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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 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 OSTI2021

MindSynchro

This report presents the developments and results of MindSynchro project as part of DOE OE FOA 1861. DOE and Pacific Northwest National Laboratory (PNNL) have made available to FOA awardees datasets containing years of real historical data recorded from various phasor measurement units (PMUs) which are installed in three large US interconnections: Texas (IC A), Western (IC B), and Eastern (IC C). The main goal of the project, which was successfully achieved, was to develop methods for detection and identification of events which are relevant for power grid operation. Tasks performed for achieving the project goals included data exploration and pre-processing, the development and application of physics-based features, data analysis and labeling based on unsupervised learning approaches, training and testing of DSSL models for classification of events which are relevant for power grid operation, and deployment of solutions to cloud environments. The methods developed in the project can potentially provide relevant benefits to power grid asset owners/operators in general in terms of situational awareness. Two main types of outcomes can be provided by these tools: Identification of specific relevant power grid event types: Semi-supervised ML methods developed in the project can adequately employ not only the relatively scarce labeled data but also the large amount of available unlabeled data to train models for detection of specific event types. Such methods enable the application of trained models for the detection of events in a population of PMUs much larger than that associated to the labeled events. Support in data labeling / label validation: Labels are critical for training of models for identification of specific types of events. However, labeling large amounts of data is a manual and tedious process. This means that such process is error prone and is not scalable. Methods developed in the project, based on ensembles of clustering models, have been successfully employed for turning manual labeling into a scalable process. Accurate identification of specific relevant events can provide the operators with immediate situational awareness that could otherwise require hours or days of analysis from domain experts. We envision that such methods could be initially employed in support of post-mortem analysis of events and, as confidence is gained, they could be employed for online/real-time support, providing, among other benefits, insights for avoiding major events which could happen due to a combination of smaller ones. On the longer term, related methods could potentially be employed to improve protection and control.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Nondestructive Damage Detection of Concrete With Alkali-Silica Reactions Using Coda Wave and Anomaly Detection

An anomaly detection model for early damage detection for concrete structures undergoing alkali-silica reaction (ASR) is presented. It is difficult to detect ASR initiation and early damage without a reference expansion measurement. Coda waves, or the multiply scattered portion of ultrasonic waves, have been found to be indicative of small changes in complex material such as concrete. The relationship between concrete damage and relative velocity change and decorrelation of coda waves has been studied, but a generalized model which detects when damage occurs in a concrete structure is still lacking. The presented method uses features extracted from coda waves to detect early damage in concrete structures. The model uses unsupervised learning and only requires data from undamaged structures for training. During the training process, the reconstruction error of the training data is minimized. When the data collected from damaged concrete structures is used as an input of the model, it returns high reconstruction errors that indicate the occurrence of damage in the structures. The performance of the model is validated using experimental studies and has been shown to generalize across two different ASR specimens.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2018

Advances in Hyperspectral Image Classification Methods for Vegetation and Agricultural Cropland Studies

