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All sources NASA NTRS DOE OSTI

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 OSTI2023

Efficient solutions of fermionic systems using artificial neural networks

In this study, we explore the similarities and differences between variational Monte Carlo techniques that employ conventional and artificial neural network representations of the ground-state wave function for fermionic systems. Our primary focus is on shallow neural network architectures, specifically the restricted Boltzmann machine, and we examine unsupervised learning algorithms that are appropriate for modeling complex many-body correlations. We assess the advantages and drawbacks of conventional and neural network wave functions by applying them to a range of circular quantum dot systems. Our findings, which include results for systems containing up to 90 electrons, emphasize the efficient implementation of these methods on both homogeneous and heterogeneous high-performance computing facilities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

NSFnets (Navier-Stokes flow nets): Physics-informed neural networks for the incompressible Navier-Stokes equations

In the last 50 years there has been a tremendous progress in solving numerically the Navier-Stokes equations using finite differences, finite elements, spectral, and even meshless methods. Yet, in many real cases, we still cannot incorporate seamlessly (multi-fidelity) data into existing algorithms, and for industrial-complexity applications the mesh generation is time consuming and still an art. Moreover, solving ill-posed problems (e.g., lacking boundary conditions) or inverse problems is often prohibitively expensive and requires different formulations and new computer codes. Here, we employ physics-informed neural networks (PINNs), encoding the governing equations directly into the deep neural network via automatic differentiation, to overcome some of the aforementioned limitations for simulating incompressible laminar and turbulent flows. We develop the Navier-Stokes flow nets (NSFnets) by considering two different mathematical formulations of the Navier-Stokes equations: the velocity-pressure (VP) formulation and the vorticity-velocity (VV) formulation. Since this is a new approach, we first select some standard benchmark problems to assess the accuracy, convergence rate, computational cost and flexibility of NSFnets; analytical solutions and direct numerical simulation (DNS) databases provide proper initial and boundary conditions for the NSFnet simulations. The spatial and temporal coordinates are the inputs of the NSFnets, while the instantaneous velocity and pressure fields are the outputs for the VP-NSFnet, and the instantaneous velocity and vorticity fields are the outputs for the VV-NSFnet. This is unsupervised learning and, hence, no labeled data are required beyond boundary and initial conditions and the fluid properties. The residuals of the VP or VV governing equations, together with the initial and boundary conditions, are embedded into the loss function of the NSFnets. No data is provided for the pressure to the VP-NSFnet, which is a hidden state and is obtained via the incompressibility constraint without extra computational cost. Unlike the traditional numerical methods, NSFnets inherit the properties of neural networks (NNs), hence the total error is composed of the approximation, the optimization, and the generalization errors. Here, we empirically attempt to quantify these errors by varying the sampling (“residual”) points, the iterative solvers, and the size of the NN architecture. For the laminar flow solutions, we show that both the VP and the VV formulations are comparable in accuracy but their best performance corresponds to different NN architectures. The initial convergence rate is fast but the error eventually saturates to a plateau due to the dominance of the optimization error. For the turbulent channel flow, we show that NSFnets can sustain turbulence at , but due to expensive training we only consider part of the channel domain and enforce velocity boundary conditions on the subdomain boundaries provided by the DNS data base. We also perform a systematic study on the weights used in the loss function for balancing the data and physics components, and investigate a new way of computing the weights dynamically to accelerate training and enhance accuracy. In the last part, we demonstrate how NSFnets should be used in practice, namely for ill-posed problems with incomplete or noisy boundary conditions as well as for inverse problems. We obtain reasonably accurate solutions for such cases as well without the need to change the NSFnets and at the same computational cost as in the forward well-posed problems. As a result, we also present a simple example of transfer learning that will aid in accelerating the training of NSFnets for different parameter settings.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Enhancing the hunt for new phenomena in dijet final states using anomaly detection filters at the high-luminosity large Hadron Collider

