015-2016
Postdoctoral Associate, University of New Hampshire. Mentor: W. H. McDowell, 2013-2015
Postdoctoral Associate, Duke University. Mentor: J. B. Heffernan, 2012-2013
Ph.D. Student and Teaching Assistant: Organismal Diversity, Aquatic Field Ecology, and General Microbiology, University Program in Ecology, Duke University, 2006-2012
Research Technician, Stanford University & Carnegie Institution of Washington, 2004-2006
Undergraduate Teaching Assistant: Programming Paradigms and Discrete Mathematics, Computer Science, Stanford University, 2001-2003
Education and Certifications
Ph.D. Ecology, 2012. Duke University, Durham, NC.
Connectivity Drives Function: Carbon and Nitrogen Dynamics in a Floodplain-Aquifer Ecosystem. Advisors: E. S. Bernhardt and R. B. Jackson
B.S. Symbolic Systems, 2004. Stanford University, Stanford, CA.
Science and Products
Integrated Water Prediction (IWP)
The USGS Integrated Water Prediction science program is focused on developing and improving model code, workflows, and applications of core water availability components at a national extent.
Filter Total Items: 20
Downscaling and multi-scale modeling of stream temperature in five watersheds of the Delaware River Basin, 1979-2021 Downscaling and multi-scale modeling of stream temperature in five watersheds of the Delaware River Basin, 1979-2021
This model archive (Fan et al. 2025a) provides all data, code, and model outputs used in the corresponding manuscript (Fan et al. 2025b) to test machine learning (ML) methods for downscaling and multi-scale modeling of stream temperature to combine an ML model and/or input data at coarse spatial resolution with an ML model and/or input data at fine spatial resolution to predict stream...
Distance matrices and river-network crosswalks for the Geospatial Fabric v1.1 to support data-driven models of water quality in U.S. rivers Distance matrices and river-network crosswalks for the Geospatial Fabric v1.1 to support data-driven models of water quality in U.S. rivers
This data release contains hydrologic network information to support national modeling of water quality in streams and rivers, including distance matrices that represent the spatial relationships among modeled river reaches. These data can be used as inputs to data-driven models that leverage information about spatial proximity to make predictions of water quantity or quality. The...
Compilation of multi-agency water temperature observations for U.S. streams, 1894-2022 Compilation of multi-agency water temperature observations for U.S. streams, 1894-2022
This data release collates stream water temperature observations from across the United States from four data sources: The U.S. Geological Survey's National Water Information System (NWIS), Water Quality Portal (WQP), Spatial Hydro-Ecological Decision Systems temperature database (EcoSHEDS), and the U.S. Fish and Wildlife's NorWeST stream temperature database. These data were compiled...
Delaware River Basin Stream Salinity Machine Learning Models and Data Delaware River Basin Stream Salinity Machine Learning Models and Data
This model archive contains the input data, model code, and model outputs for machine learning models that predict daily non-tidal stream salinity (specific conductance) for a network of 459 modeled stream segments across the Delaware River Basin (DRB) from 1984-09-30 to 2021-12-31. There are a total of twelve models from combinations of two machine learning models (Random Forest and...
Identifying structural priors in a hybrid differentiable model for stream water temperature modeling at 415 U.S. basin outlets, 2010-2016 Identifying structural priors in a hybrid differentiable model for stream water temperature modeling at 415 U.S. basin outlets, 2010-2016
This model archive (Rahmani et al. 2023a) provides all data, code, and model outputs used in Rahmani et al. (2023b) to improve model representations toward improved prediction of stream temperature and groundwater/subsurface flow contributions to stream temperature. Briefly, we modeled stream temperature at sites across the continental United States using a hybrid differentiable model...
Model Code, Outputs, and Supporting Data for Approaches to Process-Guided Deep Learning for Groundwater-Influenced Stream Temperature Predictions Model Code, Outputs, and Supporting Data for Approaches to Process-Guided Deep Learning for Groundwater-Influenced Stream Temperature Predictions
This model archive provides all data, code, and modeling results used in Barclay and others (2023) to assess the ability of process-guided deep learning stream temperature models to accurately incorporate groundwater-discharge processes. We assessed the performance of an existing process-guided deep learning stream temperature model of the Delaware River Basin (USA) and explored four...