Hyperspectral data are becoming more widely available via sensors on airborne and unmanned aerial vehicle (UAV) platforms, as well as proximal platforms. While space-based hyperspectral data continue to be limited in availability, multiple spaceborne Earth-observing missions on traditional platforms are scheduled for launch, and companies are experimenting with small satellites for constellations to observe the Earth, as well as for planetary missions. Land cover mapping via classification is one of the most important applications of hyperspectral remote sensing and will increase in significance as time series of imagery are more readily available. However, while the narrow bands of hyperspectral data provide new opportunities for chemistry-based modeling and mapping, challenges remain. Hyperspectral data are high dimensional, and many bands are highly correlated or irrelevant for a given classification problem. For supervised classification methods, the quantity of training data is typically limited relative to the dimension of the input space. The resulting Hughes phenomenon, often referred to as the curse of dimensionality, increases potential for unstable parameter estimates, overfitting, and poor generalization of classifiers. This is particularly problematic for parametric approaches such as Gaussian maximum likelihood–based classifiers that have been the backbone of pixel-based multispectral classification methods. This issue has motivated investigation of alternatives, including regularization of the class covariance matrices, ensembles of weak classifiers, development of feature selection and extraction methods, adoption of nonparametric classifiers, and exploration of methods to exploit unlabeled samples via semi-supervised and active learning. Data sets are also quite large, motivating computationally efficient algorithms and implementations. This chapter provides an overview of the recent advances in classification methods for mapping vegetation using hyperspectral data. Three data sets that are used in the hyperspectral classification literature (e.g., Botswana Hyperion satellite data and AVIRIS airborne data over both Kennedy Space Center and Indian Pines) are described in Section 3.2 and used to illustrate methods described in the chapter. An additional high-resolution hyperspectral data set acquired by a SpecTIR sensor on an airborne platform over the Indian Pines area is included to exemplify the use of new deep learning approaches, and a multiplatform example of airborne hyperspectral data is provided to demonstrate transfer learning in hyperspectral image classification. Classical approaches for supervised and unsupervised feature selection and extraction are reviewed in Section 3.3. In particular, nonlinearities exhibited in hyperspectral imagery have motivated development of nonlinear feature extraction methods in manifold learning, which are outlined in Section 3.3.1.4. Spatial context is also important in classification of both natural vegetation with complex textural patterns and large agricultural fields with significant local variability within fields. Approaches to exploit spatial features at both the pixel level (e.g., co-occurrence–based texture and extended morphological attribute profiles [EMAPs]) and integration of segmentation approaches (e.g., HSeg) are discussed in this context in Section 3.3.2. Recently, classification methods that leverage nonparametric methods originating in the machine learning community have grown in popularity. An overview of both widely used and newly emerging approaches, including support vector machines (SVMs), Gaussian mixture models, and deep learning based on convolutional neural networks is provided in Section 3.4. Strategies to exploit unlabeled samples, including active learning and metric learning, which combine feature extraction and augmentation of the pool of training samples in an active learning framework, are outlined in Section 3.5. Integration of image segmentation with classification to accommodate spatial coherence typically observed in vegetation is also explored, including as an integrated active learning system. Exploitation of multisensor strategies for augmenting the pool of training samples is investigated via a transfer learning framework in Section 3.5.1.2. Finally, we look to the future, considering opportunities soon to be provided by new paradigms, as hyperspectral sensing is becoming common at multiple scales from ground-based and airborne autonomous vehicles to manned aircraft and space-based platforms.

Pasolli, Edoardo↗

DOE OSTI2022

Unsupervised learning from three-component accelerometer data to monitor the spatiotemporal evolution of meso-scale hydraulic fractures

Enhanced geothermal systems can provide a substantial share of the global energy demand. There exist several hurdles in the engineering implementations of such geothermal systems. One such hurdle is the accurate monitoring of the fracture networks created in subsurface through hydraulic stimulation of these systems. Micro seismicity associated with the stimulation is the primary means to locate the event hypocenters for estimating the stimulated rock volume. Existing methods for location the hypocenters are restricted to only the highest amplitude impulsive signals that are simultaneously detected on several sensors. Consequently, a large portion (usually ~99%) of the measurements are left unused. In this paper, an unsupervised manifold-approximation followed by clustering of 3-component accelerometer data is used to analyze the seismicity recorded on a monitoring well. With this method, a larger portion of the measured signal is used for the monitoring of the hydraulic fracture network. We analyze the EGS Collab experiment 1 microseismic data, recorded at the Sanford Underground Research Facility, South Dakota. Using the data from a single three-component accelerometer, the polarization features viz. Azimuth, incidence, rectilinearity, and planarity are used as inputs for the unsupervised manifold approximation followed by clustering. Our study shows that density-based clusters in the projected 3D space correspond to distinct types of hydraulically fractured zones around the injection point. Finally, we show that the temporal evolution of these clusters can be used to track fracture creation and propagation.

58 GEOSCIENCES↗

DOE OSTI2023

Data-Driven Smoothers for Extreme-Scale Computing

Patch-based relaxation refers to a family of methods for solving linear systems which partitions the matrix into smaller pieces often corresponding to groups of adjacent degrees of freedom residing within patches of the computational domain. The two most common families of patch-based methods are block-Jacobi and Schwarz methods, where the former typically corresponds to non-overlapping domains and the later implies some overlap. We focus on cases where each patch consists of the degrees of freedom on a finite element method mesh cell. Patch methods often capture complex local physics much more effectively than simpler point-smoothers such as Jacobi; however, forming, inverting, and applying each patch can be prohibitively expensive in terms of both storage and computation time. To this end, we propose several approaches for performing analysis on these patches and constructing a reduced representation. The compression techniques rely on either matrix norm comparisons or unsupervised learning via a clustering approach. We illustrate how it is frequently possible to retain/factor less than 5% of all patches and still develop a method that converges only a little slower than when all patches are stored/factored.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1976

Development and application of operational techniques for the inventory and monitoring of resources and uses for the Texas coastal zone

The author has identified the following significant results. Image interpretation mapping techniques were successfully applied to test site 5, an area with a semi-arid climate. The land cover/land use classification required further modification. A new program, HGROUP, added to the ADP classification schedule provides a convenient method for examining the spectral similarity between classes. This capability greatly simplifies the task of combining 25-30 unsupervised subclasses into about 15 major classes that approximately correspond to the land use/land cover classification scheme.

