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NASA NTRS2021

Unsupervised Deep Persistent Monocular Visual Odometry and Depth Estimation in Extreme Environments

In recent years, unsupervised deep learning ap-proaches have received a significant attention to estimate depthand visual odometry (VO) from unlabelled monocular imagesequences. However, their performance is limited in challengingenvironments due to perceptual degradation, occlusions andrapid motions. Moreover, the existing unsupervised methodssuffer from the lack of scale-consistency constraints acrossframes, which causes that the VO estimators fail to providepersistent trajectories over long sequences. In this study, wepropose a unsupervised monocular deep VO framework thatpredicts 6 degrees-of-freedom pose camera motion and depthmap of the scene from unlabelled RGB image sequences.We provide detailed quantitative and qualitative evaluationsof the proposed framework on a) a challenging dataset col-lected during the DARPA Subterranean challenge1; and b)the benchmark KITTI and Cityscapes datasets. The proposedapproach outperforms both traditional and state-of-the-artunsupervised deep VO methods providing better results for bothpose estimation and depth recovery. The presented approach ispart of the solution used by the COSTAR team participatingat the DARPA Subterranean Challenge

Agha-mohammadi, Ali-akbar↗

DOE OSTI2026

Machine Learning-Based Anomaly Detection for PMT Data Quality Monitoring in the SBN and DUNE

Maintaining high-quality detector data is essential for achieving the scientific objectives of the Short-Baseline Neutrino (SBN) Program at Fermilab. Current data quality monitoring (DQM) procedures rely primarily on threshold-based metrics and manual inspection of detector monitoring plots, making the detection of subtle or gradually developing anomalies both time-consuming and dependent on expert interpretation. This project developed and evaluated a machine-learning workflow for automatically identifying anomalous photomultiplier tube (PMT) channels in the Short-Baseline Near Detector (SBND) using optical-hit amplitude data. A Python-based analysis program was developed to process ROOT files, extract statistical features describing individual PMT amplitude distributions, and generate feature vectors for anomaly detection. These features were used to train an Isolation Forest model using data representing normal detector operation. The trained model was subsequently applied to independent detector runs to identify channels exhibiting statistically unusual behavior relative to the learned reference response. To support expert interpretation, the workflow generated complementary diagnostic products, including anomaly score distributions, normalized amplitude comparisons, decision-tree visualizations, and principal component analysis (PCA) projections. This project demonstrated the feasibility of integrating unsupervised machine learning into detector data-quality monitoring and developed a complete workflow for automated PMT performance assessment to aid expert-driven review. Beyond its technical contributions, the VFP appointment fostered a research collaboration between Aurora University and Fermilab and provided direct workforce development benefits by training the visiting faculty member in detector-scale machine-learning methods that are now being incorporated into undergraduate coursework and research. The methodology developed here provides a foundation for future applications to ProtoDUNE and other liquid argon time projection chamber (LArTPC) detectors, contributing to ongoing efforts to improve detector reliability, reduce manual monitoring requirements, and enable scalable data quality monitoring for future large-scale neutrino experiments, including the Deep Underground Neutrino Experiment (DUNE).

Colón Santana, Juan A. [Unlisted, US, IL]↗

DOE OSTI2025

Unraveling Hydrogen Induced Geochemical Reaction Mechanisms through Coupled Geochemical Modeling and Machine Learning

