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At least 145 records · Page 8

Automated ICRF heating surrogate modeling via machine learning

This work introduces automated machine learning workflows that address critical bottlenecks in surrogate model development for Ion Cyclotron Range of Frequencies (ICRF) heating applications. The automated framework includes data analysis tools that transform raw datasets into actionable insights in seconds, replacing weeks of manual exploratory effort and ensuring consistent, reproducible dataset characterization. By integrating advanced hyperparameter optimization (HPO) methods including Bayesian optimization via BoTorch and Tree-structured Parzen Estimators (TPE), the framework significantly reduces model development time from weeks to hours, decreasing computational cost and required expertise, while enabling high-accuracy surrogate models. Compared to traditional hyperparameter scanning (HPS) techniques such as methodical, randomized, and grid searches, HPO methods achieve superior convergence and predictive performance, even when compared to already well-tuned reference models. On NSTX High Harmonic Fast Wave (HHFW) heating datasets, both Random Forest Regressor (RFR) and neural network surrogates demonstrate improved accuracy, achieving R 2 values beyond 0.97 and 0.98, respectively. The results show that while HPO gains are modest for robust architectures like RFR, they become essential for more sensitive models such as neural networks, highlighting the trade-offs across optimization strategies. Through automated workflows that eliminate manual hyperparameter tuning and require minimal ML expertise, this work enables widespread adoption of high-fidelity surrogate models across the fusion community for real-time plasma control, uncertainty quantification, rapid experimental scenario development, and integrated system optimization.

Sanchez-Villar, Alvaro [Princeton Plasma Physics L↗

Scalable generalized screening for high-order terms in the many-body expansion: Algorithm, open-source implementation, and demonstration

The many-body expansion lies at the heart of numerous fragment-based methods that are intended to sidestep the nonlinear scaling of ab initio quantum chemistry, making electronic structure calculations feasible in large systems. In principle, inclusion of higher-order n-body terms ought to improve the accuracy in a controllable way, but unfavorable combinatorics often defeats this in practice and applications with n ≥ 4 are rare. Here, we outline an algorithm to overcome this combinatorial bottleneck, based on a bottom-up approach to energy-based screening. This is implemented within a new open-source software application (“Fragme∩t”), which is integrated with a lightweight semi-empirical method that is used to cull subsystems, attenuating the combinatorial growth of higher-order terms in the graph that is used to manage the calculations. This facilitates applications of unprecedented size, and we report four-body calculations in (H2O)64 clusters that afford relative energies within 0.1 kcal/mol/monomer of the supersystem result using less than 10% of the unique subsystems. We also report n-body calculations in (H2O)20 clusters up to n = 8, at which point the expansion terminates naturally due to screening. These are the largest n-body calculations reported to date using ab initio electronic structure theory, and they confirm that high-order n-body terms are mostly artifacts of basis-set superposition error.

Chemistry↗

Mitigate: An Adaptive Network Data Anonymization Tool Using Condensation-Based Differential Privacy