Harwood, P.↗

DOE OSTI2021

Defect detection in atomic-resolution images via unsupervised learning with translational invariance

Abstract Crystallographic defects can now be routinely imaged at atomic resolution with aberration-corrected scanning transmission electron microscopy (STEM) at high speed, with the potential for vast volumes of data to be acquired in relatively short times or through autonomous experiments that can continue over very long periods. Automatic detection and classification of defects in the STEM images are needed in order to handle the data in an efficient way. However, like many other tasks related to object detection and identification in artificial intelligence, it is challenging to detect and identify defects from STEM images. Furthermore, it is difficult to deal with crystal structures that have many atoms and low symmetries. Previous methods used for defect detection and classification were based on supervised learning, which requires human-labeled data. In this work, we develop an approach for defect detection with unsupervised machine learning based on a one-class support vector machine (OCSVM). We introduce two schemes of image segmentation and data preprocessing, both of which involve taking the Patterson function of each segment as inputs. We demonstrate that this method can be applied to various defects, such as point and line defects in 2D materials and twin boundaries in 3D nanocrystals.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Robust Spectral Anomaly Detection in EELS Spectral Images via 3D Convolutional Variational Autoencoders

Abstract A 3D Convolutional Variational Autoencoder (3D‐CVAE) is introduced for automated anomaly detection in electron energy‐loss spectroscopy spectrum imaging (EELS‐SI) data. This approach leverages the full 3D structure of EELS‐SI data to detect subtle spectral anomalies while preserving both spatial and spectral correlations across the datacube. By employing cross‐entropy loss and training on bulk spectra, the model learns to reconstruct bulk features characteristic of the defect‐free material. In exploring methods for anomaly detection, both the 3D‐CVAE approach and principal component analysis (PCA) are evaluated, testing their performance using FeL‐edge ΔEpeak shifts designed to simulate material defects. These results show that 3D‐CVAE achieves superior anomaly detection and maintains consistent performance across various shift magnitudes. The method demonstrates clear bimodal separation between bulk and anomalous spectra, enabling reliable classification. Further analysis verifies that lower‐dimensional representations are robust to anomalies in the data. While performance advantages over PCA diminish with decreasing anomaly concentration, our method maintains high reconstruction quality even in challenging, noise‐dominated spectral regions. This approach provides a robust framework for unsupervised automated detection of spectral anomalies in EELS‐SI data, particularly valuable for analyzing complex material systems.

Chemistry↗

DOE OSTI2024

Ice Phase Classification Made Easy with Score-Based Denoising

Accurate identification of ice phases is essential for understanding various physicochemical phenomena. However, such classification for structures simulated with molecular dynamics is complicated by the complex symmetries of ice polymorphs and thermal fluctuations. For this purpose, both traditional order parameters and data-driven machine learning approaches have been employed, but they often rely on expert intuition, specific geometric information, or large training data sets. In this work, we present an unsupervised phase classification framework that combines a score-based denoiser model with a subsequent model-free classification method to accurately identify ice phases. Further, the denoiser model is trained on perturbed synthetic data of ideal reference structures, eliminating the need for large data sets and labeling efforts. The classification step utilizes the smooth overlap of atomic position (SOAP) descriptors as the atomic fingerprint, ensuring Euclidean symmetries and transferability to various structural systems. Our approach achieves a remarkable 100% accuracy in distinguishing ice phases of test trajectories using only seven ideal reference structures of ice phases as model inputs. This demonstrates the generalizability of the score-based denoiser model in facilitating phase identification for complex molecular systems. The proposed classification strategy can be broadly applied to investigate structural evolution and phase identification for a wide range of materials, offering new insights into the fundamental understanding of water and other complex systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Neural network reconstruction of the dense matter equation of state from neutron star observables

