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DOE OSTI2024

Teaching Freight Mode Choice Models New Tricks Using Interpretable Machine Learning Methods

Understanding and forecasting the intricate freight mode choice behavior under various industry, policy, and technology contexts is essential in freight planning and policymaking. Numerous models have been developed in prior studies to provide insights into freight mode selection, the majority of which use discrete choice models such as multinomial logit (MNL) models. However, logit models often rely on linear specifications of independent variables, despite potential nonlinear relationships in the data. Moreover, there often lacks a heuristic and efficient approach to identify such complex relationships to define the logit model specifications. To fill this gap, we developed an MNL model for freight mode choice using the insights from state-of-the- art machine learning (ML) models. ML models can capture the nonlinear nature of the complex decision-making process, and recent advances in 'explainable AI' have greatly improved their interpretability. The interpretable ML methods help enhance the performance of MNL models and advance knowledge of freight mode choice. Specifically, the influential factors and their relationship with individual modes are identified using SHapley Additive exPlanations (SHAP) to improve the MNL's performance. The workflow is demonstrated in a case study of Austin, Texas, and the SHAP results reveal multiple nonlinear relationships predicted by ML models. Incorporating those relationships into MNL model specifications improves the interpretability and accuracy of the MNL model compared to a conventional MNL model. Findings from this study can be used to guide freight planning and inform policymakers and practitioners on how key factors affect freight decision-making.

ADVANCED PROPULSION SYSTEMS,MATHEMATICS AND COMPUT↗

DOE OSTI2022

Control systems and methods to enable autonomous drilling

A system or method for drilling includes autonomously controlling a rotary or percussive drilling process as it transitions through multiple materials with very different dynamics. The method determines a drilling medium based on real-time measurements and comparison to prior drilling data, and identifies the material type, drilling region, and approximately optimal setpoint based on data from at least one operating condition. The controller uses these setpoints initially to execute an optimal search to maximize performance by minimizing mechanical specific energy. Near-bit depth-of-cut estimations are performed using a machine learning prediction deployed in an embedded processor to provide high-speed ROP estimates. The sensing capability is coupled with a near-bit clutching mechanism to support drilling dysfunction mitigation.

Buerger, Stephen↗

DOE OSTI2023

Control systems and methods to enable autonomous drilling

Buerger, Stephen↗

DOE OSTI2021

Autonomous Experiments in Scanning Probe Microscopy and Spectroscopy: Choosing Where to Explore Polarization Dynamics in Ferroelectrics

Polarization dynamics in ferroelectric materials are explored via automated experiment in piezoresponse force microscopy/spectroscopy (PFM/S). A Bayesian optimization (BO) framework for imaging is developed, and its performance for a variety of acquisition and pathfinding functions is explored using previously acquired data. The optimized algorithm is then deployed on an operational scanning probe microscope (SPM) for finding areas of large electromechanical response in a thin film of PbTiO 3 , with results showing that, with just 20% of the area sampled, most high-response clusters were captured. Furthermore, this approach can allow performing more complex spectroscopies in SPM that were previously not possible due to time constraints and sample stability. Improvements to the framework to enable the incorporation of more prior information and improve efficiency further are modeled and discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Variable rate neural compression for sparse detector data

Particle colliders produce data at extraordinary rates, posing major challenges for transmission and storage. High-throughput compression algorithms are therefore essential. In the sPHENIX experiment taking data at the Relativistic Heavy Ion Collider, a time projection chamber records three-dimensional (3D) particle trajectories that are highly sparse, making conventional learning-free lossy compression ineffective. Convolutional neural networks have surpassed traditional methods in compression ratio and accuracy. However, they fail to exploit sparsity for efficiency. To address these gaps, we present BCAE-VS, a bicephalous convolutional autoencoder with variable compression ratio for sparse data, which adapts compression to input complexity through key-point identification and sparse convolution. BCAE-VS achieves higher accuracy and compression ratios than prior neural approaches while being orders of magnitude smaller. Moreover, its throughput increases with sparsity—a property not observed in other methods. Although it was developed for collider experiments, BCAE-VS readily extends to other sparse data domains, such as light detection and ranging (LiDAR) sensing and 3D microscopy.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Predicting resistive wall mode stability in NSTX through balanced random forests and counterfactual explanations

