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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Applications and Techniques for Fast Machine Learning in Science

In this community review report, we discuss applications and techniques for fast machine learning (ML) in science—the concept of integrating powerful ML methods into the real-time experimental data processing loop to accelerate scientific discovery. The material for the report builds on two workshops held by the Fast ML for Science community and covers three main areas: applications for fast ML across a number of scientific domains; techniques for training and implementing performant and resource-efficient ML algorithms; and computing architectures, platforms, and technologies for deploying these algorithms. We also present overlapping challenges across the multiple scientific domains where common solutions can be found. This community report is intended to give plenty of examples and inspiration for scientific discovery through integrated and accelerated ML solutions. This is followed by a high-level overview and organization of technical advances, including an abundance of pointers to source material, which can enable these breakthroughs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Development of a Single-Phase, Transient, Subchannel Code, within the MOOSE Multi-Physics Computational Framework

Subchannel codes have been widely used for thermal-hydraulics analyses in nuclear reactors. This paper details the development of a novel subchannel code within the Idaho National Laboratory’s (INL) Multi-physics Object Oriented Simulation Environment (MOOSE). MOOSE is a parallel computational framework targeted at the solution of systems of coupled, nonlinear partial differential equations, that often arise in the simulation of nuclear processes. As such, it includes codes/modules able to solve the multiple linear and nonlinear physics that describe a nuclear reactor, under normal operation conditions or accidents. This includes thermal-hydraulics, fuel performance, and neutronics codes, between others. A MOOSE-based subchannel code is a new addition to the fleet of INL-developed codes, based on the MOOSE framework. In this work, we present the derivation of the subchannel equations for a single-phase fluid, we proceed with the description of the algorithm that is used to solve these equations and describe how this algorithm was implemented within MOOSE. We also present how this code can be coupled to the BISON fuel performance code. Next, we verify the friction model and the turbulent mixing model. We calibrate the turbulent modeling parameters for momentum mixing and enthalpy mixing, C T , β. We validate the code using experimental results and last demonstrate the coupling capabilities using a simple example.

42 ENGINEERING↗
DOE OSTI2020

A Dynamic Amplitude-Correcting Gradient Estimation Technique to Align X-ray Focusing Optics

High-brightness X-rays, as produced at synchrotrons and X-ray free electron laser (XFEL) facilities, are used to characterize materials in a variety of scientific experiments. In most cases, effective use of the high-energy light requires precisely-aligned focusing optics; one example being a compound refractive lens (CRL). To align a CRL, the position and rotation must be optimized along four axes. In practice, this is a labor-intensive, time-consuming manual process that can monopolize scarce experimental time at the necessary X-ray facilities. Models of the expected Xray transmission function suggest that this task can be automated; however, the temporally-varying intensity at X-ray free electron laser facilities preclude the direct use of standard implementations of optimization solvers such as steepest descent algorithms. In this paper, we propose a novel technique to estimate the gradient of noisy functions with temporally-varying amplitudes. We construct this dynamicamplitude correction by systematically sampling a fixed central location within the standard finite difference stencil, accounting for the observed changes in time, and normalizing the difference quotients against those fluctuations. In addition to a rigorous error analysis of the sampling technique, we demonstrate its efficacy in stochastic descent optimization methods. Further, we demonstrate how this approach may be implemented to optimize X-ray focusing optics at synchrotrons or XFEL facilities

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Lattice QCD and the Computational Frontier

The search for new physics requires a joint experimental and theoretical effort. Lattice QCD is already an essential tool for obtaining precise model-free theoretical predictions of the hadronic processes underlying many key experimental searches, such as those involving heavy flavor physics, the anomalous magnetic moment of the muon, nucleon-neutrino scattering, and rare, second-order electroweak processes. As experimental measurements become more precise over the next decade, lattice QCD will play an increasing role in providing the needed matching theoretical precision. Achieving the needed precision requires simulations with lattices with substantially increased resolution. As we push to finer lattice spacing we encounter an array of new challenges. They include algorithmic and software-engineering challenges, challenges in computer technology and design, and challenges in maintaining the necessary human resources. In this white paper we describe those challenges and discuss ways they are being dealt with. Overcoming them is key to supporting the community effort required to deliver the needed theoretical support for experiments in the coming decade.

