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Abstract. Atmospheric inverse modeling describes the process of estimating greenhouse gas fluxes or air pollution emissions at the Earth's surface using observations of these gases collected in the atmosphere. The launch of new satellites, the expansion of surface observation networks, and a desire for more detailed maps of surface fluxes have yielded numerous computational and statistical challenges for standard inverse modeling frameworks that were often originally designed with much smaller data sets in mind. In this article, we discuss computationally efficient methods for large-scale atmospheric inverse modeling and focus on addressing some of the main computational and practical challenges. We develop generalized hybrid projection methods, which are iterative methods for solving large-scale inverse problems, and specifically we focus on the case of estimating surface fluxes. These algorithms confer several advantages. They are efficient, in part because they converge quickly, they exploit efficient matrix–vector multiplications, and they do not require inversion of any matrices. These methods are also robust because they can accurately reconstruct surface fluxes, they are automatic since regularization or covariance matrix parameters and stopping criteria can be determined as part of the iterative algorithm, and they are flexible because they can be paired with many different types of atmospheric models. We demonstrate the benefits of generalized hybrid methods with a case study from NASA's Orbiting Carbon Observatory 2 (OCO-2) satellite. We then address the more challenging problem of solving the inverse model when the mean of the surface fluxes is not known a priori; we do so by reformulating the problem, thereby extending the applicability of hybrid projection methods to include hierarchical priors. We further show that by exploiting mathematical relations provided by the generalized hybrid method, we can efficiently calculate an approximate posterior variance, thereby providing uncertainty information. 

In many physiological systems, real-time endogeneous and exogenous signals in living organisms provide critical information and interpretations of physiological functions; however, these signals or variables of interest are not directly accessible and must be estimated from noisy, measured signals. In this paper, we study an inverse problem of recovering gas exchange signals of animals placed in a flow-through respirometry chamber from measured gas concentrations. For large-scale experiments (e.g., long scans with high sampling rate) that have many uncertainties (e.g., noise in the observations or an unknown impulse response function), this is a computationally challenging inverse problem. We first describe various computational tools that can be used for respirometry reconstruction and uncertainty quantification when the impulse response function is known. Then, we address the more challenging problem where the impulse response function is not known or only partially known. We describe nonlinear optimization methods for reconstruction, where both the unknown model parameters and the unknown signal are reconstructed simultaneously. Numerical experiments show the benefits and potential impacts of these methods in respirometry.