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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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At least 19 records

Ps and Qs: Quantization-Aware Pruning for Efficient Low Latency Neural Network Inference

Efficient machine learning implementations optimized for inference in hardware have wide-ranging benefits, depending on the application, from lower inference latency to higher data throughput and reduced energy consumption. Two popular techniques for reducing computation in neural networks are pruning, removing insignificant synapses, and quantization, reducing the precision of the calculations. In this work, we explore the interplay between pruning and quantization during the training of neural networks for ultra low latency applications targeting high energy physics use cases. Techniques developed for this study have potential applications across many other domains. We study various configurations of pruning during quantization-aware training, which we term quantization-aware pruning, and the effect of techniques like regularization, batch normalization, and different pruning schemes on performance, computational complexity, and information content metrics. We find that quantization-aware pruning yields more computationally efficient models than either pruning or quantization alone for our task. Further, quantization-aware pruning typically performs similar to or better in terms of computational efficiency compared to other neural architecture search techniques like Bayesian optimization. Surprisingly, while networks with different training configurations can have similar performance for the benchmark application, the information content in the network can vary significantly, affecting its generalizability.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Deep Generative Models that Solve PDEs: Distributed Computing for Training Large Data-Free Models

Recent progress in scientific machine learning (SciML) has opened up the possibility of training novel neural network architectures that solve complex partial differential equations (PDEs). Several (nearly data free) approaches have been recently reported that successfully solve PDEs, with examples including deep feed forward networks, generative networks, and deep encoder-decoder networks. However, practical adoption of these approaches is limited by the difficulty in training these models, especially to make predictions at large output resolutions (≥1024×1024). Here we report on a software framework for data parallel distributed deep learning that resolves the twin challenges of training these large SciML models - training in reasonable time as well as distributing the storage requirements. Our framework provides several out of the box functionality including (a) loss integrity independent of number of processes, (b) synchronized batch normalization, and (c) distributed higher-order optimization methods. We show excellent scalability of this framework on both cloud as well as HPC clusters, and report on the interplay between bandwidth, network topology and bare metal vs cloud. We deploy this approach to train generative models of sizes hitherto not possible, showing that neural PDE solvers can be viably trained for practical applications. We also demonstrate that distributed higher-order optimization methods are 2-3× faster than stochastic gradient-based methods and provide minimal convergence drift with higher batch-size.

PDEs↗

Continuous conditional generative adversarial networks for data-driven solutions of poroelasticity with heterogeneous material properties

Machine learning-based data-driven modeling can allow computationally efficient time-dependent solutions of PDEs, such as those that describe subsurface multiphysical problems. In this work, our previous approach (Kadeethum et al., 2021d) of conditional generative adversarial networks (cGAN) developed for the solution of steady-state problems involving highly heterogeneous material properties is extended to time-dependent problems by adopting the concept of continuous cGAN (CcGAN). The CcGAN that can condition continuous variables is developed to incorporate the time domain through either element-wise addition or conditional batch normalization. Moreover, this framework can handle training data that contain different timestamps and then predict timestamps that do not exist in the training data. As a numerical example, the transient response of the coupled poroelastic process is studied in two different permeability fields: Zinn & Harvey transformation and a bimodal transformation. The proposed CcGAN uses heterogeneous permeability fields as input parameters while pressure and displacement fields over time are model output. Our results show that the model provides sufficient accuracy with computational speed-up. This robust framework will enable us to perform real-time reservoir management and robust uncertainty quantification in poroelastic problems.

97 MATHEMATICS AND COMPUTING↗

Cooperativity in the Aldol Condensation Using Bifunctional Mesoporous Silica–Poly(styrene) MCM-41 Organic/Inorganic Hybrid Catalysts

This work explores the efficacy of silica/organic hybrid catalysts, where the organic component is built from linear aminopolymers appended to the silica support within the support mesopores. Specifically, the role of molecular weight and polymer chain composition in amine-bearing atom transfer radical polymerization-synthesized poly(styrene-co-2-(4-vinylbenzyl)isoindoline-1,3-dione) copolymers is probed in the aldol condensation of 4-nitrobenzaldehyde and acetone. Controlled polymerization produces protected amine-containing poly(styrene) chains of controlled molecular weight and dispersity, and a grafting-to thiol–ene coupling approach followed by a phthalimide deprotection step are used to covalently tether and activate the polymer hybrid catalysts prior to the catalytic reactions. Site-normalized batch kinetics are used to assess the role of polymer molecular weight and chain composition in the cooperative catalysis. Lower-molecular-weight copolymers are demonstrated to be more active than catalysts built from only molecular organic components or from higher-molecular-weight chains. Molecular dynamics simulations are used to probe the role of polymer flexibility and morphology, whereby it is determined that higher-molecular-weight hybrid structures result in congested pores that inhibit active site cooperativity and the diffusivity of reagents, thus resulting in lower rates during the reaction.