Boyle, Peter↗
DOE OSTI2020

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays allows the characterization of large numbers of enhancers for the first time. Here, we developed a framework using Drosophila STARR-seq to create shape-matching filters based on meta-profiles of epigenetic features. We integrated these features with supervised machine-learning algorithms to predict enhancers. We further demonstrated that our model could be transferred to predict enhancers in mammals. We comprehensively validated the predictions using a combination of in vivo and in vitro approaches, involving transgenic assays in mice and transduction-based reporter assays in human cell lines (153 enhancers in total). The results confirmed that our model can accurately predict enhancers in different species without re-parameterization. Finally, we examined the transcription factor binding patterns at predicted enhancers versus promoters. Here, we demonstrated that these patterns enable the construction of a secondary model that effectively distinguishes enhancers and promoters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

TEMImageNet training library and AtomSegNet deep-learning models for high-precision atom segmentation, localization, denoising, and deblurring of atomic-resolution images

Abstract Atom segmentation and localization, noise reduction and deblurring of atomic-resolution scanning transmission electron microscopy (STEM) images with high precision and robustness is a challenging task. Although several conventional algorithms, such has thresholding, edge detection and clustering, can achieve reasonable performance in some predefined sceneries, they tend to fail when interferences from the background are strong and unpredictable. Particularly, for atomic-resolution STEM images, so far there is no well-established algorithm that is robust enough to segment or detect all atomic columns when there is large thickness variation in a recorded image. Herein, we report the development of a training library and a deep learning method that can perform robust and precise atom segmentation, localization, denoising, and super-resolution processing of experimental images. Despite using simulated images as training datasets, the deep-learning model can self-adapt to experimental STEM images and shows outstanding performance in atom detection and localization in challenging contrast conditions and the precision consistently outperforms the state-of-the-art two-dimensional Gaussian fit method. Taking a step further, we have deployed our deep-learning models to a desktop app with a graphical user interface and the app is free and open-source. We have also built a TEM ImageNet project website for easy browsing and downloading of the training data.

25 ENERGY STORAGE↗
DOE OSTI2024

Analysis of neoclassical tearing mode stabilization experiment by electron cyclotron injection in KSTAR

We report the neoclassical tearing mode (NTM) stabilization experimental results by injection of the electron cyclotron (EC) beam in KSTAR, and its analysis with integrated modelling. In the KSTAR experiment, NTM was intentionally induced and the EC beam was injected by the plasma control system (PCS) to stabilize it. Here, the EC angle was controlled based on the minimum seeking algorithm for the island growth rate. Although the EC angle was not changed significantly, the island width significantly decreased towards the end of the experiment followed by the recovery of plasma performance. To assess the NTM stabilization experiment from a stability perspective, we performed integrated modelling with TRIASSIC utilizing the reconstructed equilibrium with magnetic diagnostics and motional stark effect diagnostics. As a result, we observed that the NTM is stabilized by EC.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Robust identification of multiple-input single-output system response for efficient pickup noise removal from tokamak diagnostics

We report electromagnetic pickup noise in the tokamak environment imposes an imminent challenge for measuring weak diagnostic photocurrents in the nA range. The diagnostic signal can be contaminated by an unknown mixture of crosstalk signals from coils powered by currents in the kA range. To address this issue, an algorithm for robust identification of linear multi-input single-output (MISO) systems has been developed. The MISO model describes the dynamic relationship between measured signals from power sources and observed signals in the diagnostic and allows for a precise subtraction of the noise component. The proposed method was tested on experimental diagnostic data from the DIII-D tokamak, and it has reduced noise by up to 20 dB in the 1–20 kHz range.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Scaling Out a Combinatorial Algorithm for Discovering Carcinogenic Gene Combinations to Thousands of GPUs

Cancer is a leading cause of death in the US, second only to heart disease. It is primarily a result of a combination of an estimated two-nine genetic mutations (multi-hit combinations). Although a body of research has identified hundreds of cancer-causing genetic mutations, we don’t know the specific combination of mutations responsible for specific instances of cancer for most cancer types. An approximate algorithm for solving the weighted set cover problem was previously adapted to identify combinations of genes with mutations that may be responsible for individual instances of cancer. However, the algorithm’s computational requirement scales exponentially with the number of genes, making it impractical for identifying more than three-hit combinations, even after the algorithm was parallelized and scaled up to a V100 GPU. Since most cancers have been estimated to require more than three hits, we scaled out the algorithm to identify combinations of four or more hits using 1000 nodes (6000 V100 GPUs with ≈48×106 processing cores) on the Summit supercomputer at Oak Ridge National Laboratory. Efficiently scaling out the algorithm required a series of algorithmic innovations and optimizations for balancing an exponentially divergent workload across processors and for minimizing memory latency and inter-node communication. We achieved an average strong scaling efficiency of 90.14% (80.96%–97.96% for 200 to 1000 nodes), compared to a 100 node run, with 84.18% scaling efficiency for 1000 nodes. With experimental validation, the multi-hit combinations identified here could provide further insight into the etiology of different cancer subtypes and provide a rational basis for targeted combination therapy.