Predictions and supporting data for network-wide 7-day ahead forecasts of water temperature in the Delaware River Basin Predictions and supporting data for network-wide 7-day ahead forecasts of water temperature in the Delaware River Basin
Daily maximum water temperature predictions in the Delaware River Basin (DRB) can inform decision makers who can use cold-water reservoir releases to maintain thermal habitat for sensitive fish species. This data release contains the forcings and outputs of 7-day ahead maximum water temperature forecasting models that makes predictions at 70 river reaches in the upper DRB. The modeling...
A deep learning model and associated data to support understanding and simulation of salinity dynamics in Delaware Bay A deep learning model and associated data to support understanding and simulation of salinity dynamics in Delaware Bay
Salinity dynamics in the Delaware Bay estuary are a critical water quality concern as elevated salinity can damage infrastructure and threaten drinking water supplies. Current state-of-the-art modeling approaches use hydrodynamic models, which can produce accurate results but are limited by significant computational costs. We developed a machine learning (ML) model to predict the 250 mg...
Examining the influence of deep learning architecture on generalizability for predicting stream temperature in the Delaware River Basin Examining the influence of deep learning architecture on generalizability for predicting stream temperature in the Delaware River Basin
This data release and model archive provides all data, code, and modelling results used in Topp et al. (2023) to examine the influence of deep learning architecture on generalizability when predicting stream temperature in the Delaware River Basin (DRB). Briefly, we modeled stream temperature in the DRB using two spatially and temporally aware process guided deep learning models (a...
Deep learning approaches for improving prediction of daily stream temperature in data-scarce, unmonitored, and dammed basins Deep learning approaches for improving prediction of daily stream temperature in data-scarce, unmonitored, and dammed basins
This data release provides all data and code used in Rahmani et al. (2021b) to model stream temperature and assess results. Briefly, we modeled stream temperature at sites across the continental United States using deep learning methods. The associated manuscript explores the prediction challenges posed by reservoirs, the value of additional training sites when predicting in gaged vs...
Model predictions for heterogeneous stream-reservoir graph networks with data assimilation Model predictions for heterogeneous stream-reservoir graph networks with data assimilation
This data release provides the predictions from stream temperature models described in Chen et al. 2021. Briefly, various deep learning and process-guided deep learning models were built to test improved performance of stream temperature predictions below reservoirs in the Delaware River Basin. The spatial extent of predictions was restricted to streams above the Delaware River at...
Stream temperature predictions in the Delaware River Basin using pseudo-prospective learning and physical simulations Stream temperature predictions in the Delaware River Basin using pseudo-prospective learning and physical simulations
Stream networks with reservoirs provide a particularly hard modeling challenge because reservoirs can decouple physical processes (e.g., water temperature dynamics in streams) from atmospheric signals. Including observed reservoir releases as inputs to models can improve water temperature predictions below reservoirs, but many reservoirs are not well-observed. This data release contains...
Filter Total Items: 35
Integrated Hydro-terrestrial Modeling 2.0: Progress and path forward on building a national capability Integrated Hydro-terrestrial Modeling 2.0: Progress and path forward on building a national capability
Growing societal pressures on U.S. water resources and the challenges inherent in understanding how future water risks may evolve are driving major investments to improve our knowledge of the integrated water cycle. This improved understanding as captured in innovations in our data, knowledge, and modeling capabilities, needs to be accelerated through better integration and coordination...
Authors
Katherine Skalak, Nathalie Voisin, Patrick Read, Ying Fan Reinfelder
Predictive understanding of stream salinization in a developed watershed using machine learning Predictive understanding of stream salinization in a developed watershed using machine learning
Stream salinization is a global issue, yet few models can provide reliable salinity estimates for unmonitored locations at the time scales required for ecological exposure assessments. Machine learning approaches are presented that use spatially limited high-frequency monitoring and spatially distributed discrete samples to estimate the daily stream-specific conductance across a...
