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DOE OSTI2020

Root identification in minirhizotron imagery with multiple instance learning

In this study, multiple instance learning (MIL) algorithms to automatically perform root detection and segmentation in minirhizotron imagery using only image-level labels are proposed. Root and soil characteristics vary from location to location, and thus, supervised machine learning approaches that are trained with local data provide the best ability to identify and segment roots in minirhizotron imagery. However, labeling roots for training data (or otherwise) is an extremely tedious and time-consuming task. This paper aims to address this problem by labeling data at the image level (rather than the individual root or root pixel level) and train algorithms to perform individual root pixel level segmentation using MIL strategies. Three MIL methods (multiple instance adaptive cosine coherence estimator, multiple instance support vector machine, multiple instance learning with randomized trees) were applied to root detection and compared to non-MIL approaches. The results show that MIL methods improve root segmentation in challenging minirhizotron imagery and reduce the labeling burden. In our results, multiple instance support vector machine outperformed other methods. The multiple instance adaptive cosine coherence estimator algorithm was a close second with an added advantage that it learned an interpretable root signature which identified the traits used to distinguish roots from soil and did not require parameter selection.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Simulation-based anomaly detection for multileptons at the LHC

Decays of Higgs boson-like particles into multileptons is a well-motivated process for investigating physics beyond the Standard Model (SM). A unique feature of this final state is the precision with which the SM is known. As a result, simulations are used directly to estimate the background. Current searches consider specific models and typically focus on those with a single free parameter to simplify the analysis and interpretation. In this paper, we explore recent proposals for signal model agnostic searches using machine learning in the multilepton final state. These tools can be used to simultaneously search for many models, some of which have no dedicated search at the Large Hadron Collider. We find that the machine learning methods offer broad coverage across parameter space beyond where current searches are sensitive, with a necessary loss of performance compared to dedicated searches by only about one order of magnitude.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Explainable multi-fidelity Bayesian neural network for distribution system state estimation

Distribution System State Estimation (DSSE) is frequently constrained by limited real-time measurements, the uncertainties introduced by distributed energy resources, and the presence of bad data. To address them, this paper proposes an enhanced Multi-Fidelity Bayesian Neural Network (MFBNN) DSSE approach. A low-fidelity layer based on a Deep Neural Network (DNN) is first pre-trained on pseudo-measurement data to learn fundamental state features. Subsequently, a high-fidelity Bayesian Neural Network (BNN) layer leverages limited but high-quality real-time measurements to refine these features, thereby achieving accurate DSSE. Additionally, the deep SHapley Additive exPlanation (SHAP) is developed to quantify the influence of measurement data on DSSE through dual perspectives of global feature importance and local nodal contributions, establishing a hierarchical explainability framework for machine learning-based DSSE. Comparative studies conducted on the IEEE 13-bus system and a real-world 2135-node system from Dominion Energy demonstrate that the proposed method excels in estimation accuracy, even under situations of high noise levels, bad data, and missing data. Further comparisons with Weighted Least Squares (WLS) and other machine learning-based DSSE approaches verify that the proposed framework offers higher accuracy, improved interpretability, and enhanced robustness.

Bad data↗

DOE OSTI2020

Insights into cosmological structure formation with machine learning.

Our modern understanding of cosmological structure formation posits that small matter density fluctuations present in the early Universe, as traced by the cosmic microwave background, grow via gravitational instability to form extended haloes of dark matter. A theoretical understanding of the structure, evolution and formation of dark matter haloes is an essential step towards unravelling the intricate connection between halo and galaxy formation, needed to test our cosmological model against data from upcoming galaxy surveys. Physical understanding of the process of dark matter halo formation is made difficult by the highly non-linear nature of the haloes' evolution. I describe a new approach to gain physical insight into cosmological structure formation based on machine learning. This approach combines the ability of machine learning algorithms to learn non-linear relationships, with techniques that enable us to physically interpret the learnt mapping. I describe applicatio ns of th e method, with the aim of investigating which aspects of the early universe density field impact the later formation of dark matter haloes. First I present a case where the process of halo formation is turned into a binary classification problem; the algorithm predicts whether or not dark matter `particles' in the initial conditions of a simulation will collapse into haloes of a given mass range. Second, I present its generalization to regression, where the algorithm infers the final mass of the halo to which each particle will later belong. I show that the initial tidal shear does not play a significant role compared to the initial density field in establishing final halo masses. Finally, I demonstrate that extending the framework to deep learning algorithms such as convolutional neural networks allows us to explore connections between the early universe and late time haloes beyond those studied by existing analytic approximations of halo collapse.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2019

