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DOE OSTI2026

OmicsMLMentor: A Web Application for Guided Machine Learning Analysis of Omics Data

Expression-based omics technologies (e.g. proteomics, metabolomics, transcriptomics, etc.) increasingly rely on supervised and unsupervised machine learning (ML) models to find key biomolecules distinguishing conditions, identify natural groupings in biological data, or generate predictions for outcomes of interest. Fitting ML models to omics data presents several challenges, including handling missing data, selecting a normalization method, choosing a valid model, and optimizing hyperparameters, all requiring statistical programming skills to address these challenges. Thus, the open-source web application SLOPE was designed to lower the barrier to ML modeling for omics data. SLOPE supports the fitting of 15 ML models (10 supervised and 5 unsupervised) tailored to omics datasets, such as proteomics, metabolomics, lipidomics, and transcriptomics. SLOPE offers several omics-specific features, including methods for handling missingness (imputation, conversion, removal), normalization tests, ranking of models based on the structure of a user’s data and user input, and optimal hyperparameter selections using cross-validation splits. By streamlining ML workflows for omics analysis, SLOPE address critical gaps in existing online web tools, facilitating a broader adoption of these models for omics research. Here, SLOPE is applied to data from a lignin exposure study to highlight the workflow for fitting both supervised and unsupervised models to data.

lipidomics↗

DOE OSTI2021

High temperature oxidation of corrosion resistant alloys from machine learning

Parabolic rate constants, k p , were collected from published reports and calculated from corrosion product data (sample mass gain or corrosion product thickness) and tabulated for 75 alloys exposed to temperatures between ~800 and 2000 K (~500–1700 °C; 900–3000°F). Data were collected for environments including lab air, ambient and supercritical carbon dioxide, supercritical water, and steam. Materials studied include low- and high-Cr ferritic and austenitic steels, nickel superalloys, and aluminide materials. A combination of Arrhenius analysis, simple linear regression, supervised and unsupervised machine learning methods were used to investigate the relations between composition and oxidation kinetics. The supervised machine learning techniques produced the lowest mean standard errors. The most significant elements controlling oxidation kinetics were Ni, Cr, Al, and Fe, with Mo and Co composition also found to be significant features. The activation energies produced from the machine learning analysis were in the correct distributions for the diffusion constants for the oxide scales expected to dominate in each class.

Materials Science↗

DOE OSTI2023

Automatic Point Cloud Building Envelope Segmentation (AutoCuBES)

The Auto-CuBES algorithm is based on unsupervised machine learning that automatically labels 3D point cloud data and reduces the time spent in manual segmentation. The algorithm can process high-resolution point clouds and generate a wire-frame building envelope model with a small set of calibration parameters. The algorithm inputs a 3D point cloud generated by commonly available surveying equipment and outputs a wire-frame model of the building envelope. Unsupervised machine learning methods were used to identify facades, windows, and doors while minimizing the number of calibration parameters.

Puente, BryanMaldonado↗

DOE OSTI2018

Unsupervised learning about 4D features of microparticle motion

Material clusters of different sizes are known to exist in high-temperature plasmas due to plasma-wall interactions. The facts that these clusters, ranging from sub-microns to above mm in size, can move from one location to another quickly and that there are a lot of them make high-speed imaging and tracking one of the best, effective, and sometimes only diagnostic. An unsupervised machine learning technique based on deconvolutional neural networks is developed to analyze two-camera videos of high-temperature microparticles generated from exploding wires. The neural network utilizes a locally competitive algorithm to infer representations and optimize a dictionary composed of kernels, or basis vectors, for image analysis. Our primary goal is to use this method for feature recognition and prediction of the time-dependent three-dimensional (or “4D”) microparticle motion. Features equivalent to local velocity vectors have been identified as the dictionary kernels or “building blocks” of the scene. The dictionary elements from the left and right camera views are found to be strongly correlated and satisfy the projection geometrical constraints. The results show that unsupervised machine learning techniques are promising approaches to process large sets of images for high-temperature plasmas and other scientific experiments. In conclusion, machine learning techniques can be useful to handle the large amount of data and therefore aid the understanding of plasma-wall interaction.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Annual Report for Structure-Aware Unsupervised, Transformational Machine Learning for Drug Discovery