Abstract Recent progress in the disruption event characterization and forecasting framework has shown that machine learning guided by physics theory can be easily implemented as a supporting tool for fast computations of ideal stability properties of spherical tokamak plasmas. In order to extend that idea, a customized random forest (RF) classifier that takes into account imbalances in the training data is hereby employed to predict resistive wall mode (RWM) stability for a set of high beta discharges from the NSTX spherical tokamak. More specifically, with this approach each tree in the forest is trained on samples that are balanced via a user-defined over/under-sampler. The proposed approach outperforms classical cost-sensitive methods for the problem at hand, in particular when used in conjunction with a random under-sampler, while also resulting in a threefold reduction in the training time. In order to further understand the model’s decisions, a diverse set of counterfactual explanations based on determinantal point processes (DPP) is generated and evaluated. Via the use of DPP, the underlying RF model infers that the presence of hypothetical magnetohydrodynamic activity would have prevented the RWM from concurrently going unstable, which is a counterfactual that is indeed expected by prior physics knowledge. Given that this result emerges from the data-driven RF classifier and the use of counterfactuals without hand-crafted embedding of prior physics intuition, it motivates the usage of counterfactuals to simulate real-time control by generating the β N levels that would have kept the RWM stable for a set of unstable discharges.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

High dimensional predictions of suicide risk in 4.2 million US Veterans using ensemble transfer learning

We present an ensemble transfer learning method to predict suicide from Veterans Affairs (VA) electronic medical records (EMR). A diverse set of base models was trained to predict a binary outcome constructed from reported suicide, suicide attempt, and overdose diagnoses with varying choices of study design and prediction methodology. Each model used twenty cross-sectional and 190 longitudinal variables observed in eight time intervals covering 7.5 years prior to the time of prediction. Ensembles of seven base models were created and fine-tuned with ten variables expected to change with study design and outcome definition in order to predict suicide and combined outcome in a prospective cohort. The ensemble models achieved c-statistics of 0.73 on 2-year suicide risk and 0.83 on the combined outcome when predicting on a prospective cohort of ~4.2 M veterans. The ensembles rely on nonlinear base models trained using a matched retrospective nested case-control (Rcc) study cohort and show good calibration across a diversity of subgroups, including risk strata, age, sex, race, and level of healthcare utilization. In addition, a linear Rcc base model provided a rich set of biological predictors, including indicators of suicide, substance use disorder, mental health diagnoses and treatments, hypoxia and vascular damage, and demographics. Similar content being viewed by others

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

FluxRETAP: a REaction TArget Prioritization genome-scale modeling technique for selecting genetic targets

MOTIVATION: Metabolic engineering is rapidly evolving as a result of new advances in synthetic biology tools and automation platforms that enable high throughput strain construction, as well as the development of machine learning tools (ML) for biology. However, selecting genetic engineering targets that effectively guide the metabolic engineering process is still challenging. ML can provide predictive power for synthetic biology, but current technical limitations prevent the independent use of ML approaches without previous biological knowledge. RESULTS: Here, we present FluxRETAP, a simple and computationally inexpensive method that leverages the prior mechanistic knowledge embedded in genome-scale models for suggesting targets for genetic overexpression, downregulation or deletion, with the final goal of increasing the production of a desired metabolite. This method can provide a list of desirable engineering targets that can be combined with current ML pipelines. FluxRETAP captured 100% of reaction targets experimentally verified to improve Escherichia coli isoprenol production, 50% of targets that experimentally improved taxadiene production in E. coli and ∼60% of genetic targets from a verified minimal constrained cut-set in Pseudomonas putida, while providing additional high priority targets that could be tested. Overall, FluxRETAP is an efficient algorithm for identifying a prioritized list of testable genetic and reaction targets. AVAILABILITY AND IMPLEMENTATION: FluxRETAP is implemented in python and released under the creative commons license. The implementation and code are freely available at: https://github.com/JBEI/FluxRETAP.

