Jana Thayer

Xiang Li, Till Jahnke, Rebecca Boll et al.

Capturing the structural changes that molecules undergo during chemical reactions in real space and time is a long-standing dream and an essential prerequisite for understanding and ultimately controlling femtochemistry. A key approach to tackle this challenging task is Coulomb explosion imaging, which benefited decisively from recently emerging high-repetition-rate X-ray free-electron laser sources. With this technique, information on the molecular structure is inferred from the momentum distributions of the ions produced by the rapid Coulomb explosion of molecules. Retrieving molecular structures from these distributions poses a highly non-linear inverse problem that remains unsolved for molecules consisting of more than a few atoms. Here, we address this challenge using a diffusion-based Transformer neural network. We show that the network reconstructs unknown molecular geometries from ion-momentum distributions with a mean absolute error below one Bohr radius, which is half the length of a typical chemical bond.

Ahsan Ali, Hemant Sharma, Rajkumar Kettimuthu et al.

Extracting actionable information rapidly from data produced by instruments such as the Linac Coherent Light Source (LCLS-II) and Advanced Photon Source Upgrade (APS-U) is becoming ever more challenging due to high (up to TB/s) data rates. Conventional physics-based information retrieval methods are hard-pressed to detect interesting events fast enough to enable timely focusing on a rare event or correction of an error. Machine learning~(ML) methods that learn cheap surrogate classifiers present a promising alternative, but can fail catastrophically when changes in instrument or sample result in degradation in ML performance. To overcome such difficulties, we present a new data storage and ML model training architecture designed to organize large volumes of data and models so that when model degradation is detected, prior models and/or data can be queried rapidly and a more suitable model retrieved and fine-tuned for new conditions. We show that our approach can achieve up to 100x data labelling speedup compared to the current state-of-the-art, 200x improvement in training speed, and 92x speedup in-terms of end-to-end model updating time.

Cong Wang, Eric Florin, Hsing-Yin Chang et al.

With X-ray free-electron lasers (XFELs), it is possible to determine the three-dimensional structure of noncrystalline nanoscale particles using X-ray single-particle imaging (SPI) techniques at room temperature. Classifying SPI scattering patterns, or "speckles", to extract single hits that are needed for real-time vetoing and three-dimensional reconstruction poses a challenge for high data rate facilities like European XFEL and LCLS-II-HE. Here, we introduce SpeckleNN, a unified embedding model for real-time speckle pattern classification with limited labeled examples that can scale linearly with dataset size. Trained with twin neural networks, SpeckleNN maps speckle patterns to a unified embedding vector space, where similarity is measured by Euclidean distance. We highlight its few-shot classification capability on new never-seen samples and its robust performance despite only tens of labels per classification category even in the presence of substantial missing detector areas. Without the need for excessive manual labeling or even a full detector image, our classification method offers a great solution for real-time high-throughput SPI experiments.

Cong Wang, Po-Nan Li, Jana Thayer et al.

Serial crystallography at X-ray free electron laser (XFEL) and synchrotron facilities has experienced tremendous progress in recent times enabling novel scientific investigations into macromolecular structures and molecular processes. However, these experiments generate a significant amount of data posing computational challenges in data reduction and real-time feedback. Bragg peak finding algorithm is used to identify useful images and also provide real-time feedback about hit-rate and resolution. Shot-to-shot intensity fluctuations and strong background scattering from buffer solution, injection nozzle and other shielding materials make this a time-consuming optimization problem. Here, we present PeakNet, an autonomous Bragg peak finder that utilizes deep neural networks. The development of this system 1) eliminates the need for manual algorithm parameter tuning, 2) reduces false-positive peaks by adjusting to shot-to-shot variations in strong background scattering in real-time, 3) eliminates the laborious task of manually creating bad pixel masks and the need to store these masks per event since these can be regenerated on demand. PeakNet also exhibits exceptional runtime efficiency, processing a 1920-by-1920 pixel image around 90 ms on an NVIDIA 1080 Ti GPU, with the potential for further enhancements through parallelized analysis or GPU stream processing. PeakNet is well-suited for expert-level real-time serial crystallography data analysis at high data rates.

Zhantao Chen, Cong Wang, Mingye Gao et al.

The development of X-ray Free Electron Lasers (XFELs) has opened numerous opportunities to probe atomic structure and ultrafast dynamics of various materials. Single Particle Imaging (SPI) with XFELs enables the investigation of biological particles in their natural physiological states with unparalleled temporal resolution, while circumventing the need for cryogenic conditions or crystallization. However, reconstructing real-space structures from reciprocal-space x-ray diffraction data is highly challenging due to the absence of phase and orientation information, which is further complicated by weak scattering signals and considerable fluctuations in the number of photons per pulse. In this work, we present an end-to-end, self-supervised machine learning approach to recover particle orientations and estimate reciprocal space intensities from diffraction images only. Our method demonstrates great robustness under demanding experimental conditions with significantly enhanced reconstruction capabilities compared with conventional algorithms, and signifies a paradigm shift in SPI as currently practiced at XFELs.