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Structure-Aware Unsupervised, Transformational Machine Learning for Drug Discovery (DTRA Basic Research Final Report)

The major goal of this project is to develop machine learning (ML) methods to enable improved predictive power on real drug discovery for novel targets. More specifically, we planned to demonstrate the capability and effectiveness of ML tools utilizing unlabeled large-volume protein-ligand datasets. We investigated multiple pre-training approaches for 3D protein-ligand structure-based foundation models, without relying on experimental binding data. We also addressed scenarios in which crystal structures are unavailable or binding data are limited. We also planned to develop a complete pipeline to screen novel compounds as well as to demonstrate the capability and effectiveness of the developed methods by testing on a realistic drug discovery task such as SARS-CoV-2. While the major goals and milestones remain consistent with the original proposal, certain technical details have been adjusted, based on the experimental results and related outcomes.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Machine-learned interatomic potentials by active learning: amorphous and liquid hafnium dioxide

We propose an active learning scheme for automatically sampling a minimum number of uncorrelated configurations for fitting the Gaussian Approximation Potential (GAP). Our active learning scheme consists of an unsupervised machine learning (ML) scheme coupled with a Bayesian optimization technique that evaluates the GAP model. We apply this scheme to a Hafnium dioxide (HfO 2 ) dataset generated from a "melt-quench" ab initio molecular dynamics (AIMD) protocol. Our results show that the active learning scheme, with no prior knowledge of the dataset, is able to extract a configuration that reaches the required energy fit tolerance. Further, molecular dynamics (MD) simulations performed using this active learned GAP model on 6144 atom systems of amorphous and liquid state elucidate the structural properties of HfO 2 with near ab initio precision and quench rates (i.e., 1.0 K/ps) not accessible via AIMD. The melt and amorphous X-ray structural factors generated from our simulation are in good agreement with experiment. In addition, the calculated diffusion constants are in good agreement with previous ab initio studies.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Unsupervised learning for identifying events in active target experiments

This article presents novel applications of unsupervised machine learning methods to the problem of event separation in an active target detector, the Active-Target Time Projection Chamber (AT-TPC). The overarching goal is to group similar events in the early stages of the data analysis, thereby improving efficiency by limiting the computationally expensive processing of unnecessary events. The application of unsupervised clustering algorithms to the analysis of two-dimensional projections of particle tracks from a resonant proton scattering experiment on 46 Ar is introduced. We explore the performance of autoencoder neural networks and a pre-trained VGG16 Simonyan and Zisserman (2015) convolutional neural network. We study clustering performance on both data from a simulated 46 Ar experiment, and real events from the AT-TPC detector. We find that a -means algorithm applied to simulated data in the VGG16 latent space forms almost perfect clusters. Additionally, the VGG16+-means approach finds high purity clusters of proton events for real experimental data. Here, we also explore the application of clustering the latent space of autoencoder neural networks for event separation. While these networks show strong performance, they suffer from high variability in their results.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Machine Learning-Enabled Quantitative Analysis of Optically Obscure Scratches on Nickel-Plated Additively Manufactured (AM) Samples

Additively manufactured metal components often have rough and uneven surfaces, necessitating post-processing and surface polishing. Hardness is a critical characteristic that affects overall component properties, including wear. This study employed K-means unsupervised machine learning to explore the relationship between the relative surface hardness and scratch width of electroless nickel plating on additively manufactured composite components. The Taguchi design of experiment (TDOE) L9 orthogonal array facilitated experimentation with various factors and levels. Initially, a digital light microscope was used for 3D surface mapping and scratch width quantification. However, the microscope struggled with the reflections from the shiny Ni-plating and scatter from small scratches. To overcome this, a scanning electron microscope (SEM) generated grayscale images and 3D height maps of the scratched Ni-plating, thus enabling the precise characterization of scratch widths. Optical identification of the scratch regions and quantification were accomplished using Python code with a K-means machine-learning clustering algorithm. The TDOE yielded distinct Ni-plating hardness levels for the nine samples, while an increased scratch force showed a non-linear impact on scratch widths. The enhanced surface quality resulting from Ni coatings will have significant implications in various industrial applications, and it will play a pivotal role in future metal and alloy surface engineering.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Latent Representation Learning for Structural Characterization of Catalysts