Authors
Jared David Smith, Lauren Elizabeth Koenig, Margaux Jeanne Sleckman, Alison P. Appling, Jeffrey M Sadler, Vincent T. DePaul, Zoltan Szabo
Stream nitrate dynamics driven primarily by discharge and watershed physical and soil characteristics at intensively monitored sites: Insights from deep learning Stream nitrate dynamics driven primarily by discharge and watershed physical and soil characteristics at intensively monitored sites: Insights from deep learning
We developed a suite of models using deep learning to make hindcast predictions of the 7‐day average backward‐looking nitrate concentration at 46 predominantly agricultural sites across the midwestern and eastern United States. The models used daily observations of discharge and meteorological variables and watershed attributes describing anthropogenic modification to hydrology, nitrogen...
Authors
Galen Gorski, Laurel Larsen, Jordan Wingenroth, Liang Zhang, Dino Bellugi, Alison P. Appling
Deep learning of estuary salinity dynamics is physically accurate at a fraction of hydrodynamic model computational cost Deep learning of estuary salinity dynamics is physically accurate at a fraction of hydrodynamic model computational cost
Salinity dynamics in the Delaware Bay estuary are a critical water quality concern as elevated salinity can damage infrastructure and threaten drinking water supplies. Current state-of-the-art modeling approaches use hydrodynamic models, which can produce accurate results but are limited by significant computational costs. We developed a machine learning (ML) model to predict the 250 mg...
Authors
Galen Gorski, Salme Ellen Cook, Amelia Marie Snyder, Alison P. Appling, Theodore Paul Thompson, Jared David Smith, John C. Warner, Simon Nemer Topp
Deep learning for water quality Deep learning for water quality
Understanding and predicting the quality of inland waters are challenging, particularly in the context of intensifying climate extremes expected in the future. These challenges arise partly due to complex processes that regulate water quality, and arduous and expensive data collection that exacerbate the issue of data scarcity. Traditional process-based and statistical models often fall...
Authors
Wei Zhi, Alison P. Appling, Heather E. Golden, Joel Podgorski, Li Li
Train, inform, borrow, or combine? Approaches to process-guided deep learning for groundwater-influenced stream temperature prediction Train, inform, borrow, or combine? Approaches to process-guided deep learning for groundwater-influenced stream temperature prediction
Although groundwater discharge is a critical stream temperature control process, it is not explicitly represented in many stream temperature models, an omission that may reduce predictive accuracy, hinder management of aquatic habitat, and decrease user confidence. We assessed the performance of a previously-described process-guided deep learning model of stream temperature in the...
Authors
Janet R. Barclay, Simon Nemer Topp, Lauren Elizabeth Koenig, Margaux Jeanne Sleckman, Alison P. Appling
Identifying structural priors in a hybrid differentiable model for stream water temperature modeling Identifying structural priors in a hybrid differentiable model for stream water temperature modeling
Although deep learning models for stream temperature (Ts) have recently shown exceptional accuracy, they have limited interpretability and cannot output untrained variables. With hybrid differentiable models, neural networks (NNs) can be connected to physically based equations (called structural priors) to output intermediate variables such as water source fractions (specifying what...
Authors
Farshid Rahmani, Alison P. Appling, Dapeng Feng, Kathryn Lawson, Chaopeng Shen
Differentiable modelling to unify machine learning and physical models for geosciences Differentiable modelling to unify machine learning and physical models for geosciences
Process-based modelling offers interpretability and physical consistency in many domains of geosciences but struggles to leverage large datasets efficiently. Machine-learning methods, especially deep networks, have strong predictive skills yet are unable to answer specific scientific questions. In this Perspective, we explore differentiable modelling as a pathway to dissolve the...
