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At least 325 records · Page 18

LinkML: an open data modeling framework

Background Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, nonstandardized spreadsheets, or data repositories. This lack of structure challenges interoperability, making data integration, validation, and reuse difficult. Findings LinkML (Linked Data Modeling Language) is an open framework that simplifies the process of authoring, validating, and sharing data. LinkML can describe a range of data structures, from flat, list-based models to complex, interrelated, and normalized models that utilize polymorphism and compound inheritance. It offers an approachable syntax that is not tied to any one technical architecture and can be integrated seamlessly with many existing frameworks. The LinkML syntax provides a standard way to describe schemas, classes, and relationships, allowing modelers to build well-defined, stable, and optionally ontology-aligned data structures. Once defined, LinkML schemas may be imported into other LinkML schemas. These key features make LinkML an accessible platform for interdisciplinary collaboration and a reliable way to define and share data semantics. Conclusions LinkML helps reduce heterogeneity, complexity, and the proliferation of single-use data models while simultaneously enabling compliance with FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. LinkML has seen increasing adoption in various fields, including biology, chemistry, biomedicine, microbiome research, finance, electrical engineering, transportation, and commercial software development. In short, LinkML makes implicit models explicitly computable and allows data to be standardized at their origin. LinkML documentation and code are available at https://linkml.io/.

AI-ready data↗

Performance Portability of Molecular Docking Miniapp On Leadership Computing Platforms

Rapidly changing computer architectures, such as those found at high-performance computing (HPC) facilities, present the need for mini-applications (miniapps) that capture essential algorithms used in large applications to test program performance and portability, aiding transitions to new systems. The COVID-19 pandemic has fueled a flurry of activity in computational drug discovery, including the use of supercomputers and GPU acceleration for massive virtual screens for therapeutics. Recent work targeting COVID-19 at the Oak Ridge Leadership Computing Facility (OLCF) used the GPU-accelerated program AutoDock-GPU to screen billions of compounds on the Summit supercomputer. In this paper we present the development of a new miniapp, miniAutoDock-GPU, that can be used to evaluate the performance and portability of GPU-accelerated protein-ligand docking programs on different computer architectures. These tests are especially relevant as facilities transition from petascale systems and prepare for upcoming exascale systems that will use a variety of GPU vendors. The key calculations, namely, the Lamarckian genetic algorithm combined with a local search using a Solis-Wets based random optimization algorithm, are implemented. We developed versions of the miniapp using several different programming models for GPU acceleration, including a version using the CUDA runtime API for NVIDIA GPUs, and the Kokkos middle-ware API which is facilitated by C++ template libraries. A third version, currently in progress, uses the HIP programming model. These efforts will help facilitate the transition to exascale systems for this important emerging HPC application, as well as its use on a wide range of heterogeneous platforms.

Thavappiragasam, Mathialakan↗

INTEGRATE - Inverse Network Transformations for Efficient Generation of Robust Airfoil and Turbine Enhancements