In the realm of dijet searches in high-energy physics, a significant challenge has emerged: with experiments producing more and more data, the traditional methods of using analytic functions to describe dijet mass spectra start to fail. Here, to address this, we suggest the application of an anomaly detection approach to eliminate less interesting background events based on event final states. This method not only bypasses the limitations of conventional background models but also significantly enhances our ability to detect potential signals of new physics. Through simulations that mimic the conditions of the upcoming high-luminosity large Hadron collider, we demonstrate the strength and efficiency of this approach in dealing with large data volumes. The integration of unsupervised machine learning into our experimental framework paves the way for a promising avenue to unveil hidden physics discoveries within the overwhelming influx of data.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Anomaly Detection in Seismic Data with Deep Learning: Application for Instrument Failure Detection and Forecasting

Seismic data quality assessment (QA) is the first and one of the most important steps before conducting any further data analysis. Traditional methods involve checking various metrics, such as spike detection and power spectral density, by setting strict thresholds or comparing data against synthetic benchmarks. However, these approaches often rely on pre-existing knowledge and assumptions about data anomalies, leading to potential misclassification of unusual cases. Here, in this study, we propose a deep autoencoder model, an unsupervised learning approach that evaluates data quality without making assumptions about normal and anomalous data, which can be used to identify deviations in recorded data that may indicate nascent instrument failure. We test the model with the U.S. International Monitoring System (IMS) seismic stations and demonstrate the capability of detecting anomalies on a monthly scale. This could prompt station operators to examine potential problems early, allowing sufficient time for instrument maintenance to prevent data outages. In addition, we use a new manually selected testing dataset to compare our model performance against two supervised machine learning (ML) approaches and a standard QA package, as baseline models. When applied to the dataset containing known data anomalies, performance of the supervised and unsupervised ML approaches is similar, with an accuracy of 88.1% for our model compared to ∼90% for the supervised ML approach and 78.2% for the standard QA package. Our model outperforms the baseline models when applied to new stations, where new types of data anomalies can be station-specific and not included in the training dataset. Finally, we show model transferability by training the model with data from the Global Seismograph Network only and applying it to the IMS network data. The results suggest that our model is generalizable and can be applied to new stations with good accuracy.

Lin, Jiun-Ting [Lawrence Livermore National Labora↗

DOE OSTI2024

Acoustic sensing and autoencoder approach for abnormal gas detection in a spent nuclear fuel canister mock-up

Currently, spent nuclear fuel (SNF) from commercial nuclear power plants is stored in stainless-steel canisters for interim dry storage. To provide an inert environment, these canisters are backfilled with helium after vacuum drying. However, the helium environment may be contaminated during extended storage because of the material degradation. For example, the heavier fission gas xenon may be released from the fuel rods into the canister cavity should the fuel cladding be breached. Other gases such as air and water vapor may also be present as a result of leakage caused by chloride-induced stress corrosion cracking on the canister walls or by insufficient vacuum drying. Therefore, monitoring the gas composition can provide critical information about the health of SNF canisters. In this study, noninvasive testing was conducted on a 2/3-scaled SNF canister mock-up using acoustic sensing. Ultrasonic transducers were placed on the exterior surface of the canister to probe the gas composition. A dataset was collected by sealing the canister mock-up and introducing up to 1.53% argon or 1.29% air into the helium background gas. Three methods were used to detect changes in the gas composition: the time-of-flight (TOF) method, the differential method, and the autoencoder method. Results showed that the TOF method had sufficient resolution to detect abnormal gas concentrations of less than 1.0%. The differential method demonstrated a periodic in-phase and out-of-phase behavior between the benchmark (i.e., pure helium) and abnormal (i.e., with argon or air) state signals. The variational autoencoder (VAE) and the Wasserstein autoencoder (WAE) were trained on the benchmark data and were applied directly to the abnormal state data. It was found that both the unsupervised VAE and the WAE were able to distinguish the benchmark and abnormal states of the canister mock-up based on the reconstruction error.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

Unsupervised Clustering of Microseismic Events and Focal Mechanism Analysis at the CO 2 Injection Site in Decatur, Illinois

