@article {orozco2024IPaspire,
	title = {ASPIRE: Iterative Amortized Posterior Inference for Bayesian Inverse Problems},
	journal = {Inverse Problems},
	volume = {41},
	year = {2025},
	note = {(Inverse Problems)},
	month = {3},
	abstract = {Due to their uncertainty quantification, Bayesian solutions to inverse problems are the framework of choice in applications that are risk averse. These benefits come at the cost of computations that are in general, intractable. New advances in machine learning and variational inference (VI) have lowered the computational barrier by learning from examples. Two VI paradigms have emerged that represent different tradeoffs: amortized and non-amortized. Amortized VI can produce fast results but due to generalizing to many observed datasets it produces suboptimal inference results. Non-amortized VI is slower at inference but finds better posterior approximations since it is specialized towards a single observed dataset. Current amortized VI techniques run into a sub-optimality wall that can not be improved without more expressive neural networks or extra training data. We present a solution that enables iterative improvement of amortized posteriors that uses the same networks architectures and training data. The benefits of our method requires extra computations but these remain frugal since they are based on physics-hybrid methods and summary statistics. Importantly, these computations remain mostly offline thus our method maintains cheap and reusable online evaluation while bridging the approximation gap these two paradigms. We denote our proposed method ASPIRE - Amortized posteriors with Summaries that are Physics-based and Iteratively REfined. We first validate our method on a stylized problem with a known posterior then demonstrate its practical use on a high-dimensional and nonlinear transcranial medical imaging problem with ultrasound. Compared with the baseline and previous methods from the literature our method stands out as an computationally efficient and high-fidelity method for posterior inference.},
	keywords = {Amortization Gap, Amortized Variational Inference, Bayesian inference, medical imaging, Normalizing flows, simulation-based inference},
	doi = {10.1088/1361-6420/adba3d},
	url = {https://doi.org/10.1088/1361-6420/adba3d},
	author = {Rafael Orozco and Ali Siahkoohi and Mathias Louboutin and Felix J. Herrmann}
}
@article {daskalakis2019SIAMJISasr,
	title = {Accelerating Sparse Recovery by Reducing Chatter},
	journal = {SIAM Journal on Imaging Sciences},
	volume = {13},
	number = {3},
	year = {2020},
	note = {(SIAM Journal on Imaging Sciences)},
	month = {07},
	pages = {1211{\textendash}1239},
	abstract = {Compressive Sensing has driven a resurgence of sparse recovery algorithms with l_1-norm minimization. While these minimizations are relatively well understood for small underdetermined, possibly inconsistent systems, their behavior for large over-determined and inconsistent systems has received much less attention. Specifically, we focus on large systems where computational restrictions call for algorithms that use randomized subsets of rows that are touched a limited number of times. In that regime, l_1-norm minimization algorithms exhibit unwanted fluctuations near the desired solution, and the Linear Bregman iterations are no exception. We explain this observed lack of performance in terms of chatter, a well-known phenomena observed in non-smooth dynamical systems, where intermediate solutions wander between different states stifling convergence. By identifying chatter as the culprit, we modify the Bregman iterations with chatter reducing adaptive element-wise step lengths in combination with potential support detection via threshold crossing. We demonstrate the performance of our algorithm on carefully selected stylized examples and a realistic seismic imaging problem involving millions of unknowns and matrix-free matrix-vector products that involve expensive wave-equation solves.},
	keywords = {chatter, inconsistent linear systems, Kacmarz, linearized Bregman dynamical systems, non-smooth dynamics, sparsity promotion},
	doi = {10.1137/19M129111X},
	url = {https://slim.gatech.edu/Publications/Public/Journals/SIAMJournalOnImagingSciences/2020/daskalakis2019SIAMJISasr/daskalakis2019SIAMJISasr.pdf},
	author = {Emmanouil Daskalakis and Felix J. Herrmann and Rachel Kuske}
}
@article {luporini2018aap,
	title = {Architecture and performance of Devito, a system for automated stencil computation},
	journal = {ACM Trans. Math. Softw.},
	volume = {46},
	number = {1},
	year = {2020},
	note = {(ACM Trans. Math. Softw.)},
