Jeffrey S. Whitaker’s research while affiliated with National Oceanic and Atmospheric Administration and other places

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Publications (106)


Nonlinear ensemble filtering with diffusion models: Application to the surface quasi-geostrophic dynamics
  • Article

May 2025

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17 Reads

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6 Citations

Feng Bao

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Siming Liang

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[...]

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Jeffrey S. Whitaker

The intersection between classical data assimilation methods and novel machine learning techniques has attracted significant interest in recent years. Here we explore another promising solution in which diffusion models are used to formulate a robust nonlinear ensemble filter for sequential data assimilation. Unlike standard machine learning methods, the proposed Ensemble Score Filter (EnSF) is completely training-free and can efficiently generate a set of analysis ensemble members. In this study, we apply the EnSF to a surface quasi-geostrophic model and compare its performance against the popular Local Ensemble Transform Kalman Filter (LETKF), which makes Gaussian assumptions in the analysis step. Numerical tests demonstrate that EnSF maintains stable performance in the absence of localization and for a variety of experimental settings. We find that while LETKF maintains optimal performance in the case of linear observations of the entire state and a perfect model, EnSF shows improvements over LETKF when nonlinear observations are assimilated and the system is subject to unexpected model errors. A spectral decomposition of the analysis results in this nonlinear observation regime shows that the largest improvements over LETKF occur at large scales (small wavenumbers) where LETKF lacks sufficient ensemble spread. Overall, this initial application of EnSF to a geophysical model of intermediate complexity motivates further developments of the algorithm for more realistic problems.



Time series of errors from each cycling experiment. Thick curves use three backgrounds per analysis cycle (3‐hourly backgrounds), and thin curves use one background per analysis cycle (6‐hourly backgrounds). (a) Root‐mean square analysis error of 500 hPa geopotential height (Z500), relative to ERA5, in the Northern Hemisphere (20–90 N). Curves end when the models become unstable. (b) Root‐mean square difference between observations and background fields interpolated to observation time and location. Average root mean squared error for the available time is given in the legend.
Instantaneous global kinetic energy spectra at 700 hPa of the background ensemble mean for each experiment. Each curve illustrates spectra from a different data assimilation cycle; lighter colors denote earlier dates in the experiment, and darker colors denote later dates. The Unified Forecast System curve from the final cycle (blue) is included in all panels for reference.
(a)–(b) As in Figure 1, but for the filtered GraphCast experiment. (c) As in Figure 2, but for the filtered GraphCast experiment.
Ensemble mean differences from perturbation experiments. Top row: Maps of Z500 ensemble mean difference. Bottom row: Vertical profiles of ensemble mean zonal mean geopotential height (Z) difference.
Assimilating Observed Surface Pressure Into ML Weather Prediction Models
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  • Full-text available

March 2025

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68 Reads

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3 Citations

There has been a recent surge in development of accurate machine learning (ML) weather prediction models, but evaluation of these models has mainly been focused on medium‐range forecasts, not their performance in cycling data assimilation (DA) systems. Cycling DA provides a statistically optimal estimate of the system state, which can then be used as initial conditions for model prediction, given observations and previous model forecasts. Here, real surface pressure observations are assimilated into several popular ML models using an ensemble Kalman filter, where accurate ensemble covariance estimation is essential to constrain unobserved state variables from sparse observations. In this cycling DA system, deterministic ML models accumulate small‐scale noise until they diverge. Mitigating this noise with a spectral filter can stabilize the system, but with larger errors than traditional models. Perturbation experiments illustrate that these models do not accurately represent short‐term error growth, leading to poor estimation of cross‐variable covariances.

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Assimilating Observed Surface Pressure into ML Weather Prediction Models

December 2024

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91 Reads

There has been a recent surge in development of accurate machine learning (ML) weather prediction models, but evaluation of these models has mainly been focused on medium-range forecasts, not their performance in cycling data assimilation (DA) systems. Cycling DA provides a statistically optimal estimate of model initial conditions, given observations and previous model forecasts. Here, real surface pressure observations are assimilated into several popular ML models using an ensemble Kalman filter, where accurate ensemble covariance estimation is essential to constrain unobserved state variables from sparse observations. In this cycling DA system, deterministic ML models accumulate small-scale noise until they diverge. Mitigating this noise with a spectral filter can stabilize the system, but with larger errors than traditional models. Perturbation experiments illustrate that these models do not accurately represent short-term error growth, leading to poor estimation of cross-variable covariances.


