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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 OSTI2022

Discovering hidden geothermal signatures using non-negative matrix factorization with customized k-means clustering

Discovery of hidden geothermal resources is challenging. It requires the mining of large datasets with diverse data attributes representing subsurface hydrogeological and geothermal conditions. The commonly used play fairway analysis approach typically incorporates subject-matter expertise to analyze regional data to estimate geothermal characteristics and favorability. We demonstrate an alternative approach based on machine learning (ML) to process a geothermal dataset from southwest New Mexico (SWNM). The study region includes low- and medium-temperature hydrothermal systems. Several of these systems are not well characterized because of insufficient existing data and limited past explorative work. This study discovers hidden patterns and relations in the SWNM geothermal dataset to improve our understanding of the regional hydrothermal conditions and energy-production favorability. This understanding is obtained by applying an unsupervised ML algorithm based on non-negative matrix factorization coupled with customized k-means clustering (NMFk). NMFk can automatically identify (1) hidden signatures characterizing analyzed datasets, (2) the optimal number of these signatures, (3) the dominant data attributes associated with each signature, and (4) the spatial distribution of the extracted signatures. Here, in this study, NMFk is applied to analyze 18 geological, geophysical, hydrogeological, and geothermal attributes at 44 locations in SWNM. Using NMFk, we find data patterns and identify the spatial associations of hydrothermal signatures within two physiographic provinces (Colorado Plateau and Basin and Range) and two sub-regions of these provinces (the Mogollon-Datil volcanic field and the Rio Grande rift) in SWNM. The ML algorithm extracted five hydrothermal signatures in the SWNM datasets that differentiate between low (<90°C) and medium (90-150°C)-temperature hydrothermal systems. The algorithm also suggests that the Rio Grande rift and northern Mogollon-Datil volcanic field are the most favorable regions for future geothermal resource discovery. NMFk also identified critical attributes to identify medium-temperature hydrothermal systems in the study area. The resulting NMFk model can be applied to predict geothermal conditions and their uncertainties at new SWNM locations based on limited data from unexplored regions. The code to execute the performed analyses as well as the corresponding data can be found at https://github.com/SmartTensors/GeoThermalCloud.jl.

15 GEOTHERMAL ENERGY↗
DOE OSTI2025

The Artificial Scientist: in-Transit Machine Learning of Plasma Simulations

Large-scale simulations or scientific experiments produce petabytes of data per run. This poses massive challenges for I/O and storage when scientific analysis workflows are run manually offline. Unsupervised deep learning-based techniques to extract patterns and non-linear relations from these large amounts of data provide a way to build scientific understanding from raw data, reducing the need for manual pre-selection of analysis steps, but require exascale compute and memory to process the full dataset available. In this paper, we demonstrate a heterogeneous streaming workflow in which plasma simulation data is streamed directly to a Machine Learning (ML) application training a model on the simulation data in-transit, completely circumventing the capacity-constrained filesystem bottleneck. This workflow employs openPMD to provide a high level interface to describe scientific data and also uses ADIOS2, to transfer volumes of data that exceed the capabilities of the filesystem. We employ experience replay to avoid catastrophic forgetting in learning from this non-steady state process in a continual manner and adapt it to improve model convergence while learning in-transit. As a proof-of-concept, we approach the ill-posed inverse problem of predicting particle dynamics from radiation in a particle-incell (PIConGPU) simulation of the Kelvin-Helmholtz instability (KHI). We detail hardware-software co-design challenges as we scale PIConGPU to full Frontier, the Top-1 system as of June 2024 Top500 list.

Kelling, Jeffrey [Helmholtz-Zentrum Dresden Rossen↗
DOE OSTI2023

RX-ADS: Interpretable Anomaly Detection Using Adversarial ML for Electric Vehicle CAN Data

Recent year has brought considerable advancements in Electric Vehicles (EVs) and associated infrastructures/ communications. Intrusion Detection Systems (IDS) are widely deployed for anomaly detection in such critical infrastructures. This paper presents an Interpretable Anomaly Detection System (RX-ADS) for intrusion detection in CAN protocol communication in EVs. Contributions include: 1) window based feature extraction method; 2) deep Autoencoder based anomaly detection method; and 3) adversarial machine learning based explanation generation methodology. The presented approach was tested on two benchmark CAN datasets: OTIDS and Car Hacking. The anomaly detection performance of RX-ADS was compared against the state-of-the-art approaches on these datasets: HIDS and GIDS. The RX-ADS approach presented performance comparable to the HIDS approach (OTIDS dataset) and has outperformed HIDS and GIDS approaches (Car Hacking dataset). Further, the proposed approach was able to generate explanations for detected abnormal behaviors arising from various intrusions. Furthermore, these explanations were later validated by information used by domain experts to detect anomalies. Other advantages of RX-ADS include: 1) the method can be trained on unlabeled data; 2) explanations help experts in understanding anomalies and root course analysis, and also help with AI model debugging and diagnostics, ultimately improving user trust in AI systems.