	month = {04},
	abstract = {Stencil computations are a key part of many high-performance computing applications, such as image processing, convolutional neural networks, and finite-difference solvers for partial differential equations. Devito is a framework capable of generating highly-optimized code given symbolic equations expressed in Python, specialized in, but not limited to, affine (stencil) codes. The lowering process {\textendash} from mathematical equations down to C++ code {\textendash} is performed by the Devito compiler through a series of intermediate representations. Several performance optimizations are introduced, including advanced common sub-expressions elimination, tiling and parallelization. Some of these are obtained through well-established stencil optimizers, integrated in the back-end of the Devito compiler. The architecture of the Devito compiler, as well as the performance optimizations that are applied when generating code, are presented. The effectiveness of such performance optimizations is demonstrated using operators drawn from seismic imaging applications.},
	keywords = {compiler, finite difference method, performance optimization, stencil, structured grid, symbolic processing},
	doi = {10.1145/3374916},
	url = {https://slim.gatech.edu/Publications/Public/Journals/ACMTOMS/2020/luporini2018aap/luporini2018aap.pdf},
	author = {Fabio Luporini and Mathias Louboutin and Michael Lange and Navjot Kukreja and Philipp A. Witte and Jan H{\"u}ckelheim and Charles Yount and Paul H. J. Kelly and Felix J. Herrmann and Gerard J. Gorman}
}
@article {peters2019aos,
	title = {Algorithms and software for projections onto intersections of convex and non-convex sets with applications to inverse problems},
	journal = {arXiv e-prints},
	year = {2019},
	note = {(arXiv)},
	month = {03},
	abstract = {We propose algorithms and software for computing projections onto the intersection of multiple convex and non-convex constraint sets. The software package, called SetIntersectionProjection, is intended for the regularization of inverse problems in physical parameter estimation and image processing. The primary design criterion is working with multiple sets, which allows us to solve inverse problems with multiple pieces of prior knowledge. Our algorithms outperform the well known Dykstra{\textquoteright}s algorithm when individual sets are not easy to project onto because we exploit similarities between constraint sets. Other design choices that make the software fast and practical to use, include recently developed automatic selection methods for auxiliary algorithm parameters, fine and coarse grained parallelism, and a multilevel acceleration scheme. We provide implementation details and examples that show how the software can be used to regularize inverse problems. Results show that we benefit from working with all available prior information and are not limited to one or two regularizers because of algorithmic, computational, or hyper-parameter selection issues.},
	keywords = {algorithm, software},
	url = {http://arxiv.org/abs/1902.09699},
	author = {Bas Peters and Felix J. Herrmann}
}
@article {silva2018alr,
	title = {Applications of low-rank compressed seismic data to full waveform inversion and extended image volumes},
	journal = {Geophysics},
	year = {2019},
	note = {Accepted on January 22, 2019.},
	abstract = {Conventional oil and gas fields are increasingly difficult to explore and image, resulting in the call for more complex wave-equation based inversion algorithms that require dense long-offset samplings. Consequently, there is an exponential growth in the size of data volumes and prohibitive demands on computational resources. In this work, we propose a method to compress and process seismic data directly in a low-rank tensor format, which drastically reduces the amount of storage required to represent the data. We first outline how seismic data exhibits low-rank structure in a particular transform-domain, which can be exploited to compress the dense data in one extremely storage-efficient tensor format when the data is fully sampled. In the more realistic case of missing data, we can use efficient interpolation techniques to approximate the fully sampled volume in compressed form. In either case, once we have our data represented in its compressed tensor form, we design an algorithm to extract source or receiver gathers directly from the compressed parameters. This extraction process can be done on-the-fly directly on the compressed data, in a full waveform inversion context, and does not require scanning through the entire dataset in order to form shot gathers. To the best of our knowledge, this work is one of the first major contributions to working with seismic data applications directly in the compressed domain without reconstructing the entire data volume. We use a stochastic inversion approach, which works with small subsets of source experiments at each iteration, further reducing the computational and memory costs of full waveform inversion. We also demonstrate how this data compression and extraction technique can be applied to forming full subsurface image gathers through probing techniques.},
