@conference {orozco2022SPIEadjoint,
	title = {Adjoint operators enable fast and amortized machine learning based Bayesian uncertainty quantification},
	booktitle = {SPIE Medical Imaging Conference},
	year = {2023},
	note = {(SPIE, San Diego)},
	month = {02},
	abstract = {Machine learning algorithms such as Normalizing Flows, VAEs, and GANs are powerful tools in Bayesian uncertainty quantification (UQ) of inverse problems. Unfortunately, when using these algorithms medical imaging practitioners are faced with the challenging task of manually defining neural networks that can handle complicated inputs such as acoustic data. This task needs to be replicated for different receiver types or configurations since these change the dimensionality of the input. We propose to first transform the data using the adjoint operator {\textemdash}ex: time reversal in photoacoustic imaging (PAI) or back-projection in computer tomography (CT) imaging {\textemdash} then continue posterior inference using the adjoint data as an input now that it has been standardized to the size of the unknown model. This adjoint preprocessing technique has been used in previous works but with minimal discussion on if it is biased. In this work, we prove that conditioning on adjoint data is unbiased for a certain class of inverse problems. We then demonstrate with two medical imaging examples (PAI and CT) that adjoints enable two things: Firstly, adjoints partially undo the physics of the forward operator resulting in faster convergence of an ML based Bayesian UQ technique. Secondly, the algorithm is now robust to changes in the observed data caused by differing transducer subsampling in PAI and number of angles in CT. Our adjoint-based Bayesian inference method results in point estimates that are faster to compute than traditional baselines and show higher SSIM metrics, while also providing validated UQ.},
	keywords = {Amortized Inference, Bayesian inference, deep learning, Inverse problems, machine learning, medical imaging, Normalizing flows, SPIE, Uncertainty quantification},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/SPIE/2023/orozco2022SPIEadjoint/SPIE_2022_adjoint.html},
	author = {Rafael Orozco and Ali Siahkoohi and Gabrio Rizzuti and Tristan van Leeuwen and Felix J. Herrmann}
}
@article {louboutin2023lmi,
	title = {Learned multiphysics inversion with differentiable programming and machine learning},
	journal = {The Leading Edge},
	volume = {42},
	year = {2023},
	note = {(The Leading Edge)},
	month = {07},
	pages = {452-516},
	abstract = {We present the Seismic Laboratory for Imaging and Modeling/Monitoring (SLIM) open-source software framework for computational geophysics and, more generally, inverse problems involving the wave-equation (e.g., seismic and medical ultrasound), regularization with learned priors, and learned neural surrogates for multiphase flow simulations. By integrating multiple layers of abstraction, our software is designed to be both readable and scalable. This allows researchers to easily formulate their problems in an abstract fashion while exploiting the latest developments in high-performance computing. We illustrate and demonstrate our design principles and their benefits by means of building a scalable prototype for permeability inversion from time-lapse crosswell seismic data, which aside from coupling of wave physics and multiphase flow, involves machine learning.},
	keywords = {CCS, deep learning, Fourier neural operators, GCS, Imaging, inversion, invertible networks, machine learning, monitoring, multiphysics, Normalizing flows, SLIM, software, time-lapse},
	url = {https://library.seg.org/doi/10.1190/tle42070474.1},
	presentation = {https://slim.gatech.edu/Publications/Public/Journals/TheLeadingEdge/2023/louboutin2023lmi/le_software.pdf},
	url2 = {https://slim.gatech.edu/Publications/Public/Journals/TheLeadingEdge/2023/louboutin2023lmi/le_software.html},
	author = {Mathias Louboutin and Ziyi Yin and Rafael Orozco and Thomas J. Grady II and Ali Siahkoohi and Gabrio Rizzuti and Philipp A. Witte and Olav M{\o}yner and Gerard J. Gorman and Felix J. Herrmann}
}
@conference {louboutin2022RHPCafa,
	title = {Abstractions for at-scale seismic inversion},
	booktitle = {Rice Oil and Gas High Performance Computing Conference 2022},
	year = {2022},
	note = {Rice Oil and Gas High Performance Computing Conference 2022},
	month = {03},
	pages = {Thursday Workshop: Devito Training and Hackathon},