42 ENGINEERING↗
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 OSTI2023

REC protein family expansion by the emergence of a new signaling pathway

This report presents multi-genome evidence that REC protein family expansion occurs when the emergence of new pathways gives rise to functional discordance. Specificity between residues in REC domain containing response regulators with paired histidine kinases is under negative purifying selection, constrained by the presence of other bacterial two-component systems signaling cascades that share sequence and structural identity. Presuming that the two-component systems can evolve by neutral amino acid changes (neutral drift) when purifying evolutionary constraints are relaxed, how might the REC protein family expand by amino acid changes when these constraints remain intact? Using an unsupervised machine learning approach to observe the sequence landscape of REC domains across long phylogenetic distances, we find that within-gene recombination, a subcategory of gene conversion, switched the effector domain and, consequently, the regulatory context of a duplicated response regulator from transcriptional regulation by σ54 to that by σ70. We determined that the recombined response regulator diverged from its parent by episodic diversifying selection and neutral drift. Functional experiments of the parent of recombined response regulators in a model Pseudomonas putida KT2440 model system revealed that the parent and recombined response regulators sense and respond to different carboxylic acids. Finally, a residue-switching experiment using structural predictions and functional characterization suggests that the new residues in the recombined regulator could form a new interaction interface and mediate condition-specific phosphotransfer. Overall, our study finds that genetic perturbations can create conditions of functional discordance, whereby the REC protein family can evolve by episodic diversifying selection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Why it is Unfortunate that Linear Machine Learning “Works” so well in Electromechanical Switching of Ferroelectric Thin Films

Machine learning (ML) is relied on for materials spectroscopy. It is challenging to make ML models fail because statistical correlations can mimic the physics without causality. Here, using a benchmark band-excitation piezoresponse force microscopy polarization spectroscopy (BEPS) dataset the pitfalls of the so-called “better”, “faster”, and “less-biased” ML of electromechanical switching are demonstrated and overcome. Using a toy and real experimental dataset, it is demonstrated how linear nontemporal ML methods result in physically reasonable embedding (eigenvalues) while producing nonsensical eigenvectors and generated spectra, promoting misleading interpretations. A new method of unsupervised multimodal hyperspectral analysis of BEPS is demonstrated using long-short-term memory (LSTM) β-variational autoencoders (β-VAEs) . By including LSTM neurons, the ordinal nature of ferroelectric switching is considered. Further, to improve the interpretability of the latent space, a variational Kullback–Leibler-divergency regularization is imposed . Finally, regularization scheduling of β as a disentanglement metric is leveraged to reduce user bias. Combining these experiment-inspired modifications enables the automated detection of ferroelectric switching mechanisms, including a complex two-step, three-state one. Ultimately, this work provides a robust ML method for the rapid discovery of electromechanical switching mechanisms in ferroelectrics and is applicable to other multimodal hyperspectral materials spectroscopies.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Data-Driven Supervised Dimension Reduction for Scientific Discovery (LDRD QTI Report)

This report summarizes the findings of a four months FY24 Advanced Science & Technology (AS&T) LDRD Quick Targeted Investigation (QTI) project focused on the exploration of supervised dimension reduction approaches based on autoencoders. Autoencoders have been extensively employed in literature for unsupervised learning tasks, however, their use for supervised regression tasks, which are common within scientific applications, has been limited. Motivated by linear dimension reduction strategies like Active Subspaces and Adaptive Basis, we explored the possibility of employing autoencoders to discover a non-linear manifold able to represent the original function in fewer dimensions. In this report, we discuss a neural network architecture and we perform a numerical campaign on several problems ranging from simple two-dimensional functions to a model problem for magnetohydrodynamics in five dimensions. In our preliminary results, we show that the proposed approach is found to be superior to linear dimension reduction strategies in representing the target function even with a single latent variable.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Regime Characterization of Offshore Wind Resource Using Unsupervised Learning