Deep Learning Method for Detecting Precursors to Adverse Events

With the recent advancements in Deep Learning methods, the ability to model large complex heterogeneous data sets are fundamentally changing industry and research. Coupled with hardware improvements, and ease of implementation, a wide variety of deep neural network architectures can quickly be developed to solve a sweeping range of problems such as: object detection in images, automatic healthcare diagnosis using heterogenous data sources, real time language translating and sentence prediction, upscaling low resolution images, and forecasting of multivariate timeseries. Generally, many of these architectures outperform classical machine learning approaches in their respective tasks, however, this typically comes at a cost of interpretability. These black box algorithms generally suffer from lack of transparency in both model complexity as well as the rationale behind the prediction. This lack of comprehension, is driving an emerging area of interest in “Explainable AI”. An algorithm called: “Deep Temporal Multiple Instance Learning”1 was a recently developed to identify precursors to adverse events and has been applied in the aviation domain. The deep learning architecture is designed to capture the evolution of the probability of the outcome over the time preceding the adverse event using a multiple instance learning approach as illustrated in Figure 1. Precursors are defined when the probability of the event has exceeded a threshold at some point in the timeseries, at which point, a sensitivity analysis is performed to determine contributing factors. The contributing factors are used to explain and define the precursor during the periods where the probability score is high. The identified contributing factors are then presented to subject matter experts to provide objective insights into the leading factors associated with the particular adverse event. The algorithm has been tested on flight data from a commercial airline and has the ability to discover precursors to known adverse events that take the form of safety critical operations, such as unstable approach events on final approach. Apart from detecting precursors to adverse events, the converse can also be leveraged to discover corrective actions. These positive actions manifest themselves as periods in the timeseries when the precursor score has been lowered from an elevated state; meaning that if the system had been left uncorrected, it would have eventually reached the adverse event state. Characterizing these state changes can help identify successful interventions that may not have been known before. Policy makers and procedure designers can use this additional knowledge to craft more safety and efficient resilient procedures for future operations and therefore improve the overall performance of the National Airspace.

Matthews, Bryan L.↗

DOE OSTI2025

Physics-based hybrid machine learning for critical heat flux prediction with uncertainty quantification

Critical heat flux (CHF) is a key quantity in nuclear system modeling due to its impact on heat transfer, safety margins, and reactor performance. This study develops and validates an uncertainty-aware hybrid modeling approach that combines machine learning with physics-based models to predict CHF in cases of dryout. The Biasi and Bowring empirical correlations were paired with three ML uncertainty quantification (UQ) techniques: deep neural network (DNN) ensembles, Bayesian neural networks (BNNs), and deep Gaussian processes (DGPs). A pure ML model without a base model was evaluated for comparison. Model performance was assessed under plentiful (7,350 points) and limited (9 points) training data scenarios using parity, uncertainty distributions, and calibration curves. Results show that the Biasi hybrid DNN ensemble achieved the best overall performance, with a mean absolute relative error of 1.846%, and well-calibrated uncertainty estimates. The BNN-based hybrids showed slightly higher error (2.14%) but superior uncertainty calibration. DGP models underperformed, with over 6% error and poor uncertainty calibration. All hybrid models outperformed pure machine learning configurations, demonstrating resistance against data scarcity. These findings indicate that hybrid modeling significantly improves predictive accuracy, interpretability, and resilience to data scarcity. The integration of uncertainty awareness provides actionable confidence in CHF predictions, which is vital for safety-critical decisions in nuclear applications. This hybrid approach offers a viable pathway for deploying ML models in reactor analysis tools while preserving domain knowledge and physical consistency.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Data-centric framework for crystal structure identification in atomistic simulations using machine learning