The INTEGRATE (Inverse Network Transformations for Efficient Generation of Robust Airfoil and Turbine Enhancements) project is developing a new inverse-design capability for the aerodynamic design of wind turbine rotors using invertible neural networks. This AI-based design technology can capture complex non-linear aerodynamic effects while being 100 times faster than design approaches based on computational fluid dynamics. This project enables innovation in wind turbine design by accelerating time to market through higher-accuracy early design iterations to reduce the levelized cost of energy. INVERTIBLE NEURAL NETWORKS Researchers are leveraging a specialized invertible neural network (INN) architecture along with the novel dimension-reduction methods and airfoil/blade shape representations developed by collaborators at the National Institute of Standards and Technology (NIST) learns complex relationships between airfoil or blade shapes and their associated aerodynamic and structural properties. This INN architecture will accelerate designs by providing a cost-effective alternative to current industrial aerodynamic design processes, including: - Blade element momentum (BEM) theory models: limited effectiveness for design of offshore rotors with large, flexible blades where nonlinear aerodynamic effects dominate - Direct design using computational fluid dynamics (CFD): cost-prohibitive - Inverse-design models based on deep neural networks (DNNs): attractive alternative to CFD for 2D design problems, but quickly overwhelmed by the increased number of design variables in 3D problems AUTOMATED COMPUTATIONAL FLUID DYNAMICS FOR TRAINING DATA GENERATION - MERCURY FRAMEWORK The INN is trained on data obtained using the University of Marylands (UMD) Mercury Framework, which has with robust automated mesh generation capabilities and advanced turbulence and transition models validated for wind energy applications. Mercury is a multi-mesh paradigm, heterogeneous CPU-GPU framework. The framework incorporates three flow solvers at UMD, 1) OverTURNS, a structured solver on CPUs, 2) HAMSTR, a line based unstructured solver on CPUs, and 3) GARFIELD, a structured solver on GPUs. The framework is based on Python, that is often used to wrap C or Fortran codes for interoperability with other solvers. Communication between multiple solvers is accomplished with a Topology Independent Overset Grid Assembler (TIOGA). NOVEL AIRFOIL SHAPE REPRESENTATIONS USING GRASSMAN SPACES We developed a novel representation of shapes which decouples affine-style deformations from a rich set of data-driven deformations over a submanifold of the Grassmannian. The Grassmannian representation as an analytic generative model, informed by a database of physically relevant airfoils, offers (i) a rich set of novel 2D airfoil deformations not previously captured in the data , (ii) improved low-dimensional parameter domain for inferential statistics informing design/manufacturing, and (iii) consistent 3D blade representation and perturbation over a sequence of nominal shapes. TECHNOLOGY TRANSFER DEMONSTRATION - COUPLING WITH NREL WISDEM Researchers have integrated the inverse-design tool for 2D airfoils (INN-Airfoil) into WISDEM (Wind Plant Integrated Systems Design and Engineering Model), a multidisciplinary design and optimization framework for assessing the cost of energy, as part of tech-transfer demonstration. The integration of INN-Airfoil into WISDEM allows for the design of airfoils along with the blades that meet the dynamic design constraints on cost of energy, annual energy production, and the capital costs. Through preliminary studies, researchers have shown that the coupled INN-Airfoil + WISDEM approach reduces the cost of energy by around 1% compared to the conventional design approach. This page will serve as a place to easily access all the publications from this work and the repositories for the software developed and released through this pr...

aerodynamics↗

Using MLIR Framework for Codesign of ML Architectures Algorithms and Simulation Tools

MLIR (Multi-Level Intermediate Representation), is an extensible compiler framework that supports high-level data structures and operation constructs. These higher-level code representations are particularly applicable to the artificial intelligence and machine learning (AI/ML) domain, allowing developers to more easily support upcoming heterogeneous AI/ML accelerators and develop flexible domain specific compilers/frameworks with higher-level intermediate representations (IRs) and advanced compiler optimizations. The result of using MLIR within the LLVM compiler framework is expected to yield significant improvement in the quality of generated machine code, which in turn will result in improved performance and hardware efficiency

97 MATHEMATICS AND COMPUTING↗

Extending C++ for Heterogeneous Quantum-Classical Computing

In this report we present qcor - a language extension to C++ and compiler implementation that enables heterogeneous quantum-classical programming, compilation, and execution in a single-source context. Our work provides a first-of-its-kind C++ compiler enabling high-level quantum kernel (function) expression in a quantum-language agnostic manner, as well as a hardware-agnostic, retargetable compiler workflow targeting a number of physical and virtual quantum computing backends. qcor leverages novel Clang plugin interfaces and builds upon the XACC system-level quantum programming framework to provide a state-of-the-art integration mechanism for quantum-classical compilation that leverages the best from the community at-large. qcor translates quantum kernels ultimately to the XACC intermediate representation, and provides user-extensible hooks for quantum compilation routines like circuit optimization, analysis, and placement. This work details the overall architecture and compiler workflow for qcor, and provides a number of illuminating programming examples demonstrating its utility for near-term variational tasks, quantum algorithm expression, and feed-forward error correction schemes.