Supervised machine learning-enabled mapping of the X-ray absorption near edge structure (XANES) spectra to local structural descriptors offers new methods for understanding the structure and function of working nanocatalysts. We briefly summarize a status of XANES analysis approaches by supervised machine learning methods. We present an example of an autoencoder-based, unsupervised machine learning approach for latent representation learning of XANES spectra. This new approach produces a lower-dimensional latent representation, which retains a spectrum–structure relationship that can be eventually mapped to physicochemical properties. Furthermore, the latent space of the autoencoder also provides a pathway to interpret the information content “hidden” in the X-ray absorption coefficient. Our approach (that we named latent space analysis of spectra, or LSAS) is demonstrated for the supported Pd nanoparticle catalyst studied during the formation of Pd hydride. By employing the low-dimensional representation of Pd K-edge XANES, the LSAS method was able to isolate the key factors responsible for the observed spectral changes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Creating ground truth for nanocrystal morphology: a fully automated pipeline for unbiased transmission electron microscopy analysis

Control over colloidal nanocrystal morphology (size, size distribution, and shape) is important for tailoring the functionality of individual nanocrystals and their ensemble behavior. Despite this, traditional methods to quantify nanocrystal morphology are laborious. New developments in automated morphology classification will accelerate these analyses but the assessment of machine learning models is limited by human accuracy for ground truth, causing even unsupervised machine learning models to have inherent bias. Herein, we introduce synthetic image rendering to solve the ground truth problem of nanocrystal morphology classification. By simulating 2D images of nanocrystal shapes via a function of high-dimensional parameter space, we trained a convolutional neural network to link unique morphologies to their simulated parameters, defining nanocrystal morphology quantitatively rather than qualitatively. An automated pipeline then processes, quantitatively defines, and classifies nanocrystal morphology from experimental transmission electron microscopy (TEM) images. Using improved computer vision techniques, 42,650 nanocrystals were identified, assessed, and labeled with quantitative parameters, offering a 600-fold improvement in efficiency over best-practice manual measurements. Further, a classification algorithm was trained with a prediction accuracy of 99.5%, which can successfully analyze a range of concave, convex, and irregular nanocrystal shapes. The resulting pipeline was applied to differentiating two syntheses of nominally cuboidal CsPbBr 3 nanocrystals and uniquely classifying binary nickel sulfide nanocrystal phase based on morphology. This pipeline provides a simple, efficient, and unbiased method to quantify nanocrystal morphology and represents a practical route to construct large datasets with an absolute ground truth for training unbiased morphology-based machine learning algorithms.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2020

Classical versus quantum models in machine learning: insights from a finance application

Although several models have been proposed towards assisting machine learning (ML) tasks with quantum computers, a direct comparison of the expressive power and efficiency of classical versus quantum models for datasets originating from real-world applications is one of the key milestones towards a quantum ready era. Here, we take a first step towards addressing this challenge by performing a comparison of the widely used classical ML models known as restricted Boltzmann machines (RBMs), against a recently proposed quantum model, now known as quantum circuit Born machines (QCBMs). Both models address the same hard tasks in unsupervised generative modeling, with QCBMs exploiting the probabilistic nature of quantum mechanics and a candidate for near-term quantum computers, as experimentally demonstrated in three different quantum hardware architectures to date. To address the question of the performance of the quantum model on real-world classical data sets, we construct scenarios from a probabilistic version out of the well-known portfolio optimization problem in finance, by using time-series pricing data from asset subsets of the S&P500 stock market index. It is remarkable to find that, under the same number of resources in terms of parameters for both classical and quantum models, the quantum models seem to have superior performance on typical instances when compared with the canonical training of the RBMs. Our simulations are grounded on a hardware efficient realization of the QCBMs on ion-trap quantum computers, by using their native gate sets, and therefore readily implementable in near-term quantum devices.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Selecting representative geological realizations to model subsurface CO 2 storage under uncertainty