Modern network devices collect a large amount of data that can be analyzed to identify bottlenecks, anomalies, cyber-attacks, etc. Therefore, there is often a need to analyze such collections of network data quite often by an external expert or by the research community. However, these collections of data contain sensitive, proprietary information. In order for the network data to be shared, it must first be anonymized. The overall objective of this project is to develop an innovative privacy management tool to anonymize network data and achieve sufficient privacy, acceptable data utility, and efficient data analysis at the same time. No existing anonymization methods can achieve all of these at the same time. The core of this technology is a differential private clustering algorithm that provides strong privacy protection, preserves data properties important for subsequent analysis, and allows the party receiving the anonymized data to conduct analysis directly on anonymized data without the need of decryption or any extra processing. The research carried out was to design, implement and verify a solution to this problem by completing the following tasks: 1) developing the core technology; 2) developing a context based method that automatically recommends fields that must be anonymized; 3) conducted experiments showing superior results using our approach compared to existing tools, and 4) developed an intuitive but basic user interface. The research that was conducted generated novel algorithmic techniques that utilize state-of-the-art methods such as condensation, differential privacy preservation, clustering, automated tuning based on contextual awareness, and recommendation techniques to specify columns to users for anonymization leading to optimal privacy that allows research analysis on the dataset. Experiments were conducted to evaluate the efficacy of these novel algorithmic techniques by performing analysis on original non-anonymized datasets, then conducting analysis on the same yet anonymized datasets and comparing the results of the analyses. Overall, the anonymized analysis results were within 1% of the original results, verifying that the generated technology not only guarantees a high level of privacy but also enables research analysis as if it were conducted on the original dataset. Potential applications of this technology include anonymization of any type of structured network datasets that contain sensitive identifiers, such as IP addresses, that can be used in multiple applications. For example, to create an AI or machine learning model for cyber security, e.g., to detect attacks, or for performance analysis, e.g., identify bottlenecks or predict performance. In addition, a market analysis that was conducted for potential applications of this technology identified a broader range of applications of our anonymization technology beyond the network sector that includes healthcare, banking, insurance, securities, finance (FISB), data brokering, cloud services, ad sales, and government.

97 MATHEMATICS AND COMPUTING↗

Minnowbrook VI: 2009 Workshop on Flow Physics and Control for Internal and External Aerodynamics

Topics covered include: Flow Physics and control for Internal and External Aerodynamics (not in TOC...starts on pg13); Breaking CFD Bottlenecks in Gas-Turbine Flow-Path Design; Streamwise Vortices on the Convex Surfaces of Circular Cylinders and Turbomachinery Blading; DNS and Embedded DNS as Tools for Investigating Unsteady Heat Transfer Phenomena in Turbines; Cavitation, Flow Structure and Turbulence in the Tip Region of a Rotor Blade; Development and Application of Plasma Actuators for Active Control of High-Speed and High Reynolds Number Flows; Active Flow Control of Lifting Surface With Flap-Current Activities and Future Directions; Closed-Loop Control of Vortex Formation in Separated Flows; Global Instability on Laminar Separation Bubbles-Revisited; Very Large-Scale Motions in Smooth and Rough Wall Boundary Layers; Instability of a Supersonic Boundary-Layer With Localized Roughness; Active Control of Open Cavities; Amplitude Scaling of Active Separation Control; U.S. Air Force Research Laboratory's Need for Flow Physics and Control With Applications Involving Aero-Optics and Weapon Bay Cavities; Some Issues Related to Integrating Active Flow Control With Flight Control; Active Flow Control Strategies Using Surface Pressure Measurements; Reduction of Unsteady Forcing in a Vaned, Contra-Rotating Transonic Turbine Configuration; Active Flow Control Stator With Coanda Surface; Controlling Separation in Turbomachines; Flow Control on Low-Pressure Turbine Airfoils Using Vortex Generator Jets; Reduced Order Modeling Incompressible Flows; Study and Control of Flow Past Disk, and Circular and Rectangular Cylinders Aligned in the Flow; Periodic Forcing of a Turbulent Axisymmetric Wake; Control of Vortex Breakdown in Critical Swirl Regime Using Azimuthal Forcing; External and Turbomachinery Flow Control Working Group; Boundary Layers, Transitions and Separation; Efficiency Considerations in Low Pressure Turbines; Summary of Conference; and Final Plenary Session Transcript.

LaGraff, John E.↗

Bragg Spot Finder (BSF): a new machine-learning-aided approach to deal with spot finding for rapidly filtering diffraction pattern images