Abhilasha Dave, Cong Wang, James Russell et al.

We implement a specialized version of our SpeckleNN model for real-time speckle pattern classification in X-ray Single-Particle Imaging (SPI) using the SLAC Neural Network Library (SNL) on an FPGA. This hardware is optimized for inference near detectors in high-throughput X-ray free-electron laser (XFEL) facilities like the Linac Coherent Light Source (LCLS). To fit FPGA constraints, we optimized SpeckleNN, reducing parameters from 5.6M to 64.6K (98.8% reduction) with 90% accuracy. We also compressed the latent space from 128 to 50 dimensions. Deployed on a KCU1500 FPGA, the model used 71% of DSPs, 75% of LUTs, and 48% of FFs, with an average power consumption of 9.4W. The FPGA achieved 45.015us inference latency at 200 MHz. On an NVIDIA A100 GPU, the same inference consumed ~73W and had a 400us latency. Our FPGA version achieved an 8.9x speedup and 7.8x power reduction over the GPU. Key advancements include model specialization and dynamic weight loading through SNL, eliminating time-consuming FPGA re-synthesis for fast, continuous deployment of (re)trained models. These innovations enable real-time adaptive classification and efficient speckle pattern vetoing, making SpeckleNN ideal for XFEL facilities. This implementation accelerates SPI experiments and enhances adaptability to evolving conditions.

Yuan Ni, Zhantao Chen, Alexander N. Petsch et al.

Significant challenges exist in efficient data analysis of most advanced experimental and observational techniques because the collected signals often include unwanted contributions--such as background and signal distortions--that can obscure the physically relevant information of interest. To address this, we have developed a self-supervised machine-learning approach for source separation using a dual implicit neural representation framework that jointly trains two neural networks: one for approximating distortions of the physical signal of interest and the other for learning the effective background contribution. Our method learns directly from the raw data by minimizing a reconstruction-based loss function without requiring labeled data or pre-defined dictionaries. We demonstrate the effectiveness of our framework by considering a challenging case study involving large-scale simulated as well as experimental momentum-energy-dependent inelastic neutron scattering data in a four-dimensional parameter space, characterized by heterogeneous background contributions and unknown distortions to the target signal. The method is found to successfully separate physically meaningful signals from a complex or structured background even when the signal characteristics vary across all four dimensions of the parameter space. An analytical approach that informs the choice of the regularization parameter is presented. Our method offers a versatile framework for addressing source separation problems across diverse domains, ranging from superimposed signals in astronomical measurements to structural features in biomedical image reconstructions.

Yuan Ni, Zhantao Chen, Cheng Peng et al.

Implicit neural representations (INRs) have emerged as a compact and parametric alternative to discrete array-based data representations, encoding information directly in neural network weights to enable resolution-independent representation and memory efficiency. However, existing INR approaches, when constrained to compact network sizes, struggle to faithfully represent the multi-scale structures, high-frequency information, and fine textures that characterize the majority of scientific datasets. To address this limitation, we propose WIEN-INR, a wavelet-informed implicit neural representation that distributes modeling across different resolution scales and employs a specialized kernel network at the finest scale to recover subtle details. This multi-scale architecture allows for the use of smaller networks to retain the full spectrum of information while preserving the training efficiency and reducing storage cost. Through extensive experiments on diverse scientific datasets spanning different scales and structural complexities, WIEN-INR achieves superior reconstruction fidelity while maintaining a compact model size. These results demonstrate WIEN-INR as a practical neural representation framework for high-fidelity scientific data encoding, extending the applicability of INRs to domains where efficient preservation of fine detail is essential.

Zhengchun Liu, Ahsan Ali, Peter Kenesei et al.

Extremely high data rates at modern synchrotron and X-ray free-electron laser light source beamlines motivate the use of machine learning methods for data reduction, feature detection, and other purposes. Regardless of the application, the basic concept is the same: data collected in early stages of an experiment, data from past similar experiments, and/or data simulated for the upcoming experiment are used to train machine learning models that, in effect, learn specific characteristics of those data; these models are then used to process subsequent data more efficiently than would general-purpose models that lack knowledge of the specific dataset or data class. Thus, a key challenge is to be able to train models with sufficient rapidity that they can be deployed and used within useful timescales. We describe here how specialized data center AI (DCAI) systems can be used for this purpose through a geographically distributed workflow. Experiments show that although there are data movement cost and service overhead to use remote DCAI systems for DNN training, the turnaround time is still less than 1/30 of using a locally deploy-able GPU.