We consider an inverse problem involving the reconstruction of the solution to a nonlinear partial differential equation (PDE) with unknown boundary conditions. Instead of direct boundary data, we are provided with a large dataset of boundary observations for typical solutions (collective data) and a bulk measurement of a specific realization. To leverage this collective data, we first compress the boundary data using proper orthogonal decomposition (POD) in a linear expansion. Next, we identify a possible nonlinear low-dimensional structure in the expansion coefficients using an auto-encoder, which provides a parametrization of the dataset in a lower-dimensional latent space. We then train a neural network to map the latent variables representing the boundary data to the solution of the PDE. Finally, we solve the inverse problem by optimizing a data-fitting term over the latent space. We analyze the underlying stabilized finite element method in the linear setting and establish optimal error estimates in the $H^1$ and $L^2$-norms. The nonlinear problem is then studied numerically, demonstrating the effectiveness of our approach.
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