Czajka, Jeffrey J↗

DOE OSTI2026

Bayesian Physics Informed Spatio-Temporal Network for Streamflow Data Imputation

Reliable reconstruction of incomplete streamflow records is critical for improving hydrological forecasting, flood preparedness, and water resource management. However, large observational gaps and uncertainties in governing physical parameters limit the accuracy of traditional statistical and machinelearning imputation frameworks. To address these challenges, we develop a Bayesian Physics-Informed Spatio-Temporal Network (BPI-STNet) that jointly captures spatial and temporal dependencies while enforcing hydrologic consistency through embedded physical constraints. The framework integrates a GraphSAGE-LSTM architecture to model spatial connectivity across gauges and temporal flow dynamics, coupled with a Bayesian update mechanism to estimate uncertain parameters in a simplified water-balance framework. Unlike conventional physics-informed networks that rely on sampling-based posterior estimation, BPI-STNet derives an analytic solution to the inverse problem, allowing closed-form Bayesian updates of uncertain parameters Λ={α,β,k} using Gaussian priors and likelihoods. Applied to daily observations from the Susquehanna River Basin (1980-2022), BPI-STNet achieves substantial improvements over a purely data-driven RGNN baseline, which reduced RMSE by 23 % and MAE by 9 %, and achieving an average NSE values up to 0.96. The results demonstrate that coupling Bayesian inference with physics-informed learning yields physically consistent, uncertainty-aware reconstructions that preserve the temporal persistence and statistical distribution of observed flows. The proposed framework establishes a generalizable paradigm for data-sparse hydrologic systems where both data fidelity and physical interpretability are essential.

Krishnan Kutty Ambika, Anukesh [ORNL] (ORCID:00000↗

DOE OSTI2022

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

While deep learning models have seen increasing applications in protein science, few have been implemented for protein backbone generation—an important task in structure-based problems such as active site and interface design. We present a new approach to building class-specific backbones, using a variational auto-encoder to directly generate the 3D coordinates of immunoglobulins. Our model is torsion- and distance-aware, learns a high-resolution embedding of the dataset, and generates novel, high-quality structures compatible with existing design tools. We show that the Ig-VAE can be used with Rosetta to create a computational model of a SARS-CoV2-RBD binder via latent space sampling. We further demonstrate that the model’s generative prior is a powerful tool for guiding computational protein design, motivating a new paradigm under which backbone design is solved as constrained optimization problem in the latent space of a generative model.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Machine Learning Design of Perovskite Catalytic Properties

Abstract Discovering new materials that efficiently catalyze the oxygen reduction and evolution reactions is critical for facilitating the widespread adoption of solid oxide fuel cell and electrolyzer (SOFC/SOEC) technologies. Here, machine learning (ML) models are developed to predict perovskite catalytic properties critical for SOFC/SOEC applications, including oxygen surface exchange, oxygen diffusivity, and area specific resistance (ASR). The models are based on trivial‐to‐calculate elemental features and are more accurate and dramatically faster than the best models based on ab initio‐derived features, potentially eliminating the need for ab initio calculations in descriptor‐based screening. The model of ASR enables temperature‐dependent predictions, has well calibrated uncertainty estimates and online accessibility. Use of temporal cross‐validation reveals the model to be effective at discovering new promising materials prior to their initial discovery, demonstrating the model can make meaningful predictions. Using the SHapley Additive ExPlanations (SHAP) approach, detailed discussion of different approaches of model featurization is provided for ML property prediction. Finally, the model is used to screen more than 19 million perovskites to develop a list of promising cheap, earth‐abundant, stable, and high performing materials, and find some top materials contain mixtures of less‐explored elements (e.g., K, Bi, Y, Ni, Cu) worth exploring in more detail.

25 ENERGY STORAGE↗

DOE OSTI2023

Multiverse: Bayesian model selection for neural networks

Multiverse is a code repository for a set of tools for Bayesian model selection for neural networks. The goal of the tools is to provide capabilities for selecting among prior and model specifications for Bayesian neural networks. Multiverse will include tools for creating Bayesian neural networks, evaluating the Bayesian model evidence, and performing inference in Bayesian neural networks. These components are written in Python, a high-level programming language that takes advantage of the Python ecosystem of high-quality open-source packages for machine learning and signal processing.