The Equation of State (EoS) of strongly interacting cold and hot ultra-dense QCD matter remains a major challenge in the field of nuclear astrophysics. With the advancements in measurements of neutron star masses, radii, and tidal deformabilities, from electromagnetic and gravitational wave observations, neutron stars play an important role in constraining the ultra-dense QCD matter EoS. Here, in this work, we present a novel method that exploits deep learning techniques to reconstruct the neutron star EoS from mass-radius (M-R) observations. We employ neural networks (NNs) to represent the EoS in a model-independent way, within the range of ~1-7 times the nuclear saturation density. The unsupervised Automatic Differentiation (AD) framework is implemented to optimize the EoS, so as to yield through TOV equations, an M-R curve that best fits the observations. We demonstrate that this method works by rebuilding the EoS on mock data, i.e., mass-radius pairs derived from a randomly generated polytropic EoS. The reconstructed EoS fits the mock data with reasonable accuracy, using just 11 mock M-R pairs observations, close to the current number of actual observations.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRSDate not supplied

Using Machine Learning to Infer Material Properties of Debris Fragments from X-ray Images in the DebriSat Project

The DebriSat project is a collaboration effort with the NASA Orbital Debris Program Office, the U.S. Space Force Space Systems Command Center, The Aerospace Corporation, and the University of Florida. To date, over 200,000 fragments from this ground-based, hypervelocity impact experiment have been collected, and processing is underway to determine their physical characteristics, such as material, shape, color, characteristic length, and average cross-sectional area. The x-ray process is primarily used to identify the location of the fragments and estimated size for extraction, so that these physical characteristics can be assessed. This paper proposes a machine learning-based approach to characterize materials from x-ray images of debris fragments embedded in soft-catch foam used in the DebriSat project. The novel methodology discussed in this paper will highlight the use of x-ray imagery data to characterize these fragments without extraction or a human-in-the-loop. Both supervised and unsupervised machine learning techniques are utilized with this approach to infer the physical parameters of the fragments embedded in the soft-catch foam panels used in the impact experiment based on x-ray images of the foam panels. Additionally, 3D reconstructions of the extracted fragments are created with images taken from two different angles using the structure from motion (SfM) method. The characteristic lengths and shape from the 3D reconstruction, alongside the physical characteristics of the debris, are used in the inference of the material type. To develop and test the approach, a dataset of x-ray images of debris fragments of varying sizes and materials is collected. Supervised learning methods such as convolutional neural networks (CNNs), support vector machines (SVM), decision trees, and random forest classifiers are used due to the high-dimensional feature spaces of the debris and nonlinear decision boundaries for material categorization. Given the limited pre-labeled data of embedded debris materials smaller than 10 mm, unsupervised machine learning techniques such as clustering algorithms and autoencoders are used, in addition to supervised learning methods. The clustering algorithms group similar fragments together based on their physical properties, and autoencoders reduce the dimensionality of the x ray images and extract relevant features. The performance of the proposed approach's is analyzed using a range of statistical methods, including confusion matrices, receiver operating characteristic curves, and precision-recall curves. The results are compared with those obtained using a baseline approach that relies on manual identification and classification of debris fragments. To evaluate the effectiveness of different machine learning methods, statistical tests such as t-tests, ANOVA, and cross-validation are performed, comparing the performance of CNNs, SVMs, clustering algorithms, and autoencoders. Additional analysis needs to be conducted to identify any sources of bias or variability that may affect the results, such as variations in imaging conditions or fragmentation patterns. Other topics explored are limitations, refinements, and the potential use of semi-supervised learning techniques, such as self-training to label unlabeled datasets and co-training using x-ray images taken from two different angles as two different models.

Saik Anam Siam↗

NASA NTRS2023

Using Machine Learning to Infer Material Properties of Debris Fragments from X-ray Images in the DebriSat Project

Saik Anam Siam↗

DOE OSTI2024

Single Channel Infrasound Detection Using Machine Learning

Infrasound, low frequency sound less than 20 Hz, is generated by both natural and anthropogenic sources. Infrasound sensors measure pressure fluctuations only in the vertical plane and are single channel. However, the most robust infrasound signal detection methods rely on stations with multiple sensors (arrays), despite the fact that these are sparse. Automated methods developed for seismic data, such as short-term average to long-term average ratio (STA/LTA), often have a high false alarm rate when applied to infrasound data. Leveraging single channel infrasound stations has the potential to decrease signal detection limits, though this cannot be done without a reliable detection method. Therefore, this report presents initial results using (1) a convolutional neural network (CNN) to detect infrasound signals and (2) unsupervised learning to gain insight into source type.