Predictability of wind resource conditions is critical for offshore wind design and operations. While many studies of extreme wind conditions focus on specific events such as low-level jets or ramps, these rely on threshold definitions that limit generality. Here we present a data-driven framework that combines principal component analysis (PCA), self-organizing maps (SOM), and k-means clustering to classify wind resource conditions as typical and anomalous from climatological data. Anomalies are defined not by fixed thresholds but by flagging samples located far from SOM node centers inside the baseline SOM structure. This reframes extremes as rare ebents and hence, likely difficult to anticipate by numerical weather prediction models. We applied this approach to 23 years (2000–2022) of hourly profiles from the NOW-23 hindcast model at the Humboldt Wind Energy Area. Classification is conducted on a feature space consisting of 10 m wind speed and direction, bulk shear and veer across 30–270 m, and a low-level jet index. Dimensionality reduction is achieved through PC. A 2 × 3 OM lattice trained on the PCA vectors identified six baseline regimes spanning weak to strong flow states. High quantization-error profiles are identified and re-clustered into four anomalous regimes. The baseline regimes exhibited clear seasonal and diurnal cycles. Meanwhile, the anomalous regimes represented <10 % of all hours but showed distinct combinations of speed, shear, and veer, when compared to the baseline regimes. Anomalous regimes are typically short-lived (~few hours), yet their transitions can lead to hub-height wind changes of −18 to +9 m s -1 . For a representative 15 MW turbine, these shifts imply rapid swings in capacity factor from near-full output to negligible generation. Validation with lidar buoy data showed 51% agreement in SOM labels across ~6,000 overlapping hours, with most mismatches confined to adjacent speed classes. HRRR comparisons further revealed that anomalous regimes were disproportionately associated with forecast biases exceeding 5 m s -1 . Together, these results reframe extremes in offshore wind from absolute maxima or minima to weather states that are difficult to anticipate from models.

17 WIND ENERGY↗
DOE OSTI2024

GeoThermalCloud: Cloud Fusion of Big Data and Multi-Physics Models using Machine Learning for Discovery, Exploration, and Development of Hidden Geothermal Resources