Underground hydrogen storage (UHS) provides a promising large-scale, long-term energy storage solution. A reasonable recovery of stored hydrogen is critical for a successful storage scheme. However, in subsurface reservoirs hydrogen is subject to active geochemical reactions that might result in hydrogen loss. In this study, we implemented a geochemical modeling approach coupled with an unsupervised machine learning technique called non-negative matrix factorization (NMF) to unravel the complex brine-rock-H 2 geochemical processes responsible for hydrogen losses, with particular focus on sulfate reduction reactions. NMF is applied to modeled mineral evolution and fluid component profiles to retrieve profiles that can be interpreted to more easily assess competing processes. NMF decouples simulated competing equilibrium reactions. This facilitates separation of overlapping reaction profiles from redox processes, dissolution fronts, and secondary precipitation while considering the effects of simulation parameters such as salinity, temperature, and total H 2 pressure. NMF successfully discriminates these competing effects in nonlinear ways, allowing robust interpretation. In addition, NMF reveals subtle coupled mineral associations and reaction fronts that are invisible to conventional model analysis. This integrated approach strengthens the conceptual understanding of complex nonlinear hydrogen-brine-rock interactions and advances geochemical research on UHS systems to resolve complexities in modeled geochemical systems without the need for direct experiments or prior knowledge. Furthermore, this study highlights the efficacy of combining geochemical modeling with machine learning techniques to enhance the interpretability of the intricate geochemical simulation output through deciphering the overlapping reaction path that cannot be achieved only using conventional analysis of geochemical models alone.

08 HYDROGEN↗

DOE OSTI2024

Anomaly detection in collider physics via factorized observables

To maximize the discovery potential of high-energy colliders, experimental searches should be sensitive to unforeseen new physics scenarios. This goal has motivated the use of machine learning for unsupervised anomaly detection. In this paper, we introduce a new anomaly detection strategy called : factorized observables for regressing conditional expectations. Our approach is based on the inductive bias of factorization, which is the idea that the physics governing different energy scales can be treated as approximately independent. Assuming factorization holds separately for signal and background processes, the appearance of nontrivial correlations between low- and high-energy observables is a robust indicator of new physics. Under the most restrictive form of factorization, a machine-learned model trained to identify such correlations will in fact converge to the optimal new physics classifier. We test on a benchmark anomaly detection task for the Large Hadron Collider involving collimated sprays of particles called jets. By teasing out correlations between the kinematics and substructure of jets, our method can reliably extract percent-level signal fractions. This strategy for uncovering new physics adds to the growing toolbox of anomaly detection methods for collider physics with a complementary set of assumptions. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

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↗

DOE OSTI2024

Investigation of acoustic waves under subsurface conditions to improve the predictions of rock mechanical properties and natural fracture characteristics

Mechanical properties and natural fracture characteristics are critical to investigate for subsurface engineering applications, including carbon storage, well drilling, and stimulation, as they govern rock stability, fluid flow, and mechanical behavior under stress. This dissertation integrates experimental and machine learning approaches to enhance the prediction and understanding of these properties by analyzing acoustic wave behavior under varied subsurface conditions. First, the influence of temperature, pore pressure, and supercritical CO2 (scCO2) saturation on poroelastic properties is examined using Gray Berea sandstone samples. The results show that temperature and pore pressure significantly affect the bulk modulus and Biot’s coefficient, while scCO2 saturation impacts rock compressibility, informing strategies for effective geological carbon storage. The study extends this understanding by experimentally evaluating the impact of reservoir depletion on the dynamic mechanical properties of the emerging Caney shale in South Oklahoma with the employment of unsupervised machine learning to predict static mechanical properties across the Caney shale. Integrating petrophysical data and chemostratigraphy, the workflow—featuring K-means clustering, principal component analysis (PCA), and inverse distance weighting (IDW)—improves stratigraphic characterization and the estimation of static-to-dynamic modulus ratios, which is vital for optimizing drilling and stimulation strategies. Finally, the work explores how natural fracture characteristics in shale influence acoustic waveforms and shear wave splitting (SWS) analysis. Experimental data on fractured samples under different stress and temperature conditions, combined with machine learning models such as K-nearest neighbors (KNN) and extreme gradient boosting (XGBoost), reveal key fracture properties impacting SWS and wave propagation. Together, these studies provide a comprehensive framework for linking acoustic wave behavior with rock properties, advancing the methods for monitoring and predicting geomechanical changes. The insights offered valuable implications for safer, more efficient CO2 injection, hydrocarbon extraction, and subsurface management.

