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DOE OSTI2023

Deep learning uncertainty quantification for clinical text classification

Machine learning algorithms are expected to work side-by-side with humans in decision-making pipelines. Thus, the ability of classifiers to make reliable decisions is of paramount importance. Deep neural networks (DNNs) represent the state-of-the-art models to address real-world classification. Although the strength of activation in DNNs is often correlated with the network’s confidence, in-depth analyses are needed to establish whether they are well calibrated. In this paper, we demonstrate the use of DNN-based classification tools to benefit cancer registries by automating information extraction of disease at diagnosis and at surgery from electronic text pathology reports from the US National Cancer Institute (NCI) Surveillance, Epidemiology, and End Results (SEER) population-based cancer registries. In particular, we introduce multiple methods for selective classification to achieve a target level of accuracy on multiple classification tasks while minimizing the rejection amount—that is, the number of electronic pathology reports for which the model’s predictions are unreliable. We evaluate the proposed methods by comparing our approach with the current in-house deep learning-based abstaining classifier. Overall, all the proposed selective classification methods effectively allow for achieving the targeted level of accuracy or higher in a trade-off analysis aimed to minimize the rejection rate. On in-distribution validation and holdout test data, with all the proposed methods, we achieve on all tasks the required target level of accuracy with a lower rejection rate than the deep abstaining classifier (DAC). Interpreting the results for the out-of-distribution test data is more complex; nevertheless, in this case as well, the rejection rate from the best among the proposed methods achieving 97% accuracy or higher is lower than the rejection rate based on the DAC. We show that although both approaches can flag those samples that should be manually reviewed and labeled by human annotators, the newly proposed methods retain a larger fraction and do so without retraining—thus offering a reduced computational cost compared with the in-house deep learning-based abstaining classifier.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Updates to Relevance Vector Machine: Multiclass Classification, Variable Selection, and Proof-of-Concept Application to Safeguards Fresh Fuel Verification using List-Mode Neutron Collar Data

To expand the capabilities of safeguards authorities to verify the integrity of fresh fuel assemblies, Oak Ridge National Laboratory has retrofit the existing electronics of the JCC-71 uranium neutron coincidence collar, which contains 18 3 He neutron detectors and an external 241 AmLi(α, n) neutron interrogation source arranged to surround a fresh nuclear fuel assembly. The new electronics system allows analysts to record list-mode neutron multiplicity data in addition to the singles and doubles rates that are currently measured. Based on previous proof-of-concept research, analysis of these new data will identify off-normal fuel configurations in an assembly and characterize or localize the specific partial fuel defects. The purpose of this report it to document the analysis algorithm development and then to demonstrate its capability for the safeguards verification of fresh fuel assemblies using list mode neutron collar data. To analyze the complex list-mode data collected with the upgraded uranium neutron collar, multivariate classification algorithms are being developed using a novel classification method, the relevance vector machine. This approach may be applied to multiclass problems to estimate the probability that test data belongs to one of many possible classes of data. In addition, our method identifies the most useful variables/channels for making predictions, which illuminates the basis for the model’s predictions, and this interpretability is largely unique among data analytics methods. Variable selection occurs during model training and parameter tuning and does not need any external hyperparameter tuning routines. Finally, we apply the modified relevance vector machine to a simulated dataset of list-mode neutron collar data generated with the radiation transport code MCNP. The method can correctly identify off-normal fuel configurations, categorize the data according to four fuel defect scenarios, and rank the channels in the data according to prediction utility. For nuclear safeguards applications, it is concluded that this method has the potential to increase the sensitivity and reliability to detect missing fuel rods from a standard 17 x 17 Pressurized Water Reactor (PWR) fresh fuel assembly. Within this analysis, “off-normal” (i.e., missing fuel rods) were correctly classified in 17 simulated test scenarios with one quarter (25%) of the fresh fuel rods missing using a training data set of 58 simulated measurements.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2020

Machine learning-based multidomain processing for texture-based image segmentation and analysis

