Patch-Based Deep Kernel Learning for Data Assimilation and Bias Correction with Extremely Sparse Observations
Emanuele Mele, Angelo Coluccia, Massimo Cafaro, Italo Epicoco, Paola Nassisi
Abstract
Data Assimilation (DA) reconstructs the state of a spatio-temporal system by combining sensor observations with the output of a numerical model. Since model states are high-dimensional while observations cover only a small fraction of the domain, DA is a challenging large-scale estimation problem, central to weather forecasting and oceanography. Classical variational methods such as 3D-Var rely on a hand-crafted background error covariance that assumes unbiased errors, and therefore cannot capture state-dependent correlations or systematic model biases. Moreover, their cost grows with the size of the domain. Deep learning (DL) methods can perform DA and bias correction (BC) non-linearly, but typically offer limited interpretability and no calibrated uncertainty estimates. We propose a hybrid framework that couples a convolutional neural network (CNN) with a learnable-kernel Gaussian Process (GP) to jointly perform DA and BC from extremely sparse observations. The model is trained end-to-end by maximizing the marginal log-likelihood, learns a data-driven covariance over the whole grid, and provides both the Maximum A Posteriori analysis and its uncertainty by design. A patch-based strategy reduces the $O(N^3)$ training cost of exact GPs over $N$ grid points to $O(N)$ for a fixed patch size. Inference remains exact and only requires solving a linear system whose $O(m^3)$ cost depends on the number of observations $m \ll N$, not on the domain. The learned covariance can also replace the hand-crafted one in 3D-Var, improving its accuracy without changing the variational formulation. Experiments on sea surface temperature and salinity, with both synthetic and real, extremely sparse in-situ observations, show that the framework outperforms 3D-Var, a classical GP and a competing DL model, while reducing inference time by more than 98% with respect to 3D-Var.