Macromolecular crystallography contributes significantly to understanding diseases and, more importantly, how to treat them by providing atomic resolution 3D structures of proteins. This is achieved by collecting X-ray diffraction images of protein crystals from important biological pathways. Spotfinders are used to detect the presence of crystals with usable data, and the spots from such crystals are the primary data used to solve the relevant structures. Having fast and accurate spot finding is essential, but recent advances in synchrotron beamlines used to generate X-ray diffraction images have brought us to the limits of what the best existing spotfinders can do. This bottleneck must be removed so spotfinder software can keep pace with the X-ray beamline hardware improvements and be able to see the weak or diffuse spots required to solve the most challenging problems encountered when working with diffraction images. In this paper, we first present Bragg Spot Detection (BSD), a large benchmark Bragg spot image dataset that contains 304 images with more than 66 000 spots. We then discuss the open source extensible U-Net-based spotfinder Bragg Spot Finder (BSF), with image pre-processing, a U-Net segmentation backbone, and post-processing that includes artifact removal and watershed segmentation. Finally, we perform experiments on the BSD benchmark and obtain results that are (in terms of accuracy) comparable to or better than those obtained with two popular spotfinder software packages ( Dozor and DIALS ), demonstrating that this is an appropriate framework to support future extensions and improvements.

36 MATERIALS SCIENCE↗

Development of high throughput light-sheet fluorescence lifetime imaging microscopy for 3D functional imaging of metabolic pathways in plant and microorganisms (Final Technical Report)

This research program will enable new biochemical contrast in the nanosecond lifetime domain through use of the recently demonstrated electro-optic fluorescence lifetime imaging technique (EO-FLIM) for wide-field lifetime imaging. The Stanford/Stanford Linear Accelerator Center multidisciplinary collaboration -- physics, applied physics, and structural biology -- will develop a light-sheet fluorescence lifetime imaging microscope for functional studies of microbial and plant metabolic pathways and dynamic interactions between plants and microorganisms in the rhizosphere. The proposed approach overcomes the imaging time bottleneck associated with existing fluorescence lifetime imaging methods. Initial demonstrations have shown a factor of 100,000 improvement in photon throughput compared to existing methods. High photon efficiency allowed the first wide-field fluorescence lifetime imaging of single molecules. Recent work has improved the technique’s repetition rate to enable compatibility with mode-locked lasers and demonstrated the combination of wide-field fluorescence lifetime imaging with super-resolution localization microscopy, observations of single molecule dynamics, and observation of donor lifetime quenching in single-molecule imaging. These results were achieved on standard camera sensors and would not have been possible with other wide-field approaches. The throughput and photon economy of the EO-FLIM method enables new BER-relevant imaging opportunities. In particular, scanned single- and two-photon light-sheet excitation will be used to achieve volumetric imaging with time-domain contrast.

47 OTHER INSTRUMENTATION↗

Automated Instrumentation and Monitoring of Data Movement for Parallel Programs

Writing efficient parallel programs is complicated by the need to select the right data structure alignments and distributions, which determine the nature and volume of inter-processor communications. A large number of performance tools for parallel programs have been developed recently to expose these inter-processor communications. However, none of them support performance views or provide statistics in terms of inter-processor data structure interactions. A performance tool that tracks the interaction between individual data structures and the context of these interactions is essential for understanding the performance of both explicit message passing programs and data-parallel languages such as HPF. In this paper we discuss the use of compiler front end tools for automatically tracking data structure movements in message passing programs, and low-overhead monitoring and postprocessing of such codes. We demonstrate that robust instrumentation and low overhead monitoring of inter-processor data structure movements is possible, with the use of a number of NAS benchmark codes, run on the i860 hypercube. We also show that the data so collected can be used effectively by post processing tools that expose performance bottlenecks using graphical displays and performance statistics.

Sarukkai, Sekhar↗

In Situ Growth of Crystalline and Polymer-Incorporated Amorphous ZIFs in Polybenzimidazole Achieving Hierarchical Nanostructures for Carbon Capture