Atomic and molecular resolved atomic force microscopy (AFM) images offer unique insights into materials' properties such as local ordering, molecular orientation, and topological defects, which can be used to pinpoint physical and chemical interactions occurring at the surface. Utilizing machine learning for extracting underlying physical parameters increases the throughput of AFM data processing and eliminates inconsistencies intrinsic to manual image analysis, thus enabling the creation of reliable frameworks for qualitative and quantitative evaluation of experimental data. Here, we present a robust and scalable approach to the segmentation of AFM images based on flexible pre-selected classification criteria. The usage of supervised learning and feature extraction allows us to retain the consideration of specific problem-dependent features (such as types of periodical structures observed in the images and the associated numerical parameters: spacing, orientation, etc.). We highlight the applicability of this approach for the segmentation of molecular resolved AFM images based on the crystal orientation of the observed domains, automated selection of boundaries, and collection of relevant statistics. Finally, we outline a general strategy for machine learning-enabled analysis of nanoscale systems exhibiting periodic order that could be applied to any analytical imaging technique

36 MATERIALS SCIENCE↗

DOE OSTI2024

Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography

Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e - Å -2 , achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Data-driven selection and spectral classification of white dwarf stars

The next generation of spectroscopic surveys is expected to provide spectra for hundreds of thousands of white dwarf (WD) candidates in the upcoming years. Currently, spectroscopic classification of white dwarfs is mostly done by visual inspection, requiring substantial amounts of expert attention. We propose a data-driven pipeline for fast, automatic selection, and spectroscopic classification of WD candidates, trained using spectroscopically confirmed objects with available Gaia astrometry, photometry, and Sloan Digital Sky Survey (SDSS) spectra with signal-to-noise ratios ≥9. The pipeline selects WD candidates with improved accuracy and completeness over existing algorithms, classifies their primary spectroscopic type with ≥ 90 % accuracy, and spectroscopically detects main sequence companions with similar performance. We apply our pipeline to the Gaia Data Release 3 cross-matched with the SDSS Data Release 17 (DR17), identifying 424 096 high-confidence WD candidates and providing the first catalogue of automated and quantifiable classification for 36 523 WD spectra. Both the catalogue and pipeline are made available online. Such a tool will prove particularly useful for the undergoing SDSS-V survey, allowing for rapid classification of thousands of spectra at every data release.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Grain boundary slip transfer classification and metric selection with artificial neural networks

An artificial neural network is used to evaluate the effectiveness of six metrics and their combinations to assess whether slip transfers across grain boundaries in coarse-grained oligocrystalline Al foils. This approach extends the one- or two-dimensional projections formerly applied to analyze slip transfer. The accuracy of this binary classification reaches around 87% for the best single metric and around 90% when considering two or more metrics simultaneously. Here, the results suggest slip transfer mostly depends on the geometric relationship between grains. Training a double-layer network having 10 nodes per hidden layer with 40 measurements is sufficient to render the maximum accuracy.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Training data selection for event classification in a highly variable environment

A problem of interest for nuclear nonproliferation is monitoring activities at nuclear facilities, where proliferation events may only take place a few times and often under variable conditions. Machine learning has revolutionized data analytics by enabling the use of measurable signatures to generate predictive models of facility operations. However, traditional methods for training these models require large, reliable data sets with labeled observations, a challenge for nonproliferation. Highly variable conditions further complicate this as events from training data may have occurred in conditions quite different from the event of interest. Our hypothesis is that when events occur in a highly variable environment, careful training data selection for each test event could outperform the standard approach of using all available training data. We developed a method to optimize training data selection for the given test event and applied it to predicting the power level of the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory. In this study, the reactor startup exhibits variability between occurrences due to natural variability in environmental conditions and operational procedures. Using a combination of analysis techniques, a similitude assessment was performed on data collected from HFIR to isolate clusters that were optimal for training a predictive model. Concepts such as dynamic time warping and Jaccard similarity were used in conjunction with clustering analysis. In order to validate this approach, the model was trained on every combination of unique training events and the predictive performance was compared to the performance using a subset of the training data selected by isolated clusters found through the similitude assessment.