	abstract = {We present the SLIM open-source software framework for computational geophysics, and more generally, inverse problems based on the wave-equation (e.g., medical ultrasound). We developed a software environment aimed at scalable research and development by designing multiple layers of abstractions. This environment allows the researchers to easily formulate their problem in an abstract fashion, while still being able to exploit the latest developments in high-performance computing. We illustrate and demonstrate the benefits of our software design on many geophysical applications, including seismic inversion and physics-informed machine learning for geophysics (e.g., loop unrolled imaging, uncertainty quantification), all while facilitating the integration of external software.},
	keywords = {CCS, devito, FWI, HPC, inversion, JUDI, machine learning, RHPC, software, Uncertainty quantification},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/RHPC/2022/louboutin2022RHPCafa/RiceHPC22.pdf},
	url2 = {https://youtu.be/scRTbP8w6Wk?t=4542},
	author = {Mathias Louboutin and Ali Siahkoohi and Ziyi Yin and Rafael Orozco and Thomas J. Grady II and Yijun Zhang and Philipp A. Witte and Gabrio Rizzuti and Felix J. Herrmann}
}
@conference {louboutin2022SEGais,
	title = {Accelerating innovation with software abstractions for scalable computational geophysics},
	booktitle = {International Meeting for Applied Geoscience and Energy Expanded Abstracts},
	year = {2022},
	note = {(IMAGE, Houston)},
	month = {05},
	abstract = {We present the SLIM open-source software framework for computational geophysics, and more generally, inverse problems based on the wave-equation (e.g., medical ultrasound). We developed a software environment aimed at scalable research and development by designing multiple layers of abstractions. This environment allows the researchers to easily formulate their problem in an abstract fashion, while still being able to exploit the latest developments in high-performance computing. We illustrate and demonstrate the benefits of our software design on many geophysical applications, including seismic inversion and physics-informed machine learning for geophysics(e.g., loop unrolled imaging, uncertainty quantification), all while facilitating the integration of external software.},
	keywords = {CCS, devito, FWI, HPC, inversion, JUDI, machine learning, SEG, software, Uncertainty quantification},
	doi = {10.1190/image2022-3750561.1},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2022/louboutin2022SEGais/louboutin_seg22.html},
	presentation = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2022/louboutin2022SEGais/index.html},
	author = {Mathias Louboutin and Philipp A. Witte and Ali Siahkoohi and Gabrio Rizzuti and Ziyi Yin and Rafael Orozco and Felix J. Herrmann}
}
@presentation {orozco2022ML4SEISMICaos,
	title = {Adjoint operators as summary functions in amortized Bayesian inference frameworks},
	year = {2022},
	month = {11},
	abstract = {An important concern in seismic inverse problems is the large and varying size of observed data. The large size can cause computational cost concerns and its varying size (such as when changing receiver geometries) implies the need to rerun inference algorithms from scratch for each new observation. Motivated by these two problems, we take inspiration from the statistics literature which commonly relies on summary statistic of observed data. Summary statistic compress the observed data leaving only information needed for inference. In this work, we argue that the adjoint operator provides a natural candidate for a summary function in the context of physics-based inverse problems. We first mathematically show that for certain general assumptions transforming data under the adjoint operator defines a new conditional distribution which preserves the expectations of the original posterior. We validate our hypothesis by evaluating our framework in a learned amortized inference algorithm. Our seismic and medical synthetic experiments show computational gains and increased quality of point estimates using our framework. We discuss statistical metrics that show our learned posterior is well calibrated therefore justifying its use in uncertainty quantification.},
	keywords = {Amortized Inference, Bayesian inference, deep learning, Inverse problems, machine learning, medical imaging, ML4SEISMIC, Normalizing flows, SLIM, Uncertainty quantification},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/ML4SEISMIC/2022/orozco2022ML4SEISMICaos/index.html},
	author = {Rafael Orozco and Mathias Louboutin and Ali Siahkoohi and Gabrio Rizzuti and Felix J. Herrmann}
}
@presentation {yin2022TRANSFORMjulia,
	title = {Julia for Geoscience},
	year = {2022},
	month = {04},