We report mixed matrix materials (MMMs) hold great potential for membrane gas separations by merging nanofillers with unique nanostructures and polymers with excellent processability. In situ growth of the nanofillers is adapted to mitigate interfacial incompatibility to avoid the selectivity loss. Surprisingly, functional polymers have not been exploited to co-grow the nanofillers for membrane applications. Herein, in situ synergistic growth of crystalline zeolite imidazole framework-8 (ZIF-8) in polybenzimidazole (PBI), creating highly porous structures with high gas permeability, is demonstrated. More importantly, PBI contains benzimidazole groups (similar to the precursor for ZIF-8, i.e., 2-methylimidazole) and induces the formation of amorphous ZIFs, enhancing interfacial compatibility and creating highly size-discriminating bottlenecks. For instance, the formation of 15 mass% ZIF-8 in PBI improves H- 2 permeability and H- 2 /CO 2 selectivity by approximate to 100% at 35 degrees C, breaking the permeability/selectivity tradeoff. This work unveils a new platform of MMMs comprising functional polymer-incorporated amorphous ZIFs with hierarchical nanostructures for various applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Stochastic Constrained Extended System Dynamics for Solving Charge Equilibration Models

In this work, we present a new stochastic extended Lagrangian molecular dynamics solution to charge equilibration that eliminates self-consistent field (SCF) calculations, thus eliminating the computational bottleneck in solving the charge distribution with standard SCF solvers. By formulating both charges and chemical potential as latent variables and introducing a holonomic constraint that satisfies charge conservation, the SC-XLMD method accurately reproduces thermodynamic, dynamic, and structural properties within the framework of ReaxFF for a bulk water system and highly reactive RDX molecules simulated at high temperature. The SC-XLMD method shows excellent computational performance and is available in the publicly available LAMMPS package.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scalable Comparative Visualization of Ensembles of Call Graphs

Optimizing the performance of large-scale parallel codes is critical for efficient utilization of computing resources. Code developers often explore various execution parameters, such as hardware configurations, system software choices, and application parameters, and are interested in detecting and understanding bottlenecks in different executions. They often collect hierarchical performance profiles represented as call graphs, which combine performance metrics with their execution contexts. The crucial task of exploring multiple call graphs together is tedious and challenging because of the many structural differences in the execution contexts and significant variability in the collected performance metrics (e.g., execution runtime). In this paper, we present Ensemble CallFlow to support the exploration of ensembles of call graphs using new types of visualizations, analysis, graph operations, and features. We introduce ensemble-Sankey , a new visual design that combines the strengths of resource-flow (Sankey) and box-plot visualization techniques. Whereas the resource-flow visualization can easily and intuitively describe the graphical nature of the call graph, the box plots overlaid on the nodes of Sankey convey the performance variability within the ensemble. Our interactive visual interface provides linked views to help explore ensembles of call graphs, e.g., by facilitating the analysis of structural differences, and identifying similar or distinct call graphs. Finally, we demonstrate the effectiveness and usefulness of our design through case studies on large-scale parallel codes.

97 MATHEMATICS AND COMPUTING↗

Preventing Failures By Dataset Shift Detection in Safety-Critical Graph Applications

Dataset shift refers to the problem where the input data distribution may change over time (e.g., between training and test stages). Since this can be a critical bottleneck in several safety-critical applications such as healthcare, drug-discovery, etc., dataset shift detection has become an important research issue in machine learning. Though several existing efforts have focused on image/video data, applications with graph-structured data have not received sufficient attention. Therefore, in this paper, we investigate the problem of detecting shifts in graph structured data through the lens of statistical hypothesis testing. Specifically, we propose a practical two-sample test based approach for shift detection in large-scale graph structured data. Our approach is very flexible in that it is suitable for both undirected and directed graphs, and eliminates the need for equal sample sizes. Using empirical studies, we demonstrate the effectiveness of the proposed test in detecting dataset shifts. We also corroborate these findings using real-world datasets, characterized by directed graphs and a large number of nodes.

97 MATHEMATICS AND COMPUTING↗

Information processing in the primate visual system - An integrated systems perspective

The primate visual system contains dozens of distinct areas in the cerebral cortex and several major subcortical structures. These subdivisions are extensively interconnected in a distributed hierarchical network that contains several intertwined processing streams. A number of strategies are used for efficient information processing within this hierarchy. These include linear and nonlinear filtering, passage through information bottlenecks, and coordinated use of multiple types of information. In addition, dynamic regulation of information flow within and between visual areas may provide the computational flexibility needed for the visual system to perform a broad spectrum of tasks accurately and at high resolution.