The primary goals of this project are exploring hidden geothermal resources in the U.S.A. and designing profitable enhanced geothermal systems (EGS). Many processes and parameters control geothermal exploration and energy production from geothermal fields. Diverse datasets (e.g., geology, geochemistry, geophysics, satellite, airborne geophysics) are available to help characterize subsurface geothermal conditions. Sparse and multi-scale characteristics of these datasets prohibit properly leveraging these datasets for geothermal exploration and profitable EGS design. Recent advancements in machine learning (ML) promise to resolve these issues. The tremendous challenges and risks of geothermal exploration and production bring the demand for novel ML methods and tools that can (1) analyze large field datasets, (2) assimilate model simulations (large inputs and outputs), (3) process sparse datasets, (4) perform transfer learning (between sites with different exploratory levels), (5) extract hidden geothermal signatures in the field and simulation data, (6) label geothermal resources and processes, (7) identify high-value data acquisition targets, and (8) guide geothermal exploration and production by selecting optimal exploration, production, and drilling strategies. To address these necessities, ML-based geothermal resources exploration and enhanced geothermal systems (EGS) design tools have been developed. The exploration tool is called GeoThermalCloud and EGS design tool is called GeoDT-ML. GeoThermalCloud (https://github.com/SmartTensors/GeoThermalCloud.jl) utilizes a LANL unsupervised ML platform called SmartTensors (https://tensors.lanl.gov/) to automate data analyses and interpretations by extracting hidden signatures to identify geothermal prospects. Also, it enables the identification of critical measurements needed to identify geothermal resource signatures. Alternatively, GeoDT-ML (https://github.com/SmartTensors/GeoThermalCloud.jl/tree/master/EGS) is an ML-based alternative to GeoDT (https://github.com/GeoDesignTool/GeoDT.git), a fast, simplified multi-physics solver to evaluate EGS project designs in uncertain geologic systems. GeoDT-ML leverages recent advances in deep learning and high-performance computing. It is a faster and simpler version of GeoDT. To make this project a success, we used capabilities of LANL, PNNL, Google, Stanford, and Julia Computing. We analyzed eight datasets of the U.S.A. using GeothermalCloud and demonstrated potential highly prospective geothermal resources and identified key factors defining highly prospective sites. The first data set includes 44 locations in southwest New Mexico and 18 geological, hydrogeological, geophysical, geothermal, geochemical attributes. We defined low- and medium-temperature hydrothermal systems and discovered a new highly prospective site. The second data set analyzed 18 shallow water chemistry attributes at 14,342 locations in the Great Basin. It demarcated modestly, moderately, and highly prospective sites including key attributes for each type of prospectivity. The third data set analyzed Utah FORGE data including satellite (InSAR), geophysical (gravity, seismic), geochemical, and geothermal attributes. Here, we performed prospectivity analysis to identify future drilling locations using geological, geochemical, and geophysical attributes. Maps of temperature at depth and heat flow are constructed based on the available data. Prospectivity maps were generated, and drilling locations were proposed for future geothermal field exploration. The fourth data set analyzed 21 attributes at 120 locations in Tularosa Basin, New Mexico; data comes from past play fairway analyses in this region. ML analyses identified geothermal signatures associated with modestly, moderately, and highly hydrothermal systems. We also defined dominant attributes and spatial distribution of the geothermal signatures. The fifth, sixth, seventh, and eighth datasets include Tohatchi Springs, New Mexico, Hawaii, Brady site, Nevada, and EGS Collab, respectively. Moreover, we coupled GeothermalCloud and magnetotellurics data to pinpoint drilling locations for developing geothermal projects in the Tularosa Basin, New Mexico. GeothermalCloud found potential prospective locations for geothermal resources near White Sands Missile Range and McGregor Range at Fort Bliss. Magnetotellurics data determined the potential depth (~1800m) of geothermal prospects at McGregor Range based on apparent resistivity structures/layers in the subsurface. The McGregor Range consists of three resistivity layers and two resistivity structures. Magnetotellurics data also helps identify that the western portion of the McGregor Range has thick and low-resistivity earth materials. The low resistivity to the west is most likely for a fault system. Assuming temperature is consistent with a geothermal reservoir, the west-central part of the McGregor Range has the highest geothermal potential because of the increase in porosity and associated permeability attributed to the interpreted fault system. Also, we devised a coupling strategy between a process model and GeothermalCloud to characterize hydrogeological conditions and geothermal conditions, respectively. The process model characterizes hydrogeological and geothermal conditions on highly prospective geothermal sites provided by GeothermalCloud. We developed a physics-informed neural network (PINN) version of the Burns equation that can be easily coupled with GeothermalCloud. Furthermore, we performed an optimal design decision maximizing the economic value of an EGS power plant. This study optimized the range of well spacing between injection and production wells maximizing net present value in dollars (NPV). For this task, we used the GeoDT to simulate the Utah FORGE EGS development cycle from the initial well design to the end of production. Next, we accomplished another crucial task, which is predicting permeability of geothermal reservoirs. Predicting permeability of geothermal reservoirs is a non-trivial task because of huge computational runtime of simulation and lack of measurements. To avoid these limitations, we used easy-to-measure chemical concentrations in the subsurface as measurement data and convolutional neural network based ML model of a high-fidelity model. Next, we predicted permeability using Markov chain Monte Carlo simulation. We found that Markov chain Monte Carlo simulation predicts permeability with a high certainty if the prediction zone in the simulation area has chemical concentration data. Finally, we analyzed the DOE funded INGENIOUS and GeoDAWN projects data. For discovering hidden geothermal systems in the Great Basin, the INGENIOUS project accumulated old data, collected new data, and released them in 2022. The dataset includes a total of 24 geological, geophysical, and geochemical attributes. Data resolution and scale significantly vary prohibiting an appropriate usage. To avoid such limitations, we brought all data in the same resolution and scale by applying the inverse distance weighting interpolation technique for predicting data in unsampled locations. Subsequently, we analyzed LiDAR data of the GeoDAWN project. We received data in tiles format. The DOE’s overarching goal is to use ML on LiDAR data for finding favorable geological structures (e.g., step up faults in Brady, Nevada). To serve the purpose, we need to label favorable geologic structures that correspond to LiDAR data. We wrote an algorithm to label the LiDAR data with the favorable geologic structures.