An Adaptive Channel Selection Method for Assimilating the Hyperspectral Infrared Radiances

January 2024

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80 Reads

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1 Citation

Hyperspectral infrared (IR) satellites can provide high-resolution vertical profiles of the atmospheric state, which significantly contributes to the forecast skill of numerical weather prediction, especially for regions with sparse observations. One challenge in assimilating the hyperspectral radiances is how to effectively extract the observation information, due to the interchannel correlations and correlated observation errors. An adaptive channel selection method is proposed, which is implemented within the data assimilation scheme and selects the radiance observation with the maximum reduction of variance in observation space. Compared to the commonly used channel selection method based on the maximum entropy reduction (ER), the adaptive method can provide flow-dependent and time-varying channel selections. The performance of the adaptive selection method is evaluated by assimilating only the synthetic Fengyun-4A ( FY-4A ) GIIRS IR radiances in an observing system simulation experiment (OSSE), with model resolutions from 7.5 to 1.5 km and then 300 m. For both clear-sky and all-sky conditions, the adaptive method generally produces smaller RMS errors of state variables than the ER-based method given similar amounts of assimilated radiances, especially with fine model resolutions. Moreover, the adaptive method has minimum RMS errors smaller than or approaching those with all channels assimilated. For the intensity of the tropical cyclone, the adaptive method also produces smaller errors of the minimum dry air mass and maximal wind speed at different levels, compared to the ER-based selection method. Significance Statement Assimilating satellite radiances has been essential for numerical weather prediction. Hyperspectral infrared satellites provide high-resolution vertical profiles for the atmospheric state and can further improve the numerical weather prediction. Due to limited computational resources, and correlated observations and associated errors, efficient and effective ways to assimilate the hyperspectral radiances are needed. An adaptive channel selection method that is incorporated with data assimilation is proposed. The adaptive channel selection can effectively extract the information from hyperspectral radiances under both clear- and all-sky conditions, with increased model resolutions from kilometers to subkilometers.



Local volume solvers for Earth system data assimilation: implementation in the framework for Joint Effort for Data Assimilation Integration

March 2023

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35 Reads

The Joint Effort for Data assimilation Integration (JEDI) is an international collaboration aimed at developing an open software ecosystem for model agnostic data assimilation. This paper considers implementation of the model-agnostic family of the local volume solvers in the JEDI framework. The implemented solvers include the Local Ensemble Transform Kalman Filter (LETKF), the Gain form Ensemble Transform Kalman Filter (GETKF), and the optimal interpolation variant of the LETKF filter (LETKF-OI). This paper documents the implementation choices and strategies that allow model agnostic implementation. We also document an expansive set of localization approaches that includes generic distance-based localization, localization based on modulated ensemble products, but also localizations specific to ocean (based on the Rossby radius of deformation), and land (based on the terrain difference between observation and model grid point). Finally, we apply the developed solvers in a limited set of experiments, including single-observation experiments in atmosphere and ocean, and cycling experiments for the ocean, land, and aerosol assimilation. We also provide a proof of concept that illustrates how JEDI Ensemble Kalman Filter solvers can be used in a strongly coupled framework providing increments to the ocean based on the combined observations from the ocean and the atmosphere.


Correcting Systematic and State‐Dependent Errors in the NOAA FV3‐GFS Using Neural Networks

October 2022

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201 Reads

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29 Citations

Weather forecasts made with imperfect models contain state‐dependent errors. Data assimilation (DA) partially corrects these errors with new information from observations. As such, the corrections, or “analysis increments,” produced by the DA process embed information about model errors. An attempt is made here to extract that information to improve numerical weather prediction. Neural networks (NNs) are trained to predict corrections to the systematic error in the National Oceanic and Atmospheric Administration's FV3‐GFS model based on a large set of analysis increments. A simple NN focusing on an atmospheric column significantly improves the estimated model error correction relative to a linear baseline. Leveraging large‐scale horizontal flow conditions using a convolutional NN, when compared to the simple column‐oriented NN, does not improve skill in correcting model error. The sensitivity of model error correction to forecast inputs is highly localized by vertical level and by meteorological variable, and the error characteristics vary across vertical levels. Once trained, the NNs are used to apply an online correction to the forecast during model integration. Improvements are evaluated both within a cycled DA system and across a collection of 10‐day forecasts. It is found that applying state‐dependent NN‐predicted corrections to the model forecast improves the overall quality of DA and improves the 10‐day forecast skill at all lead times.