Van Essen, David C.↗

Discovering Ni/Cu Single-Atom Alloy as a Highly Active and Selective Catalyst for Direct Methane Conversion to Ethylene: A First-Principles Kinetic Study

Direct methane conversion to liquid fuels or value-added chemicals is a promising technology to utilize natural resources without resorting to further petroleum extraction. However, discovering efficient catalysts for this reaction is challenging due to either coke formation or unfavorable C-H bond activation. Herein, we design single-atom alloy (SAA) catalysts to simultaneously eliminate the above two bottlenecks based on mechanism-guided strategies: (1) the active single atom enables favorable C-H bond breaking and (2) the less reactive host metal facilitates C-C coupling and thus avoids strong binding of carbonaceous species. Employing electronic structure theory calculations, we screened the stability of multiple SAAs with 3d-5d transition metals atomically dispersed on a copper surface in terms of avoiding dopant aggregation and segregation. We then evaluated reactivities of the stable SAAs as catalysts for direct methane conversion to C2 products, including methane dehydrogenation and C-C coupling mechanisms. Combining selectivity analysis with kinetic modeling, we predicted that nickel dispersed on copper, i.e., Ni/Cu SAA, is a highly active and selective catalyst that can efficiently transform methane to ethylene. This work designs efficient SAA catalysts for direct methane activation and provides chemical insights into engineering compositions of SAAs to tune their catalytic performances.

Kothakonda, Manish↗

Unsupervised physics-informed disentanglement of multimodal data

Here, we introduce physics-informed multimodal autoencoders (PIMA) - a variational inference framework for discovering shared information in multimodal datasets. Individual modalities are embedded into a shared latent space and fused through a product-of-experts formulation, enabling a Gaussian mixture prior to identify shared features. Sampling from clusters allows cross-modal generative modeling, with a mixture-of-experts decoder that imposes inductive biases from prior scientific knowledge and thereby imparts structured disentanglement of the latent space. This approach enables cross-modal inference and the discovery of features in high-dimensional heterogeneous datasets. Consequently, this approach provides a means to discover fingerprints in multimodal scientific datasets and to avoid traditional bottlenecks related to high-fidelity measurement and characterization of scientific datasets.

97 MATHEMATICS AND COMPUTING↗

Revealing EDL-driven reduction mechanisms in binary, ternary, and quaternary fluorinated electrolytes via an integrated MD–DFT–ML framework

Accurately predicting solid electrolyte interphase (SEI) formation requires explicitly resolving the electric double layer (EDL) structure, which deviates significantly from that of the bulk electrolyte. Although an established molecular dynamics (MD) and Density Functional Theory (DFT) framework can model SEI formation by evaluating reduction reactions of local clusters in the EDL, it suffers from a combinatorial computational bottleneck. To overcome this limitation, we introduce a machine-learning-accelerated simulation workflow (MD–DFT–ML), integrating a gradient-boosted regression model trained on EDL composition data to efficiently predict reduction potentials. We apply this framework to seven fluorinated electrolytes comprising fluorinated anions, a fluorinated ester solvent, two types of diluent (ion-solvating ester vs. non-solvating ether), and an FEC additive. The analysis shows that the EDL selectively accumulates cation-binding species; consequently, the non–cation-binding ether diluent rarely enters the EDL and makes minimal contributions to SEI formation. DFT calculations on statistically representative EDL clusters provide reduction potentials and fluorine-release pathways, while the ML model, which substantially reduces the DFT workload, predicts cluster reduction energies with a mean absolute error of 0.1 eV. The combined MD–DFT–ML approach also quantifies contributions from different sources to LiF formation in the SEI. This methodology establishes a generalizable route for multiscale modeling electrolyte and interphase design for next-generation electrochemical energy-storage systems.