36 MATERIALS SCIENCE↗

Navigating the Noise: Bringing Clarity to ML Parameterization Design With O $\boldsymbol{\mathcal{O}}$(100) Ensembles

Abstract Machine‐learning (ML) parameterizations of subgrid processes (here of turbulence, convection, and radiation) may one day replace conventional parameterizations by emulating high‐resolution physics without the cost of explicit simulation. However, uncertainty about the relationship between offline and online performance (i.e., when integrated with a large‐scale general circulation model) hinders their development. Much of this uncertainty stems from limited sampling of the noisy, emergent effects of upstream ML design decisions on downstream online hybrid simulation. Our work rectifies the sampling issue via the construction of a semi‐automated, end‐to‐end pipeline for size ensembles of hybrid simulations, revealing important nuances in how systematic reductions in offline error manifest in changes to online error and online stability. For example, removing dropout and switching from a Mean Squared Error to a Mean Absolute Error loss both reduce offline error, but they have opposite effects on online error and online stability. Other design decisions, like incorporating memory, converting moisture input from specific humidity to relative humidity, using batch normalization, and training on multiple climates do not come with any such compromises. Finally, we show that ensemble sizes of may be necessary to reliably detect causally relevant differences online. By enabling rapid online experimentation at scale, we can empirically settle debates regarding subgrid ML parameterization design that would have otherwise remained unresolved in the noise.

Lin, Jerry [Department of Earth System Sciences Un↗

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate

Abstract Photosynthetic microalgae are responsible for 50% of the global atmospheric CO2 fixation into organic matter and hold potential as a renewable bioenergy source. Their metabolic interactions with the surrounding microbial community (the algal microbiome) play critical roles in carbon cycling, but due to methodological limitations, it has been challenging to examine how community development is influenced by spatial proximity to their algal host. Here we introduce a copolymer-based porous microplate to co-culture algae and bacteria, where metabolites are constantly exchanged between the microorganisms while maintaining physical separation. In the microplate, we found that the diatom Phaeodactylum tricornutum accumulated to cell abundances ~20 fold higher than under normal batch conditions due to constant replenishment of nutrients through the porous structure. We also demonstrate that algal-associated bacteria, both single isolates and complex communities, responded to inorganic nutrients away from their host as well as organic nutrients originating from the algae in a spatially predictable manner. These experimental findings coupled with a mathematical model suggest that host proximity and algal culture growth phase impact bacterial community development in a taxon-specific manner through organic and inorganic nutrient availability. Our novel system presents a useful tool to investigate universal metabolic interactions between microbes in aquatic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

PRODeepSyn: predicting anticancer synergistic drug combinations by embedding cell lines with protein–protein interaction network

Abstract Although drug combinations in cancer treatment appear to be a promising therapeutic strategy with respect to monotherapy, it is arduous to discover new synergistic drug combinations due to the combinatorial explosion. Deep learning technology holds immense promise for better prediction of in vitro synergistic drug combinations for certain cell lines. In methods applying such technology, omics data are widely adopted to construct cell line features. However, biological network data are rarely considered yet, which is worthy of in-depth study. In this study, we propose a novel deep learning method, termed PRODeepSyn, for predicting anticancer synergistic drug combinations. By leveraging the Graph Convolutional Network, PRODeepSyn integrates the protein–protein interaction (PPI) network with omics data to construct low-dimensional dense embeddings for cell lines. PRODeepSyn then builds a deep neural network with the Batch Normalization mechanism to predict synergy scores using the cell line embeddings and drug features. PRODeepSyn achieves the lowest root mean square error of 15.08 and the highest Pearson correlation coefficient of 0.75, outperforming two deep learning methods and four machine learning methods. On the classification task, PRODeepSyn achieves an area under the receiver operator characteristics curve of 0.90, an area under the precision–recall curve of 0.63 and a Cohen’s Kappa of 0.53. In the ablation study, we find that using the multi-omics data and the integrated PPI network’s information both can improve the prediction results. Additionally, the case study demonstrates the consistency between PRODeepSyn and previous studies.