Authors
Chaopeng Shen, Alison P. Appling, Pierre Gentine, Toshiyuki Bandai, Hoshin Gupta, Alexandre Tartakovsky, Marco Baity-Jesi, Fabrizio Fenicia, Daniel Kifer, Li Li, Xiaofeng Liu, Wei Ren, Yi Zheng, Ciaran Harman, Martyn Clark, Matthew Farthing, Dapeng Feng, Praveen Kumar, Doaa Aboelyazeed, Farshid Rahmani, Yalan Song, Hylke E. Beck, Tadd Bindas, Dipankar Dwivedi, Kuai Fang, Marvin Höge, Chris Rackauckas, Binayak Mohanty, Tirthankar Roy, Chonggang Xu, Kathryn Lawson
Evaluating deep learning architecture and data assimilation for improving water temperature forecasts at unmonitored locations Evaluating deep learning architecture and data assimilation for improving water temperature forecasts at unmonitored locations
Deep learning (DL) models are increasingly used to forecast water quality variables for use in decision making. Ingesting recent observations of the forecasted variable has been shown to greatly increase model performance at monitored locations; however, observations are not collected at all locations, and methods are not yet well developed for DL models for optimally ingesting recent...
Authors
Jacob Aaron Zwart, Jeremy Alejandro Diaz, Scott Douglas Hamshaw, Samantha K. Oliver, Jesse Cleveland Ross, Margaux Jeanne Sleckman, Alison P. Appling, Hayley R. Corson-Dosch, Xiaowei Jia, Jordan S Read, Jeffrey M Sadler, Theodore Paul Thompson, David Watkins, Elaheh (Ellie) White
Stream temperature prediction in a shifting environment: The influence of deep learning architecture Stream temperature prediction in a shifting environment: The influence of deep learning architecture
Stream temperature is a fundamental control on ecosystem health. Recent efforts incorporating process guidance into deep learning models for predicting stream temperature have been shown to outperform existing statistical and physical models. This performance is in part because deep learning architectures can actively learn spatiotemporal relationships that govern how water and energy...
Authors
Simon Nemer Topp, Janet R. Barclay, Jeremy Alejandro Diaz, Alexander Y. Sun, Xiaowei Jia, Daniel Lubin, Jeffrey M Sadler, Alison P. Appling
Near-term forecasts of stream temperature using deep learning and data assimilation in support of management decisions Near-term forecasts of stream temperature using deep learning and data assimilation in support of management decisions
Deep learning (DL) models are increasingly used to make accurate hindcasts of management-relevant variables, but they are less commonly used in forecasting applications. Data assimilation (DA) can be used for forecasts to leverage real-time observations, where the difference between model predictions and observations today is used to adjust the model to make better predictions tomorrow...
Authors
Jacob Aaron Zwart, Samantha K. Oliver, William Watkins, Jeffrey Michael Sadler, Alison P. Appling, Hayley R. Corson-Dosch, Xiaowei Jia, Vipin Kumar, Jordan Read
Physics-guided architecture (PGA) of LSTM models for uncertainty quantification in lake temperature modeling Physics-guided architecture (PGA) of LSTM models for uncertainty quantification in lake temperature modeling
This chapter focuses on meeting the need to produce neural network outputs that are physically consistent and also express uncertainties, a rare combination to date. It explains the effectiveness of physics-guided architecture - long-short-term-memory (PGA-LSTM) in achieving better generalizability and physical consistency over data collected from Lake Mendota in Wisconsin and Falling...
Authors
Arka Daw, R. Quinn Thomas, Cayelan C. Carey, Jordan Read, Alison P. Appling, Anuj Karpatne
Non-USGS Publications**
J. S. Read, J. I. Walker, A. P. Appling, D. L. Blodgett, E. K. Read, and L. A. Winslow. 2015. geoknife: reproducible web-processing of large gridded datasets. Ecography. https://doi.org/10.1111/ecog.01880
S.A. Sistla, A. P. Appling, A. M. Lewandowska, B. N. Taylor, and A. A. Wolf. 2015. Stoichiometric flexibility in response to fertilization along gradients of environmental and organismal nutrient richness. Oikos, 124: 949-959. https://doi.org/10.1111/oik.02385
A. P. Appling, M. C. Leon, and W. H. McDowell. 2015. Reducing bias and quantifying uncertainty in watershed flux estimates: The R package loadflex. Ecosphere 6(12):269. https://doi.org/10.1890/ES14-00517.1
A. P. Appling and J. B. Heffernan. 2014. Nutrient limitation and physiology mediate the fine-scale [de]coupling of biogeochemical cycles. The American Naturalist 184:384-406. https://doi.org/10.1086/677282
A. P. Appling, E. S. Bernhardt, and J. A. Stanford. 2014. Floodplain biogeochemical mosaics: a multidimensional view of alluvial soils. Journal of Geophysical Research: Biogeosciences 119:2013JG002543. https://doi.org/10.1002/2013JG002543
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Science and Products
Integrated Water Prediction (IWP)
The USGS Integrated Water Prediction science program is focused on developing and improving model code, workflows, and applications of core water availability components at a national extent.