Carbon capture and storage (CCS) is one of the quickest and most effective solutions for reducing carbon emissions. The majority of subsurface storage occurs in saline aquifers, for which geological information is lacking which in turn results in geological uncertainty. To evaluate uncertainty in CO 2 injection projections, the use of multiple geological realizations (GRs) has been practiced very commonly. In this approach, hundreds or thousands of high-resolution GRs is used that quickly becomes computationally expensive. This issue can be addressed with representative geological realizations (RGRs) that preserve the uncertainty domain of the ensemble GRs. Here, in this study, we propose the use of unsupervised machine learning (UML) frameworks, including dissimilarity measurement, dimensionality reduction, clustering and sampling algorithms ta select a predetermined number of RGRs. We compare the simulation outputs of the RGR sets and the ensemble using the Kolmogorov–Smirnov (KS) test to select the best UML. The UML frameworks and their associated selection processes are evaluated using a saline aquifer with a single CO 2 injection well and 200 GRs with varying uncertain petrophysical characteristics. The best UML framework is selected to use only 5% of the GRs while maintaining the uncertainty domain of the ensemble GRs. In addition, the best UML framework is tested using a saline aquifer with three CO 2 injection wells and varied GRs. The results show that our proposed UML framework can be used to choose RGRs, capturing the whole uncertainty domain. Our approach leads to a significant reduction in the computational cost associated with scenario testing, decision-making, and development planning for CO 2 storage sites under geological uncertainty.

58 GEOSCIENCES↗

DOE OSTI2026

FIB-ToF-SIMS characterization of irradiated U-10Zr

Post-irradiation examination (PIE) is critical for the performance assessment and qualification of nuclear fuels. Secondary ion mass spectrometry (SIMS) is a powerful materials characterization technique that allows for elemental and isotopic mapping with a depth resolution greater than EDS and EPMA. However, it has not yet been applied to PIE of metallic nuclear fuel. Here, in this work, we characterize an fast neutron spectrum irradiated U-10Zr fuel sample using a time-of-flight SIMS (ToF-SIMS) system connected to a FIB/SEM system, which allows for flexible sample analysis compared to a dedicated ToF-SIMS instrument. Analysis of the resulting hyperspectral micrograph data was aided by the development of an unsupervised machine learning (ML) algorithm that iterates on existing methods to segment the 3D micrographic datasets based on the similarity of mass spectra. The results showed that the FIB-ToF-SIMS instrument was potentially capable of spatially resolving closed fission gas bubbles in 3D by continued ion sputtering of the analyzed volume. Additionally, the ML algorithm proved useful in revealing the chemical segregation of light fission products (those with an atomic mass between approximately 85–105 amu, such as ruthenium and rhodium) plus matrix zirconium, heavy fission products (those with an atomic mass between approximately 135–150 amu, such as the lanthanides) and uranium. Future studies are planned to conduct FIB-ToF-SIMS analysis on more irradiated U-Zr samples to study the constituent redistribution.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2020

Remote Sensing-Informed Zonation for Understanding Snow, Plant and Soil Moisture Dynamics within a Mountain Ecosystem

In the headwater catchments of the Rocky Mountains, plant productivity and its dynamics are largely dependent upon water availability, which is influenced by changing snowmelt dynamics associated with climate change. Understanding and quantifying the interactions between snow, plants and soil moisture is challenging, since these interactions are highly heterogeneous in mountainous terrain, particularly as they are influenced by microtopography within a hillslope. Recent advances in satellite remote sensing have created an opportunity for monitoring snow and plant dynamics at high spatiotemporal resolutions that can capture microtopographic effects. In this study, we investigate the relationships among topography, snowmelt, soil moisture and plant dynamics in the East River watershed, Crested Butte, Colorado, based on a time series of 3-meter resolution PlanetScope normalized difference vegetation index (NDVI) images. To make use of a large volume of high-resolution time-lapse images (17 images total), we use unsupervised machine learning methods to reduce the dimensionality of the time lapse images by identifying spatial zones that have characteristic NDVI time series. We hypothesize that each zone represents a set of similar snowmelt and plant dynamics that differ from other identified zones and that these zones are associated with key topographic features, plant species and soil moisture. We compare different distance measures (Ward and complete linkage) to understand the effects of their influence on the zonation map. Results show that the identified zones are associated with particular microtopographic features; highly productive zones are associated with low slopes and high topographic wetness index, in contrast with zones of low productivity, which are associated with high slopes and low topographic wetness index. The zones also correspond to particular plant species distributions; higher forb coverage is associated with zones characterized by higher peak productivity combined with rapid senescence in low moisture conditions, while higher sagebrush coverage is associated with low productivity and similar senescence patterns between high and low moisture conditions. In addition, soil moisture probe and sensor data confirm that each zone has a unique soil moisture distribution. This cluster-based analysis can tractably analyze high-resolution time-lapse images to examine plant-soil-snow interactions, guide sampling and sensor placements and identify areas likely vulnerable to ecological change in the future.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Uranium Oxide Synthetic Pathway Discernment through Unsupervised Morphological Analysis