Iyer, A↗

DOE OSTI2020

Risk-Informed Approach for Event Selection and Component Classification

Develop a report summarizing a structured approach for the incorporation of risk insights when making facility safety assessments and regulatory decisions is proposed to supplement the deterministic approach, with the following expected benefits: Increased confidence that key safety issues have been fully identified and addressed Better understanding of safety margins Facilitates more structured dialogue among international regulators Reduced reliance on “expert judgement” through a rigorous, pre-defined process with more predictable outcomes Proposed outcome is development of a report summarizing the structure and key considerations for applying this approach that: Is inclusive of advanced reactor technologies Provides for flexible implementation recognizing unique and varying sovereign regulatory structures Builds upon existing/current GIF safety approaches (e.g., GIF Basic Safety Approach, Integrated Safety Assessment Methodology)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

The miniJPAS survey quasar selection – II. Machine learning classification with photometric measurements and uncertainties

Astrophysical surveys rely heavily on the classification of sources as stars, galaxies, or quasars from multiband photometry. Surveys in narrow-band filters allow for greater discriminatory power, but the variety of different types and redshifts of the objects present a challenge to standard template-based methods. In this work, which is part of a larger effort that aims at building a catalogue of quasars from the miniJPAS survey, we present a machine learning-based method that employs convolutional neural networks (CNNs) to classify point-like sources including the information in the measurement errors. We validate our methods using data from the miniJPAS survey, a proof-of-concept project of the Javalambre Physics of the Accelerating Universe Astrophysical Survey (J-PAS) collaboration covering ∼1 deg 2 of the northern sky using the 56 narrow-band filters of the J-PAS survey. Due to the scarcity of real data, we trained our algorithms using mocks that were purpose-built to reproduce the distributions of different types of objects that we expect to find in the miniJPAS survey, as well as the properties of the real observations in terms of signal and noise. We compare the performance of the CNNs with other well-established machine learning classification methods based on decision trees, finding that the CNNs improve the classification when the measurement errors are provided as inputs. The predicted distribution of objects in miniJPAS is consistent with the putative luminosity functions of stars, quasars, and unresolved galaxies. Our results are a proof of concept for the idea that the J-PAS survey will be able to detect unprecedented numbers of quasars with high confidence.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Selective Sampling for Sensor Type Classification in Buildings

A key barrier to applying any smart technology to a building is the requirement of locating and connecting to the necessary resources among the thousands of sensing and control points, i.e., the metadata mapping problem. Existing solutions depend on exhaustive manual annotation of sensor metadata --- a laborious, costly, and hardly scalable process. To reduce the amount of manual effort required, this paper presents a multi-oracle selective sampling framework to leverage noisy labels from information sources with unknown reliability such as existing buildings, which we refer to as weak oracles, for metadata mapping. This framework involves an interactive process, where a small set of sensor instances are progressively selected and labeled for it to learn how to aggregate the noisy labels as well as to predict sensor types. Two key challenges arise in designing the framework, namely, weak oracle reliability estimation and instance selection for querying. To address the first challenge, we develop a clustering-based approach for weak oracle reliability estimation to capitalize on the observation that weak oracles perform differently in different groups of instances. For the second challenge, we propose a disagreement-based query selection strategy to combine the potential effect of a labeled instance on both reducing classifier uncertainty and improving the quality of label aggregation. We evaluate our solution on a large collection of real-world building sensor data from 5 buildings with more than 11,000 sensors of 18 different types. The experiment results validate the effectiveness of our solution, which outperforms a set of state-of-the-art baselines.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2024

Data-driven search for promising intercalating ions and layered materials for metal-ion batteries

The rise in demand for lithium-ion batteries has led to a large-scale search for electrode materials and intercalating ion species to meet the demands of next-generation energy technologies. Recent efforts largely focus on searching for cathodes that can accommodate large amounts of intercalating ions, but similar work on anodes is relatively limited. This study utilizes machine learning methods to find alternative two-dimensional (2D) materials and intercalating ions beyond Li for metal-ion batteries with high-power efficiencies. The approach first uses density functional theory (DFT) calculations to estimate the theoretical capacities and voltages of various metal ions on 2D materials. The DFT-generated data also provide insights into the local structural accommodation upon ion intercalation on various 2D materials. Significant changes to the lattice can result in irreversible changes to the bonding environments in the anode material, resulting in poor cycling stability. Next, this study develops a binding energy and structural accommodation-based classification model to screen anode materials for next-generation batteries. The classification model selects intercalating ions and 2D material pairs suitable for batteries based on the calculated voltage and volumetric changes in the 2D material upon intercalation. Finally, this study builds a regression model to accurately predict the binding energies of the various intercalating ions on 2D materials. The approach highlights the importance of different elemental and structural features for classification and regression tasks. In conclusion, the insights gained from this study on the role of involved features, such as electronegativities of the constituent ions and the presence of unfilled electronic levels, will help to streamline further studies towards the search for future layered battery materials.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Using ensembles and distillation to optimize the deployment of deep learning models for the classification of electronic cancer pathology reports

