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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Brochure for the DOE Office of Science Workshop on Envisioning Frontiers in AI and Computing for Biological Research

In February of 2025 a joint ASCR/BER workshop was held to identify key transformational research directions for understanding biology using artificial intelligence (AI), digital twins and high-performance (HPC) computational methods to facilitate scientific discovery and innovation in support of the Department of Energy mission. AI technologies offer exciting new groundbreaking methods to analyze large volumes of complex biological data, thereby greatly accelerating the ability to understand, predict, and design biological processes for beneficial purposes. In the laboratory, the bridging of AI-enabled automated experimental technologies, HPC and digital twins will provide potent tools for researchers to explore the fundamental nature of biology and harness its inherent metabolic potential for a variety of beneficial purposes. The focus of this workshop was on how high-performance computational methods can impact this objective by exploring digital twins, foundational models, and data-driven approaches with applications to advance automated laboratory experiments, modeling of complex living systems and engineering new functions into plants and microbial systems relevant to DOE mission. Workshop attendees with expertise in plant science, microbiology, mathematics, computer science, and AI assessed the current state of the science, trends, and AI challenges at the interface of plant and microbial systems biology and computational science to identify opportunities for high-impact research. This collaborative effort capitalized on ASCR's advancements in applied mathematics, computer science, and Exascale systems, and BER's expertise in basic genomics-enabled research on DOE relevant plant and microbial systems. The workshop culminated in four key priority research directions to guide future research and development within DOE Office of Science programs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

NuGraph2 with explainability: post-hoc explanations for geometric neural network predictions

With the growing popularity of artificial intelligence (AI) used for scientific applications, the ability of attribute a result to a reasoning process from the network is in high demand for robust scientific generalizations to hold. In this work we aim to motivate the need for and demonstrate the use of post-hoc explainability methods when applied to AI methods used in scientific applications. To this end, we introduce explainability add-ons to the existing graph neural network (GNN) for neutrino tagging, NuGraph2. The explanations take the form of a suite of techniques examining the output of the network (node classifications) and the edge connections between them, and probing of the latent space using novel general-purpose tools applied to this network. We show how none of these methods are singularly sufficient to show network ‘understanding’, but together can give insights into the processes used in classification. While these methods are tested on the NuGraph2 application, they can be applied to a broad range of networks, not limited to GNNs. The code for this work is publicly available on GitHub at https://github.com/voetberg/XNuGraph.

Voetberg, Margaret [Fermilab] (ORCID:0009000527154↗
DOE OSTI2022

Performance and power modeling and prediction using MuMMI and 10 machine learning methods

Energy-efficient scientific applications require insight into how high performance computing system features impact the applications' power and performance. This insight can result from the development of performance and power models. Here, in this article, we use the modeling and prediction tool MuMMI (Multiple Metrics Modeling Infrastructure) and 10 machine learning methods to model and predict performance and power consumption and compare their prediction error rates. We use an algorithm-based fault-tolerant linear algebra code and a multilevel checkpointing fault-tolerant heat distribution code to conduct our modeling and prediction study on the Cray XC40 Theta and IBM BG/Q Mira at Argonne National Laboratory and the Intel Haswell cluster Shepard at Sandia National Laboratories. Our experimental results show that the prediction error rates in performance and power using MuMMI are less than 10% for most cases. By utilizing the models for runtime, node power, CPU power, and memory power, we identify the most significant performance counters for potential application optimizations, and we predict theoretical outcomes of the optimizations. Based on two collected datasets, we analyze and compare the prediction accuracy in performance and power consumption using MuMMI and 10 machine learning methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Numerical characterization of support recovery in sparse regression with correlated design