Atomic-level modeling performed at large scales enables the investigation of mesoscale materials properties with atom-by-atom resolution. The spatial complexity of such cross-scale simulations renders them unsuitable for simple human visual inspection. Instead, specialized structure characterization techniques are required to aid interpretation. These have historically been challenging to construct, requiring significant intuition and effort. Here we propose an alternative framework for a fundamental structural characterization task: classifying atoms according to the crystal structure to which they belong. Our approach is data-centric and favors the employment of Machine Learning over heuristic rules of classification. A group of data-science tools and simple local descriptors of atomic structure are employed together with an efficient synthetic training set. We also introduce the first standard and publicly available benchmark data set for evaluation of algorithms for crystal-structure classification. Further, it is demonstrated that our data-centric framework outperforms all of the most popular heuristic methods—especially at high temperatures when lattices are the most distorted—while introducing a systematic route for generalization to new crystal structures. Moreover, through the use of outlier detection algorithms our approach is capable of discerning between amorphous atomic motifs (i.e., noncrystalline phases) and unknown crystal structures, making it uniquely suited for exploratory materials synthesis simulations.

36 MATERIALS SCIENCE↗

DOE OSTI2024

A Science Gateway for the Repeatable Analysis of Machine Learning Predicted Gravity Anomalies

In recent years, deep learning has become an increasingly popular alternative for modeling in geoscience applications due to its scalability and efficiency. However, the interpretability, compute, data volume, and hyperparameter tuning requirements of deep learning models make development and monitoring difficult. Furthermore, model explainability and communicating results obtained by these models to users or domain experts is a challenge, as domain experts in geoscience also need to have a deep understanding of how those models function in order to support their scientific works. Here, we describe a science gateway and machine learning pipeline for predicting gravity anomalies from geophysical data. The gateway, built on open-source technologies, provides a holistic view of the pipeline through interactive visualizations aimed at enabling efficient exploratory data analysis. The repeatability, reproducibility, and monitoring capabilities of this overall system allow us to iterate and analyze at scale. Using this pipeline and gateway, we can repeatedly produce accurate high-resolution gravity anomaly datasets. By describing the underlying technologies, implementation, and results, here we provide a foundation for the broader adoption of science gateways into cross-cutting geoscience and machine learning research projects as a means to improve the scientific discovery and collaboration in the geophysics and computational sciences community.

58 GEOSCIENCES↗

DOE OSTI2018

A Deep Look Into the Future of Quantitative Imaging in Oncology: A Statement of Working Principles and Proposal for Change

The adoption of enterprise digital imaging, along with the development of quantitative imaging methods and the re-emergence of statistical learning, has opened the opportunity for more personalized cancer treatments through transformative data science research. In the last 5 years, accumulating evidence has indicated that noninvasive advanced imaging analytics (i.e., radiomics) can reveal key components of tumor phenotype for multiple lesions at multiple time points over the course of treatment. Many groups using homegrown software have extracted engineered and deep quantitative features on 3-dimensional medical images for better spatial and longitudinal understanding of tumor biology and for the prediction of diverse outcomes. These developments could augment patient stratification and prognostication, buttressing emerging targeted therapeutic approaches. Unfortunately, the rapid growth in popularity of this immature scientific discipline has resulted in many early publications that miss key information or use underpowered patient data sets, without production of generalizable results. Quantitative imaging research is complex, and key principles should be followed to realize its full potential. The fields of quantitative imaging and radiomics in particular require a renewed focus on optimal study design and reporting practices, standardization, interpretability, data sharing, and clinical trials. Standardization of image acquisition, feature calculation, and statistical analysis (i.e., machine learning) are required for the field to move forward. A new data-sharing paradigm enacted among open and diverse participants (medical institutions, vendors and associations) should be embraced for faster development and comprehensive clinical validation of imaging biomarkers. In this review and critique of the field, we propose working principles and fundamental changes to the current scientific approach, with the goal of high-impact research and development of actionable prediction models that will yield more meaningful applications of precision cancer medicine.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

NASA NTRSDate not supplied

TPSAS-NF1676L-35322-DND

This talk discusses emerging methods that seek to fuse and integrate physics-based modeling with machine learning. With the recent rise of machine learning and artificial intelligence, there has been a huge surge in data-driven approaches to solve computational science and engineering problems. However, neglecting a priori knowledge of established physical laws and relying solely on data-driven methods can yield unreliable, less interpretable, and/or non-physical results, especially when data is sparse or predictions are required outside of the training data domain. This two part talk presents two distinct approaches for accelerating predictions with machine learning that are grounded and constrained by relevant physics and their application to problems at NASA.

