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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 OSTI2024

A Deep Learning-Driven Sampling Technique to Explore the Phase Space of an RNA Stem-Loop

The folding and unfolding of RNA stem-loops are critical biological processes; however, their computational studies are often hampered by the ruggedness of their folding landscape, necessitating long simulation times at the atomistic scale. Here, we adapted DeepDriveMD (DDMD), an advanced deep learning-driven sampling technique originally developed for protein folding, to address the challenges of RNA stem-loop folding. Although tempering- and order parameter-based techniques are commonly used for similar rare-event problems, the computational costs or the need for a priori knowledge about the system often present a challenge in their effective use. DDMD overcomes these challenges by adaptively learning from an ensemble of running MD simulations using generic contact maps as the raw input. DeepDriveMD enables on-the-fly learning of a low-dimensional latent representation and guides the simulation toward the undersampled regions while optimizing the resources to explore the relevant parts of the phase space. We showed that DDMD estimates the free energy landscape of the RNA stem-loop reasonably well at room temperature. Our simulation framework runs at a constant temperature without external biasing potential, hence preserving the information on transition rates, with a computational cost much lower than that of the simulations performed with external biasing potentials. Here, we also introduced a reweighting strategy for obtaining unbiased free energy surfaces and presented a qualitative analysis of the latent space. This analysis showed that the latent space captures the relevant slow degrees of freedom for the RNA folding problem of interest. Finally, throughout the manuscript, we outlined how different parameters are selected and optimized to adapt DDMD for this system. We believe this compendium of decision-making processes will help new users adapt this technique for the rare-event sampling problems of their interest.

Gupta, Ayush↗
DOE OSTI2023

Combining variational autoencoders and physical bias for improved microscopy data analysis *

Electron and scanning probe microscopy produce vast amounts of data in the form of images or hyperspectral data, such as electron energy loss spectroscopy or 4D scanning transmission electron microscope, that contain information on a wide range of structural, physical, and chemical properties of materials. To extract valuable insights from these data, it is crucial to identify physically separate regions in the data, such as phases, ferroic variants, and boundaries between them. In order to derive an easily interpretable feature analysis, combining with well-defined boundaries in a principled and unsupervised manner, here we present a physics augmented machine learning method which combines the capability of variational autoencoders to disentangle factors of variability within the data and the physics driven loss function that seeks to minimize the total length of the discontinuities in images corresponding to latent representations. Our method is applied to various materials, including NiO-LSMO, BiFeO 3 , and graphene. The results demonstrate the effectiveness of our approach in extracting meaningful information from large volumes of imaging data. The customized codes of the required functions and classes to develop phyVAE is available at https://github.com/arpanbiswas52/phy-VAE.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Disentangling Ferroelectric Wall Dynamics and Identification of Pinning Mechanisms via Deep Learning

Field-induced domain-wall dynamics in ferroelectric materials underpins multiple applications ranging from actuators to information technology devices and necessitates a quantitative description of the associated mechanisms including giant electromechanical couplings, controlled nonlinearities, or low coercive voltages. While the advances in dynamic piezoresponse force microscopy measurements over the last two decades have rendered visualization of polarization dynamics relatively straightforward, the associated insights into the local mechanisms have been elusive. This work explores the domain dynamics in model polycrystalline materials using a workflow combining deep-learning-based segmentation of the domain structures with nonlinear dimensionality reduction using multilayer rotationally invariant autoencoders (rVAE). The former allows unambiguous identification and classification of the ferroelectric and ferroelastic domain walls. Here, the rVAE discovers the latent representations of the domain wall geometries and their dynamics, consequently providing insight into the intrinsic mechanisms of polarization switching, that can further be compared to simple physical models. The rVAE disentangles the factors affecting the pinning efficiency of ferroelectric walls, offering insights into the correlation of ferroelastic wall distribution and ferroelectric wall pinning.