Klein, Natalie↗

DOE OSTI2024

FY2024 Mid-Year Report: Verification of Spent Fuel Inside Dry Storage Casks by Cask Top Fast Neutron Mapping

This project is developing a prototype scanner array verification system for detection of missing fuel assemblies in spent-fuel storage casks. The prototype consists of six fast-neutron scintillator detectors mounted to a linear actuator frame that is placed on the top of a spent fuel cask to scan across all fuel assembly positions. The scanner array was assembled and tested at LLNL in prior years. A field test schedule has been requested at the Idaho National Laboratory (INL) Cask Farm site for FY2024. Following the Field Test, we will present results and discuss the technology with the IAEA. The IAEA may have special requirements for portability, shipping, lifting, and installation. We will incorporate additional improvements to the system based on lessons learned from the Field Test and feedback from the IAEA. If successful, the technology can be transferred to the IAEA or other stakeholders for assessment.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Preparing for the next pandemic via transfer learning from existing diseases with hierarchical multi-modal BERT: a study on COVID-19 outcome prediction

Abstract Developing prediction models for emerging infectious diseases from relatively small numbers of cases is a critical need for improving pandemic preparedness. Using COVID-19 as an exemplar, we propose a transfer learning methodology for developing predictive models from multi-modal electronic healthcare records by leveraging information from more prevalent diseases with shared clinical characteristics. Our novel hierarchical, multi-modal model ( $${\textsc {TransMED}}$$ T R A N S MED ) integrates baseline risk factors from the natural language processing of clinical notes at admission, time-series measurements of biomarkers obtained from laboratory tests, and discrete diagnostic, procedure and drug codes. We demonstrate the alignment of $${\textsc {TransMED}}$$ T R A N S MED ’s predictions with well-established clinical knowledge about COVID-19 through univariate and multivariate risk factor driven sub-cohort analysis. $${\textsc {TransMED}}$$ T R A N S MED ’s superior performance over state-of-the-art methods shows that leveraging patient data across modalities and transferring prior knowledge from similar disorders is critical for accurate prediction of patient outcomes, and this approach may serve as an important tool in the early response to future pandemics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Constrained non-negative matrix factorization enabling real-time insights of in situ and high-throughput experiments

Non-negative matrix factorization (NMF) is an appealing class of methods for performing unsupervised learning on streaming spectral data, particularly in time-sensitive applications such as in situ characterization of materials. These methods seek to decompose a dataset into a small number of components and weights that can compactly represent the underlying signal while effectively reconstructing the observations with minimal error. However, canonical NMF methods have no underlying requirement that the reconstruction uses components or weights that are representative of the true physical processes. In this work, we demonstrate how constraining a subset of the NMF weights or components as rigid priors, provided as known or assumed values, can provide significant improvement in revealing true underlying phenomena. We present a PyTorch-based method for efficiently applying constrained NMF and demonstrate its application to several synthetic examples. Our implementation allows an expert researcher-in-the-loop to provide and dynamically adjust the constraints during a live experiment involving streaming spectral data. Such interactive priors allow researchers to specify known or identified independent components, as well as functional expectations about the mixing or transitions between the components. We further demonstrate the application of this method to measured synchrotron x-ray total scattering data from in situ beamline experiments. In such a context, constrained NMF can result in a more interpretive and scientifically relevant decomposition than canonical NMF or other decomposition techniques. As a result, the details of the method are provided, along with general guidance for employing constrained NMF in the extraction of critical information and insights during time-sensitive experimental applications.

36 MATERIALS SCIENCE↗

DOE OSTI2026

In-situ sensor monitoring of multi-class gas porosity formation in laser powder bed fusion using convolutional neural network

In-situ monitoring of defect formation remains a significant challenge in the laser powder bed fusion (LPBF) process. Recent advances have enabled real-time defect detection with machine learning and in-situ sensing technologies; however, most studies focus on binary classification of keyhole pores, limiting nuanced multi-class pore differentiation and formation mechanisms. This work introduces a multi-class pore detection framework (no pore, small pores < 15 µm, and large pores > 15 µm) by leveraging photodiode sensor data alongside high-fidelity synchrotron X-ray imaging. The 15 µm threshold is selected to distinguish between two fundamentally different defect mechanisms, following the physical size-mechanism boundary established by prior high-resolution synchrotron X-ray characterization of Al6061 LPBF. Distinguishing these classes is critical because large keyhole pores are structurally detrimental, whereas small gas pores are often benign, requiring different process control strategies. Thermal emission monitoring data collected simultaneously with high-speed X-ray imaging at the Stanford Synchrotron Radiation Lightsource (SSRL), are correlated with subsurface melt pool dynamics to establish ground truth. Continuous Wavelet Transform (CWT) with optimized parameters converts the photodiode time-series signals into time–frequency images, facilitating feature extraction. Convolutional Neural Networks (CNN) are then applied for real-time multi-class pore classification in an average inference time of 1 ms per signal window. It achieves 79% accuracy and an Area Under the Receiver Operating Characteristic curve (AUC ROC) score of 0.89 with five-fold cross-validation. The results demonstrate that coupling CWT-based feature engineering with CNN architecture enables reliable multi-class pore detection in Al6061 builds using affordable in-situ sensors. This approach advances scalable and affordable quality assurance in additive manufacturing by moving beyond binary defect detection toward more nuanced classification of porosity mechanisms with in-situ sensors and machine learning.

