Decision-Oriented Uncertainty Quantification for Risk Control in Earth System Spatiotemporal Foundation Models

Foundation models (FMs) for the Earth system learn statistical relationships between physical variables across massive datasets to enable versatile downstream applications through finetuning, separating them from task-specific weather models. Here, we introduce Earth System Foundation Model (ESFM), a fully open model building on the 3D Swin UNet backbone of the pioneering Aurora model. ESFM introduces extensions that increase functionality and foster adoption in climate sciences. First, the encoding scheme and training protocols have been extended to handle diverse datasets, including those containing missing values across all spatio-temporal dimensions such as satellite data, as well as station data, all under one backbone. Axial attention is introduced to capture inter-variable dependencies. As a result ESFM skillfully predicts variables in regions or on pressure levels where no data is present at the initial time, while preserving inter-variable relationships, for example between temperature, pressure, and humidity. Individual variable tokenization enables different sets of variables to be shuffled during training and simplifies the process of building extensions for new downstream tasks. Adaptive layer norm-based ensembles allow for a simple yet effective way to transform deterministic ESFM to a probabilistic FM. We present findings using dense gridded data (ERA5, CMIP6), regionally masked dense data, sparse gridded MODIS satellite data, and station data. Results demonstrate competitive or superior performance relative to state-of-the-art benchmarks. Case studies of Super Typhoon Doksuri (2023) and 2024 sudden stratospheric warming events show accurate positional and magnitude estimations of extreme weather. ESFM retains the strengths of previous foundation models, such as long-term stability, but facilitates application to a variety of downstream tasks.

Reliable forecasting of several interrelated environmental variables - such as regional precipitation and temperature, or other correlated geophysical fields - across many locations calls for accurate predictions accompanied by trustworthy statements of their uncertainty. Modern deep-learning models forecast such variables accurately but usually report no uncertainty, and forcing them to output uncertainty through maximum likelihood tends to degrade their accuracy, especially when the variables are strongly correlated. Motivated by this tension, we develop TSCoNet, a two-stage convolutional-recurrent model coupled with a Gaussian copula that jointly forecasts multiple variables over space and time while quantifying predictive uncertainty. The method first learns accurate mean forecasts and then, holding the mean fixed, refines a shared representation to estimate the predictive variance, yielding calibrated prediction intervals after a standard recalibration, so that uncertainty is added without sacrificing point accuracy. We study the approach on simulated non-stationary spatial fields on the sphere and on a real dataset of monthly precipitation and temperature for fifty cities over 2000-2020. The model matches the accuracy of a strong deterministic forecaster while supplying calibrated prediction intervals that the deterministic model cannot, giving a single tool that provides both accurate point forecasts and reliable uncertainty for multivariate spatio-temporal data.

Deep learning weather models now match numerical weather prediction accuracy while running orders of magnitude faster, but produce deterministic forecasts without uncertainty estimates, a critical gap for high-stakes decisions during extreme weather events. This paper proposes Neural Tangent Kernel-based uncertainty quantification (NTK-UQ) using last-layer empirical features. Theoretical analysis predicts that UQ quality is architecture-dependent through two mechanisms. First, a variance collapse mechanism explains when UQ fails: when the eigenvalue truncation rank approaches the effective rank of the feature space, the GP correction term consumes nearly all prior variance, destroying discrimination between tropical cyclones and routine conditions; architectures with concentrated spectra (spectral operators) require aggressive truncation ($k \leq 10$), while attention-based models tolerate full-rank computation. Second, decomposition performance depends on the non-Gaussian, heavy-tailed structure of extreme weather: Independent Component Analysis exploits higher-order statistics (kurtosis, negentropy) to isolate heavy-tailed extreme-event features, achieving higher discrimination than singular value decomposition, which captures only second-order variance. A data-driven selection rule chooses ICA or SVD from the feature eigenspectrum concentration ratio, correctly prescribing the superior decomposition for all four evaluated architectures. Compared to split conformal prediction (the natural post-hoc baseline), NTK-UQ achieves 31--37% sharper prediction intervals at 90% coverage, and uniquely produces \emph{adaptive} intervals that scale with extreme event severity, which conformal prediction cannot achieve by construction. The framework requires no retraining; inference-time uncertainty requires only a single matrix-vector product per sample.