We present a novel unsupervised machine learning method for quantitative representation of scanning electron micrographs and its applications and performance for nuclear forensic analysis of uranium ore concentrates. The method uses a vector quantizing variational autoencoder followed by a histogram operation to encode a micrograph into a single dimensional representation, called the latent vector. The method requires no extant labeling of the data and can be applied over large datasets of micrographs with minimal human interaction. The representations generated are broadly descriptive of each micrograph and the microstructure of the material imaged. In the case of uranium ore concentrate analysis, the representations were amenable to processing reagent and ore concentrate species classification with accuracy of 81:8%, which is competitive with state-of-the-art supervised networks. The representations were also used to classify previously unseen processing routes, were able to classify imaging parameters such as magnification (to 76:0% accuracy), were able to classify fine grained process parameters such as calcining temperature (to 74:4% accuracy), and their informatic properties indicate that they are generally descriptive of the image represented. This method can be applied across microstructure analysis fields to perform quantitative analysis without the need for labor intensive and possibly biased human analysis.

Scanning Electron Microscopy, Vector Quantizing Va↗

DOE OSTI2021

Machine learning to identify geologic factors associated with production in geothermal fields: A casestudy using 3D geologic data, Brady geothermal field, Nevada

In this paper, we present an analysis using unsupervised machine learning (ML) to identify the key geologic factors that contribute to the geothermal production in the Brady geothermal field. Brady is a hydrothermal system in northwestern Nevada that supports both electricity production and direct use of hydrothermal fluids. Transmissive fluid flow pathways are relatively rare in the subsurface but are critical components of hydrothermal systems like Brady and many other types of fluid flow systems in fractured rock. The ML method, non-negative matrix factorization with k-means clustering (NMFk), is applied to a library of fourteen 3D geologic characteristics hypothesized to control hydrothermal circulation in the Brady geothermal field. Our results indicate the macro-scale faults and a local step-over in the fault system preferentially occur along with production wells when compared to injection wells and non-productive wells. We infer that these are the key geologic characteristics that control the through-going hydrothermal transmission pathways at Brady. Our results demonstrate 1) the specific geologic controls on the Brady hydrothermal system and 2) the efficacy of pairing ML techniques with 3D geologic characterization to enhance the understanding of subsurface processes.

15 GEOTHERMAL ENERGY↗

DOE OSTI2017

Semi-supervised learning approach for crack detection and identification in advanced gas-cooled reactor graphite bricks - 111

One of the life-limiting components of an Advanced Gas cooled Reactor (AGR) is its graphite core. The bricks present in the core undergo radiolytic oxidation throughout their lifetime which causes graphite weight loss and irradiation which can result in some of the bricks developing cracks. Understanding the nature and extent of brick cracking within the core is key to ensuring continued and extended operation of the AGR fleet. A semi-supervised machine learning classification algorithm is proposed as a method for improving the detection of cracked graphite bricks, by combining the labels derived from infrequent, detailed inspections of the core, with unlabeled, more frequent monitoring measurements taken during refueling operations. Semi-supervised machine learning, which is an emerging field in nuclear power condition monitoring, is the combination of ideas from both supervised and unsupervised machine learning whereby the data that is used to train the algorithm is a combination of labeled and unlabeled data. This paper introduces the initial research that has been undertaken in creating a semi-supervised self-training algorithm to detect the presence of graphite brick cracks and then proceeds to show that there is an improvement in the classification of graphite bricks using a semi-supervised machine learning classifier compared to supervised machine learning classifiers. This improved classification performance is encouraging as it does not require time consuming and costly human analysis to obtain extra learning information from available data. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