One of the goals of the Surveillance, Epidemiology, and End Results (SEER) program is to estimate incidence, prevalence, and mortality of all cancers. To that end, cancer registries across the country maintain a massive database of cancer pathology reports which contain rich information to understand cancer trends. However, these reports are stored in the form of unstructured text, and human annotators are required to read and extract relevant information. In this article, we show that existing deep learning models for automating information extraction from cancer pathology reports can be significantly improved by using ensemble model distillation. We found that by training multiple predictive models and transferring their knowledge to a single, low-resource model, we can reduce the number of highly confident wrong predictions. Our results show that our implemented methods could save 1000s of manual annotation hours.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Toward memory-efficient melt pool monitoring: a classification framework using event-based imaging and sparse sensing technique

Vision sensors like CMOS and CCD cameras are often used for in-process monitoring of melt pools in laser-based additive and welding processes, but they require transferring large amounts of data and computational processing resources. Event-based neuromorphic imagery, on the other hand, detects only the change in pixel intensity, thus potentially reducing the data amount and latency. With an event imager, this study develops a framework for melt pool condition classification, including image construction, time scale selection, optimal pixel selection, and sparse classification, to achieve a highly memory-efficient scheme. These are based on sparse sensing techniques with singular value decomposition (SVD) and QR pivoting, the two fundamental matrix transformations for linear dimensionality reduction. The framework is then validated by classifying a controlled experiment by exciting various mode shapes of liquid gallium pools of varying depths (3, 6, and 8 mm). At 200 pixels, the classifier can reach overall accuracy of 75%, while at 2000 pixels (0.013% of the total possible pixels), the accuracy is nearly 90% (89.86%). At the same number of pixels, random selection can only achieve 46% and 67%, respectively. The memory savings of the sparsely sampled event data compared to a conventional imager is about 500 times. In addition to performance, implementation and limitations of the framework are also discussed.

42 ENGINEERING↗

DOE OSTI2022

The miniJPAS survey quasar selection – I. Mock catalogues for classification

In this series of papers, we employ several machine learning (ML) methods to classify the point-like sources from the miniJPAS catalogue, and identify quasar candidates. Since no representative sample of spectroscopically confirmed sources exists at present to train these ML algorithms, we rely on mock catalogues. In this first paper, we develop a pipeline to compute synthetic photometry of quasars, galaxies, and stars using spectra of objects targeted as quasars in the Sloan Digital Sky Survey . To match the same depths and signal-to-noise ratio distributions in all bands expected for miniJPAS point sources in the range 17.5 ≤ r < 24, we augment our sample of available spectra by shifting the original r-band magnitude distributions towards the faint end, ensure that the relative incidence rates of the different objects are distributed according to their respective luminosity functions, and perform a thorough modelling of the noise distribution in each filter, by sampling the flux variance either from Gaussian realizations with given widths, or from combinations of Gaussian functions. Finally, we also add in the mocks the patterns of non-detections which are present in all real observations. Although the mock catalogues presented in this work are a first step towards simulated data sets that match the properties of the miniJPAS observations, these mocks can be adapted to serve the purposes of other photometric surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Osprey Framework v0.2.2

The Alpha Berkeley Framework is a software architecture for building agentic AI systems that coordinate multi-step workflows in scientific and industrial environments. It is based on a plan-first orchestration model, where natural language requests are translated into execution plans with explicit dependencies and optional human approval. The framework includes capability classification, which selects relevant tools on a per-task basis to keep orchestration efficient as the number of available tools grows. It incorporates task extraction methods that compress conversational context and integrate external resources such as databases, APIs, and knowledge bases into structured, machine-readable tasks. Execution is supported by modular services with checkpointing, artifact management, and error handling, allowing workflows to be paused, inspected, and resumed. The system is designed for deployment in production environments, supporting both local and containerized execution as well as integration with HPC clusters. Interfaces include command-line tools, browser-based workflows, and containerized services. The framework has been demonstrated in tutorial examples and deployed at the Advanced Light Source, where it coordinates accelerator control and analysis workflows.