Wang, Xiaowen↗

TorchBraid: High-Performance Layer-Parallel Training of Deep Neural Networks with MPI and GPU Acceleration

TorchBraid is a high-performance implementation of layer-parallel training for deep neural networks (DNNs) supporting MPI-based parallelism and GPU acceleration. Layer-parallel training has been developed to overcome the serialization inherent in forward and backward propagation of DNNs that limits utilization of computational resources in the strong scaling limit. To achieve this, TorchBraid integrates the PyTorch neural network framework with the state-of-the-art XBraid time-parallel library. Furthermore, this article presents the use and performance of TorchBraid, in addition to solutions for overcoming the algorithmic challenges inherent in combining automatic differentiation with layer-parallel. Results are presented with and without GPU acceleration for the Tiny ImageNet and MNIST image classification data sets, as well as recurrent neural networks. Overall, TorchBraid enables fast training of DNNs, both in a strong and weak scaling context. In addition to the TorchBraid software, several new advances in applying layer-parallel algorithms are detailed. Integration of layer-parallel with data-parallel algorithms is presented for the first time, showing the computational advantages of the combination. Standard deep learning techniques, like batch-normalization, are developed for layer-parallel training. Finally, a new approach combining layer-parallel with spatial coarsening in order to accelerate training for 3D image classification shows roughly a 10× speedup over serial execution.

Layer-parallel↗

DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network

Abstract Background Estimation of the accuracy (quality) of protein structural models is important for both prediction and use of protein structural models. Deep learning methods have been used to integrate protein structure features to predict the quality of protein models. Inter-residue distances are key information for predicting protein’s tertiary structures and therefore have good potentials to predict the quality of protein structural models. However, few methods have been developed to fully take advantage of predicted inter-residue distance maps to estimate the accuracy of a single protein structural model. Result We developed an attentive 2D convolutional neural network (CNN) with channel-wise attention to take only a raw difference map between the inter-residue distance map calculated from a single protein model and the distance map predicted from the protein sequence as input to predict the quality of the model. The network comprises multiple convolutional layers, batch normalization layers, dense layers, and Squeeze-and-Excitation blocks with attention to automatically extract features relevant to protein model quality from the raw input without using any expert-curated features. We evaluated DISTEMA’s capability of selecting the best models for CASP13 targets in terms of ranking loss of GDT-TS score. The ranking loss of DISTEMA is 0.079, lower than several state-of-the-art single-model quality assessment methods. Conclusion This work demonstrates that using raw inter-residue distance information with deep learning can predict the quality of protein structural models reasonably well. DISTEMA is freely at https://github.com/jianlin-cheng/DISTEMA

59 BASIC BIOLOGICAL SCIENCES↗

PNNL-Predictive-Phenomics/ProteoMeter

ProteoMeter is a Python package that assists in the statistical analysis of global proteomics, protein post-translation modification (PTM), and limited proteolysis (LiP) data. It contains batch correction, normalization, and statistical testing methods, as well as functions that "roll up" peptide-level data to the single-site level. It has a robust user configuration system, allowing it to flexibly integrate different types of experiment designs. For basic usage, a simple configuration file provides the essential functionality. Advanced users have access to the entire statistical pipeline for fine-tuning analyses. Processed data is easily exported to many common spreadsheet and data-frame formats.

Rozum, Jordan [Pacific Northwest National Lab]↗

Control Selection for the Neutralization Tank in the Aqueous Recovery System at SRPPF

• Neutralization and solidification is the last step in the Aqueous Recovery Process • All waste streams are acidic and must be neutralized before being combined with grout in a solidification drum • The neutralization tank is a 250 L, 24” diameter, 45” high tank • The batch tank is a 125 L tank • The solidification drum is a 55-gallon drum, pre-filled with grout & a sacrificial mixing paddle • Normal mass in neutralization tank: 50 g Pu • Normal mass in batch tank or drum: 25 g Pu

Dressman, Phillip M. [Savannah River Nuclear Solut↗

Learning functional priors and posteriors from data and physics

In this work, we develop a new Bayesian framework based on deep neural networks to be able to extrapolate in space-time using historical data and to quantify uncertainties arising from both noisy and gappy data in physical problems. Specifically, the proposed approach has two stages: (1) prior learning and (2) posterior estimation. At the first stage, we employ the physics-informed Generative Adversarial Networks (PI-GAN) to learn a functional prior either from a prescribed function distribution, e.g., Gaussian process, or from historical data and physics. At the second stage, we employ the Hamiltonian Monte Carlo (HMC) method to estimate the posterior in the latent space of PI-GANs. In addition, we use two different approaches to encode the physics: (1) automatic differentiation, used in the physicsinformed neural networks (PINNs) for scenarios with explicitly known partial differential equations (PDEs), and (2) operator regression using the deep operator network (DeepONet) for PDE-agnostic scenarios. We then test the proposed method for (1) meta-learning for one-dimensional regression, and forward/inverse PDE problems (combined with PINNs); (2) PDE-agnostic physical problems (combined with DeepONet), e.g., fractional diffusion as well as saturated stochastic (100-dimensional) flows in heterogeneous porous media; and (3) spatial-temporal regression problems, i.e., inference of a marine riser displacement field using experimental data from the Norwegian Deepwater Programme (NDP). The results demonstrate that the proposed approach can provide accurate predictions as well as uncertainty quantification given very limited scattered and noisy data, since historical data could be available to provide informative priors. In summary, the proposed method is capable of learning flexible functional priors, e.g., both Gaussian and non-Gaussian process, and can be readily extended to big data problems by enabling mini-batch training using stochastic HMC or normalizing flows since the latent space is generally characterized as low dimensional.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Part II: Predicting performance of $\mathrm{DOWEX 21K}$ resin for remediation of comingled contaminants in groundwater

