@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}
}
@conference {orozco2023MIDLanf,
	title = {Amortized normalizing flows for transcranial ultrasound with uncertainty quantification},
	booktitle = {Medical Imaging with Deep Learning},
	year = {2023},
	note = {(MIDL, Nashville)},
	month = {07},
	abstract = {We present a novel approach to transcranial ultrasound computed tomography that utilizes normalizing flows to improve the speed of imaging and provide Bayesian uncertainty quantification. Our method combines physics-informed methods and data-driven methods to accelerate the reconstruction of the final image. We make use of a physics-informed summary statistic to incorporate the known ultrasound physics with the goal of compressing large incoming observations. This compression enables efficient training of the normalizing flow and standardizes the size of the data regardless of imaging configurations. The combinations of these methods results in fast uncertainty-aware image reconstruction that generalizes to a variety of transducer configurations. We evaluate our approach with in silico experiments and demonstrate that it can significantly improve the imaging speed while quantifying uncertainty. We validate the quality of our image reconstructions by comparing against the traditional physics-only method and also verify that our provided uncertainty is calibrated with the error.},
	keywords = {Bayesian Estimation, invertible networks, medical imaging, MIDL, Physics and Machine Learning Hybrid, Uncertainty quantification},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/MIDL/2023/orozco2023MIDLanf/paper.pdf},
	author = {Rafael Orozco and Mathias Louboutin and Ali Siahkoohi and Gabrio Rizzuti and Tristan van Leeuwen and Felix J. Herrmann}
}
@conference {vanleeuwen2015EAGEafs,
	title = {Affordable full subsurface image volume{\textendash}-an application to WEMVA},
	booktitle = {EAGE Annual Conference Proceedings},
	year = {2015},
	note = {(EAGE Workshop on Wave Equation based Migration Velocity Analysis, Madrid)},
	month = {06},
	abstract = {Common image gathers are used in building velocity models, inverting for anisotropy parameters, and analyzing reservoir attributes. In this paper, we offer a new perspective on image gathers, where we glean information from the image volume via efficient matrix-vector products. The proposed formulation make the computation of full subsurface image volume feasible. We illustrate how this matrix-vector product can be used to construct objective functions for automatic MVA.},
	keywords = {EAGE, MVA, randomized trace estimation, wave-equation},
	doi = {10.3997/2214-4609.201413498},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/EAGE/2015/vanleeuwen2015EAGEafs/vanleeuwen2015EAGEafs.pdf},
	presentation = {https://slim.gatech.edu/Publications/Public/Conferences/EAGE/2015/vanleeuwen2015EAGEafs/vanleeuwen2015EAGEafs_pres.pdf},
	author = {Tristan van Leeuwen and Rajiv Kumar and Felix J. Herrmann}
}
@presentation {kumar2015SINBADFaoi,
	title = {Affordable omnidirectional image volumes extension to 3D},
	year = {2015},
	publisher = {SINBAD},
	abstract = {Image gathers are an important tool for velocity analysis, AVA analysis and targeted imaging, however, the computational cost involving in forming the image volumes makes them prohibitively expensive in case of large scale 3D seismic data acquisition. In this work, we propose the extension of our probing techniques from 2D to 3D to form the extended image volumes efficiently. We show the efficacy of proposed formulation on synthetic data set.},
	keywords = {Presentation, SINBAD, SINBADFALL2015, SLIM},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/SINBAD/2015/Fall/kumar2015SINBADFaoi/kumar2015SINBADFaoi.pdf},
	url2 = {https://slim.gatech.edu/Publications/Public/Conferences/SINBAD/2015/Fall/kumar2015SINBADFaoi/kumar2015SINBADFaoi.mov},
	author = {Rajiv Kumar and Tristan van Leeuwen and Felix J. Herrmann}
}
@conference {esser2015SEGasd,
	title = {Automatic salt delineation {\textendash}- Wavefield Reconstruction Inversion with convex constraints},
	booktitle = {SEG Technical Program Expanded Abstracts},
	year = {2015},
	note = {(SEG, New Orleans)},
	month = {10},
	pages = {1337-1343},