Elkholy, Sherif↗

DOE OSTI2026

Real-Time Anomaly Detection for Beyond Standard Model Searches in ProtoDUNE Horizontal Drift

This paper summarizes work conducted throughout a SULI internship at Fermi National Accelerator Laboratory focused on building an unsupervised machine learning model for real-time anomaly detection in ProtoDUNE Horizontal Drift. Using simulated data, we trained an autoencoder model on a pure cosmic dataset, and evaluated it on both cosmic and neutrino events---making the model an anomaly detector. The goal was to make a model which matches or exceeds the current ADC Simple Window trigger algorithm so that our model can perform at the same rate but provide sensitivity to potential beyond-the-Standard-Model (BSM) signatures. In the end, we were able to construct a model which slightly exceeds the capabilities of the ADC Simple Window while remaining completely unsupervised, achieving $31.9 \pm 0.2$\% ($26.6 \pm 0.2$\%) $\nu$ efficiency at 5 Hz (2 Hz), a 3.6 (3.2) percentage point increase. Additionally, $17.5 \pm 0.3$\% ($18.3 \pm 0.3$\%) of the events that passed the autoencoder at 5 Hz (2 Hz) were missed by the current trigger algorithm. Future work will investigate alternative normalization methods, including quantile transformation, and evaluate the model on ProtoDUNE-HD detector-glitch data if that data becomes available.

Wilson, Cameron C. [Cincinnati U., RWC]↗

DOE OSTI2026

Real-Time Anomaly Detection for Beyond Standard Model Searches in ProtoDUNE Horizontal Drift

Wilson, Cameron C. [Cincinnati U., RWC]↗

DOE OSTI2026

Real-Time Anomaly Detection for Searches Beyond the Standard Model in the ProtoDUNE Horizontal Drift Detector

This paper summarizes work conducted throughout a SULI internship at Fermi National Accelerator Laboratory focused on building an unsupervised machine learning model for real-time anomaly detection in ProtoDUNE Horizontal Drift. Using simulated data, we trained an autoencoder model on a pure cosmic dataset, and evaluated it on both cosmic and neutrino events—making the model an anomaly detector. The goal was to make a model which matches or exceeds the current ADC Simple Window trigger algorithm so that our model can perform at the same rate but provide sensitivity to potential beyond-the-Standard-Model (BSM) signatures. In the end, we were able to construct a model which slightly exceeds the capabilities of the ADC Simple Window while remaining completely unsupervised, achieving 31.9 ± 0.2% (26.6 ± 0.2%) ν efficiency at 5 Hz (2 Hz), a 3.6 (3.2) percentage point increase. Additionally, 17.5 ± 0.3% (18.3 ± 0.3%) of the events that passed the autoencoder at 5 Hz (2 Hz) were missed by the current trigger algorithm. Future work will investigate alternative normalization methods, including quantile transformation, and evaluate the model on ProtoDUNE-HD detector-glitch data if that data becomes available.

Wilson, C. [Cincinnati U., RWC]↗

DOE OSTI2025

Real-time tracking and analysis of gas bubble dynamics in laser powder bed fusion using in-situ X-ray characterization and machine learning

Porosity defects remain a significant challenge in the laser powder bed fusion (LPBF) process, adversely affecting the mechanical properties and reliability of additively manufactured components. Here, this study investigates the real-time formation and trajectory of gas bubbles during LPBF of Al6061 alloy using advanced in-situ X-ray characterization and machine learning. The unsupervised Gaussian mixture model and particle tracking algorithm developed are able to precisely track and quantify the properties of gas bubbles and keyhole pores. Our analysis identified five distinct types of gas bubble formation and movement patterns, emphasizing the diverse origins and behaviors of these defects. It enables precise quantification of trajectories, velocities, and morphological changes of gas bubbles, offering a granular view of the subsurface dynamics within the melt pool. Additionally, we explored keyhole-induced pore dynamics, revealing the critical role of keyhole oscillation and collapse for the formation of both large and small gas pores. It defines four different regions of gas bubble movement within the melt pool, providing a clearer understanding of how local fluid dynamics affect pore behavior. The results underscore the importance of integrating in-situ experimental observation and automated machine learning to develop a more robust predictive model for defect formation in LPBF.