Sparse regression is employed in diverse scientific settings as a feature selection method. A pervasive aspect of scientific data is the presence of correlations between predictive features. These correlations hamper both feature selection and estimation and jeopardize conclusions drawn from estimated models. On the other hand, theoretical results on sparsity-inducing regularized regression have largely addressed conditions for selection consistency via asymptotics, and disregard the problem of model selection, whereby regularization parameters are chosen. In this numerical study, we address these issues through exhaustive characterization of the performance of several regression estimators, coupled with a range of model selection strategies. These estimators and selection criteria were examined across correlated regression problems with varying degrees of signal to noise, distributions of non-zero model coefficients, and model sparsity. Our results reveal a fundamental tradeoff between false positive and false negative control in all regression estimators and model selection criteria examined. Additionally, we numerically explore a transition point modulated by the signal-to-noise ratio and spectral properties of the design covariance matrix at which the selection accuracy of all considered algorithms degrades. Overall, we find that SCAD coupled with BIC or empirical Bayes model selection performs the best feature selection across the regression problems considered.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A data integration framework of additive manufacturing based on FAIR principles

Abstract Laser-powder bed fusion (L-PBF) is a popular additive manufacturing (AM) process with rich data sets coming from both in situ and ex situ sources. Data derived from multiple measurement modalities in an AM process capture unique features but often have different encoding methods; the challenge of data registration is not directly intuitive. In this work, we address the challenge of data registration between multiple modalities. Large data spaces must be organized in a machine-compatible method to maximize scientific output. FAIR (findable, accessible, interoperable, and reusable) principles are required to overcome challenges associated with data at various scales. FAIRified data enables a standardized format allowing for opportunities to generate automated extraction methods and scalability. We establish a framework that captures and integrates data from a L-PBF study such as radiography and high-speed camera video, linking these data sets cohesively allowing for future exploration. Graphical abstract

36 MATERIALS SCIENCE↗
DOE OSTI2026

Make the Fastest Faster: Importance Mask Synthesis for Interactive Volume Visualization using Reconstruction Neural Networks

Visualizing a large-scale volumetric dataset with high resolution is challenging due to the substantial computational time and space complexity. Recent deep learning-based image inpainting methods significantly improve rendering latency by reconstructing a high-resolution image for visualization in constant time on GPU from a partially rendered image where only a portion of pixels go through the expensive rendering pipeline. However, existing solutions need to render every pixel of either a predefined regular sampling pattern or an irregular sample pattern predicted from a low-resolution image rendering. Both methods require a significant amount of expensive pixel-level rendering. In this work, we provide Importance Mask Learning (IML) and Synthesis (IMS) networks, which are the first attempts to directly synthesize important regions of the regular sampling pattern from the user’s view parameters, to further minimize the number of pixels to render by jointly considering the dataset, user behavior, and the downstream reconstruction neural network. Our solution is a unified framework to handle various types of inpainting methods through the proposed differentiable compaction/decompaction layers. Experiments show our method can further improve the overall rendering latency of state-of-the-art volume visualization methods using reconstruction neural network for free when rendering scientific volumetric datasets. Our method can also directly optimize the off-the-shelf pre-trained reconstruction neural networks without elongated retraining.

Large-scale data↗
DOE OSTI2022

Science and Solutions for a Planet Under Pressure: Synthetic Research, Analytics, and Community Engagement on Five Priority Theme Areas

Support from the Department of Energy proved instrumental in supporting the work of Global Council for Science and the Environment (GCSE) on synthetic research, analysis, and community engagement, oriented around the themes and discussions from the GCSE Drawdown 2021 Conference — Research to Action: Science and Solutions for a Planet Under Pressure. These efforts helped inform and enhance the societal relevance of the knowledge that has been generated through the conference and, at the same time, advance the scientific insights acquired through synthesis and scientific translation efforts. The work centered on three main objectives: 1) documentation of findings from the completed GCSE 2021, culminating in the publication of a synthesis report; 2) development and vetting of integrated use cases that illustrate synthesis methods and enable scientific outreach, communications, and translational discussions among universities and the broader research community; and 3) strengthening the scientific basis for energy education research by sharing findings in university-educator fora.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Accelerating scientific discoveries through data-driven innovations