Julian Cuevas Paniagua↗

DOE OSTI2023

Adaptively driven X-ray diffraction guided by machine learning for autonomous phase identification

Machine learning (ML) has become a valuable tool to assist and improve materials characterization, enabling automated interpretation of experimental results with techniques such as X-ray diffraction (XRD) and electron microscopy. Because ML models are fast once trained, there is a key opportunity to bring interpretation in-line with experiments and make on-the-fly decisions to achieve optimal measurement effectiveness, which creates broad opportunities for rapid learning and information extraction from experiments. Here, we demonstrate such a capability with the development of autonomous and adaptive XRD. By coupling an ML algorithm with a physical diffractometer, this method integrates diffraction and analysis such that early experimental information is leveraged to steer measurements toward features that improve the confidence of a model trained to identify crystalline phases. We validate the effectiveness of an adaptive approach by showing that ML-driven XRD can accurately detect trace amounts of materials in multi-phase mixtures with short measurement times. The improved speed of phase detection also enables in situ identification of short-lived intermediate phases formed during solid-state reactions using a standard in-house diffractometer. Our findings showcase the advantages of in-line ML for materials characterization and point to the possibility of more general approaches for adaptive experimentation.

36 MATERIALS SCIENCE↗

DOE OSTI2025

DeepBench: A simulation package for physical benchmarking data

We introduce **DeepBench**, a python library that generates simple simulated image data from first principles, such as basic geometric shapes and astronomical objects. These data are highly valuable for developing (calibration, testing, and benchmarking) statistical and machine learning models because they make it possible to connect the final data product to physically interpretable inputs. This software includes tools to curate and store the datasets to maximize reproducibility.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2018

Embedding Python for In-Situ Analysis

We describe our work to embed a Python interpreter in S3D, a highly scalable parallel direct numerical simulation reacting flow solver written in Fortran. Although S3D had no in-situ capability when we began, embedding the interpreter was surprisingly easy, and the result is an extremely flexible platform for conducting machine-learning experiments in-situ.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Unsupervised machine learning based on non-negative tensor factorization for analyzing reactive-mixing

Analysis of reactive-diffusion simulations representing complex mixing processes requires a large number of independent model runs. For each high-fidelity model simulation, the model inputs are varied and the predicted mixing behavior is represented by temporal and spatial changes in species concentration. It is then required to discern how the model inputs (such as diffusivity, dispersion, anisotropy, and velocity field properties) impact the mixing process. This task is challenging and typically involves interpretation of large model outputs representing temporal and spatial changes of species concentration within the model domain. Yet, the task can be automated and substantially simplified by applying Machine Learning (ML) methods. Here, we present an application of an unsupervised ML method (called NTF k ) using Non-negative Tensor Factorization (NTF) coupled with a custom clustering procedure based on k-means to reveal the temporal and spatial features in product concentrations. An attractive and unique aspect of the proposed ML method is that it ensures the extracted features are non-negative, which is important to obtain a meaningful deconstruction of the mixing processes. The ML methodology is applied to a large set of high-resolution finite-element model simulations representing anisotropic reaction-diffusion processes in perturbed vortex-based velocity fields. The applied finite-element method ensures that spatial and temporal species concentration are always non-negative, even in the case of high anisotropic contrasts. The simulated reaction is a fast irreversible bimolecular reaction A+B→C , where species A and B react to form species C. The reactive-diffusion model input parameters that control mixing include properties of the velocity field (such as vortex structures), anisotropic dispersion, and molecular diffusion. We demonstrate the applicability of the ML feature extraction method to produce a meaningful deconstruction of model outputs to discriminate between different physical processes impacting the reactants, their mixing, and the spatial distribution of the product C. The introduced ML analysis allowed us to identify additive temporal and spatial features that characterize mixing behavior. The application of the proposed NTF k approach is not limited to reactive-mixing. NTFk can be readily applied to any observed or simulated datasets that can be represented as tensors (multi-dimensional arrays) and have separable latent signatures or features.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Using Ultrasound Image Augmentation and Ensemble Predictions to Prevent Machine-Learning Model Overfitting