The selectivity of ion exchange (IX) resins for aqueous contaminant removal can be impacted by changing concentrations of competing natural groundwater ions. In a two-part investigation, the Hanford Site 200 West Area pump-and-treat (P&T) facility in Washington State, USA is used as a case study to evaluate the performance of two IX resins for groundwater treatment: Purolite® A532E for pertechnetate (TcO 4 - ) removal, explored in Part I, and DOWEX 21K (DOWEX) for uranium (U) removal. In Part II, DOWEX selectivity for U, as uranyl carbonate species, and uptake kinetics is quantified in a series of laboratory-scale aqueous batch experiments containing Hanford-relevant concentrations of competing anions nitrate (NO 3 - ), sulfate (SO 4 2- ), chloride (Cl - ), and carbonate (CO 3 2- ), as well as co-mingled contaminant TcO 4 - . Here the results demonstrate that DOWEX trimethylammonium functional groups are highly selective for U carbonate species (85–100 % uptake) under all conditions investigated. Only NO 3 - concentrations of 100 mM were shown to decrease U removal, with the extent (85–99 %) depending on competing anion concentrations present in solution. However, at the highest NO 3 - concentrations reported for groundwaters treated at the P&T facility (25 mM), the effect on U uptake is minimal. The batch sorption results are modeled to obtain chloride normalized equilibrium exchange coefficients (K) for predicting DOWEX performance: K SO4--/Cl- = 2.0, K NO3-/Cl- = 5.0, K HCO3-/Cl- = 1.5, K TcO4-/Cl- = 2,000, and K U/Cl- = 50,000. These K values predict little effect of current and future influent chemistries on U removal by DOWEX, where both uranyl carbonate species and TcO 4 - are removed such that effluent concentrations meet groundwater treatment requirements.

54 ENVIRONMENTAL SCIENCES↗

Catalytic Consequences of Hierarchical Pore Architectures within MFI and FAU Zeolites for Polyethylene Conversion

The benefits of hierarchical zeolites for the conversion of bulky molecules like polymeric waste have been reported in the literature; however, the impact of mesopore sizes and connectivities on rates, product selectivities, and catalyst deactivation in the context of plastic upcycling has not been systematically probed. Here, in this study, we synthesized a suite of hierarchical MFI and FAU zeolites via desilication under varying conditions for metal-free polyethylene conversion reactions under batch and flow conditions (473–523 K). Polyethylene (solid) conversion rates (normalized by Bro̷nsted acid site density) were higher on hierarchical than parent microporous MFI regardless of mesopore connectivities, i.e., open or constricted, suggesting that the incorporation of mesopores facilitates diffusion of intermediate products to access medium-pore protons for successive scission events. Furthermore, higher branched:linear gaseous product ratios were produced on hierarchical than parent MFI, since mesopores allow for egress of bulkier molecules without undergoing further secondary events, e.g., isomerization back to linear alkanes/alkenes or beta scission. Solid conversion rates on hierarchical FAU synthesized via desilication with cetyltrimethylammonium bromide (CTABr), however, were not higher than parent FAU, likely because the presence of CTABr facilitates recrystallization of leached species to form composites (hierarchical FAU and ordered mesoporous materials) with more isolated mesopores. The stagnation in rates, despite increased mesopore volumes (>0.22 cm 3 g –1 ), highlights the importance of confinement effects provided by micropores for cleaving C–C bonds at modest reaction conditions. In situ 1 H MAS NMR performed on polyethylene with MFI zeolite show that PE isomerizes (and potentially deconstructs) at temperatures near 450 K, highlighting the role of Bro̷nsted acid sites in activating C–C bonds under mild reaction conditions. Catalyst recyclability studies showed that all catalysts undergo deactivation during plastic upcycling reactions, but to varying extents. Overall, hierarchical materials have better catalyst stability than parent materials, although the differences in stability between hierarchical and parent FAU are smaller than those for MFI. Taken together, these findings demonstrate how rates, selectivities, and catalyst deactivation from plastic upcycling reactions can be controlled via fine-tuning the identity and connectivity of mesopores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

