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Authors:Anakha V Babu, Tekin Bicer, Saugat Kandel, Tao Zhou, Daniel J. Ching, Steven Henke, Siniša Veseli, Ryan Chard, Antonino Miceli, Mathew Joseph Cherukara

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Abstract:We present an end-to-end automated workflow that uses large-scale remote compute resources and an embedded GPU platform at the edge to enable AI/ML-accelerated real-time analysis of data collected for x-ray ptychography. Ptychography is a lensless method that is being used to image samples through a simultaneous numerical inversion of a large number of diffraction patterns from adjacent overlapping scan positions. This acquisition method can enable nanoscale imaging with x-rays and electrons, but this often requires very large experimental datasets and commensurately high turnaround times, which can limit experimental capabilities such as real-time experimental steering and low-latency monitoring. In this work, we introduce a software system that can automate ptychography data analysis tasks. We accelerate the data analysis pipeline by using a modified version of PtychoNN -- an ML-based approach to solve phase retrieval problem that shows two orders of magnitude speedup compared to traditional iterative methods. Further, our system coordinates and overlaps different data analysis tasks to minimize synchronization overhead between different stages of the workflow. We evaluate our workflow system with real-world experimental workloads from the 26ID beamline at Advanced Photon Source and ThetaGPU cluster at Argonne Leadership Computing Resources.

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Authors:Anakha V Babu, Tao Zhou, Saugat Kandel, Tekin Bicer, Zhengchun Liu, William Judge, Daniel J. Ching, Yi Jiang, Sinisa Veseli, Steven Henke(+8 more)

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Abstract:Coherent microscopy techniques provide an unparalleled multi-scale view of materials across scientific and technological fields, from structural materials to quantum devices, from integrated circuits to biological cells. Driven by the construction of brighter sources and high-rate detectors, coherent X-ray microscopy methods like ptychography are poised to revolutionize nanoscale materials characterization. However, associated significant increases in data and compute needs mean that conventional approaches no longer suffice for recovering sample images in real-time from high-speed coherent imaging experiments. Here, we demonstrate a workflow that leverages artificial intelligence at the edge and high-performance computing to enable real-time inversion on X-ray ptychography data streamed directly from a detector at up to 2 kHz. The proposed AI-enabled workflow eliminates the sampling constraints imposed by traditional ptychography, allowing low dose imaging using orders of magnitude less data than required by traditional methods.

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Authors:Saugat Kandel, S. Maddali, Youssef S G Nashed, Stephan O Hruszkewycz, Chris Jacobsen, Marc Allain

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Abstract:The phase retrieval problem, where one aims to recover a complex-valued image from far-field intensity measurements, is a classic problem encountered in a range of imaging applications. Modern phase retrieval approaches usually rely on gradient descent methods in a nonlinear minimization framework. Calculating closed-form gradients for use in these methods is tedious work, and formulating second order derivatives is even more laborious. Additionally, second order techniques often require the storage and inversion of large matrices of partial derivatives, with memory requirements that can be prohibitive for data-rich imaging modalities. We use a reverse-mode automatic differentiation (AD) framework to implement an efficient matrix-free version of the Levenberg-Marquardt (LM) algorithm, a longstanding method that finds popular use in nonlinear least-square minimization problems but which has seen little use in phase retrieval. Furthermore, we extend the basic LM algorithm so that it can be applied for general constrained optimization problems beyond just the least-square applications. Since we use AD, we only need to specify the physics-based forward model for a specific imaging application; the derivative terms are calculated automatically through matrix-vector products, without explicitly forming any large Jacobian or Gauss-Newton matrices. We demonstrate that this algorithm can be used to solve both the unconstrained ptychographic object retrieval problem and the constrained "blind" ptychographic object and probe retrieval problems, under both the Gaussian and Poisson noise models, and that this method outperforms best-in-class first-order ptychographic reconstruction methods: it provides excellent convergence guarantees with (in many cases) a superlinear rate of convergence, all with a computational cost comparable to, or lower than, the tested first-order algorithms.

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Authors:Ming Du, Saugat Kandel, Junjing Deng, Xiaojing Huang, Arnaud Demortiere, Tuan Tu Nguyen, Remi Tucoulou, Vincent De Andrade, Qiaoling Jin, Chris Jacobsen

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Abstract:We describe and demonstrate an optimization-based x-ray image reconstruction framework called Adorym. Our framework provides a generic forward model, allowing one code framework to be used for a wide range of imaging methods ranging from near-field holography to and fly-scan ptychographic tomography. By using automatic differentiation for optimization, Adorym has the flexibility to refine experimental parameters including probe positions, multiple hologram alignment, and object tilts. It is written with strong support for parallel processing, allowing large datasets to be processed on high-performance computing systems. We demonstrate its use on several experimental datasets to show improved image quality through parameter refinement.

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Authors:Henry Chan, Youssef S. G. Nashed, Saugat Kandel, Stephan Hruszkewycz, Subramanian Sankaranarayanan, Ross J. Harder, Mathew J. Cherukara

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Abstract:Phase retrieval, the problem of recovering lost phase information from measured intensity alone, is an inverse problem that is widely faced in various imaging modalities ranging from astronomy to nanoscale imaging. The current process of phase recovery is iterative in nature. As a result, the image formation is time-consuming and computationally expensive, precluding real-time imaging. Here, we use 3D nanoscale X-ray imaging as a representative example to develop a deep learning model to address this phase retrieval problem. We introduce 3D-CDI-NN, a deep convolutional neural network and differential programming framework trained to predict 3D structure and strain solely from input 3D X-ray coherent scattering data. Our networks are designed to be "physics-aware" in multiple aspects; in that the physics of x-ray scattering process is explicitly enforced in the training of the network, and the training data are drawn from atomistic simulations that are representative of the physics of the material. We further refine the neural network prediction through a physics-based optimization procedure to enable maximum accuracy at lowest computational cost. 3D-CDI-NN can invert a 3D coherent diffraction pattern to real-space structure and strain hundreds of times faster than traditional iterative phase retrieval methods, with negligible loss in accuracy. Our integrated machine learning and differential programming solution to the phase retrieval problem is broadly applicable across inverse problems in other application areas.

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