97 MATHEMATICS AND COMPUTING↗

Supercomputing systems - A projection to 2000

Advances in computer architecture, computer science, computational methods, and constituent technologies are expected to lead to significant advances in the performance of scientific supercomputing system capabilities over the next decade. By the year 2000, single 1-in-sq dies are projected to incorporate four processors, each of which would be operating faster than 750 million instructions per second (MIPS) for a total on-chip processing performance in excess of 2000 MIPS. Scalable parallel processors can be expected to contain thousands of such multiple processor chips. In general, semiconductor performance advances appear to change about one order of magnitude every five years. Rotating magnetic memory and communications technology are not advancing as rapidly, with the result that the allocation of functions within the system configurations fo future supercomputer systems will require important changes. Availability of massively parallel heterogeneous processing capabilities should be a catalyst leading to new approaches for applications.

Lundstrom, S. F.↗

Developing an Evolutionary Baseline Model for Humans: Jointly Inferring Purifying Selection with Population History

Building evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics—including quantifying the relative contributions of adaptive versus nonadaptive processes—but also essential for identifying candidate loci experiencing relatively rare and episodic forms of selection (e.g., positive or balancing selection). Here, a baseline model was developed for a human population of West African ancestry, the Yoruba, comprising processes constantly operating on the genome (i.e., purifying and background selection, population size changes, recombination rate heterogeneity, and gene conversion). Specifically, to perform joint inference of selective effects with demography, an approximate Bayesian approach was employed that utilizes the decay of background selection effects around functional elements, taking into account genomic architecture. This approach inferred a recent 6-fold population growth together with a distribution of fitness effects that is skewed towards effectively neutral mutations. Importantly, these results further suggest that, although strong and/or frequent recurrent positive selection is inconsistent with observed data, weak to moderate positive selection is consistent but unidentifiable if rare.

59 BASIC BIOLOGICAL SCIENCES↗

Application of artificial intelligence methods in the international roughness index prediction of rigid and composite pavements: a systematic review

The International Roughness Index (IRI) is a widely adopted metric for quantifying pavement roughness, directly influencing vehicle safety, ride comfort, and overall roadway performance. In recent years, the use of Machine Learning (ML) models for IRI prediction has gained momentum, with the goal of improving the allocation of maintenance and rehabilitation resources by enabling accurate assessments of pavement conditions. Most prior reviews, however, have concentrated on flexible pavements, leaving a notable gap regarding rigid and composite pavements. To address this gap, the present study conducts a systematic review of Artificial Intelligence (AI) methods applied to IRI prediction for rigid and composite pavements. Literature published between 2004 and 2025 is synthesized to highlight prevailing trends, methodological contributions, and directions for future research. Particular attention is given to the types of models employed, the datasets used for training and validation, and the role of input variables and data-processing strategies. Across the included studies, ensemble learning methods (especially gradient boosting variants such as XGBoost), artificial neural networks, and hybrid architectures frequently achieved high predictive skill, with several models reporting test-set coefficients of determination approaching 0.9–0.96, indicating strong potential for capturing the influence of traffic, pavement structure, and climatic factors. Since these results are obtained from heterogeneous datasets and evaluation protocols, they are interpreted qualitatively rather than as strict cross-study rankings. Analysis of input variables revealed that pavement age and initial IRI were included in 91% (21 of 23) and 78% (18 of 23) of studies, respectively. Climatic variables such as the freezing index appeared in 57% (13 of 23), while traffic-related factors were considered in 65% (15 of 23). The findings underscore the importance of standardized, high-quality datasets, such as those from the Long-Term Pavement Performance (LTPP) program, along with data consistency, model interpretability, computational efficiency, and replicability in enhancing IRI prediction. Future research should focus on incorporating input variable selection techniques to identify the most influential predictors, thereby improving accuracy and robustness. Integrating these approaches with advanced non-linear data-driven models, coupled with robust hyperparameter optimization, holds considerable promise for strengthening the reliability of IRI prediction and supporting resilient pavement management strategies.