	abstract = {We extend full-waveform inversion by Wavefield Reconstruction Inversion by including convex constraints on the model. Contrary to the conventional adjoint-state formulations, Wavefield Reconstruction Inversion has the advantage that the Gauss-Newton Hessian is well approximated by a diagonal scaling, which allows us to add convex constraints, such as the box- and the edge-preserving total-variation constraint, on the square slowness without incurring significant increases in computational costs. As the examples demonstrate, including these constraints yields far superior results in complex geological areas that contain high-velocity high-contrast bodies (e.g. salt or basalt). Without these convex constraints, adjoint-state and Wavefield Reconstruction Inversion get trapped in local minima for poor starting models.},
	keywords = {convex constraints, Full-waveform inversion, salt, SEG, total-variation norm},
	doi = {10.1190/segam2015-5877995.1},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2015/esser2015SEGasd/esser2015SEGasd.html},
	presentation = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2015/esser2015SEGasd/esser2015SEGasd_pres.pdf},
	author = {Ernie Esser and Llu{\'\i}s Guasch and Tristan van Leeuwen and Aleksandr Y. Aravkin and Felix J. Herrmann}
}
@conference {petrenko2014EAGEaih,
	title = {Accelerating an iterative Helmholtz solver with FPGAs},
	booktitle = {EAGE Annual Conference Proceedings},
	year = {2014},
	month = {06},
	abstract = {We implement the Kaczmarz row-projection algorithm (Kaczmarz (1937)) on a CPU host + FPGA accelerator platform using techniques of dataflow programming. This algorithm is then used as the preconditioning step in CGMN, a modified version of the conjugate gradients method (Bj{\"o}rck and Elfving (1979)) that we use to solve the time-harmonic acoustic isotropic constant density wave equation. Using one accelerator we achieve a speed-up of over 2{\texttimes} compared with one Intel core.},
	keywords = {CGMN, EAGE, FPGA, Helmholtz equation, Kaczmarz, reconfigurable computing},
	doi = {10.3997/2214-4609.20141141},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/EAGE/2014/petrenko2014EAGEaih/petrenko2014EAGEaih.pdf},
	presentation = {https://slim.gatech.edu/Publications/Public/Conferences/EAGE/2014/petrenko2014EAGEaih/petrenko2014EAGEaih_pres.pdf},
	author = {Art Petrenko and Tristan van Leeuwen and Diego Oriato and Simon Tilbury and Felix J. Herrmann}
}
@presentation {petrenko2014SINBADaih,
	title = {Accelerating an iterative Helmholtz solver with FPGAs},
	year = {2014},
	publisher = {SINBAD},
	abstract = {An implementation of seismic wave simulation on a platform consisting of a conventional host processor and a reconfigurable hardware accelerator is presented. This research is important in the field of exploration for oil and gas resources, where a 3D model of the subsurface is frequently required. By comparing seismic data collected in a real-world survey with synthetic data generated by simulated waves, it is possible to deduce such a model. However this requires many time-consuming simulations with different Earth models to find the one that best fits the measured data. Speeding up the wave simulations would allow more models to be tried, yielding a more accurate estimate of the subsurface. The reconfigurable hardware accelerator employed in this work is a field programmable gate array (FPGA). FPGAs are computer chips that consist of electronic building blocks that the user can configure and reconfigure to represent their algorithm in hardware. Whereas a traditional processor can be viewed as a pipeline for processing instructions, an FPGA is a pipeline for processing data. The chief advantage of the FPGA is that all the instructions in the algorithm are already hardwired onto the chip. This means that execution time depends only on the amount of data to be processed, and not on the complexity of the algorithm. The main contribution is an implementation of the well-known Kaczmarz row projection algorithm on the FPGA, using techniques of dataflow programming. This kernel is used as the preconditioning step of CGMN, a modified version of the conjugate gradients method that is used to solve the time-harmonic acoustic isotropic constant density wave equation. Using one FPGA accelerator, the current implementation allows seismic wave simulations to be performed over twice as fast, compared to running on one Intel Xeon E5-2670 core. I also discuss the effect of modifications of the algorithm necessitated by the hardware on the convergence properties of CGMN. Finally, a specific plan for future work is set-out in order to fully exploit the accelerator platform, and my work is set in its larger context},