DFT-MD-ML workflow↗

Massive all-atom analysis of 2D materials with quantum properties (Final report)

Improvements in microscopy have enabled the acquisition of data at a scale that is difficult to process manually, making automated machine learning approaches to analyzing experimental images essential. In this project, we developed and applied machine learning (ML) workflows for atomic resolution scanning transmission electron microscopy (STEM) images. This development included improving both methodology as well as generating user-friendly codes. We developed machine learning architectures which, after training, automatically identify the location and types of defects throughout a material. We used these data to produce class-averaged images of 2D atomic coordinates with up to 0.3 pm precision, uncovering the structure and oscillations of long-range strain fields around point defects in WSe 2-2x Te 2x . We also resolved a long-standing problem in this field in the training of ML models, a lack of labeled experimental data, by developing a cycle-GAN that transformed simulated-generated labeled data into labeled data indistinguishable from experiment and therefore suitable for training. This removed the remaining parts of the ML data processing workflow where human intervention was still critical and therefore a bottleneck to working at scale. Codes have been developed and released for this full machine learning workflow. ML approaches to partially automate STEM acquisition were also developed. Finally we applied ML and other advanced data processing methods to several materials science problems in two-dimensional materials, including studying the evolution of hyperuniformity with defect concentration in WSe2, understanding phase transformations in transition metal dichalcogenides during in-situ heating in the STEM, and exploring how 2D interfaces transform from twisted into aligned structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Root hairs vs. trichomes: Not everyone is straight!

Trichomes show 47 morphological phenotypes, while literature reports only two root hair phenotypes in all plants. However, could hair-like structures exist below-ground in a similar wide range of morphologies like trichomes? Genetic mutants and root hair stress phenotypes point to the possibility of uncharacterized morphological variation existing belowground. For example, such root hairs in Arabidopsis (Arabidopsis thaliana) can be wavy, curled, or branched. We found hints in the literature about hair-like structures that emerge before root hairs belowground. As such, these early emerging hair structures can be potential exceptions to the contrasting morphological variation between trichomes and root hairs. Here, in this work, we show a previously unreported ‘hooked’ hair structure growing below-ground in common bean. The unique ‘hooking’ shape distinguishes the ‘hooked hair’ morphologically from root hairs. Currently, we cannot fully characterize the phenotype of our observation due to the lack of automated methods for phenotyping root hairs. This phenotyping bottleneck also handicaps the discovery of more morphology types that might exist below-ground as manual screening across species is slower than computer-assisted high-throughput screening.

59 BASIC BIOLOGICAL SCIENCES↗

Comparability of Liquid Chromatography Tandem Mass Spectrometry Analysis of Dissolved Organic Matter across Laboratories

Non-targeted liquid chromatography tandem highresolution mass spectrometry (LC−MS/MS) is increasingly applied for the structure-resolved chemical analysis of dissolved organic matter (DOM). With new developments in MS instrumentation and analysis software, the approach has gained substantial momentum over the past decade. However, achieving high-quality analytical data that is reproducible and comparable across laboratories can be a bottleneck in non-targeted metabolomics and organic matter chemical analysis, especially for data reuse in repository-scale analyses. Understanding the capabilities as well as challenges of comparing LC−MS/MS data from different laboratories is necessary for inferring global trends from public data sets. To illuminate instrumentation factors that drive differences and variability, we used a standardized data analysis pipeline, including classical (CMN) and featurebased molecular networking (FBMN), to analyze data from a ring trial by 24 laboratories on identical sample sets of algal and DOM extracts that were mixed in predefined concentrations and spiked with standards. Our results showed that data sets from similar mass spectrometer types with unified instrument parameters were qualitatively comparable, resolving the same general trends and shared mass spectral features. Interlaboratory comparability was best for high-intensity features, while low-intensity features showed greater detection variability. Our analysis also highlights challenges when comparing data from instruments with different acquisition rates or operating with less standardized methods. Lastly, we provide recommendations for data integration, public data sharing, standardization, and best practices for standardized LC−MS/MS data acquisition, which will be critical for long-term time series and intercomparability of DOM chemical analyses.

DOM↗