Developing artificial intelligence (AI) and machine learning (ML) methods that can accelerate scientific discoveries and advance science has become one of the important research directions for the AI/ML research community. It has been gaining increasing attention from researchers in diverse scientific areas, including biomedical science, materials science, climate science, physics, chemistry, and many others. Data-driven AI/ML innovations to enable reliable predictions and optimal decision making for scientific discoveries face several critical challenges, among which are high system complexity, large search space, incomplete knowledge, and small data, all of which demand novel strategies to effectively address them. Meeting these challenges and thereby accelerating scientific discoveries and industrial innovations, calls for research that can take full advantage of the latest advances in AI/ML to integrate data-driven techniques with scientific knowledge and is able to execute them in modern high-performance computing (HPC) environments at scale. This Patterns special collection "Accelerating scientific discoveries through data-driven innovations" features articles that showcase the promising roles of AI/ML and data-driven modeling in accelerating scientific discoveries and may inspire the next wave of data-driven innovations in various scientific domains.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Towards a Software Development Framework for Interconnected Science Ecosystems

The innovative science of the future must be multi-domain and interconnected to usher in the next generation of “self-driving” laboratories enabling consequential discoveries and transformative inventions. Such a disparate and interconnected ecosystem of scientific instruments will need to evolve using a system-of-systems (SoS) approach. The key to enabling application integration with such an SoS will be the use of Software Development Kits (SDKs). Currently, SDKs facilitate scientific research breakthroughs via algorithmic automation, databases and storage, optimization and structure, pervasive environmental monitoring, among others. However, existing SDKs lack instrument-interoperability and reusability capabilities, do not effectively work in an open federated architectural environment, and are largely isolated within silos of the respective scientific disciplines. Inspired by the scalable SoS framework, this work proposes the development of INTERSECT-SDK to provide a coherent environment for multi-domain scientific applications to benefit from the open federated architecture in an interconnected ecosystem of instruments. This approach will decompose functionality into loosely coupled software services for interoperability among several solutions that do not scale beyond a single domain and/or application. Furthermore, the proposed environment will allow operational and managerial inter-dependence while providing opportunities for the researchers to reuse software components from other domains and build universal solution libraries. We demonstrate this research for microscopy use-case, where we show how INTERSECT-SDK is developing the tools necessary to enable advanced scanning methods and accelerate scientific discovery.

Malviya, Addi Thakur↗
DOE OSTI2022

Performance assessment of ensembles of in situ workflows under resource constraints

Summary Scientific breakthroughs in biomolecular methods and improvements in hardware technology have shifted from a long‐running simulation to a large set of shorter simulations running simultaneously, called an ensemble. In an ensemble, simulations are usually coupled with analyses of data produced by the simulations. In situ methods can be used to analyze large volumes of data generated by scientific simulations at runtime (i.e., simulations and analyses are performed concurrently). In this work, we study the execution of ensemble‐based simulations paired with in situ analyses using in‐memory staging methods. Using an ensemble of molecular dynamics in situ workflows with multiple simulations and analyses, we first show that collecting traditional metrics such as makespan, instructions per cycle, memory usage, or cache miss ratio is not sufficient to characterize complex behaviors of ensembles. We propose a method to evaluate the performance of ensembles of workflows that captures multiple resource usage aspects: resource efficiency, resource allocation, and resource provisioning. Experimental results demonstrate that the proposed method can effectively distinguish the performance of different component placements in an ensemble with up to 32 ensemble members. By evaluating different co‐location scenarios, our proposed performance indicators demonstrate benefits of co‐locating simulation and coupled analyses within a compute node.

Do, Tu Mai Anh↗
DOE OSTI2024

Polymer Waste Valorization into Advanced Carbon Nanomaterials for Potential Energy and Environment Applications

The rise in universal population and accompanying demands have directed toward an exponential surge in the generation of polymeric waste. The estimate predicts that world-wide plastic production will rise to ≈590 million metric tons by 2050, whereas 5000 million more tires will be routinely abandoned by 2030. Handling this waste and its detrimental consequences on the Earth's ecosystem and human health presents a significant challenge. Converting the wastes into carbon-based functional materials viz. activated carbon, graphene, and nanotubes is considered the most scientific and adaptable method. Herein, this world provides an overview of the various sources of polymeric wastes, modes of build-up, impact on the environment, and management approaches. Update on advances and novel modifications made in methodologies for converting diverse types of polymeric wastes into carbon nanomaterials over the last 5 years are given. A remarkable focus is made to comprehend the applications of polymeric waste-derived carbon nanomaterials (PWDCNMs) in the CO 2 capture, removal of heavy metal ions, supercapacitor-based energy storage and water splitting with an emphasis on the correlation between PWDCNMs' properties and their performances. In conclusion, this review offers insights into emerging developments in the upcycling of polymeric wastes and their applications in environment and energy.