36 MATERIALS SCIENCE↗
DOE OSTI2026

AI-assisted object condensation clustering for calorimeter shower reconstruction at CLAS12

Several nuclear physics studies using the CLAS12 detector rely on the accurate reconstruction of neutrons and photons from its forward angle calorimeter system. These studies often place restrictive cuts when measuring neutral particles due to an overabundance of false clusters created by the existing calorimeter reconstruction software. In this work, we present a new AI approach to clustering CLAS12 calorimeter hits based on the object condensation framework. The model learns a latent representation of the full detector topology using GravNet layers, serving as the positional encoding for an event’s calorimeter hits which are processed by a Transformer encoder. This unique structure allows the model to contextualize local and long range information, improving its performance. Evaluated on one million simulated $e^-$ $+$ $p$ collision events, our method significantly improves cluster trustworthiness: the fraction of reliable neutron clusters, increasing from 8.88% to 30.73%, and photon clusters, increasing from 51.07% to 64.73%. In conclusion, our study also marks the first application of AI clustering techniques for hodoscopic detectors, showing potential for usage in many other experiments.

Calorimeters↗
DOE OSTI2026

Dense autoencoders, clustering techniques, and semi-supervised learning for HPGe $γ$-spectra

Classifying high-resolution gamma spectra by their isotopic content is an essential task in nuclear forensics and other applications. Traditional analysis methods are often time-intensive, but machine learning (ML) may help analysts quickly process many spectra. Such methods tend to rely on abundant, well-labeled data for training. Historical gamma data exists in various fields but is not uniformly useful for supervised ML due to inconsistent labeling. Here, to address some of these challenges, we present a method to classify and organize unlabeled data from high-purity germanium detectors using an autoencoding neural network (autoencoder). We trained dense autoencoders to compress gamma data into latent representations that enable efficient data characterization. By clustering the encoded spectra or lower-dimensional mappings of them, we identified and removed portions of over-abundant data categories, resulting in a more balanced dataset and improved autoencoder performance. This encoding and clustering pipeline also enabled the organization of spectra into self-consistent categories. Finally, we found that encoded representations showed potential as inputs for semi-supervised learning of nuclide identification (NID) labels, achieving an average F1 score of 0.85 ± 0.03 when mapping encodings to a set of 65 isotope labels.

Autoencoders↗
DOE OSTI2026

Decoding the proton’s gluonic density with lattice QCD-informed machine learning

We present a first machine learning-based decoding of the gluonic structure of the proton from lattice QCD using a variational autoencoder inverse mapper (VAIM). Harnessing the power of generative AI, we predict the parton distribution function (PDF) of the gluon given information on the reduced pseudo-Ioffe-time distributions (RpITDs) as calculated from an ensemble with lattice spacing a ≈ 0.09 fm and a pion mass of M π ≈ 310 MeV. The resulting gluon PDF is consistent with phenomenological global fits within uncertainties, particularly in the intermediate-to-high-x region where lattice data are most constraining. A subsequent correlation analysis confirms that the VAIM learns a meaningful latent representation, highlighting the potential of generative AI to bridge lattice QCD and phenomenological extractions within a unified analysis framework.

Gluon parton distribution function↗
DOE OSTI2022

Data-driven model for divertor plasma detachment prediction

We present a fast and accurate data-driven surrogate model for divertor plasma detachment prediction leveraging the latent feature space concept in machine learning research. Our approach involves constructing and training two neural networks: an autoencoder that finds a proper latent space representation (LSR) of plasma state by compressing the multi-modal diagnostic measurements and a forward model using multi-layer perception (MLP) that projects a set of plasma control parameters to its corresponding LSR. By combining the forward model and the decoder network from autoencoder, this new data-driven surrogate model is able to predict a consistent set of diagnostic measurements based on a few plasma control parameters. In order to ensure that the crucial detachment physics is correctly captured, highly efficient 1D UEDGE model is used to generate training and validation data in this study. The benchmark between the data-driven surrogate model and UEDGE simulations shows that our surrogate model is capable of providing accurate detachment prediction (usually within a few per cent relative error margin) but with at least four orders of magnitude speed-up, indicating that performance-wise, it has the potential to facilitate integrated tokamak design and plasma control. Comparing with the widely used two-point model and/or two-point model formatting, the new data-driven model features additional detachment front prediction and can be easily extended to incorporate richer physics. This study demonstrates that the complicated divertor and scrape-off-layer plasma state has a low-dimensional representation in latent space. Understanding plasma dynamics in latent space and utilising this knowledge could open a new path for plasma control in magnetic fusion energy research.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Deep Learning for Simultaneous Inference of Hydraulic and Transport Properties