The Impact of Incremental Analysis Update on Regional Simulations for Typhoons

September 2022

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179 Reads

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6 Citations

The analyses produced by intermittent data assimilation methods can be dynamically inconsistent and unbalanced. By gradually distributing the analysis increment along model integration, the incremental analysis update (IAU) is effective to combat the inconsistences and imbalances. Different implementations of IAU with time constant or time‐varying increments using different increment frequencies are systematically evaluated for regional simulations, especially for fast‐moving typhoons. Results show that experiments with IAU generally produce smaller forecast errors of temperature, specific humidity, and wind speed than experiment CTRL without initialization. Three‐dimensional IAUs (3DIAUs) with time‐constant increments have smaller errors than four‐dimensional IAUs (4DIAUs) with time‐varying increments interpolated from 3‐hr and hourly increments. Thus, for regional simulations, 3DIAU that imposes stronger filtering has advantages over 4DIAUs with different increment frequencies. For two typhoon cases, experiments with IAU obtain better intensity and structure of vortex than experiment CTRL; thus, the application of IAU can better retain the observation information and build the improved TC structure. But due to the displacement errors in priors and posteriors, the advantage of 4DIAU that considers the propagation of increment is limited compared to 3DIAU. As a trade‐off between the filtering and time‐varying increment, 4DIAU with 3‐hr increment that considers time‐varying increments compared to 3DIAU but imposes stronger filtering than 4DIAU with hourly increment could be preferred for TCs.


A Comparison of Hybrid‐Gain Versus Hybrid‐Covariance Data Assimilation for Global NWP

August 2022

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120 Reads

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2 Citations

Plain Language Summary Accurate forecasts of the earth system rely on accurate estimates of the initial state of the system, which are created by updating a model forecast with the latest observations using a technique called data assimilation. A crucial aspect of the problem is an accurate estimation of the error of the background model forecast being updated. Ensemble‐based estimates of background‐forecast error covariances are often used, but their accuracy is limited by sample size. To mitigate this, the ensemble‐based estimate is often combined with a static, or climatological estimate that is not dependent on the current model state but can be higher dimensional. Rather than blending the two error covariance estimates directly within the update (the hybrid‐covariance approach), the updates computed separately using the static and ensemble‐based covariances can be combined (the hybrid‐gain approach). The simpler and less expensive hybrid‐gain approach is shown here to perform similarly to the hybrid‐covariance approach, aside from the beneficial impact of extra dynamical balance constraints that are available in the hybrid‐covariance approach but have not yet been implemented in the hybrid‐gain system.


Citations (86)


... Both the reservoir and wave simulators support multiple options for parallelization (via multithreading and/or the Message-Passing Interface) while amortized training and multisource wave physics permit embarrassing parallelism. More importantly, our approach does not require many simulations for the dynamics and observations or unfeasible complete historical knowledge of plume evolution (Rozet & Louppe 2023 ;Bao et al. 2025 ), rendering it computationally feasible. Preliminary results, included in Fig. 12 , demonstrate our digital shadow's ability to scale to 3-D (Gahlot et al. 2025a ). ...

Reference:

An uncertainty-aware Digital Shadow for underground multimodal CO2 storage monitoring
Nonlinear ensemble filtering with diffusion models: Application to the surface quasi-geostrophic dynamics
  • Citing Article
  • May 2025

... Perhaps more importantly, the fundamental physical balances were not conserved and derived quantities were not realistically represented. Slivinski et al. (2025) identified that when used to assimilate surface pressure data, nearly all of the MLWP models produced growing errors that exploded beyond control. This is troubling because the estimation of the full 3D atmosphere from surface pressure observations was one of the great successes in data assimilation in the last two decades-enabling the reconstruction of historical weather patterns going as far back as the 1800's (Compo et al., 2011;Laloyaux et al., 2018;Slivinski et al., 2019Slivinski et al., , 2021. ...

Assimilating Observed Surface Pressure Into ML Weather Prediction Models

... While all-sky assimilation requires significantly more computational resources than clear-sky approaches, case-dependent channel selection for FY-4A GIIRS could optimize efficiency. Recent studies have shown that such selection can improve the performance of several features in high-resolution tropical cyclone simulations [51]. ...