	abstract = {In this tutorial, we will introduce the Julia programming language to the geoscience community, covering topics such as I/O, data processing, inversion, and machine learning. We will begin by installing Julia and relevant packages. Through a series of tutorials, we will demonstrate Julia{\textquoteright}s abstraction power and show how to load and plot data, write your own functions/operators, form and solve a geophysical inverse problem, and demonstrate how to integrate wave-equation solvers in Julia with machine learning frameworks. The intent of this presentation is to provide an introductory level tutorial that will be useful to members of the geoscience community.},
	keywords = {JOLI, JUDI, Julia, machine learning, SLIM, software, TRANSFORM},
	url = {https://transform.softwareunderground.org/2022-julia-for-geoscience},
	url2 = {https://www.youtube.com/watch?v=HyWfp3NzIbg},
	software = {https://github.com/slimgroup/SLIMTutorials},
	author = {Ziyi Yin and Mathias Louboutin and Philipp A. Witte and Ali Siahkoohi and Gabrio Rizzuti and Rafael Orozco and Henryk Modzelewski and Felix J. Herrmann}
}
@presentation {siahkoohi2021ML4SEISMICuqi,
	title = {Uncertainty quantification in imaging and automatic horizon tracking{\textemdash}a Bayesian deep-prior based approach},
	year = {2021},
	month = {11},
	abstract = {In inverse problems, uncertainty quantification (UQ) deals with a probabilistic description of the solution nonuniqueness and data noise sensitivity. Setting seismic imaging into a Bayesian framework allows for a principled way of studying uncertainty by solving for the model posterior distribution. Imaging, however, typically constitutes only the first stage of a sequential workflow, and UQ becomes even more relevant when applied to subsequent tasks that are highly sensitive to the inversion outcome. In this paper, we focus on how UQ trickles down to horizon tracking for the determination of stratigraphic models and investigate its sensitivity with respect to the imaging result. As such, the main contribution of this work consists in a data-guided approach to horizon tracking uncertainty analysis. This work is fundamentally based on a special reparameterization of reflectivity, known as {\textquotedblleft}deep prior{\textquotedblright}. Feasible models are restricted to the output of a convolutional neural network with a fixed input, while weights and biases are Gaussian random variables. Given a deep prior model, the network parameters are sampled from the posterior distribution via a Markov chain Monte Carlo method, from which the conditional mean and point-wise standard deviation of the inferred reflectivities are approximated. For each sample of the posterior distribution, a reflectivity is generated, and the horizons are tracked automatically. In this way, uncertainty on model parameters naturally translates to horizon tracking. As part of the validation for the proposed approach, we verified that the estimated confidence intervals for the horizon tracking coincide with geologically complex regions, such as faults.},
	keywords = {horizon picking, Imaging, machine learning, ML4SEISMIC, SLIM, Uncertainty quantification},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/ML4SEISMIC/2021/siahkoohi2021ML4SEISMICuqi/Mon-11-20-Siahkoohi.pdf},
	author = {Ali Siahkoohi and Gabrio Rizzuti and Felix J. Herrmann}
}
@conference {siahkoohi2020SEGuqi,
	title = {Uncertainty quantification in imaging and automatic horizon tracking{\textemdash}a Bayesian deep-prior based approach},
	booktitle = {SEG Technical Program Expanded Abstracts},
	year = {2020},
	note = {(SEG, virtual)},
	month = {09},
	pages = {1636-1640},
	abstract = {In inverse problems, uncertainty quantification (UQ) deals with a probabilistic description of the solution nonuniqueness and data noise sensitivity. Setting seismic imaging into a Bayesian framework allows for a principled way of studying uncertainty by solving for the model posterior distribution. Imaging, however, typically constitutes only the first stage of a sequential workflow, and UQ becomes even more relevant when applied to subsequent tasks that are highly sensitive to the inversion outcome. In this paper, we focus on how UQ trickles down to horizon tracking for the determination of stratigraphic models and investigate its sensitivity with respect to the imaging result. As such, the main contribution of this work consists in a data-guided approach to horizon tracking uncertainty analysis. This work is fundamentally based on a special reparameterization of reflectivity, known as "deep prior". Feasible models are restricted to the output of a convolutional neural network with a fixed input, while weights and biases are Gaussian random variables. Given a deep prior model, the network parameters are sampled from the posterior distribution via a Markov chain Monte Carlo method, from which the conditional mean and point-wise standard deviation of the inferred reflectivities are approximated. For each sample of the posterior distribution, a reflectivity is generated, and the horizons are tracked automatically. In this way, uncertainty on model parameters naturally translates to horizon tracking. As part of the validation for the proposed approach, we verified that the estimated confidence intervals for the horizon tracking coincide with geologically complex regions, such as faults.},