Abstract Identification of a heterogeneous conductivity field and reconstruction of a contaminant release history are key aspects of subsurface remediation. These two goals are achieved by combining model predictions with sparse and noisy hydraulic head and concentration measurements. Solution of this inverse problem is notoriously difficult due to, in part, high dimensionality of the parameter space and high computational cost of repeated forward solves. We use a convolutional adversarial autoencoder (CAAE) to parameterize a heterogeneous non‐Gaussian conductivity field via a low‐dimensional latent representation. A three‐dimensional dense convolutional encoder‐decoder (DenseED) network serves as a forward surrogate of the flow and transport model. The CAAE‐DenseED surrogate is fed into the ensemble smoother with multiple data assimilation (ESMDA) algorithm to sample from the Bayesian posterior distribution of the unknown parameters, forming a CAAE‐DenseED‐ESMDA inversion framework. The resulting CAAE‐DenseED‐ESMDA inversion strategy is used to identify a three‐dimensional contaminant source and conductivity field. A comparison of the inversion results from CAAE‐ESMDA with physical flow and transport simulator and from CAAE‐DenseED‐ESMDA shows that the latter yields accurate reconstruction results at the fraction of the computational cost of the former.

Zhou, Zitong↗
DOE OSTI2021

Probing atomic-scale symmetry breaking by rotationally invariant machine learning of multidimensional electron scattering

Abstract The 4D scanning transmission electron microscopy (STEM) method maps the structure and functionality of solids on the atomic scale, yielding information-rich data sets describing the interatomic electric and magnetic fields, structural and electronic order parameters, and other symmetry breaking distortions. A critical bottleneck is the dearth of analytical tools that can reduce complex 4D-STEM data to physically relevant descriptors. We propose an approach for the systematic exploration of 4D-STEM data using rotationally invariant variational autoencoders (rrVAE), which disentangle the general rotation of the object from other latent representations. The implementation of purely rotational rrVAE is discussed as are applications to simulated data for graphene and zincblende structures. The rrVAE analysis of experimental 4D-STEM data of defects in graphene is illustrated and compared to the classical center-of-mass analysis. This approach is universal for probing symmetry-breaking phenomena in complex systems and can be implemented for a broad range of diffraction methods.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Normalizing flows for domain adaptation when identifying Λ hyperon events

Here this study focuses on the application of a normalizing flow as a method of domain adaptation when classifying physics data. Normalizing flows offer a way to transform data points between two different distributions. The present study investigates a novel method of transforming latent representations of physics data to a normal distribution and then to a physics distribution again. The final distribution models a simulated distribution. After being transformed, the data can be classified by a neural network trained on labeled simulation data. The present study succeeds in training two normalizing flows that can transform between data (or simulation) and a Gaussian distribution.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

A variational encoder–decoder approach to precise spectroscopic age estimation for large Galactic surveys

Constraints on the formation and evolution of the Milky Way Galaxy require multidimensional measurements of kinematics, abundances, and ages for a large population of stars. Ages for luminous giants, which can be seen to large distances, are an essential component of studies of the Milky Way, but they are traditionally very difficult to estimate precisely for a large data set and often require careful analysis on a star-by-star basis in asteroseismology. Because spectra are easier to obtain for large samples, being able to determine precise ages from spectra allows for large age samples to be constructed, but spectroscopic ages are often imprecise and contaminated by abundance correlations. Here we present an application of a variational encoder–decoder on cross-domain astronomical data to solve these issues. The model is trained on pairs of observations from APOGEE and Kepler of the same star in order to reduce the dimensionality of the APOGEE spectra in a latent space while removing abundance information. The low dimensional latent representation of these spectra can then be trained to predict age with just ∼1000 precise seismic ages. We demonstrate that this model produces more precise spectroscopic ages (∼ 22 per cent overall, ∼ 11 per cent for red-clump stars) than previous data-driven spectroscopic ages while being less contaminated by abundance information (in particular, our ages do not depend on [α/M]). We create a public age catalogue for the APOGEE DR17 data set and use it to map the age distribution and the age-[Fe/H]-[α/M] distribution across the radial range of the Galactic disc.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Infrared-safe energy weighting does not guarantee small nonperturbative effects