Filter Total Items: 20
Downscaling and multi-scale modeling of stream temperature in five watersheds of the Delaware River Basin, 1979-2021 Downscaling and multi-scale modeling of stream temperature in five watersheds of the Delaware River Basin, 1979-2021
This model archive (Fan et al. 2025a) provides all data, code, and model outputs used in the corresponding manuscript (Fan et al. 2025b) to test machine learning (ML) methods for downscaling and multi-scale modeling of stream temperature to combine an ML model and/or input data at coarse spatial resolution with an ML model and/or input data at fine spatial resolution to predict stream...
Distance matrices and river-network crosswalks for the Geospatial Fabric v1.1 to support data-driven models of water quality in U.S. rivers Distance matrices and river-network crosswalks for the Geospatial Fabric v1.1 to support data-driven models of water quality in U.S. rivers
This data release contains hydrologic network information to support national modeling of water quality in streams and rivers, including distance matrices that represent the spatial relationships among modeled river reaches. These data can be used as inputs to data-driven models that leverage information about spatial proximity to make predictions of water quantity or quality. The...
Compilation of multi-agency water temperature observations for U.S. streams, 1894-2022 Compilation of multi-agency water temperature observations for U.S. streams, 1894-2022
This data release collates stream water temperature observations from across the United States from four data sources: The U.S. Geological Survey's National Water Information System (NWIS), Water Quality Portal (WQP), Spatial Hydro-Ecological Decision Systems temperature database (EcoSHEDS), and the U.S. Fish and Wildlife's NorWeST stream temperature database. These data were compiled...
Delaware River Basin Stream Salinity Machine Learning Models and Data Delaware River Basin Stream Salinity Machine Learning Models and Data
This model archive contains the input data, model code, and model outputs for machine learning models that predict daily non-tidal stream salinity (specific conductance) for a network of 459 modeled stream segments across the Delaware River Basin (DRB) from 1984-09-30 to 2021-12-31. There are a total of twelve models from combinations of two machine learning models (Random Forest and...
Identifying structural priors in a hybrid differentiable model for stream water temperature modeling at 415 U.S. basin outlets, 2010-2016 Identifying structural priors in a hybrid differentiable model for stream water temperature modeling at 415 U.S. basin outlets, 2010-2016
This model archive (Rahmani et al. 2023a) provides all data, code, and model outputs used in Rahmani et al. (2023b) to improve model representations toward improved prediction of stream temperature and groundwater/subsurface flow contributions to stream temperature. Briefly, we modeled stream temperature at sites across the continental United States using a hybrid differentiable model...
Model Code, Outputs, and Supporting Data for Approaches to Process-Guided Deep Learning for Groundwater-Influenced Stream Temperature Predictions Model Code, Outputs, and Supporting Data for Approaches to Process-Guided Deep Learning for Groundwater-Influenced Stream Temperature Predictions
This model archive provides all data, code, and modeling results used in Barclay and others (2023) to assess the ability of process-guided deep learning stream temperature models to accurately incorporate groundwater-discharge processes. We assessed the performance of an existing process-guided deep learning stream temperature model of the Delaware River Basin (USA) and explored four...