In-situ X-ray imaging↗

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

Assessing the Application of a Genomic Network Analysis in Population Ecology: Inferring Patterns of Dispersal and Geographic Structure in the Emerging Pathogen, Coccidioides

A challenge in population ecology studies is identifying how to best group individuals into populations, especially when individual origin is unknown. Machine learning has improved upon traditional methods of identifying population structure and is more efficient at handling large, complex datasets. We demonstrate the applicability of a machine learning method to identify hierarchical population structure in an emerging pathogen, Coccidioides spp., the causative agent of Valley fever. We compared the network clusters to structure identified by traditional tools as a validation of the network performance. We used publicly available whole-genome data for 48 C. immitis and 102 C. posadasii, resulting in 168,211 genome-wide SNPs among the two species. The network analysis grouped samples into populations comparable to the literature for these species but also identified fine-scale geographic structure and travel-associated cases not reported thus far. Exploring different resolutions in the network made it easy to identify unique genotypes specific to California and possibly Nevada, as well as Phoenix- and Tucson-acquired infections in non-endemic areas, regardless of reported travel history. The present study provides a promising example of how a ML-based network analysis can improve our ability to understand pathogen ecology, group cases into populations and infer travel-associated infections.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Oleaginous Yeast Biology Elucidated With Comparative Transcriptomics

ABSTRACT Extremophilic yeasts have favorable metabolic and tolerance traits for biomanufacturing‐ like lipid biosynthesis, flavinogenesis, and halotolerance – yet the connection between these favorable phenotypes and strain genotype is not well understood. To this end, this study compares the phenotypes and gene expression patterns of biotechnologically relevant yeasts Yarrowia lipolytica , Debaryomyces hansenii , and Debaryomyces subglobosus grown under nitrogen starvation, iron starvation, and salt stress. To analyze the large data set across species and conditions, two approaches were used: a “network‐first” approach where a generalized metabolic network serves as a scaffold for mapping genes and a “cluster‐first” approach where unsupervised machine learning co‐expression analysis clusters genes. Both approaches provide insight into strain behavior. The network‐first approach corroborates that Yarrowia upregulates lipid biosynthesis during nitrogen starvation and provides new evidence that riboflavin overproduction in Debaryomyces yeasts is overflow metabolism that is routed to flavin cofactor production under salt stress. The cluster‐first approach does not rely on annotation; therefore, the coexpression analysis can identify known and novel genes involved in stress responses, mainly transcription factors and transporters. Therefore, this work links the genotype to the phenotype of biotechnologically relevant yeasts and demonstrates the utility of complementary computational approaches to gain insight from transcriptomics data across species and conditions.

Weintraub, Sarah J. [Department of Bioinformatics ↗

DOE OSTI2025

Exploring urban typologies using comprehensive analysis of transportation dynamics