Laser powder bed fusion, Multi-class pores, In-sit↗

DOE OSTI2025

The Effects of Compounded Model Size Reductions on Adversarial Robustness

Recent advances in Edge AI and Tiny Machine Learning (TinyML) have enabled the deployment of machine learning models on resource-constrained environments. However, deploying these models on edge devices, such as micro-controllers, requires significant model footprint reduction through a variety of techniques such as quantization, pruning, and clustering. While these optimization methods offer considerable advantages, they potentially introduce AI-related security vulnerabilities, particularly concerning model robustness with respect to adversarial AI attacks. Prior research has extensively examined the impact of quantization on adversarial robustness; however, the effects of alternative reduction techniques and their combinations remain understudied. This paper investigates the impact of model size reduction techniques on adversarial robustness, when applied individually and combined. We utilized Fast Gradient Sign Method (FGSM) and Projected Gradient Descent (PGD) attacks to generate adversarial perturbations for both training and testing data, and then evaluated the models' accuracy under adversarial training conditions. Our findings revealed that reduction techniques generally diminished robustness; although, combining techniques was not found to make robustness any worse than when applied individually. Moreover, specific techniques can potentially enhance resistance to small size perturbations. This research provides insights into the trade-offs between model size reduction and security, establishing a foundation for future investigations into improving adversarial training techniques and methodologies for maintaining robustness while preserving memory footprint benefits.

Austria, Phillipe [ORNL] (ORCID:0000000236223973)↗

DOE OSTI2022

Installation and imaging of thousands of minirhizotrons to phenotype root systems of field-grown plants

Roots are vital to plant performance because they acquire resources from the soil and provide anchorage. However, it remains difficult to assess root system size and distribution because roots are inaccessible in the soil. Existing methods to phenotype entire root systems range from slow, often destructive, methods applied to relatively small numbers of plants in the field to rapid methods that can be applied to large numbers of plants in controlled environment conditions. Much has been learned recently by extensive sampling of the root crown portion of field-grown plants. But, information on large-scale genetic and environmental variation in the size and distribution of root systems in the field remains a key knowledge gap. Minirhizotrons are the only established, non-destructive technology that can address this need in a standard field trial. Prior experiments have used only modest numbers of minirhizotrons, which has limited testing to small numbers of genotypes or environmental conditions. This study addressed the need for methods to install and collect images from thousands of minirhizotrons and thereby help break the phenotyping bottleneck in the field. Over three growing seasons, methods were developed and refined to install and collect images from up to 3038 minirhizotrons per experiment. Modifications were made to four tractors and hydraulic soil corers mounted to them. High quality installation was achieved at an average rate of up to 84.4 minirhizotron tubes per tractor per day. A set of four commercially available minirhizotron camera systems were each transported by wheelbarrow to allow collection of images of mature maize root systems at an average rate of up to 65.3 tubes per day per camera. This resulted in over 300,000 images being collected in as little as 11 days for a single experiment. The scale of minirhizotron installation was increased by two orders of magnitude by simultaneously using four tractor-mounted, hydraulic soil corers with modifications to ensure high quality, rapid operation. Image collection can be achieved at the corresponding scale using commercially available minirhizotron camera systems. Along with recent advances in image analysis, these advances will allow use of minirhizotrons at unprecedented scale to address key knowledge gaps regarding genetic and environmental effects on root system size and distribution in the field.

54 ENVIRONMENTAL SCIENCES↗