Characterization of induced microseismicity at a carbon dioxide (CO 2 ) storage site is critical for preserving reservoir integrity and mitigating seismic hazards. We apply a multilevel machine learning (ML) approach that combines the nonnegative matrix factorization and hidden Markov model to extract spectral representations of microseismic events and cluster them to identify seismic patterns at the Illinois Basin-Decatur Project. Unlike traditional waveform correlation methods, this approach leverages spectral characteristics of first arrivals to improve event classification and detect previously undetected planes of weakness. By integrating ML-based clustering with focal mechanism analysis, we resolve small-scale fault structures that are below the detection limits of conventional seismic imaging. Our findings reveal temporal bursts of microseismicity associated with brittle failure, providing insights into the spatio-temporal evolution of fault reactivation during CO 2 injection. This approach enhances seismic monitoring capabilities at CO 2 injection sites by improving fault characterization beyond the resolution of standard geophysical surveys.

Willis, Rachel Marie [Sandia National Laboratories↗

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]↗

NASA NTRSDate not supplied

Natural Language Processing Methods for Air Traffic Management Text and Speech Data

This presentation discusses two efforts of the NARI AI/ML Intern team during the Fall 2021 OSTEM Internship term. For Letters of Agreement (LoA), we have studied how LoAs are structured and explored the question ‘What is an LoA constraint?’ To do this, our approach is data-driven, iterative, and assisted by machine learning when available. In this presentation, we will walk through our tasks of manually scanning through documents, performing a preliminary entity labelling task, and our unsupervised analysis on LoA procedures sections. After this research phase, we define the smallest constraint unit in an LoA, and start to perform entity extraction. Looking towards constraint extraction, we are also exploring the use of a one-class support vector machine (OneClassSVM) model to identify patterns within the data. The second effort of our team this term is focused on Air Traffic Control System Command Center (ATCSCC) advisory meetings, and the subsequent advisory documents that get published from their content. These advisory documents are important to give readily accessible summaries of daily operations, so that data centers, airline officials, and other stakeholders can easily understand the context of these meetings in real time. In applying machine learning to this scenario, two natural language processing tasks are used. First is developing machine learning models to convert the meeting speech data into text. With this text, use of extractive and abstractive text summarization models are used to automatically generate preliminary versions of the advisory documents.

Natural Language Processing↗

DOE OSTI2023

Unsupervised machine learning discovery of structural units and transformation pathways from imaging data

We show that unsupervised machine learning can be used to learn chemical transformation pathways from observational Scanning Transmission Electron Microscopy (STEM) data. To enable this analysis, we assumed the existence of atoms, a discreteness of atomic classes, and the presence of an explicit relationship between the observed STEM contrast and the presence of atomic units. With only these postulates, we developed a machine learning method leveraging a rotationally invariant variational autoencoder (VAE) that can identify the existing molecular fragments observed within a material. The approach encodes the information contained in STEM image sequences using a small number of latent variables, allowing the exploration of chemical transformation pathways by tracing the evolution of atoms in the latent space of the system. The results suggest that atomically resolved STEM data can be used to derive fundamental physical and chemical mechanisms involved, by providing encodings of the observed structures that act as bottom-up equivalents of structural order parameters. The approach also demonstrates the potential of variational (i.e., Bayesian) methods in the physical sciences and will stimulate the development of more sophisticated ways to encode physical constraints in the encoder–decoder architectures and generative physical laws and causal relationships in the latent space of VAEs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Unsupervised anomaly detection in MeV ultrafast electron diffraction

MeV ultrafast electron diffraction (MUED) is a pump-probe technique used to study the dynamic structural evolution of materials. An ultrashort laser pulse triggers structural changes, which are then probed by an ultrashort relativistic electron beam. To overcome low signal-to-noise ratios, diffraction patterns are averaged over thousands of shots. However, shot-to-shot instabilities in the electron beam can distort individual patterns, introducing uncertainty. Improving MUED accuracy requires detecting and removing these anomalous patterns from large datasets. In this work, we developed a fully unsupervised methodology for the detection of anomalous diffraction patterns. Using a convolutional autoencoder, we calculate the reconstruction mean squared error of the diffraction patterns. Based on the statistical analysis of this error, we provide the user an estimation of the probability that the pattern is normal, which also allows a posterior visual inspection of the images that are difficult to classify. This method has been trained with only 100 diffraction patterns and tested on 1521 patterns, resulting in a false positive rate between 0.2% and 0.4%, with a training time of 10 s per image and a test time of about 1 s per image. Here, the proposed methodology can also be applied to other diffraction techniques in which large datasets are collected that include faulty images due to instrumental instabilities.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