Deep learning predictive models have the potential to simplify and automate medical imaging diagnostics by lowering the skill threshold for image interpretation. However, this requires predictive models that are generalized to handle subject variability as seen clinically. Here, we highlight methods to improve test accuracy of an image classifier model for shrapnel identification using tissue phantom image sets. Using a previously developed image classifier neural network—termed ShrapML—blind test accuracy was less than 70% and was variable depending on the training/test data setup, as determined by a leave one subject out (LOSO) holdout methodology. Introduction of affine transformations for image augmentation or MixUp methodologies to generate additional training sets improved model performance and overall accuracy improved to 75%. Further improvements were made by aggregating predictions across five LOSO holdouts. This was done by bagging confidences or predictions from all LOSOs or the top-3 LOSO confidence models for each image prediction. Top-3 LOSO confidence bagging performed best, with test accuracy improved to greater than 85% accuracy for two different blind tissue phantoms. This was confirmed by gradient-weighted class activation mapping to highlight that the image classifier was tracking shrapnel in the image sets. Overall, data augmentation and ensemble prediction approaches were suitable for creating more generalized predictive models for ultrasound image analysis, a critical step for real-time diagnostic deployment.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Workshop Report on Basic Research Needs for Scientific Machine Learning: Core Technologies for Artificial Intelligence

Scientific Machine Learning (SciML) and Artificial Intelligence (AI) will have broad use and transformative effects across the Department of Energy. Accordingly, the January 2018 Basic Research Needs workshop identified six Priority Research Directions (PRDs). The first three PRDs describe foundational research themes that correspond to the need for domain-awareness (PRD #1), interpretability (PRD #2), and robustness (PRD #3). The other three PRDs describe capability research themes and correspond to the three major use cases for massive scientific data analysis (PRD #4), machine learning-enhanced modeling and simulation (PRD #5), and intelligent automation and decision-support for complex systems (PRD #6). The Priority Research Directions provide a sound basis for a coherent, long-term research and development strategy in SciML and AI. Over the last decade, DOE investments in applied mathematics have laid the groundwork for the type of basic research that will underpin key advances in the six PRDs. Such advances will build on the work from leading researchers in optimization, linear algebra, high-performance solvers and algorithms, multiscale modeling and simulation, complex systems research, uncertainty quantification, and the new basic research areas that will emerge from the pursuit of transformative technologies.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Brochure on Basic Research Needs for Scientific Machine Learning: Core Technologies for Artificial Intelligence [Slides]

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Machine Learned Empirical Numerical Integrator from Simulated Data

Recently, a number of state-of-the-art surrogate machine learning (ML) models have been designed for global weather and climate prediction, which have been trained using reanalysis data products. Reanalysis data products are constructed using numerical model simulations that combine numerical integration of partial differential equations and parameterization schemes. These products are typically only archived and made available using coarsened spatial and temporal resolutions. This study explores the impact of the numerical generation methods used to produce the training datasets and the temporal resolution of those datasets on machine learning surrogate models. Using the nonlinear vector autoregression (NVAR) machine as an explainable ML technique, simple dynamical systems are emulated with ML models trained on data produced by three classical numerical integration schemes. NVAR is validated as a skillful ML method, capable of producing accurate predictions and, more importantly, reconstructing both the underlying dynamics and the numerical integration scheme used to generate the training data. However, the machine fails to generalize predictions on unseen test data generated by different numerical integration schemes, despite the underlying dynamical system being the same. This result provides a word of caution for the growing field of machine learning emulation of weather and climate dynamics. Furthermore, we illustrate using NVAR that training on temporally coarsened data may increase the required complexity of ML models and potentially introduce new numerical challenges. Finally, we discover that empirical integration schemes with arbitrary time-stepping sizes can be constructed directly from the data, which implies a potential for the development of empirical numerical integration schemes.

54 ENVIRONMENTAL SCIENCES↗