Abstract As urban areas continue to expand and develop, categorizing cities into typologies offers a valuable framework for understanding metropolitan dynamics and fostering inter-city collaboration. However, existing typologies related to urban mobility have limitations, failing to consider cities within a single large urban region and often overlooking crucial dimensions such as trip demand and traffic flow. In this paper, we introduce a transportation-focused characterization for cities within a large urban region, specifically the San Francisco Bay Area, California. We incorporate over 40 metrics across five transportation dimensions: trip demand, road network, multi-modal network, traffic flow, and land use. Specifically, for the trip demand dimension, we include metrics capturing residents’ trip characteristics, such as mode share, intra-city trips, and inter-city trips. Additionally, we analyze the purpose of trips entering the city to gain a deeper understanding of incoming trip patterns. In the traffic flow dimension, we examine metrics like vehicle miles traveled, delay, and congestion to assess the traffic conditions on the street network. These, combined with other dimensions, provide a comprehensive view of a city’s transportation dynamics. Using unsupervised machine learning clustering methods, we identified eight distinct typologies for the Bay Area: Live Work Cities; Job and Activity Magnet Cities; Anchor Cities; Multi-modal Cities; Hyper-connected Cities; Low-density Residential Cities; Medium-density Residential Cities; and Mixed-use Residential Cities. Our findings show that many clusters are strongly influenced by trip demand and traffic flow metrics. Finally, we examine the practicality of this typology and its potential to guide collaborative transportation management strategies. The typologies provide a foundation for dialogue among Bay Area cities, focusing on evaluating shared characteristics and leveraging successes or challenges to develop unified strategies for transportation management.

Kuncheria, Anu↗

DOE OSTI2026

Time-resolved spray characterization via unified optical flow and binarization technique

This work leverages an unsupervised machine learning and advanced image processing techniques to characterize the breakup of fuel sprays in a small-scale combustor under reacting conditions, providing valuable insights into near-nozzle flow phenomenology. The proposed methodology integrates an improved optical flow model on a convolutional neural network to extract flow vectors with a binarization technique to assess droplets’ size and shape across the region of interest. The velocimetry approach demonstrates superior performance compared to a state-of-the-art optical flow model when applied to high-speed X-ray phase contrast spray images, achieving more accurate and reliable flow predictions. Moreover, breakup processes are quantified by breakup length and sphericity in accordance with velocity estimations, allowing a more complete characterization of the flow. This study establishes a robust methodology for analyzing spray morphology and primary breakup in compact combustors, contributing valuable means of understanding and optimizing fuel spray behavior in advanced combustion systems.

42 ENGINEERING↗

DOE OSTI2024

AI-NERD: Elucidation of relaxation dynamics beyond equilibrium through AI-informed X-ray photon correlation spectroscopy

Abstract Understanding and interpreting dynamics of functional materials in situ is a grand challenge in physics and materials science due to the difficulty of experimentally probing materials at varied length and time scales. X-ray photon correlation spectroscopy (XPCS) is uniquely well-suited for characterizing materials dynamics over wide-ranging time scales. However, spatial and temporal heterogeneity in material behavior can make interpretation of experimental XPCS data difficult. In this work, we have developed an unsupervised deep learning (DL) framework for automated classification of relaxation dynamics from experimental data without requiring any prior physical knowledge of the system. We demonstrate how this method can be used to accelerate exploration of large datasets to identify samples of interest, and we apply this approach to directly correlate microscopic dynamics with macroscopic properties of a model system. Importantly, this DL framework is material and process agnostic, marking a concrete step towards autonomous materials discovery.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Real-space visualization of a defect-mediated charge density wave transition

Here, we study the coupled charge density wave (CDW) and insulator-to-metal transitions in the 2D quantum material 1T-TaS 2 . By applying in situ cryogenic 4D scanning transmission electron microscopy with in situ electrical resistance measurements, we directly visualize the CDW transition and establish that the transition is mediated by basal dislocations (stacking solitons). We find that dislocations can both nucleate and pin the transition and locally alter the transition temperature T c by nearly ~75 K. This finding was enabled by the application of unsupervised machine learning to cluster five-dimensional, terabyte scale datasets, which demonstrate a one-to-one correlation between resistance—a global property—and local CDW domain-dislocation dynamics, thereby linking the material microstructure to device properties. This work represents a major step toward defect-engineering of quantum materials, which will become increasingly important as we aim to utilize such materials in real devices.

4D-STEM↗

DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