DISSIDE: Dynamic In Silico Sample Identification for Discrete Evaluation

DISSIDE uses novel unsupervised learning to select samples that best represent the strongest a priori discrete pattern in a given data set. It further removes major outliers and "noisy" samples that do not fit discrete patterns well or represent outliers in groups below a defined n value. It then estimates the fit and strength of the a priori discrete pattern using both unconstrained and constrained methods for raw and cleaned data

LeBrun, Erick↗

NASA NTRS2006

Enabling the Discovery of Recurring Anomalies in Aerospace System Problem Reports using High-Dimensional Clustering Techniques

This paper describes the results of a significant research and development effort conducted at NASA Ames Research Center to develop new text mining techniques to discover anomalies in free-text reports regarding system health and safety of two aerospace systems. We discuss two problems of significant importance in the aviation industry. The first problem is that of automatic anomaly discovery about an aerospace system through the analysis of tens of thousands of free-text problem reports that are written about the system. The second problem that we address is that of automatic discovery of recurring anomalies, i.e., anomalies that may be described m different ways by different authors, at varying times and under varying conditions, but that are truly about the same part of the system. The intent of recurring anomaly identification is to determine project or system weakness or high-risk issues. The discovery of recurring anomalies is a key goal in building safe, reliable, and cost-effective aerospace systems. We address the anomaly discovery problem on thousands of free-text reports using two strategies: (1) as an unsupervised learning problem where an algorithm takes free-text reports as input and automatically groups them into different bins, where each bin corresponds to a different unknown anomaly category; and (2) as a supervised learning problem where the algorithm classifies the free-text reports into one of a number of known anomaly categories. We then discuss the application of these methods to the problem of discovering recurring anomalies. In fact the special nature of recurring anomalies (very small cluster sizes) requires incorporating new methods and measures to enhance the original approach for anomaly detection. ?& pant 0-

Srivastava, Ashok, N.↗

DOE OSTI2023

The AXEAP2 program for K β X-ray emission spectra analysis using artificial intelligence

The processing and analysis of synchrotron data can be a complex task, requiring specialized expertise and knowledge. Our previous work addressed the challenge of X-ray emission spectrum (XES) data processing by developing a standalone application using unsupervised machine learning. However, the task of analyzing the processed spectra remains another challenge. Although the non-resonant K β XES of 3 d transition metals are known to provide electronic structure information such as oxidation and spin state, finding appropriate parameters to match experimental data is a time-consuming and labor-intensive process. Here, a new XES data analysis method based on the genetic algorithm is demonstrated, applying it to Mn, Co and Ni oxides. This approach is also implemented as a standalone application, Argonne X-ray Emission Analysis 2 ( AXEAP2 ), which finds a set of parameters that result in a high-quality fit of the experimental spectrum with minimal intervention. AXEAP2 is able to find a set of parameters that reproduce the experimental spectrum, and provide insights into the 3 d electron spin state, 3 d –3 p electron exchange force and K β emission core-hole lifetime.

36 MATERIALS SCIENCE↗

NASA NTRS1981

Multiresource analysis and information system concepts for incorporating LANDSAT and GIS technology into large area forest surveys

A method of relating different classifications at each stage of a multistage, multiresource inventory using remotely sensed imagery is discussed. A class transformation matrix allowing the conversion of a set of proportions at one stage, to a set of proportions at the subsequent stage through use of a linear model, is described. The technique was tested by applying it to Kershaw County, South Carolina. Unsupervised LANDSAT spectral classifications were correlated with interpretations of land use aerial photography, the correlations employed to estimate land use classifications using the linear model, and the land use proportions used to stratify current annual increment (CAI) field plot data to obtain a total CAI for the county. The estimate differed by 1% from the published figure for land use. Potential sediment loss and a variety of land use classifications were also obtained.