	keywords = {common shot/receiver gather, extended image volume, full waveform inversion, low rank, tensor},
	doi = {10.1190/geo2018-0116.1},
	url = {https://slim.gatech.edu/Publications/Public/Journals/Geophysics/2019/silva2018alr/silva2018alr.pdf},
	author = {Curt Da Silva and Yiming Zhang and Rajiv Kumar and Felix J. Herrmann}
}
@article {shahidi2013GPars,
	title = {Application of randomized sampling schemes to curvelet-based sparsity-promoting seismic data recovery},
	journal = {Geophysical Prospecting},
	volume = {61},
	number = {5},
	year = {2013},
	month = {09},
	pages = {973-997},
	abstract = {Reconstruction of seismic data is routinely used to improve the quality and resolution of seismic data from incomplete acquired seismic recordings. Curvelet-based Recovery by Sparsity-promoting Inversion, adapted from the recently-developed theory of compressive sensing, is one such kind of reconstruction, especially good for recovery of undersampled seismic data. Like traditional Fourier-based methods, it performs best when used in conjunction with randomized subsampling, which converts aliases from the usual regular periodic subsampling into easy-to-eliminate noise. By virtue of its ability to control gap size, along with the random and irregular nature of its sampling pattern, jittered (sub)sampling is one proven method that has been used successfully for the determination of geophone positions along a seismic line. In this paper, we extend jittered sampling to two-dimensional acquisition design, a more difficult problem, with both underlying Cartesian, and hexagonal grids. We also study what we term separable and non-separable two-dimensional jittered samplings. We find hexagonal jittered sampling performs better than Cartesian jittered sampling, while fully non-separable jittered sampling performs better than separable jittered sampling. Two other 2D randomized sampling methods, Poisson Disk sampling and Farthest Point sampling, both known to possess blue-noise spectra, are also shown to perform well.},
	keywords = {curvelets, Geophysical Prospecting, randomized sampling},
	doi = {10.1111/1365-2478.12050},
	url = {https://slim.gatech.edu/Publications/Public/Journals/GeophysicalProspecting/2013/shahidi2013GPars/shahidi2013GPars.pdf},
	author = {Reza Shahidi and Gang Tang and Jianwei Ma and Felix J. Herrmann}
}
@article {herrmann2008GEOPacd,
	title = {Adaptive curvelet-domain primary-multiple separation},
	journal = {Geophysics},
	volume = {73},
	number = {3},
	year = {2008},
	month = {08},
	pages = {A17-A21},
	publisher = {SEG},
	abstract = {In many exploration areas, successful separation of primaries and multiples greatly determines the quality of seismic imaging. Despite major advances made by surface-related multiple elimination (SRME), amplitude errors in the predicted multiples remain a problem. When these errors vary for each type of multiple in different ways (as a function of offset, time, and dip), they pose a serious challenge for conventional least-squares matching and for the recently introduced separation by curvelet-domain thresholding. We propose a data-adaptive method that corrects amplitude errors, which vary smoothly as a function of location, scale (frequency band), and angle. With this method, the amplitudes can be corrected by an elementwise curvelet-domain scaling of the predicted multiples. We show that this scaling leads to successful estimation of primaries, despite amplitude, sign, timing, and phase errors in the predicted multiples. Our results on synthetic and real data show distinct improvements over conventional least-squares matching in terms of better suppression of multiple energy and high-frequency clutter and better recovery of estimated primaries. \copyright2008 Society of Exploration Geophysicists},
	keywords = {Geophysics, Processing, SLIM},
	doi = {10.1190/1.2904986},
	url = {https://slim.gatech.edu/Publications/Public/Journals/Geophysics/2008/herrmann08GEOacd/herrmann08GEOacd.pdf},
	author = {Felix J. Herrmann and Deli Wang and D. J. Verschuur}
}