Infrared and collinear (IRC) safety has long been used a proxy for robustness when developing new jet substructure observables. This guiding philosophy has been carried into the deep learning era, where IRC-safe neural networks have been used for many jet studies. For graph-based neural networks, the most straightforward way to achieve IRC safety is to weight particle inputs by their energies. However, energy-weighting by itself does not guarantee that perturbative calculations of machine-learned observables will enjoy small nonperturbative corrections. Here, in this paper, we demonstrate the sensitivity of IRC-safe networks to nonperturbative effects, by training an energy flow network (EFN) to maximize its sensitivity to hadronization. We then show how to construct Lipschitz energy flow networks (L-EFNs), which are both IRC safe and relatively insensitive to nonperturbative corrections. We demonstrate the performance of L-EFNs on generated samples of quark and gluon jets, and showcase fascinating differences between the learned latent representations of EFNs and L-EFNs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

OmniXAS: A universal deep-learning framework for materials x-ray absorption spectra

X-ray absorption spectroscopy (XAS) is a powerful characterization technique for probing the local chemical environment of absorbing atoms. However, analyzing XAS data presents significant challenges, often requiring extensive, computationally intensive simulations, as well as significant domain expertise. These limitations hinder the development of fast, robust XAS analysis pipelines that are essential in high-throughput studies and for autonomous experimentation. Here, we address these challenges with OmniXAS, a framework that contains a suite of transfer learning approaches for XAS prediction, each uniquely contributing to improved accuracy and efficiency, as demonstrated on the K-edge spectra database covering eight 3⁢d transition metals (Ti–Cu). The OmniXAS framework is built upon three distinct strategies. First, we use M3GNet [Nat. Comput. Sci. 2, 718 (2022)] to derive latent representations of the local chemical environment of absorption sites as input for XAS prediction, achieving significant improvements over conventional featurization techniques. Second, we employ a hierarchical transfer learning strategy, training a universal multitask model across elements before fine-tuning for element-specific predictions. Models based on this cascaded approach after elementwise fine-tuning outperform element-specific models by up to 69%. Third, we implement cross-fidelity transfer learning, adapting a universal model to predict spectra generated by simulation of a different fidelity with a much higher computational cost. This approach improves prediction accuracy by up to 11% over models trained on the target fidelity alone. Our approach significantly boosts the throughput of XAS modeling by orders of magnitude as compared to first-principles simulations and is extendable to XAS prediction for a broader range of elements. The proposed transfer learning framework is generalizable to enhance deep-learning models that target other properties in materials research.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Clustering High-dimensional Toxicogenomics Data with Rare Signals

Toxicogenomics studies the gene and protein activities to drug treatments or toxic exposures. As the drugs and genes are numerous, toxicogenomics data are naturally high dimensional, with dimension sizes up to millions. In addition, the distribution of toxicogenomics data is oftentimes skewed, and they contain rare but important signals representing a cell or organism’s response to toxicity. The combination of high dimension and extremely skewed distribution of toxicogenomics data makes clustering analysis extremely challenging.We present our study of clustering toxicogenomics data using classical approaches such as principal component analysis as well as deep learning approaches such as auto-encoders. Our experiments show that these approaches fail to preserve rare signals and produce high-quality clusters. We then explore augmenting matrix factorization with deep learning techniques such as attention mechanism to produce latent representations for clustering. Our technique is able to better preserve rare signals after dimensionality reduction than prior approaches. Furthermore, we combine our augmented matrix factorization with a mechanism similar to autoencoder to balance separable clusters and low regeneration errors. Our experiments demonstrate better clustering with our proposed approach.