An Adaptive Channel Selection Method for Assimilating the Hyperspectral Infrared Radiances
  • Citing Article
  • January 2024

... Similar to the Model Output Statistics (MOS) of Glahn and Lowry (1972), an alternative use of neural networks applied to weather forecasting has been to specifically map the model forecast back to a better estimate of the nature system (Bonavita & Laloyaux, 2020;Chen et al., 2022;Farchi et al., 2023Farchi et al., , 2025. This post-processing neural network attempts to learn a mapping from the known model attractor to the approximately known nature attractor in order to better agree with the observations. ...

Correcting Systematic and State‐Dependent Errors in the NOAA FV3‐GFS Using Neural Networks

... Several studies showed an improvement in the model performance for meteorological prediction by using IAU [22][23][24]. However, the impact of these improved initialization techniques on ozone predictions, especially during high ozone episodes, remains to be understood. ...

The Impact of Incremental Analysis Update on Regional Simulations for Typhoons

... The physics-based one-dimensional heat conduction equation is ubiquitous in periglacial research (Lachenbruch 1962;Nakano and Brown 1972;Kane et al. 1991;Ling and Zhang 2004) and resolves general ground temperatures with depth well. Despite the success of the heat conduction equation, the reductionist approach given by this model prevents analysis in locations with sparse data such as the Arctic since physics-based numerical models may fail in situations where the model intends to calculate a value in which numerical inputs are not directly or precisely known, or a reasonable estimate cannot be determined (Chen et al. 2022). In such cases, artificial intelligence (AI) may provide an alternative. ...

Correcting systematic and state-dependent errors in the NOAA FV3-GFS using neural networks
  • Citing Preprint
  • July 2022

... Such updates can be performed independently of each other and can scale well on modern computer architectures. The family of local volume solvers includes the Optimal Interpolation (OI) (Gandin, 1963), the Local Ensemble Transform Kalman Filter (LETKF) (Hunt et al., 2007), the Gain form of the Ensemble Transform Kalman Filter (GETKF) Lei et al., 2018), and LETKF-OI/GETKF-OI (Frolov et al., 2022) algorithms. Local volume updates are in contrast to global updates that are achieved by inverting global covariance matrices through a gradient descent algorithm employed by variational solvers (Daley, 1991). ...

Including parameterized error covariance in local ensemble solvers: Experiments in a 1D model with balance constraints

... The development of numerical weather prediction (NWP) is guided by the goal of generating forecasts with greater accuracy (Palmer [1] ; Bauer et al. [2] ; Swinbank et al. [3] ; Powers et al. [4] ; Wong et al. [5] ; Cafaro et al. [6] ; Wolff et al. [7] ). The minutely/hourly updated convection-permitting highresolution rapid refresh (HRRR) system aims to achieve this goal by swiftly assimilating a more significant number of the latest weather observations (Benjamin et al. [8] ; Bytheway et al. [9] ; Slivinski et al. [10] ). In the United States, the National Centers for Environmental Prediction (NCEP), an arm of the NOAAs National Weather Service, released the first convection-permitting HRRR version (3km grid spacing and 1-h cycling) in 2014 (https:// rapidrefresh.noaa.gov/hrrr/), ...

Overlapping Windows in a Global Hourly Data Assimilation System
  • Citing Article
  • March 2022

... As a result, they can generate forecasts for any event where observations are available, including those drawn from extended historical records, stochastic weather or streamflow generators, or climate change projections. In contrast, current hindcasting capabilities typically yield a single ensemble forecast sequence spanning only the past 30-40 years (Guan et al., 2022). Synthetic forecasts overcome this limitation by enabling plausible forecast generation across a much broader and more diverse set of hydrologic scenarios, including extreme and low-probability events. ...

GEFSv12 Reforecast Dataset for Supporting Subseasonal and Hydrometeorological Applications
  • Citing Article
  • January 2022

... This is evidenced by higher correlation coefficients and lower scatter indices. In this paper, we select NOAA's Global Ensemble Forecast System version 12 (GEFSv12) due to its high quality, derived from a combination of accurate wind forcing Hamill et al., 2022) and optimization (Gorman and Oliver, 2018) of the wave model WAVEWATCH III (WW3DG, 2019) -as described by Alves et al. (2024) and validated by Campos et al. (2024a) using 20 years of reforecast data. GEFSv12 operates with four cycles per day, at 00Z, 06Z, 12Z, and 18Z, and includes 31 members: 1 control member and 30 perturbed members. ...

The Reanalysis for the Global Ensemble Forecast System, Version 12
  • Citing Article
  • November 2021