	keywords = {Presentation, SINBAD, SINBADSPRING2014, SLIM},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/SINBAD/2014/Spring/petrenko2014SINBADaih/petrenko2014SINBADaih.pdf},
	author = {Art Petrenko and Tristan van Leeuwen and Diego Oriato and Simon Tilbury and Felix J. Herrmann}
}
@conference {petrenko2014OGHPCaih,
	title = {Accelerating an iterative Helmholtz solver with FPGAs},
	booktitle = {OGHPC},
	year = {2014},
	month = {03},
	abstract = {We implement the Kaczmarz row-projection algorithm [Kaczmarz, 1937] on a CPU host + FPGA accelerator platform using techniques of dataflow programming. This algorithm is then used as the preconditioning step in CGMN, a modified version of the conjugate gradients method [Bj?rck and Elfving, 1979] that we use to solve the time-harmonic acoustic isotropic constant density wave equation.},
	keywords = {CGMN, FPGA, Helmholtz equation, Kaczmarz, OGHPC, reconfigurable computing},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/OGHPC/2014/petrenko2014OGHPCaih/petrenko2014OGHPCaih.pdf},
	presentation = {https://slim.gatech.edu/Publications/Public/Conferences/OGHPC/2014/petrenko2014OGHPCaih/petrenko2014OGHPCaih_poster.pdf},
	author = {Art Petrenko and Felix J. Herrmann and Diego Oriato and Simon Tilbury and Tristan van Leeuwen}
}
@presentation {petrenko2013SINBADaih,
	title = {Accelerating an iterative Helmholtz solver with FPGAs},
	year = {2013},
	publisher = {SINBAD},
	abstract = {Solution of the Helmholtz equation is the main computational burden of full-waveform inversion in the frequency domain. For this task we employ the CARP-CG algorithm (Gordon \& Gordon 2010), an iterative solver that preconditions the original Helmholtz system into an equivalent symmetric positive definite system and then applies the method of conjugate gradients. Forming the matrix for the new system is not necessary as its multiplicative action on a vector is implemented using a series of projections onto the rows of the original system. Our contribution is implementing CARP-CG for a host + accelerator (FPGA) computing environment. The computational paradigm is one of dataflow: vector and matrix elements are streamed from memory through the accelerator which applies the row projections. The advantage of an FPGA to process streams of data is that unless the algorithm is memory bandwidth limited, computation time is directly proportional to the amount of data. The complexity of the algorithm implemented on the FPGA is irrelevant since all the operations programmed onto the FPGA happen in the same clock tick. In contrast, on a CPU, more complex algorithms require more clock ticks as the instructions are executed sequentially, or with only a small amount of parallelism. Ongoing work porting the CARP-CG algorithm to the accelerator is presented.},
	keywords = {Presentation, SINBAD, SINBADFALL2013, SLIM},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/SINBAD/2013/Fall/petrenko2013SINBADaih/petrenko2013SINBADaih.pdf},
	author = {Art Petrenko and Tristan van Leeuwen and Felix J. Herrmann and Diego Oriato and Simon Tilbury}
}
@conference {kumar2013SEGAVA,
	title = {AVA analysis and geological dip estimation via two-way wave-equation based extended images},
	booktitle = {SEG Technical Program Expanded Abstracts},
	volume = {32},
	year = {2013},
	month = {09},
	pages = {423-427},
	abstract = {In this paper, we present an efficient way to compute extended images for all subsurface offsets without explicitly calculating the source and receiver wavefields for all the sources. Because the extended images contain all possible subsurface offsets, we compute the angle-domain image gathers by selecting the subsurface offset that is aligned with the local dip. We also propose a method to compute the local dip information directly from common-image-point gathers. To assess the quality of the angle-domain common-image-points gathers we compute the angle-dependent reflectivity coefficients and compare them with theoretical reflectivity coefficients yielded by the (linearized) Zoeppritz equations for a few synthetic models.},
	keywords = {AVA, dip, extended images, SEG, wave-equation},
	doi = {10.1190/segam2013-1348.1},
	url = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2013/kumar2013SEGAVA/kumar2013SEGAVA.pdf},
	presentation = {https://slim.gatech.edu/Publications/Public/Conferences/SEG/2013/kumar2013SEGAVA/kumar2013SEGAVA_pres.pdf},
	author = {Rajiv Kumar and Tristan van Leeuwen and Felix J. Herrmann}
}