Predictions and supporting data for network-wide 7-day ahead forecasts of water temperature in the Delaware River Basin Predictions and supporting data for network-wide 7-day ahead forecasts of water temperature in the Delaware River Basin
Daily maximum water temperature predictions in the Delaware River Basin (DRB) can inform decision makers who can use cold-water reservoir releases to maintain thermal habitat for sensitive fish species. This data release contains the forcings and outputs of 7-day ahead maximum water temperature forecasting models that makes predictions at 70 river reaches in the upper DRB. The modeling...
A deep learning model and associated data to support understanding and simulation of salinity dynamics in Delaware Bay A deep learning model and associated data to support understanding and simulation of salinity dynamics in Delaware Bay
Salinity dynamics in the Delaware Bay estuary are a critical water quality concern as elevated salinity can damage infrastructure and threaten drinking water supplies. Current state-of-the-art modeling approaches use hydrodynamic models, which can produce accurate results but are limited by significant computational costs. We developed a machine learning (ML) model to predict the 250 mg...
Examining the influence of deep learning architecture on generalizability for predicting stream temperature in the Delaware River Basin Examining the influence of deep learning architecture on generalizability for predicting stream temperature in the Delaware River Basin
This data release and model archive provides all data, code, and modelling results used in Topp et al. (2023) to examine the influence of deep learning architecture on generalizability when predicting stream temperature in the Delaware River Basin (DRB). Briefly, we modeled stream temperature in the DRB using two spatially and temporally aware process guided deep learning models (a...
Deep learning approaches for improving prediction of daily stream temperature in data-scarce, unmonitored, and dammed basins Deep learning approaches for improving prediction of daily stream temperature in data-scarce, unmonitored, and dammed basins
This data release provides all data and code used in Rahmani et al. (2021b) to model stream temperature and assess results. Briefly, we modeled stream temperature at sites across the continental United States using deep learning methods. The associated manuscript explores the prediction challenges posed by reservoirs, the value of additional training sites when predicting in gaged vs...
Model predictions for heterogeneous stream-reservoir graph networks with data assimilation Model predictions for heterogeneous stream-reservoir graph networks with data assimilation
This data release provides the predictions from stream temperature models described in Chen et al. 2021. Briefly, various deep learning and process-guided deep learning models were built to test improved performance of stream temperature predictions below reservoirs in the Delaware River Basin. The spatial extent of predictions was restricted to streams above the Delaware River at...
Stream temperature predictions in the Delaware River Basin using pseudo-prospective learning and physical simulations Stream temperature predictions in the Delaware River Basin using pseudo-prospective learning and physical simulations
Stream networks with reservoirs provide a particularly hard modeling challenge because reservoirs can decouple physical processes (e.g., water temperature dynamics in streams) from atmospheric signals. Including observed reservoir releases as inputs to models can improve water temperature predictions below reservoirs, but many reservoirs are not well-observed. This data release contains...
Filter Total Items: 35
Integrated Hydro-terrestrial Modeling 2.0: Progress and path forward on building a national capability Integrated Hydro-terrestrial Modeling 2.0: Progress and path forward on building a national capability
Growing societal pressures on U.S. water resources and the challenges inherent in understanding how future water risks may evolve are driving major investments to improve our knowledge of the integrated water cycle. This improved understanding as captured in innovations in our data, knowledge, and modeling capabilities, needs to be accelerated through better integration and coordination...
Authors
Katherine Skalak, Nathalie Voisin, Patrick Read, Ying Fan Reinfelder
Predictive understanding of stream salinization in a developed watershed using machine learning Predictive understanding of stream salinization in a developed watershed using machine learning
Stream salinization is a global issue, yet few models can provide reliable salinity estimates for unmonitored locations at the time scales required for ecological exposure assessments. Machine learning approaches are presented that use spatially limited high-frequency monitoring and spatially distributed discrete samples to estimate the daily stream-specific conductance across a...