42 ENGINEERING↗

KokkACC: Enhancing Kokkos with OpenACC

Template metaprogramming is gaining popularity as a high-level solution for achieving performance portability on heterogeneous computing resources. Kokkos is a representative approach that offers programmers high-level abstractions for generic programming while most of the device-specific code generation and optimizations are delegated to the compiler through template specializations. For this, Kokkos provides a set of device-specific code specializations in multiple back ends, such as CUDA and HIP. Unlike CUDA or HIP, OpenACC is a high-level and directive-based programming model. This descriptive model allows developers to insert hints (pragmas) into their code that help the compiler to parallelize the code. The compiler is responsible for the transformation of the code, which is completely transparent to the programmer. This paper presents an OpenACC back end for Kokkos: KokkACC. As an alternative to Kokkos’s existing device-specific back ends, KokkACC is a multi-architecture back end providing a high-productivity programming environment enabled by OpenACC’s high-level and descriptive programming model. Moreover, we have observed competitive performance; in some cases, KokkACC is faster (up to 9×) than NVIDIA’s CUDA back end and much faster than OpenMP’s GPU offloading back end. This work also includes implementation details and a detailed performance study conducted with a set of mini-benchmarks (AXPY and DOT product) and three mini-apps (LULESH, miniFE and SNAP, a LAMMPS proxy mini-app).

Valero Lara, Pedro↗

Benchmarking and Performance of the NASA Multiscale Analysis Tool

The NASA Multiscale Analysis Tool (NASMAT) is as a “plug and play,” software package which utilizes multiscale recursive micromechanics as a platform for massively multiscale modeling of hierarchical materials and structures subjected to thermomechanical. This paper is intended to give an overview of the design of NASMAT and how the design supports modularity, upgradability and maintainability, interoperability, and utility. First, the software architecture and hierarchy will be explored. Details on each of the 11 NASMAT procedures and the arrangement of NASMAT data will be presented. Application program interfaces (APIs) that were developed to facilitate the communication of NASMAT with other programs will be described. The intended application for NASMAT is massively multiscale modeling on high performance computing systems. As such, results benchmarking the performance of the integration of NASMAT with the Abaqus commercial finite element method software are also presented.

Multiscale Modeling↗

Towards Use of Mixed Precision in ECP Math Libraries

The use of multiple types of precision in mathematical software has the potential to increase its performance on new heterogeneous architectures. The xSDK project focuses both on the investigation and development of multiprecision algorithms as well as their inclusion into xSDK member libraries. This report summarizes current efforts on including and/or using mixed precision capabilities in the math libraries Ginkgo, heFFTe, hypre, MAGMA, PETSc/TAO, SLATE, SuperLU, and Trilinos, including KokkosKernels. It contains both numerical results from libraries that already provide mixed precision capabilities, as well as descriptions of the strategies to incorporate multiprecision into established libraries.

97 MATHEMATICS AND COMPUTING↗

Evaluating Application Characteristics for GPU Portability Layer Selection

GPUs have become the dominant source of computing power for high performance computing and are increasingly being used across the High Energy Physics computing landscape for a wide variety of tasks. Though NVIDIA is currently the main provider of GPUs, AMD and Intel are rapidly increasing their market share. As a result, programming using a vendor-specific language such as CUDA can significantly reduce deployment choices. There are a number of portability layers such as Kokkos, Alpaka, SYCL, OpenMP and std::par that permit execution on a broad range of GPU and CPU architectures, significantly increasing the flexibility of application programmers. However, each of these portability layers has its own characteristics, performing better at some tasks and worse at others, or placing limitations on aspects of the application. In this presentation, we report on a study of application and kernel characteristics that can influence the choice of a portability layer and show how each layer handles these characteristics. We have analyzed representative heterogeneous applications from CMS (patatrack and p2r), DUNE (Wire-Cell Toolkit), and ATLAS (FastCaloSim) to identify key application characteristics that have different behaviors for the various portability technologies. Using these results, developers can make more informed decisions on which GPU portability technology is best suited to their application.