Dash, Sajal↗
DOE OSTI2023

High-Level Synthesis of Irregular Applications: A Case Study on Influence Maximization

The Influence Maximization problem is the problem of identifying a small cohort of actors from a broader population that, when initially activated in a diffusion process, are expected to result in a large number of activations in the population. While the problem is known to be NP-hard, several approximation algorithms have been devised by leveraging its submodular structure. While these algorithms are theoretically efficient, they are computationally very expensive in practice. This work advances the current state-of-the-art parallelization scheme for the IMM algorithm by devising the adoption of custom hardware accelerators implemented on FPGAs by leveraging High Level Synthesis from OpenCL. We study the performance of our proposed approach by exploring optimizations tailored at improving the parallel efficiency of the accelerators and highlight their effects and limitations in accelerating complex graph analytic applications. Our experimental evaluation shows that FPGA acceleration can improve the performance of the LT diffusion model up to 1.72x for the entire application and up to 2.90x for its most important kernel with respect to a CPU only parallel execution. The FPGA acceleration of the LT model shows also a 1.54x reduction in energy consumption when compared to a parallel CPU only run.

Neff, Reece W.↗
DOE OSTI2020

Determining the Length Scale of Transport Impedances in Li-Ion Electrodes: Li(Ni 0.33 Mn 0.33 Co 0.33 )O 2

Battery cathodes are complex multiscale, multifunctional materials. The length scale at which the dominant impedance arises may be difficult to determine even with the most advanced experimental characterization efforts, and thus modeling can play an important role in analysis. Discharge and voltage relaxation curves, interrogated with theory, are used to distinguish between transport impedance that arise on the scale of the active crystal and on the scale of agglomerates (secondary particles) comprised of nanoscale crystals. Model-selection algorithms are applied to determine that the agglomerate scale is dominant in the Li Ni 0.33 Mn 0.33 Co 0.33 O 2 electrode studied here. Furthermore, conditions where the agglomerate and crystal-scale models yield distinct simulation results are demonstrated, providing approaches that can be applied to other systems.

25 ENERGY STORAGE↗
DOE OSTI2021

Optimal dimensionality selection for independent component analysis of transcriptomic data

Independent component analysis is an unsupervised machine learning algorithm that separates a set of mixed signals into a set of statistically independent source signals. Applied to high-quality gene expression datasets, independent component analysis effectively reveals both the source signals of the transcriptome as co-regulated gene sets, and the activity levels of the underlying regulators across diverse experimental conditions. Two major variables that affect the final gene sets are the diversity of the expression profiles contained in the underlying data, and the user-defined number of independent components, or dimensionality, to compute. Availability of high-quality transcriptomic datasets has grown exponentially as high-throughput technologies have advanced; however, optimal dimensionality selection remains an open question. We computed independent components across a range of dimensionalities for four gene expression datasets with varying dimensions (both in terms of number of genes and number of samples). We computed the correlation between independent components across different dimensionalities to understand how the overall structure evolves as the number of user-defined components increases. We then measured how well the resulting gene clusters reflected known regulatory mechanisms, and developed a set of metrics to assess the accuracy of the decomposition at a given dimension. We found that over-decomposition results in many independent components dominated by a single gene, whereas under-decomposition results in independent components that poorly capture the known regulatory structure. From these results, we developed a new method, called OptICA, for finding the optimal dimensionality that controls for both over- and under-decomposition. Specifically, OptICA selects the highest dimension that produces a low number of components that are dominated by a single gene. We show that OptICA outperforms two previously proposed methods for selecting the number of independent components across four transcriptomic databases of varying sizes. OptICA avoids both over-decomposition and under-decomposition of transcriptomic datasets resulting in the best representation of the organism’s underlying transcriptional regulatory network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Iterative wavefront optimization of ultrafast laser beams carrying orbital angular momentum

Structured intense laser beams offer degrees of freedom that are highly attractive for high-field science applications. However, the performance of high-power laser beams in these applications is often hindered by deviations from the desired spatiotemporal profile. This study reports the wavefront optimization of ultrafast Laguerre-Gaussian beams through the synergy of adaptive optics and genetic algorithm-guided feedback. The results indicate that the intensity fluctuations along the perimeter of the target ring-shaped profile can be reduced up to ~15%. Furthermore, the radius of the ring beam profile can be tailored to a certain extent by establishing threshold fitting criteria. The versatility of this approach is experimentally demonstrated in conjunction with different focusing geometries.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