Authors
Jared David Smith, Lauren Elizabeth Koenig, Margaux Jeanne Sleckman, Alison P. Appling, Jeffrey M Sadler, Vincent T. DePaul, Zoltan Szabo
Stream nitrate dynamics driven primarily by discharge and watershed physical and soil characteristics at intensively monitored sites: Insights from deep learning Stream nitrate dynamics driven primarily by discharge and watershed physical and soil characteristics at intensively monitored sites: Insights from deep learning
We developed a suite of models using deep learning to make hindcast predictions of the 7‐day average backward‐looking nitrate concentration at 46 predominantly agricultural sites across the midwestern and eastern United States. The models used daily observations of discharge and meteorological variables and watershed attributes describing anthropogenic modification to hydrology, nitrogen...
Authors
Galen Gorski, Laurel Larsen, Jordan Wingenroth, Liang Zhang, Dino Bellugi, Alison P. Appling
Deep learning of estuary salinity dynamics is physically accurate at a fraction of hydrodynamic model computational cost Deep learning of estuary salinity dynamics is physically accurate at a fraction of hydrodynamic model computational cost
Salinity dynamics in the Delaware Bay estuary are a critical water quality concern as elevated salinity can damage infrastructure and threaten drinking water supplies. Current state-of-the-art modeling approaches use hydrodynamic models, which can produce accurate results but are limited by significant computational costs. We developed a machine learning (ML) model to predict the 250 mg...
Authors
Galen Gorski, Salme Ellen Cook, Amelia Marie Snyder, Alison P. Appling, Theodore Paul Thompson, Jared David Smith, John C. Warner, Simon Nemer Topp
Deep learning for water quality Deep learning for water quality
Understanding and predicting the quality of inland waters are challenging, particularly in the context of intensifying climate extremes expected in the future. These challenges arise partly due to complex processes that regulate water quality, and arduous and expensive data collection that exacerbate the issue of data scarcity. Traditional process-based and statistical models often fall...
Authors
Wei Zhi, Alison P. Appling, Heather E. Golden, Joel Podgorski, Li Li
Train, inform, borrow, or combine? Approaches to process-guided deep learning for groundwater-influenced stream temperature prediction Train, inform, borrow, or combine? Approaches to process-guided deep learning for groundwater-influenced stream temperature prediction
Although groundwater discharge is a critical stream temperature control process, it is not explicitly represented in many stream temperature models, an omission that may reduce predictive accuracy, hinder management of aquatic habitat, and decrease user confidence. We assessed the performance of a previously-described process-guided deep learning model of stream temperature in the...
Authors
Janet R. Barclay, Simon Nemer Topp, Lauren Elizabeth Koenig, Margaux Jeanne Sleckman, Alison P. Appling
Identifying structural priors in a hybrid differentiable model for stream water temperature modeling Identifying structural priors in a hybrid differentiable model for stream water temperature modeling
Although deep learning models for stream temperature (Ts) have recently shown exceptional accuracy, they have limited interpretability and cannot output untrained variables. With hybrid differentiable models, neural networks (NNs) can be connected to physically based equations (called structural priors) to output intermediate variables such as water source fractions (specifying what...
Authors
Farshid Rahmani, Alison P. Appling, Dapeng Feng, Kathryn Lawson, Chaopeng Shen
Differentiable modelling to unify machine learning and physical models for geosciences Differentiable modelling to unify machine learning and physical models for geosciences
Process-based modelling offers interpretability and physical consistency in many domains of geosciences but struggles to leverage large datasets efficiently. Machine-learning methods, especially deep networks, have strong predictive skills yet are unable to answer specific scientific questions. In this Perspective, we explore differentiable modelling as a pathway to dissolve the...
Authors
Chaopeng Shen, Alison P. Appling, Pierre Gentine, Toshiyuki Bandai, Hoshin Gupta, Alexandre Tartakovsky, Marco Baity-Jesi, Fabrizio Fenicia, Daniel Kifer, Li Li, Xiaofeng Liu, Wei Ren, Yi Zheng, Ciaran Harman, Martyn Clark, Matthew Farthing, Dapeng Feng, Praveen Kumar, Doaa Aboelyazeed, Farshid Rahmani, Yalan Song, Hylke E. Beck, Tadd Bindas, Dipankar Dwivedi, Kuai Fang, Marvin Höge, Chris Rackauckas, Binayak Mohanty, Tirthankar Roy, Chonggang Xu, Kathryn Lawson
Evaluating deep learning architecture and data assimilation for improving water temperature forecasts at unmonitored locations Evaluating deep learning architecture and data assimilation for improving water temperature forecasts at unmonitored locations
Deep learning (DL) models are increasingly used to forecast water quality variables for use in decision making. Ingesting recent observations of the forecasted variable has been shown to greatly increase model performance at monitored locations; however, observations are not collected at all locations, and methods are not yet well developed for DL models for optimally ingesting recent...