Atif, Mohammad [Brookhaven]↗

MLCommons Science Benchmarks

Benchmarks are a cornerstone of modern machine learning practice, providing standardized eval- uations that enable reproducibility, comparison, and scientific progress. Yet, as AI systems particularly deep learning models become increasingly dynamic, traditional static benchmarking approaches are losing their relevance. Models rapidly evolve in architecture, scale, and capability; datasets shift; and deployment contexts continuously change, creating a moving target for evaluation. Without adaptive benchmarking frame- works, both scientific assessment and real-world de- ployment risk becoming misaligned with actual system behavior. Drawing on our experience from MLCommons, educa- tional initiatives, and government programs such as the DOE s Million Parameter Consortium, we identify key barriers that hinder the broader adoption and utility of benchmarking in AI. These include substantial resource demands, limited access to specialized hardware, lack of expertise in benchmark design, and uncertainty among practitioners about how to relate benchmark results to their own application domains. Moreover, current benchmarks often emphasize peak performance on leadership-class hardware, offering limited guidance for more diverse, real-world deployment scenarios. We argue that benchmarking itself must become dy- namic in order to incorporate evolving models, updated data, and heterogeneous computational platforms while maintaining transparency, reproducibility, and inter- pretability. Democratizing this process requires not only technical innovation, but also systematic educational efforts spanning undergraduate to professional levels to develop sustained expertise in benchmark design and use. Finally, benchmarks should be framed and com- municated to support application-relevant comparisons, enabling both developers and users to make informed, context-sensitive decisions. Advancing dynamic and inclusive benchmarking practices will be essential to ensure that evaluation keeps pace with the evolving AI landscape and supports responsible, reproducible, and accessible AI deployment.

Hawks, Benjamin G. [Fermilab]↗

OmniFed: A Modular Framework for Configurable Federated Learning from Edge to HPC

Federated Learning (FL) is critical for edge and High Performance Computing (HPC) where data is not centralized and privacy is crucial. We present OmniFed, a modular framework designed around decoupling and clear separation of concerns for configuration, orchestration, communication, and training logic. Its architecture supports configuration-driven prototyping and code-level override-what-you-need customization. We also support different topologies, mixed communication protocols within a single deployment, and popular training algorithms. It also offers optional privacy mechanisms including Differential Privacy (DP), Homomorphic Encryption (HE), and Secure Aggregation (SA), as well as compression strategies. These capabilities are exposed through well-defined extension points, allowing users to customize topology and orchestration, learning logic, and privacy/compression plugins, all while preserving the integrity of the core system. We evaluate multiple models and algorithms to measure various performance metrics. By unifying topology configuration, mixed-protocol communication, and pluggable modules in one stack, OmniFed streamlines FL deployment across heterogeneous environments. Github repository is available at https://github.com/at-aaims/OmniFed.

Tyagi, Sahil [ORNL] (ORCID:0009000783144745)↗

New Deformation Mechanisms in Nanocrystalline Nano-porous Small Scale Metals as Defined by Kinetically-driven Microstructures

This report describes recent advances in the design and fabrication of nanostructured metallic pillars with hierarchical microstructures using a novel nanoscale additive manufacturing approach. Through a hydrogel-infusion-based two-photon lithography (TPL) method, we successfully fabricated 3D nickel nanopillars exhibiting both nanocrystalline and nanoporous features. The resulting “bamboo-like” internal architecture comprises 30–50 nm grains and voids with similarly scaled pores. These geometrically tunable pillars, with diameters ranging from ~130 to 550 nm, serve as an ideal platform for probing deformation mechanisms in structurally heterogeneous metals at the nanoscale.