A DATA EFFICIENT SPARSE MODELING FRAMEWORK FOR POWER ESTIMATION IN WATER TREATMENT SENSING OPERATIONS

With increasing freshwater scarcity, advanced process design mechanisms such as Closed-Circuit Reverse Osmosis (CCRO) and Digital/Physical Twin systems are gaining traction in water treatment and reuse operations. While digital and physical twin models enable improved system insight and control, their development is often expensive and computationally intensive, requiring large volumes of synthetic or experimental data to characterize underlying process dynamics. This work introduces a sparse surrogate modeling framework to estimate power consumption from measured flow and pressure variables, along with their nonlinear polynomial and interaction expansions. To ensure model reliability and reduce overfitting, a two-stage pipeline is proposed. First, a dynamic data filtering algorithm is employed to remove uninformative observations and transient operational states. Second, a sparse penalized regression technique is applied to select a minimal set of parsimonious features. The proposed model achieves high sparsity, retaining only 7 out of 34 candidate features (≈79.41% sparsity) while delivering a root mean square error (RMSE) of 0.072 on the test dataset.

Mukherjee, Subrata [ORNL] (ORCID:0000000309930338)↗
DOE OSTI2022

Particle Swarm Optimization Algorithm for Critical Experiment Design

Nuclear criticality experiments are used to validate nuclear cross section data used by simulation software. This is typically achieved by designing a critical system with a high sensitivity to a certain material’s cross section. Once the experiment has been carried out, a high fidelity model of the system is developed into a benchmark. When this benchmark model is simulated by a transport code, some of the difference between the experimental and computational effective neutron multiplication factor can be attributed to inaccurate nuclear data. Nuclear data evaluators then can make adjustments accordingly to improve cross section data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Bayesian sequential optimal experimental design for nonlinear models using policy gradient reinforcement learning

We present a mathematical framework and computational methods for optimally designing a finite sequence of experiments. This sequential optimal experimental design (sOED) problem is formulated as a finite-horizon partially observable Markov decision process (POMDP) under a Bayesian setting and with information-theoretic utilities. The formulation is general and may accommodate continuous random variables, non-Gaussian posteriors, and nonlinear forward models. The sOED design policy incorporates elements of feedback and lookahead simultaneously, and we show it to generalize the commonly-used batch and greedy design strategies. We solve for the sOED policy using the policy gradient (PG) method from reinforcement learning, and provide a derivation for the PG expression in the sOED context. Adopting an actor-critic approach, the policy and value functions are parameterized using deep neural networks and improved via PG estimates produced from simulated episodes of designs and observations. The new PG-sOED algorithm is first validated on a linear-Gaussian benchmark, and then compared against other design baselines on a sensor movement problem for contaminant source inversion in a convection-diffusion field. As a result, we provide explanation for the policy behaviors using knowledge of the underlying physical process.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

The Pixel Anomaly Detection Tool : a user-friendly GUI for classifying detector frames using machine-learning approaches

Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining structure-factor amplitudes for serial crystallography or single-particle imaging experiments. Here, a new data-classification tool is reported that offers a variety of machine-learning algorithms to sort data trained either on manual data sorting by the user or by profile fitting the intensity distribution on the detector based on the experiment. This is integrated into an easy-to-use graphical user interface, specifically designed to support the detectors, file formats and software available at most X-ray free electron laser facilities. The highly modular design makes the tool easily expandable to comply with other X-ray sources and detectors, and the supervised learning approach enables even the novice user to sort data containing unwanted artefacts or perform routine data-analysis tasks such as hit finding during an experiment, without needing to write code.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina

Abstract Structure‐based virtual high‐throughput screening involves docking chemical libraries to targets of interest. A parameter pertinent to the accuracy of the resulting pose is the root mean square deviation (RMSD) from a known crystallographic structure, i. e., the ‘docking power’. Here, using a popular algorithm, Autodock Vina, as a model program, we evaluate the effects of varying two common docking parameters: the box size (the size of docking search space) and the exhaustiveness of the global search (the number of independent runs starting from random ligand conformations) on the RMSD from the PDBbind v2017 refined dataset of experimental protein‐ligand complexes. Although it is clear that exhaustiveness is an important parameter, there is wide variation in the values used, with variation between 1 and >100. We, therefore, evaluated a combination of cubic boxes of different sizes and five exhaustiveness values (1, 8, 25, 50, 75, 100) within the range of those commonly adopted. The results show that the default exhaustiveness value of 8 performs well overall for most box sizes. In contrast, for all box sizes, but particularly for large boxes, an exhaustiveness value of 1 led to significantly higher median RMSD (mRMSD) values. The docking power was slightly improved with an exhaustiveness of 25, but the mRMSD changes little with values higher than 25. Therefore, although low exhaustiveness is computationally faster, the results are more likely to be far from reality, and, conversely, values >25 led to little improvement at the expense of computational resources. Overall, we recommend users to use at least the default exhaustiveness value of 8 for virtual screening calculations.

Agarwal, Rupesh↗