15 GEOTHERMAL ENERGY↗
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 OSTI2022

Deep structural clustering for single-cell RNA-seq data jointly through autoencoder and graph neural network

Abstract Single-cell RNA sequencing (scRNA-seq) permits researchers to study the complex mechanisms of cell heterogeneity and diversity. Unsupervised clustering is of central importance for the analysis of the scRNA-seq data, as it can be used to identify putative cell types. However, due to noise impacts, high dimensionality and pervasive dropout events, clustering analysis of scRNA-seq data remains a computational challenge. Here, we propose a new deep structural clustering method for scRNA-seq data, named scDSC, which integrate the structural information into deep clustering of single cells. The proposed scDSC consists of a Zero-Inflated Negative Binomial (ZINB) model-based autoencoder, a graph neural network (GNN) module and a mutual-supervised module. To learn the data representation from the sparse and zero-inflated scRNA-seq data, we add a ZINB model to the basic autoencoder. The GNN module is introduced to capture the structural information among cells. By joining the ZINB-based autoencoder with the GNN module, the model transfers the data representation learned by autoencoder to the corresponding GNN layer. Furthermore, we adopt a mutual supervised strategy to unify these two different deep neural architectures and to guide the clustering task. Extensive experimental results on six real scRNA-seq datasets demonstrate that scDSC outperforms state-of-the-art methods in terms of clustering accuracy and scalability. Our method scDSC is implemented in Python using the Pytorch machine-learning library, and it is freely available at https://github.com/DHUDBlab/scDSC.

Gan, Yanglan↗
DOE OSTI2024

Physics and chemistry from parsimonious representations: image analysis via invariant variational autoencoders

Electron, optical, and scanning probe microscopy methods are generating ever increasing volume of image data containing information on atomic and mesoscale structures and functionalities. This necessitates the development of the machine learning methods for discovery of physical and chemical phenomena from the data, such as manifestations of symmetry breaking phenomena in electron and scanning tunneling microscopy images, or variability of the nanoparticles. Variational autoencoders (VAEs) are emerging as a powerful paradigm for the unsupervised data analysis, allowing to disentangle the factors of variability and discover optimal parsimonious representation. Here, we summarize recent developments in VAEs, covering the basic principles and intuition behind the VAEs. The invariant VAEs are introduced as an approach to accommodate scale and translation invariances present in imaging data and separate known factors of variations from the ones to be discovered. We further describe the opportunities enabled by the control over VAE architecture, including conditional, semi-supervised, and joint VAEs. Several case studies of VAE applications for toy models and experimental datasets in Scanning Transmission Electron Microscopy are discussed, emphasizing the deep connection between VAE and basic physical principles. Python codes and datasets discussed in this article are available at https://github.com/saimani5/VAE-tutorials and can be used by researchers as an application guide when applying these to their own datasets.

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 OSTI2023

Finding simplicity: unsupervised discovery of features, patterns, and order parameters via shift-invariant variational autoencoders *

Abstract Recent advances in scanning tunneling and transmission electron microscopies (STM and STEM) have allowed routine generation of large volumes of imaging data containing information on the structure and functionality of materials. The experimental data sets contain signatures of long-range phenomena such as physical order parameter fields, polarization, and strain gradients in STEM, or standing electronic waves and carrier-mediated exchange interactions in STM, all superimposed onto scanning system distortions and gradual changes of contrast due to drift and/or mis-tilt effects. Correspondingly, while the human eye can readily identify certain patterns in the images such as lattice periodicities, repeating structural elements, or microstructures, their automatic extraction and classification are highly non-trivial and universal pathways to accomplish such analyses are absent. We pose that the most distinctive elements of the patterns observed in STM and (S)TEM images are similarity and (almost-) periodicity, behaviors stemming directly from the parsimony of elementary atomic structures, superimposed on the gradual changes reflective of order parameter distributions. However, the discovery of these elements via global Fourier methods is non-trivial due to variability and lack of ideal discrete translation symmetry. To address this problem, we explore the shift-invariant variational autoencoders (shift-VAEs) that allow disentangling characteristic repeating features in the images, their variations, and shifts that inevitably occur when randomly sampling the image space. Shift-VAEs balance the uncertainty in the position of the object of interest with the uncertainty in shape reconstruction. This approach is illustrated for model 1D data, and further extended to synthetic and experimental STM and STEM 2D data. We further introduce an approach for training shift-VAEs that allows finding the latent variables that comport to known physical behavior. In this specific case, the condition is that the latent variable maps should be smooth on the length scale of the atomic lattice (as expected for physical order parameters), but other conditions can be imposed. The opportunities and limitations of the shift VAE analysis for pattern discovery are elucidated.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Leveraging BERT and Network-Based Attention Analysis for Identifying Treatment Milestones in EHRs