TransPlatformer

We propose TransPlatformer for translating toxicogenomics from one platform to another. Transcriptomic profiling has evolved through multiple generations of technology, from microarrays (e.g., Affymetrix, CodeLink) to more recent high-throughput sequencing and targeted panels such as S1500+. Microarrays, which dominated gene expression studies in the early 2000s, provided affordable and high-throughput transcript quantification but suffered from cross-hybridization issues and limited dynamic range . RNA-Seq, introduced in the late 2000s, revolutionized transcriptomics by enabling unbiased and comprehensive gene expression analysis, albeit at higher costs and computational demands . Despite advances, many studies rely on historical microarray data, necessitating the translation of legacy data into modern platforms to ensure continuity and comparability. This translation is complicated by factors such as platform-specific probe design, differences in transcript coverage, and batch effects . Existing methods for cross-platform mapping include statistical normalization, machine learning models, and biological anchoring approaches. The ability to translate transcriptomic data between platforms has broad implications, including enhanced meta-analyses, improved toxicological modeling, and better integration of historical datasets with contemporary research. TransPlatformer seeks to contribute to this effort by evaluating translation methodologies and proposing novel strategies to improve cross-platform gene expression harmonization. In this repository there are code examples for TransPlatformer implementation

Cong, Guojing↗

Composition Measurements of the HFG1 Glasses

This report provides results from the analyses of glass compositions for the High Fluoride Glasses-1, a series of simulated nuclear waste glasses fabricated at the Pacific Northwest National Laboratory. The series included the quenched version of the glasses. These data will be used to validate or identify areas of potential characterization improvements in the current glass property/composition models. Chemical analyses were performed on a representative sample of each of the quenched glasses to allow for comparisons with the targeted compositions. The relative differences between the targeted and measured concentrations of F, K 2 0, and Li 2 O for some of the glasses were greater than 10%. Overall, there were no indications of errors in batching of the simulated waste glasses. These results can be used in further characterization of this series of glasses, including the normalization of Product Consistency Test results.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Summary Report for the Analysis of the Sludge Batch 7b (Macrobatch 9) DWPF Pour Stream Glass Sample for Canister S04023

In order to comply with the Defense Waste Processing Facility (DWPF) Waste Form Compliance Plan for Sludge Batch 7b, Savannah River National Laboratory (SRNL) personnel characterized the Defense Waste Processing Facility (DWPF) pour stream (PS) glass sample collected while filling canister S04023. This report summarizes the results of the compositional analysis for reportable oxides and radionuclides and the normalized Product Consistency Test (PCT) results. The PCT responses indicate that the DWPF produced glass that is significantly more durable than the Environmental Assessment glass. Results and further details are documented in SRNL-STI-2013-00462, Revision 1 “Analysis of the DWPF Sludge Batch 7b (Macrobatch 9) Pour Stream Glass Sample.”

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Grid Operator Analytics and Assessment Tools for Inverter- Based Resources Dominated Grid (GOAAT-IBR) Project Update

This presentation provides an update on the OPTIMA GOAAT project, with emphasis on the cloud-native data platform developed in-house to ingest, manage, and operationalize high-resolution power system data. Since our last NASPI presentation, accessible via OSTI ID #2671437, the project team advanced the design and deployment of a scalable architecture capable of handling both synchronized and non-synchronized streams, including PMU, point-on-wave (POW), COMTRADE, and SCADA data. These materials review the project status, recent progress, and key lessons learned. The core of the presentation examines the architecture and engineering of our cloud-native ingestion and data management platform. We then explain how pipelines were designed to collect, normalize, time-align, store, and serve heterogeneous data at scale. We will discuss design choices such as data models, streaming versus batch ingestion, storage tiers, and interoperability with analytics applications. Practical experiences with cloud-native technologies were shared during the event, including benefits, limitations, and integration challenges in a utility environment, along with methods used to improve performance, reduce latency, and optimize resource usage. The presentation also showcases user interface designs and visualization tools that convert raw measurements and analytics results into intuitive, actionable insights for operators and engineers. During the presentation examples were provided demonstrating how visualization, event views, and summarized analytics enhance situational awareness and support operational decision-making. These use cases illustrate how a well-designed data infrastructure can bridge the gap between high-volume measurements and practical grid operations.

Aminifar, Farrokh↗