36 MATERIALS SCIENCE↗
DOE OSTI2025

STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. In conclusion, STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Metal additive manufacturing simulation across length, time, and computing scales

Metal additive manufacturing (AM) offers a unique opportunity for production of advanced materials and complex geometries. However, variability in microstructure and properties challenges conventional approaches to design, process optimization, qualification, and materials selection. Modeling and simulation can improve understanding of AM processing and materials, but also poses major challenges for existing computational methods. Simultaneously, modern scientific computing hardware has become increasingly complex, most notably with the adoption of hybrid architectures such as Graphical Processing Units (GPUs). If appropriately utilized, emerging computational capabilities provide an opportunity to reveal new insight into AM processing and the resulting material structure and properties. In this review we describe the computational AM landscape, identify critical gaps, and highlight opportunities to impact the development and application of AM. First, the requirements and challenges of representative AM problem statements will be defined. Here, these problems range from scientific studies to industrial applications and are designed to capture the breadth of challenges facing the AM community. Next, the current state of AM modeling and simulation is evaluated, broken down by enabling hardware and software, process simulation, microstructure simulation, and property simulation. Each section describes the diversity of simulation approaches and associated trade-offs in physical fidelity and computational expense. Each area is then assessed based on their suitability and readiness for current and developing computational architectures. Lastly, the greatest opportunities for future research and application are highlighted, including gaps in modeling capabilities, opportunities for near-term application, and key scientific challenges.

additive manufacturing↗
DOE OSTI2025

Loss Landscape Analysis for Reliable Quantized ML Models for Scientific Sensing

In this paper, we propose a method to perform empirical analysis of the loss landscape of machine learning (ML) models. The method is applied to two ML models for scientific sensing, which necessitates quantization to be deployed and are subject to noise and perturbations due to experimental conditions. Our method allows assessing the robustness of ML models to such effects as a function of quantization precision and under different regularization techniques -- two crucial concerns that remained underexplored so far. By investigating the interplay between performance, efficiency, and robustness by means of loss landscape analysis, we both established a strong correlation between gently-shaped landscapes and robustness to input and weight perturbations and observed other intriguing and non-obvious phenomena. Our method allows a systematic exploration of such trade-offs a priori, i.e., without training and testing multiple models, leading to more efficient development workflows. This work also highlights the importance of incorporating robustness into the Pareto optimization of ML models, enabling more reliable and adaptive scientific sensing systems.

Baldi, Tommaso [Pisa, Scuola Normale Superiore]↗
DOE OSTI2023

Coarse-grained methods for heterogeneous vesicles with phase-separated domains: Elastic mechanics of shape fluctuations, plate compression, and channel insertion

We develop coarse-grained particle approaches for studying the elastic mechanics of vesicles with heterogeneous membranes having phase-separated domains. We perform simulations both of passive shape fluctuations and of active systems where vesicles are subjected to compression between two plates or subjected to insertion into narrow channels. Analysis methods are developed for mapping particle configurations to continuum fields with spherical harmonics representations. Heterogeneous vesicles are found to exhibit rich behaviors where the heterogeneity can amplify surface two-point correlations, reduce resistance during compression, and augment vesicle transport times in channels. The developed methods provide general approaches for characterizing the mechanics of coarse-grained heterogeneous systems taking into account the roles of thermal fluctuations, geometry, and phase separation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Physics-Informed Learning Machines for Multiscale and Multiphysics Problems (PHILMS) (Technical Report)