Hellert, Thorsten [Lawrence Berkeley National Labo↗

DOE OSTI2020

Survey of Image Denoising Methods for Medical Image Classification

Medical imaging devices, such as X-ray machines, inherently produce images that suffer from visual noise. Our objectives were to (i.) determine the effect of image denoising on a medical image classification task, and (ii.) determine if there exists a correlation between image denoising performance and medical image classification performance. We performed the medical image classification task on chest X-rays using the DenseNet-121 convolutional neural network (CNN) and used the peak signal-to-noise ratio (PSNR) and structural similarity (SSIM) metrics as the image denoising performance measures. We first found that different denoising methods can make a statistically significant difference in classification performance for select labels. We also found that denoising methods affect fine-tuned models more than randomly-initialized models and that fine-tuned models have significantly higher and more uniform performance than randomly-initialized models. Lastly, we found that there is no significant correlation between PSNR and SSIM values and classification performance for our task.

Michael, Peter↗

DOE OSTI2024

Identification of integrated proteomics and transcriptomics signature of alcohol-associated liver disease using machine learning

Distinguishing between alcohol-associated hepatitis (AH) and alcohol-associated cirrhosis (AC) remains a diagnostic challenge. In this study, we used machine learning with transcriptomics and proteomics data from liver tissue and peripheral mononuclear blood cells (PBMCs) to classify patients with alcohol-associated liver disease. The conditions in the study were AH, AC, and healthy controls. We processed 98 PBMC RNAseq samples, 55 PBMC proteomic samples, 48 liver RNAseq samples, and 53 liver proteomic samples. First, we built separate classification and feature selection pipelines for transcriptomics and proteomics data. The liver tissue models were validated in independent liver tissue datasets. Next, we built integrated gene and protein expression models that allowed us to identify combined gene-protein biomarker panels. For liver tissue, we attained 90% nested-cross validation accuracy in our dataset and 82% accuracy in the independent validation dataset using transcriptomic data. We attained 100% nested-cross validation accuracy in our dataset and 61% accuracy in the independent validation dataset using proteomic data. For PBMCs, we attained 83% and 89% accuracy with transcriptomic and proteomic data, respectively. The integration of the two data types resulted in improved classification accuracy for PBMCs, but not liver tissue. We also identified the following gene-protein matches within the gene-protein biomarker panels: CLEC4M-CLC4M, GSTA1-GSTA2 for liver tissue and SELENBP1-SBP1 for PBMCs. In this study, machine learning models had high classification accuracy for both transcriptomics and proteomics data, across liver tissue and PBMCs. The integration of transcriptomics and proteomics into a multi-omics model yielded improvement in classification accuracy for the PBMC data. The set of integrated gene-protein biomarkers for PBMCs show promise toward developing a liquid biopsy for alcohol-associated liver disease.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Better understanding and prediction of antiviral peptides through primary and secondary structure feature importance

The emergence of viral epidemics throughout the world is of concern due to the scarcity of available effective antiviral therapeutics. The discovery of new antiviral therapies is imperative to address this challenge, and antiviral peptides (AVPs) represent a valuable resource for the development of novel therapies to combat viral infection. We present a new machine learning model to distinguish AVPs from non-AVPs using the most informative features derived from the physicochemical and structural properties of their amino acid sequences. To focus on those features that are most likely to contribute to antiviral performance, we filter potential features based on their importance for classification. These feature selection analyses suggest that secondary structure is the most important peptide sequence feature for predicting AVPs. Our Feature-Informed Reduced Machine Learning for Antiviral Peptide Prediction (FIRM-AVP) approach achieves a higher accuracy than either the model with all features or current state-of-the-art single classifiers. Understanding the features that are associated with AVP activity is a core need to identify and design new AVPs in novel systems. The FIRM-AVP code and standalone software package are available at https://github.com/pmartR/FIRM-AVP with an accompanying web application at https://msc-viz.emsl.pnnl.gov/AVPR.

59 BASIC BIOLOGICAL SCIENCES↗