36 MATERIALS SCIENCE↗

A deep learning approach for semantic segmentation of unbalanced data in electron tomography of catalytic materials

In computed TEM tomography, image segmentation represents one of the most basic tasks with implications not only for 3D volume visualization, but more importantly for quantitative 3D analysis. In case of large and complex 3D data sets, segmentation can be an extremely difficult and laborious task, and thus has been one of the biggest hurdles for comprehensive 3D analysis. Heterogeneous catalysts have complex surface and bulk structures, and often sparse distribution of catalytic particles with relatively poor intrinsic contrast, which possess a unique challenge for image segmentation, including the current state-of-the-art deep learning methods. To tackle this problem, we apply a deep learning-based approach for the multi-class semantic segmentation of a γ-Alumina/Pt catalytic material in a class imbalance situation. Specifically, we used the weighted focal loss as a loss function and attached it to the U-Net’s fully convolutional network architecture. We assessed the accuracy of our results using Dice similarity coefficient (DSC), recall, precision, and Hausdorff distance (HD) metrics on the overlap between the ground-truth and predicted segmentations. Our adopted U-Net model with the weighted focal loss function achieved an average DSC score of 0.96 ± 0.003 in the γ-Alumina support material and 0.84 ± 0.03 in the Pt NPs segmentation tasks. We report an average boundary-overlap error of less than 2 nm at the 90th percentile of HD for γ-Alumina and Pt NPs segmentations. The complex surface morphology of γ-Alumina and its relation to the Pt NPs were visualized in 3D by the deep learning-assisted automatic segmentation of a large data set of high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) tomography reconstructions.

36 MATERIALS SCIENCE↗

Grey-Box System Identification of Grid-Forming Inverters

This paper demonstrates the use of grey-box system identification methods for simplifying and understanding the nonlinear power dynamics of grid-forming inverters (GFMs). The power and frequency outputs of complex high-order GFM models are fed into system identification software in order to fit them to a predetermined LTI system and learn system parameters such as (synthetic) inertia and droop constants. The same process is then run for a high-order synchronous generator model, and the outputs are fit to the same set of LTI equations. Simulation of a network of GFM inverters with diverse control architecture is also performed for the same process. The intent is threefold: first, to demonstrate the appropriateness of unified LTI models for describing the power and frequency dynamics of individual resources and connected networks, in order to facilitate analysis of larger heterogeneous networked systems; second, to discover the relationship between internal control parameters of GFMs and their externally observed values; and third, to validate that grey-box data-driven system identification techniques can be a valuable tool to discover the values of important parameters in the absence of explicit vendor models.

analytical models↗

Using the ATLAS experiment software on heterogeneous resources

With the large dataset expected from 2030 onwards by the HL-LHC at CERN, the ATLAS experiment is reaching the limits of the current data processing model in terms of traditional CPU resources based on x86_64 architectures and an extensive program for software upgrades towards the HL-LHC has been set up. The ARM CPU architecture is becoming a competitive and energy efficient alternative. Accelerators like GPUs are available in any recent HPC. In the past years ATLAS has successfully ported its full data processing and simulation software framework Athena to ARM and has invested significant effort in porting parts of the reconstruction and simulation algorithms to GPUs. We report on the successful usage of the ATLAS experiment offline and online software framework Athena on ARM and GPUs through the PanDA workflow management system at various WLCG sites. Furthermore we report on performance optimizations of the builds for ARM CPUs and the GPU integration efforts. We will discuss performance comparisons of different ARM and x86_64 architectures on WLCG resources and Cloud compute providers like GCP and AWS using ATLAS productions workflows as used in the Hep-Score23 benchmark suite.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