Langley, P. G.↗

DOE OSTI2022

Automated identification of dominant physical processes

The identification of processes that locally and approximately dominate dynamical system behavior has enabled significant advances in understanding and modeling nonlinear differential dynamical systems. Conventional methods of dominant process identification involve piecemeal and ad hoc (non-rigorous, informal) scaling analyses to identify dominant balances of governing equation terms and to delineate the spatiotemporal boundaries (boundaries in space and/or time) of each dominant balance. For the first time, we present an objective global measure of the fit of dominant balances to observations, which is desirable for automation, and was previously undefined. Furthermore, we propose a formal definition of the dominant balance identification problem in the form of an optimization problem. Here, we show that the optimization can be performed by various machine learning algorithms, enabling the automatic identification of dominant balances. Our method is algorithm agnostic and it eliminates reliance upon expert knowledge to identify dominant balances which are not known beforehand.

42 ENGINEERING↗

DOE OSTI2021

Machine Learning to Identify Geologic Factors Associated with Production in Geothermal Fields: A Case-Study Using 3D Geologic Data from Brady Geothermal Field and NMFk

In this paper, we present an analysis using unsupervised machine learning (ML) to identify the key geologic factors that contribute to the geothermal production in Brady geothermal field. Brady is a hydrothermal system in northwestern Nevada that supports both electricity production and direct use of hydrothermal fluids. Transmissive fuid-fow pathways are relatively rare in the subsurface, but are critical components of hydrothermal systems like Brady and many other types of fuid-fow systems in fractured rock. Here, we analyze geologic data with ML methods to unravel the local geologic controls on these pathways. The ML method, non-negative matrix factorization with k-means clustering (NMFk), is applied to a library of 14 3D geologic characteristics hypothesized to control hydrothermal circulation in the Brady geothermal field. Our results indicate that macro-scale faults and a local step-over in the fault system preferentially occur along production wells when compared to injection wells and non-productive wells. We infer that these are the key geologic characteristics that control the through-going hydrothermal transmission pathways at Brady. Our results demonstrate: (1) the specific geologic controls on the Brady hydrothermal system and (2) the efficacy of pairing ML techniques with 3D geologic characterization to enhance the understanding of subsurface processes. This submission includes the published journal article detailing this work, the published 3D geologic map of the Brady Geothermal Area used as a basis to develop structural and geological variables that are hypothesized to control or effect permeability or connectivity, 3D well data, along which geologic data were sampled for PCA analyses, and associated metadata file. This work was done using the GeoThermalCloud framework, which is part of SmartTensors (both are linked below).

15 GEOTHERMAL ENERGY↗

DOE OSTI2021

GeoThermalCloud framework for fusion of big data and multi-physics models in Nevada and Southwest New Mexico

Our GeoThermalCloud framework is designed to process geothermal datasets using a novel toolbox for unsupervised and physics-informed machine learning called SmartTensors. More information about GeoThermalCloud can be found at the GeoThermalCloud GitHub Repository. More information about SmartTensors can be found at the SmartTensors Github Repository and the SmartTensors page at LANL.gov. Links to these pages are included in this submission. GeoThermalCloud.jl is a repository containing all the data and codes required to demonstrate applications of machine learning methods for geothermal exploration. GeoThermalCloud.jl includes: - site data - simulation scripts - jupyter notebooks - intermediate results - code outputs - summary figures - readme markdown files GeoThermalCloud.jl showcases the machine learning analyses performed for the following geothermal sites: - Brady: geothermal exploration of the Brady geothermal site, Nevada - SWNM: geothermal exploration of the Southwest New Mexico (SWNM) region - GreatBasin: geothermal exploration of the Great Basin region, Nevada Reports, research papers, and presentations summarizing these machine learning analyses are also available and will be posted soon.

15 GEOTHERMAL ENERGY↗