Authors
Jacob Aaron Zwart, Jeremy Alejandro Diaz, Scott Douglas Hamshaw, Samantha K. Oliver, Jesse Cleveland Ross, Margaux Jeanne Sleckman, Alison P. Appling, Hayley R. Corson-Dosch, Xiaowei Jia, Jordan S Read, Jeffrey M Sadler, Theodore Paul Thompson, David Watkins, Elaheh (Ellie) White
Stream temperature prediction in a shifting environment: The influence of deep learning architecture Stream temperature prediction in a shifting environment: The influence of deep learning architecture
Stream temperature is a fundamental control on ecosystem health. Recent efforts incorporating process guidance into deep learning models for predicting stream temperature have been shown to outperform existing statistical and physical models. This performance is in part because deep learning architectures can actively learn spatiotemporal relationships that govern how water and energy...
Authors
Simon Nemer Topp, Janet R. Barclay, Jeremy Alejandro Diaz, Alexander Y. Sun, Xiaowei Jia, Daniel Lubin, Jeffrey M Sadler, Alison P. Appling
Near-term forecasts of stream temperature using deep learning and data assimilation in support of management decisions Near-term forecasts of stream temperature using deep learning and data assimilation in support of management decisions
Deep learning (DL) models are increasingly used to make accurate hindcasts of management-relevant variables, but they are less commonly used in forecasting applications. Data assimilation (DA) can be used for forecasts to leverage real-time observations, where the difference between model predictions and observations today is used to adjust the model to make better predictions tomorrow...
Authors
Jacob Aaron Zwart, Samantha K. Oliver, William Watkins, Jeffrey Michael Sadler, Alison P. Appling, Hayley R. Corson-Dosch, Xiaowei Jia, Vipin Kumar, Jordan Read
Physics-guided architecture (PGA) of LSTM models for uncertainty quantification in lake temperature modeling Physics-guided architecture (PGA) of LSTM models for uncertainty quantification in lake temperature modeling
This chapter focuses on meeting the need to produce neural network outputs that are physically consistent and also express uncertainties, a rare combination to date. It explains the effectiveness of physics-guided architecture - long-short-term-memory (PGA-LSTM) in achieving better generalizability and physical consistency over data collected from Lake Mendota in Wisconsin and Falling...
Authors
Arka Daw, R. Quinn Thomas, Cayelan C. Carey, Jordan Read, Alison P. Appling, Anuj Karpatne
Non-USGS Publications**
J. S. Read, J. I. Walker, A. P. Appling, D. L. Blodgett, E. K. Read, and L. A. Winslow. 2015. geoknife: reproducible web-processing of large gridded datasets. Ecography. https://doi.org/10.1111/ecog.01880
S.A. Sistla, A. P. Appling, A. M. Lewandowska, B. N. Taylor, and A. A. Wolf. 2015. Stoichiometric flexibility in response to fertilization along gradients of environmental and organismal nutrient richness. Oikos, 124: 949-959. https://doi.org/10.1111/oik.02385
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A. P. Appling and J. B. Heffernan. 2014. Nutrient limitation and physiology mediate the fine-scale [de]coupling of biogeochemical cycles. The American Naturalist 184:384-406. https://doi.org/10.1086/677282
A. P. Appling, E. S. Bernhardt, and J. A. Stanford. 2014. Floodplain biogeochemical mosaics: a multidimensional view of alluvial soils. Journal of Geophysical Research: Biogeosciences 119:2013JG002543. https://doi.org/10.1002/2013JG002543
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