Petrus H. Zwart

Eric J Roberts, Tanny Chavez, Alexander Hexemer et al.

We introduce DLSIA (Deep Learning for Scientific Image Analysis), a Python-based machine learning library that empowers scientists and researchers across diverse scientific domains with a range of customizable convolutional neural network (CNN) architectures for a wide variety of tasks in image analysis to be used in downstream data processing, or for experiment-in-the-loop computing scenarios. DLSIA features easy-to-use architectures such as autoencoders, tunable U-Nets, and parameter-lean mixed-scale dense networks (MSDNets). Additionally, we introduce sparse mixed-scale networks (SMSNets), generated using random graphs and sparse connections. As experimental data continues to grow in scale and complexity, DLSIA provides accessible CNN construction and abstracts CNN complexities, allowing scientists to tailor their machine learning approaches, accelerate discoveries, foster interdisciplinary collaboration, and advance research in scientific image analysis.

Zhuowen Zhao, Tanny Chavez, Elizabeth A. Holman et al.

Machine learning (ML) algorithms are showing a growing trend in helping the scientific communities across different disciplines and institutions to address large and diverse data problems. However, many available ML tools are programmatically demanding and computationally costly. The MLExchange project aims to build a collaborative platform equipped with enabling tools that allow scientists and facility users who do not have a profound ML background to use ML and computational resources in scientific discovery. At the high level, we are targeting a full user experience where managing and exchanging ML algorithms, workflows, and data are readily available through web applications. Since each component is an independent container, the whole platform or its individual service(s) can be easily deployed at servers of different scales, ranging from a personal device (laptop, smart phone, etc.) to high performance clusters (HPC) accessed (simultaneously) by many users. Thus, MLExchange renders flexible using scenarios -- users could either access the services and resources from a remote server or run the whole platform or its individual service(s) within their local network.

Bowen Zheng, Katayun Kamdin, David Shapiro et al.

Iterative ptychographic reconstruction algorithms are widely used for coherent diffractive imaging but can exhibit slow convergence under realistic experimental conditions. We propose a machine learning-augmented approach that accelerates iterative ptychographic reconstruction by introducing a learned fast-forward operator applied during reconstruction. Following an initial warm-up using standard iterations, the fast-forward operator advances the reconstruction toward a more converged state, after which conventional iterative updates are resumed. This strategy preserves the physical consistency and flexibility of established ptychographic solvers while reducing the number of iterations required for convergence. The model is trained on diverse ptychographic datasets and evaluated on experimental data acquired in a different year, demonstrating robustness and temporal generalization. Compared with conventional iterative solvers, the machine learning-augmented method achieves comparable reconstruction quality while converging faster in terms of Poisson negative log-likelihood, yielding over a two-fold reduction in wall-clock time. The approach has been integrated into an existing reconstruction pipeline and deployed in production at a synchrotron beamline, demonstrating practicality for real-time experimental operation.

Howard Yanxon, Eric Roberts, Hannah Parraga et al.

Scientific researchers frequently use the in situ synchrotron high-energy powder X-ray diffraction (XRD) technique to examine the crystallographic structures of materials in functional devices such as rechargeable battery materials. We propose a method for identifying artifacts in experimental XRD images. The proposed method uses deep learning convolutional neural network architectures, such as tunable U-Nets to identify the artifacts. In particular, the predicted artifacts are evaluated against the corresponding ground truth (manually implemented) using the overall true positive rate or recall. The result demonstrates that the U-Nets can consistently produce great recall performance at 92.4% on the test dataset, which is not included in the training, with a 34% reduction in average false positives in comparison to the conventional method. The U-Nets also reduce the time required to identify and separate artifacts by more than 50%. Furthermore, the exclusion of the artifacts shows major changes in the integrated 1D XRD pattern, enhancing further analysis of the post-processing XRD data.

Monika Choudhary, Xiaoya Chong, Runbo Jiang et al.

Scientific user facilities generate X-ray scattering data faster than traditional workflows can process them. We address this challenge across two settings, offline dataset exploration and live on-the-fly analysis. We train a domain-specific attention-based Convolutional Variational Autoencoder (C-VAE) on 1.5 million X-ray scattering images to learn low-dimensional representations capturing structural variation across diverse experimental conditions. The learned latent space reveals well-organized clusters and smooth trajectories reflecting experimental progression. It further supports controlled synthetic scattering image generation across diverse structural states. When deployed without retraining, the model organizes time-resolved film formation experiments at two synchrotron facilities into interpretable latent structures. Benchmarking against DINOv3 (ViT-7B), a general-purpose vision foundation model, demonstrates that domain-specific training yields more interpretable latent organization for scattering data. Both workflows are integrated within Latent Space Explorer, a component of the MLExchange platform, supporting interactive structural exploration across archived datasets and live experiments.

Petrus H. Zwart

Deployed conformal predictors are long-lived decision infrastructure operating over finite operational windows. The real-world question is not only ``Does the true label lie in the prediction set at the target rate?'' (marginal coverage), but ``How often does the system commit versus defer? What error exposure does it induce when it acts? How do these rates trade off?'' Marginal coverage does not determine these deployment-facing quantities: the same calibrated thresholds can yield different operational profiles depending on score geometry. We provide a framework for operational certification and planning beyond coverage with three contributions. (1) Small-Sample Beta Correction (SSBC): we invert the exact finite-sample Beta/rank law for split conformal to map a user request $(α^\star,δ)$ to a calibrated grid point with PAC-style semantics, yielding explicit finite-window coverage guarantees. (2) Calibrate-and-Audit: since no distribution-free pivot exists for rates beyond coverage, we introduce a two-stage design in which an independent audit set produces a reusable region -- label table and certified finite-window envelopes (Binomial/Beta-Binomial) for operational quantities -- commitment frequency, deferral, decisive error exposure, and commit purity -- via linear projection. (3) Geometric characterization: we describe feasibility constraints, regime boundaries (hedging vs.\ rejection), and cost-coherence conditions induced by a fixed conformal partition, explaining why operational rates are coupled and how calibration navigates their trade-offs. The output is an auditable operational menu: for a fixed scoring model, we trace attainable operational profiles across calibration settings and attach finite-window uncertainty envelopes. We demonstrate the approach on Tox21 toxicity prediction (12 endpoints) and aqueous solubility screening using AquaSolDB.

Petrus H. Zwart

Conformal prediction provides distribution-free prediction sets with guaranteed marginal coverage. However, in split conformal prediction this guarantee is training-conditional only in expectation: across many calibration draws, the average coverage equals the nominal level, but the realized coverage for a single calibration set may vary substantially. This variance undermines effective risk control in practical applications. Here we introduce the Small Sample Beta Correction (SSBC), a plug-and-play adjustment to the conformal significance level that leverages the exact finite-sample distribution of conformal coverage to provide probabilistic guarantees, ensuring that with user-defined probability over the calibration draw, the deployed predictor achieves at least the desired coverage.

Luca Pion-Tonachini, Kristofer Bouchard, Hector Garcia Martin et al.

We outline emerging opportunities and challenges to enhance the utility of AI for scientific discovery. The distinct goals of AI for industry versus the goals of AI for science create tension between identifying patterns in data versus discovering patterns in the world from data. If we address the fundamental challenges associated with "bridging the gap" between domain-driven scientific models and data-driven AI learning machines, then we expect that these AI models can transform hypothesis generation, scientific discovery, and the scientific process itself.