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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 OSTI2020

Methods and Experiences for Developing Abstractions for Data-intensive, Scientific Applications

Developing software for scientific applications that require the integration of diverse types of computing, instruments, and data present challenges that are distinct from commercial software. These applications require scale, and the need to integrate various programming and computational models with evolving and heterogeneous infrastructure. Pervasive and effective abstractions for distributed infrastructures are thus critical; however, the process of developing abstractions for scientific applications and infrastructures is not well understood. While theory-based approaches for system development are suited for well-defined, closed environments, they have severe limitations for designing abstractions for scientific systems and applications. The design science research (DSR) method provides the basis for designing practical systems that can handle real-world complexities at all levels. In contrast to theory-centric approaches, DSR emphasizes both practical relevance and knowledge creation by building and rigorously evaluating all artifacts. In this work, we show how DSR provides a well-defined framework for developing abstractions and middleware systems for distributed systems. Specifically, we address the critical problem of distributed resource management on heterogeneous infrastructure over a dynamic range of scales, a challenge that currently limits many scientific applications. We use the pilot-abstraction, a widely used resource management abstraction for high-performance, high throughput, big data, and streaming applications, as a case study for evaluating the DSR activities. For this purpose, we analyze the research process and artifacts produced during the design and evaluation of the pilot-abstraction. We find DSR provides a concise framework for iteratively designing and evaluating systems. Finally, we capture our experiences and formulate different lessons learned.

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 OSTI2020

A Review of Computational Models for the Flow of Milled Biomass Part II: Continuum-Mechanics Models

The design of efficient material-handling systems for milled lignocellulosic biomass is challenging due to their complex particle morphologies and frictional interactions. Computational modeling, including the discrete element method (DEM) and continuum-based finite-element/volume methods, may offer scientific insight and predictive capabilities for the flow of milled biomass in hoppers and feeders. Herein, this article (Part II) presents a review of current state-of-the-art continuum models for the flow of milled biomass, whereas DEM models are reviewed in a companion article (Part I). Advances of numerical methods to solve the global governing equations are discussed first, followed by a comprehensive review of constitutive models for granular materials, including Drucker–Prager, hypoplastic, Cambridge-type, inertial-rheology, and nonlocal granular fluidity models. Specifically, we provide in-depth discussion on the suitability of those models for milled lignocellulosic biomass materials in terms of nonlinear elasticity, dependence of flow strength on pressure, density and shear rate, and compaction (dilation) associated with hardening (softening). Furthermore, our study shows that, despite the recent advances in continuum granular flow modeling, the most suitable constitutive models still need further development to account for material parametrization, multiflow regimes, and multiscale behavior before they can be reliably used to optimize the design and operation of biomass handling systems.

09 BIOMASS FUELS↗

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 OSTI2020

Seasonal grassland productivity forecast for the U.S. Great Plains using Grass–Cast

Every spring, ranchers in the drought-prone U.S. Great Plains face the same difficult challenge —trying to estimate how much forage will be available for livestock to graze during the upcoming summer grazing season. To reduce this uncertainty in predicting forage availability, we developed an innovative new grassland productivity forecast system, named Grass-Cast, to provide science-informed estimates of growing season above ground net primary production (ANPP). Grass-Cast uses over 30 yr of historical data including weather and the satellite-derived normalized vegetation difference index (NDVI)—combined with ecosystem modeling and seasonal precipitation forecasts—to predict if rangelands in individual counties are likely to produce below-normal, near-normal, or above-normal amounts of grass biomass (lbs/ac). Grass-Cast also provides a view of rangeland productivity in the broader region, to assist in larger scale decision-making—such as where forage resources for grazing might be more plentiful if a rancher’s own region is at risk of drought. Grass-Cast is updated approximately every two weeks from April through July. Each Grass-Cast forecast provides three scenarios of ANPP for the upcoming growing season based on different precipitation outlooks. Near real-time 8-d NDVI can be used to supplement Grass-Cast in predicting cumulative growing season NDVI and ANPP starting in mid-April for the Southern Great Plains and mid-May to early June for the Central and Northern Great Plains. Here, we present the scientific basis and methods for Grass-Cast along with the county-level production forecasts from 2017 and 2018 for ten states in the U.S. Great Plains. The correlation between early growing season forecasts and the end-of growing season ANPP estimate is >50% by late May or early June. In a retrospective evaluation, we compared Grass-Cast end-of-growing season ANPP results to an independent dataset and found that the two agreed 69% of the time over a 20-yr period. Although some predictive tools exist for forecasting upcoming growing season conditions, none predict actual productivity for the entire Great Plains. The Grass-Cast system could be adapted to predict grassland ANPP outside of the Great Plains or to predict perennial biofuel grass production.

54 ENVIRONMENTAL SCIENCES↗

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 OSTI2021

Change-point Detection and Image Segmentation for Time Series of Astrophysical Images

Many astrophysical phenomena are time-varying, in the sense that their intensity, energy spectrum, and/or the spatial distribution of the emission suddenly change. This paper develops a method for modeling a time series of images. Under the assumption that the arrival times of the photons follow a Poisson process, the data are binned into 4D grids of voxels (time, energy band, and x-y coordinates), and viewed as a time series of non-homogeneous Poisson images. The method assumes that at each time point, the corresponding multiband image stack is an unknown 3D piecewise constant function including Poisson noise. It also assumes that all image stacks between any two adjacent change points (in time domain) share the same unknown piecewise constant function. The proposed method is designed to estimate the number and the locations of all of the change points (in time domain), as well as all of the unknown piecewise constant functions between any pairs of the change points. The method applies the minimum description length principle to perform this task. A practical algorithm is also developed to solve the corresponding complicated optimization problem. Simulation experiments and applications to real data sets show that the proposed method enjoys very promising empirical properties. Applications to two real data sets, the XMM observation of a flaring star and an emerging solar coronal loop, illustrate the usage of the proposed method and the scientific insight gained from it.

79 ASTRONOMY AND ASTROPHYSICS↗

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↗