Cong, Guojing↗
DOE OSTI2024

An explainable variational autoencoder model for three-dimensional acoustic emission source localization in hollow cylindrical structures

We introduce an explainable variational autoencoder for three-dimensional (3D) localization of acoustic emission sources in hollow cylindrical structures, with an unsupervised approach. This research capitalizes on multi-arrival waveforms generated by helical path propagation in cylindrical geometries to enable efficient two-receiver localization. By integrating the modal characteristics of Lamb modes under multi-path conditions, we demonstrate that two sets of time-of-arrival differences and peak amplitudes extracted from one receiver can serve as effective localization features. This initial approach identifies four potential source locations, highlighting the feasibility of two-receiver source localization using traditional feature extraction methods. However, direct extraction can be challenging when mode overlaps occur, complicating the localization process. To address this, our work proposes a novel waveform-based method. This method leverages the consistent dispersion characteristics within isotropic materials, where each unique combination of mode arrival times and peak amplitudes constructs a distinct waveform. This distinctiveness overcomes the ambiguities associated with mode overlaps, significantly enhancing the method’s precision and robustness. Our approach adopts a data-driven strategy for waveform-based localization using variational autoencoder (VAE). VAE discerns waveform patterns for localization, while also addressing data uncertainties. The VAE’s encoder and decoder networks capture the localization process and the source’s influence on waveform generation, respectively, guiding latent variables to segregate waveforms by source in the latent space. The design of the learning process focuses on specific localization characteristics to enhance result explainability. Localization predictions are generated by projecting test waveforms, not included in the training set, onto a trained latent space. The prediction is determined using a nearest-neighbor approach based on the closest latent representation of a source. Validation with pencil-lead-break tests on a metallic pipe confirmed our method’s effectiveness, achieving an averaged 3D localization accuracy of 0.84.

Lee, Guan-Wei↗
DOE OSTI2021

Transfer Learning using Denoising Auto-Encoders for Cellular-Level Annotation of Tumor in Pathology Slides

Adversarial examples can produce altered classifications using only seemingly innocuous, imperceptible perturbations to the original image. The imperceptibility of adversarial perturbations suggests that the corresponding classifiers use decision criteria different than those of a human. In a medical setting, inexplicable decision criteria confound a pathologist’s willingness to trust machine-generated annotations. Here, we analyze denoising tumor detection models to see if they are robust to imperceptible adversarial perturbations. Moreover, to be more fully trusted by pathologists, we require tumor detectors that generate interpretable annotations which segment pathology slides into tumorous and normal regions at the cellular level. We therefore compare transfer learning based on two different autoencoder architectures, one derived from a deep denoising bottleneck autoencoder and one from an over-complete sparse autoencoder. Both autoencoders were first trained in an unsupervised manner on a set of pathology slides drawn from the Camelyon16 dataset. The latent representations produced by each autoencoder were then passed to separate neural networks that were trained in a supervised manner on binary tumor-normal masks generated by pathologists at cellular resolution. Both tumor detectors supported better than 90% AUC PR as measured by the area under the precision/recall curve on a held-out pathology slide. To assess the underlying decision criteria used by both tumor detectors, we constructed imperceptible adversarial examples which reduced the AUC PR of both models to less than 70%. Random noise of the same amplitude had almost no effect on the AUC PR of either model. Additionally, each tumor detector was resistant to adversarial “transfer” attacks targeting the other. The adversarial perturbations showed strong characteristic differences: the deep denoising models perturbations were a very diffuse, seemingly unrecognizable pattern while the sparse coding models perturbations showed traces of tissue cells.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

CrossMP: Enabling Cross-Modality Translation between Single-Cell RNA-Seq and Single-Cell ATAC-Seq through Web-Based Portal

In recent years, there has been a growing interest in profiling multiomic modalities within individual cells simultaneously. One such example is integrating combined single-cell RNA sequencing (scRNA-seq) data and single-cell transposase-accessible chromatin sequencing (scATAC-seq) data. Integrated analysis of diverse modalities has helped researchers make more accurate predictions and gain a more comprehensive understanding than with single-modality analysis. However, generating such multimodal data is technically challenging and expensive, leading to limited availability of single-cell co-assay data. Here, we propose a model for cross-modal prediction between the transcriptome and chromatin profiles in single cells. Our model is based on a deep neural network architecture that learns the latent representations from the source modality and then predicts the target modality. It demonstrates reliable performance in accurately translating between these modalities across multiple paired human scATAC-seq and scRNA-seq datasets. Additionally, we developed CrossMP, a web-based portal allowing researchers to upload their single-cell modality data through an interactive web interface and predict the other type of modality data, using high-performance computing resources plugged at the backend.

59 BASIC BIOLOGICAL SCIENCES↗