	keywords = {horizon picking, Imaging, machine learning, SEG, Uncertainty quantification},
	doi = {10.1190/segam2020-3417560.1},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2020/siahkoohi2020SEGuqi/siahkoohi2020SEGuqi.html},
	presentation = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2020/siahkoohi2020SEGuqi/siahkoohi2020SEGuqi_pres.pdf},
	url2 = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2020/siahkoohi2020SEGuqi/siahkoohi2020SEGuqi_pres.mp4},
	software = {https://github.com/slimgroup/Software.SEG2020},
	author = {Ali Siahkoohi and Gabrio Rizzuti and Felix J. Herrmann}
}
@conference {siahkoohi2020SEGwdp,
	title = {Weak deep priors for seismic imaging},
	booktitle = {SEG Technical Program Expanded Abstracts},
	year = {2020},
	note = {(SEG, virtual)},
	month = {09},
	pages = {2998-3002},
	abstract = {Incorporating prior knowledge on model unknowns of interest is essential when dealing with ill-posed inverse problems due to the nonuniqueness of the solution and data noise. Unfortunately, it is not trivial to fully describe our priors in a convenient and analytical way. Parameterizing the unknowns with a convolutional neural network (CNN), and assuming an uninformative Gaussian prior on its weights, leads to a variational prior on the output space that favors "natural" images and excludes noisy artifacts, as long as overfitting is prevented. This is the so-called deep-prior approach. In seismic imaging, however, evaluating the forward operator is computationally expensive, and training a randomly initialized CNN becomes infeasible. We propose, instead, a weak version of deep priors, which consists of relaxing the requirement that reflectivity models must lie in the network range, and letting the unknowns deviate from the network output according to a Gaussian distribution. Finally, we jointly solve for the reflectivity model and CNN weights. The chief advantage of this approach is that the updates for the CNN weights do not involve the modeling operator, and become relatively cheap. Our synthetic numerical experiments demonstrate that the weak deep prior is more robust with respect to noise than conventional least-squares imaging approaches, with roughly twice the computational cost of reverse-time migration, which is the affordable computational budget in large-scale imaging problems.},
	keywords = {deep prior, machine learning, SEG, seismic imaging},
	doi = {10.1190/segam2020-3417568.1},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2020/siahkoohi2020SEGwdp/siahkoohi2020SEGwdp.html},
	presentation = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2020/siahkoohi2020SEGwdp/siahkoohi2020SEGwdp_pres.pdf},
	url2 = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2020/siahkoohi2020SEGwdp/siahkoohi2020SEGwdp_pres.mp4},
	software = {https://github.com/slimgroup/Software.SEG2020},
	author = {Ali Siahkoohi and Gabrio Rizzuti and Felix J. Herrmann}
}
@conference {rizzuti2019EAGElis,
	title = {Learned iterative solvers for the Helmholtz equation},
	booktitle = {EAGE Annual Conference Proceedings},
	year = {2019},
	note = {(EAGE, Copenhagen)},
	month = {06},
	abstract = {We propose a {\textquoteleft}learned{\textquoteright} iterative solver for the Helmholtz equation, by combining traditional Krylov-based solvers with machine learning. The method is, in principle, able to circumvent the shortcomings of classical iterative solvers, and has clear advantages over purely data-driven ap- proaches. We demonstrate the effectiveness of this approach under a 1.5-D assumption, when ade- quate a priori information about the velocity distribution is known.},
	keywords = {EAGE, Helmholtz, Iterative, machine learning},
	doi = {10.3997/2214-4609.201901542},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/EAGE/2019/rizzuti2019EAGElis/rizzuti2019EAGElis.pdf},
	presentation = {https://slim.gatech.edu/Publications/Public/Conferences/EAGE/2019/rizzuti2019EAGElis/rizzuti2019EAGElis_pres.pdf},
	author = {Gabrio Rizzuti and Ali Siahkoohi and Felix J. Herrmann}
}