47 OTHER INSTRUMENTATION↗

NASA NTRS2024

Sensor Fault Detection in Smart Extraterrestrial Habitats Using Unsupervised Learning

Various types of sensors are needed to monitor the health state of smart deep-space habitats. However, measured data can be affected by sensor faults, which influence the health management system and consequently the decision-making. In this paper, an unsupervised learning approach based on convolutional autoencoders (CAEs) is developed to detect anomalies in temperature and pressure sensors. The proposed method is systematically investigated using a habitat simulator (HabSim). Several illustrative examples are demonstrated in the nominal and hazardous states of the habitat, including micrometeorite impact and fire scenarios. The performance of the proposed method using CAEs is compared with that of existing methods using auto-associative neural networks (AANNs) and variational autoencoders. This comparison is based on typical evaluation metrics, including precision, recall, F1 score, training time, and testing time. The effect of temperature–pressure coupling on the detection performance of CAEs and AANNs is explored by training different data-driven models, including one with temperature sensors, one with pressure sensors, and one with both temperature and pressure sensors. The effect of the number of faulty sensors on the performance of CAEs is studied, as with an increase in the number of faulty sensors, redundant information among the sensors is reduced. The capability of CAEs to change the number of sensors without redesigning the network architecture and retraining the neural network is investigated and demonstrated. The capabilities and limitations of the proposed solution are discussed.

Zixin Wang↗

DOE OSTI2023

Sensor Anomaly Detection for Nuclear Reactor Systems Utilizing Linear Regression and K-Means Unsupervised Machine Learning

Nuclear reactors and related systems are becoming increasingly complex due to advancing technologies in next-generation power reactors. This increased complexity necessitates enhanced automation and data management capabilities. To successfully realize autonomous systems, methods must be developed to handle vast volumes of data and effectively distinguish anomalous data from noise and expected data. While impressive models utilizing digital twins and similar approaches are under development, here we propose a simplified model for analyzing fundamental methods and techniques. Initially, we created a general dataset by using initial data from PCTRAN in order to represent ideal steady-state conditions. We then inserted anomalies based on prevalent sensor anomaly types (e.g., point anomalies, linear drift, and downward deviations), along with unusual anomalies such as exponential drift and upward deviations. To detect anomalies, we developed a program that employs data partitioning and linear regression to preprocess and filter the anomalous data. A K-Means machine learning (ML) method was then applied to separate and count the data within the anomalous partition. The results from all datasets—apart from exponential growth—demonstrated positive outcomes, with each returning multiple instances of greaterthan-95% accuracy. We conducted further investigations using Idaho National Laboratory’s RAVEN software to perform a sensitivity analysis on the input variables (R 2 Tolerance, Slope Tolerance, and Window Size) and found that the output variables (Accuracy and Time) were most sensitive to the Window Size. Despite the promising results published, further development is required to effectively apply these methods to nuclear systems. Nevertheless, the strengths of this approach are evident and hold promise for future applications in the field.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2025

Distinguishing isotropic and anisotropic signals for X-ray total scattering using machine learning

Understanding structure–property relationships is essential for advancing technologies based on thin films. X-ray pair distribution function (PDF) analysis can access relevant atomic structure details spanning local-, mid- and long-range structure. While X-ray PDF has been adapted for thin films on amorphous substrates, measurements on single-crystal substrates are necessary to accurately determine structure origins for some thin film materials, especially those for which the substrate changes the accessible structure and properties. However, when measuring films on single-crystal substrates, high-intensity anisotropic Bragg spots saturate 2D detector images, overshadowing the thin films' isotropic scattering signal. This renders previous data processing methods for films on amorphous substrates unsuitable for films on single-crystal substrates. To address this measurement need, we developed IsoDAT2D, an innovative data processing approach using unsupervised machine learning algorithms. The program combines dimensionality reduction and clustering algorithms to separate thin film and single-crystal substrate X-ray scattering signals. We use SimDAT2D , a program we developed to generate simulated thin film data, to validate IsoDAT2D . Here we also use IsoDAT2D to isolate X-ray total scattering signal from a thin film on a single-crystal substrate. The resulting PDF data are compared with similar data processed using previous methods, especially substrate subtraction for single-crystal and amorphous substrates. PDF data from IsoDAT2D -identified X-ray total scattering data are significantly better than from single-crystal substrate subtraction, but not as reliable as PDF data from amorphous substrate subtraction. With IsoDAT2D , there are new opportunities to expand PDF to a wider variety of thin films, including those on single-crystal substrates, with which new structure–property relationships can be elucidated to enable fundamental understanding and technological advances.

36 MATERIALS SCIENCE↗