The research work at University of California Santa Barbara (UCSB) resulted in several new developments in the areas of scientific machine learning, numerical analysis, and practical methods for data-driven modeling, prediction, reductions, and simulation. Many of the projects were carried out in collaboration with members of the national laboratories at Sandia National Laboratories (SNL), Pacific Northwestern National Laboratories (PNNL), and other institutions. Results included developing new scientific machine learning methods, related theory and mathematical frameworks for analysis and training, data-driven numerical solvers, and related tools and software for scientific computation. During the support period, over 16+ papers were submitted for publication, and 4 open-source software packages were developed and released (available at http://atzberger.org/). In addition, 7+ students and 2 post-docs were mentored in collaboration with the laboratory staff for future careers in academia, government labs, and industry.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

The Science of Scientific Software Development and Use

Increasingly powerful and affordable computing has revolutionized scientific and scholarly discovery across a broad range of fields. Computing relies on software, which has been rapidly growing in scope, diversity, and complexity. At the same time, the methods, processes, and tools used to produce and utilize this essential software are often ad hoc, and the study and improvement of them is often done without the benefit of direct funding or prioritization. Consequently, concerns are growing about the productivity of the developers and users of scientific software, its sustainability, and the trustworthiness of the results that it produces. The US Department of Energy Office of Science (DOE-SC) is at the forefront of modern software-enabled scientific discovery across numerous areas of computational, experimental, and observational science, including major investments in national user facilities that support these activities. In December 2021, the DOE-SC Office of Advanced Scientific Computing Research (ASCR) convened a workshop on basic research needs for the Science of Scientific Software Development and Use (SSSDU). Through keynote presentations, lightning talks, and breakout groups, participants discussed the current practice of software development, maintenance, evolution, and use, and considered how the scientific method could be used to examine these practices and develop more evidence-based approaches to enhance the impact of software and computing on all areas of science. Workshop participants identified three priority research directions (PRDs) and three important crosscutting themes that center on the following overarching insight: software has become an essential part of modern science that impacts new discovery, policy, and technological development. To have full confidence in science delivered via software, we must improve the processes and tools that help us create and use it, and this enhancement requires a deep understanding of the diverse array of teams and individuals doing the work. The full workshop report will be available at https://doi.org/10.2172/1846009.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Basic Research Needs in The Science of Scientific Software Development and Use: Investment in Software is Investment in Science

Increasingly powerful and affordable computing has revolutionized scientific and scholarly discovery across a broad range of fields. Computing relies on software, which has been rapidly growing in scope, diversity, and complexity. At the same time, the methods, processes, and tools used to produce and utilize this essential software are often ad hoc, and the study and improvement of them are often done without the benefit of direct funding or prioritization. Consequently, concerns are growing about the productivity of the developers and users of scientific software, its sustainability, and the trustworthiness of the results that it produces. Increased investment, especially in the characterization and improvement of how scientific software is developed and used, is important for sustaining and improving the impact of software as the scope and complexity of scientific efforts expand. Without this investment, we face the risk of diminishing returns on our software investments because the demands for increased functionality, usability, reliability, and more will not be sufficiently met. The US Department of Energy Office of Science (DOE/SC) is at the forefront of modern software-enabled scientific discovery across numerous areas of computational, experimental, and observational science, including major investments in national user facilities that support these activities. For many years, DOE/SC software investments have provided tremendous value to the scientific community. We want to continue and further improve the value of DOE/SC software efforts by using a scientific approach to understanding and improving how scientific software is developed and used. In December 2021, the DOE/SC Office of Advanced Scientific Computing Research (ASCR) convened a workshop on basic research needs for the Science of Scientific-Software Development and Use (SSSDU). Through keynote presentations, lightning talks, and breakout groups, which built on insights from 124 pre-workshop position papers, participants discussed the current practice of software development, maintenance, evolution, and use, and considered how the scientific method could be used to examine these practices and develop more evidence-based approaches to enhance the impact of software and computing on all areas of science. Workshop participants identified three priority research directions (PRDs) and three important crosscutting themes that center on the following overarching insight: Software has become an essential part of modern science, impacting discoveries, policy, and technological development. To maintain and improve confidence in science delivered via software, we must improve the processes and tools that help us create and use software, and this enhancement requires a deep understanding of the diverse array of teams and individuals doing the work.

97 MATHEMATICS AND COMPUTING↗