This study introduces a sophisticated data-driven framework for analyzing Electronic Health Records (EHRs) using transformer-based models to identify and disentangle overlapping treatment contexts. The framework leverages a preprocessing pipeline that transforms structured procedural codes into semantically enriched descriptive text, enabling the use of attention mechanisms to cluster medical events into treatment milestones—cohesive and distinct components of care processes. The methodology is rigorously validated using synthetic datasets derived from the MIMIC-III database, designed to simulate the heterogeneity and overlapping procedural contexts characteristic of real-world EHR scenarios. Quantitative evaluation highlights the framework’s robustness in disentangling concurrent care pathways, with attention metrics and unsupervised clustering approaches demonstrating the ability to preserve intra-context relationships while distinguishing inter-context dependencies. By addressing challenges inherent in data heterogeneity, this approach provides a foundation for uncovering complex treatment patterns, advancing clinical decision-making, and optimizing resource allocation in diverse healthcare environments.

Kim, Minsu [ORNL] (ORCID:0000000224185535)↗
DOE OSTI2020

Generalized Canonical Polyadic Tensor Decomposition

Tensor decomposition is a fundamental unsupervised machine learning method in data science, with applications including network analysis and sensor data processing. This work develops a generalized canonical polyadic (GCP) low-rank tensor decomposition that allows other loss functions besides squared error. For instance, we can use logistic loss or Kullback--Leibler divergence, enabling tensor decomposition for binary or count data. We present a variety of statistically motivated loss functions for various scenarios. We provide a generalized framework for computing gradients and handling missing data that enables the use of standard optimization methods for fitting the model. Furthermore, we demonstrate the flexibility of the GCP decomposition on several real-world examples including interactions in a social network, neural activity in a mouse, and monthly rainfall measurements in India.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Denoising Autoencoder for Reconstructing Sensor Observation Data and Predicting Evapotranspiration: Noisy and Missing Values Repair and Uncertainty Quantification

Abstract Machine learning (ML) methods applied in scientific research often deal with interrelated features in high‐dimensional data. Reducing data noise and redundancy is needed to increase prediction accuracy and efficiency especially when dealing with data from field sensors. We explored an unsupervised learning method, the denoising autoencoder (DAE), to extract the underlying data structure from noisy raw data in the context of predicting hydrologic quantities from multiple field sensors. These sensors have intrinsic instrumental noise and occasional malfunctions that cause missing values. Our DAE neural network reconstructed meteorological sensor data containing noise and missing values to predict evapotranspiration in a mountainous watershed. The DAE reconstructed the sensor variables with a mean coefficient of determination value of 0.77 across 15 dimensions representing individual sensors. It reduced variance and bias uncertainties compared to a classical autoencoder model. The reconstruction quality varied across dimensions depending on their cross‐correlation and alignment with the underlying data structure. Uncertainties arising from the model structure were overall higher than those resulting from data corruption. We attached the DAE structure to a downstream ET‐prediction neural network in three formats and achieved reasonably accurate ET predictions . The use of the DAE notably reduced variance uncertainty in ET prediction. However, excessive variance reduction may be accompanied by an increase in bias due to the intrinsic bias‐variance tradeoff. Our method of evaluating and reducing uncertainties in aggregated data from different sources can be used to improve predictive models, process understanding, and uncertainty quantification for better water resource management. Plain Language Summary We present a machine learning method, namely the denoising autoencoder, which reduces the effects of data noise and missing values typically present in scientific data sets collected through sensor measurements. This method selects the most relevant information from noisy raw data collected by the instruments and fills in missing values. To demonstrate the effectiveness of our method, we applied it to predict evapotranspiration, a hydrologic variable that represents the water moved from the land surface to the atmosphere through a combination of evaporation and plant water use (transpiration). We also used a random sampling technique (the Monte Carlo method) to compare the uncertainty in the predictions when using the raw and noisy data versus the reconstructed data. The denoising process produced more accurate predictions of evapotranspiration with less uncertainty. Improved predictions of evapotranspiration can lead to a better understanding and accounting of water budgets. This ML approach is broadly suitable for a wide variety of applications that involve noisy sensor data with missing values. Key Points We used a denoising autoencoder (DAE) neural network to reduce noise in meteorological and soil sensor observations by on average We used Monte Carlo sampling to estimate the bias and variance of all model outputs, including uncertainty sources from data and the model We attached the DAE component to a downstream neural network to predict ET with the variance reduced by , compared to that without the DAE

denoising autoencoder↗