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DOE OSTI2025

Neural Network Analysis of Nuclear Magnetic Resonance and Infrared Spectra

Nuclear magnetic resonance (NMR) spectroscopy and infrared (IR) spectroscopy are powerful chemical characterization techniques with broad general usage. However, the manual evaluation of the resulting spectra is time-consuming and requires significant expertise, preventing insights from being used in real-time applications. With recent advances in computation and artificial intelligence (AI), new tools are available for automating spectral interpretation. In this work, machine learning (ML) algorithms using 1-dimensional convolutional neural networks (CNNs) were applied to identify common functional groups from spectral information. Raw spectra were collected virtually from the Human Metabolome Database (HMDB) and National Institute of Standards and Technology (NIST) Chemistry WebBook and processed into a suitable standard. Algorithm design was tailored to best fit the nature of the problem, with built-in flexibility to accommodate relevant parameters beyond the raw spectral input, specifically solvent identity and magnetic frequency for NMR. The predictive capability of the algorithm in identifying functional groups is displayed in several examples. This methodology has been compiled into a code repository and could easily be modified to adapt alternative data sources, including other spectrum types. To mitigate overfitting, a common problem in mathematical modeling where overfamiliarity with training data produces trends that are not representative of the general data, a novel metric was developed, referred to as Accufit. Accufit includes a parameter that penalizes substantial differences in the training accuracy and the accuracy of an independent validation set. Examples are presented showing the effectiveness of Accufit in maintaining the model’s predictive capability while controlling the overfitting when used as a custom metric for hyperparameter tuning.

Sturgill, James↗

DOE OSTI2026

Artificial Intelligence for Event Reconstruction and Higgs Physics at CMS and Future Colliders

This dissertation charts a trajectory in which advances in artificial intelligence (AI) play a central role in pushing the high-energy physics frontier, complementing progress driven by higher collision energies and larger colliders. The discovery potential of the LHC and future colliders relies on accurate reconstruction of increasingly complex particle collision events. In the CMS experiment, this task is performed by the particle-flow (PF) algorithm. This dissertation presents the first implementation of a machine-learning-based particle-flow (MLPF) reconstruction in the CMS detector based on transformer architectures. In simulated top quark--antiquark pair (ttbar) events under LHC Run~3 (2023--2024) conditions, MLPF improves jet energy resolution by 10--20\% compared to standard PF for jets with transverse momentum between 30--100\GeV. Runtime performance is evaluated using simulated multijet events, with a median inference time of 20\unit{ms} per event on an NVIDIA L4 GPU, compa red to approximately 110\unit{ms} for standard PF. The MLPF algorithm is also validated on Run~3 collision data, representing the first data-validated ML-based reconstruction pipeline at any LHC experiment. We then extend MLPF toward future electron--positron colliders and introduce the first full-simulation cross-detector transfer learning workflow for PF reconstruction. The model is pre-trained on simulated events from the Compact Linear Collider detector (CLICdet) and fine-tuned on the CLIC-like detector (CLD) proposed for the Future Circular Collider (FCC). This approach achieves up to a 40\% improvement in jet energy resolution over rule-based reconstruction while reducing the required training dataset size by an order of magnitude, demonstrating the potential of AI to accelerate detector development and optimization. This dissertation also demonstrates how modern AI techniques enhance the sensitivity of LHC physics analyses. A CMS search for highly Lorentz-boosted Higgs bosons decaying to \textrm{W} boson pairs is presented, focusing on the single-lepton final state. A dedicated fine-tuning strategy for \ParT yields an approximately 70\% increase in expected sensitivity relative to the baseline model. The analysis uses proton--proton collision data at a center-of-mass energy of \ensuremath{\sqrt{s}=13\TeV} collected by CMS between 2016 and 2018, corresponding to an integrated luminosity of 138\ensuremath{\ \mathrm{fb}^{-1}}. The expected significance of the search is $1.86\sigma$, with an observed signal strength of $-0.19^{+0.48}_{-0.46}$. Finally, explainable AI techniques are applied to the MLPF and \ParticleNet algorithms using layerwise relevance propagation, showing that both models base their predictions on physically meaningful features consistent with our physics intuition. Together, these results demonstrate how advanced AI methods can enhance reconstruction, analysis sensitivity, and interpretability, shaping the next era of experimental parti cle physics.

Mokhtar, Farouk [UC, San Diego]↗

DOE OSTI2022

Genetic programming for understanding cognitive biases that generate polarization in social networks

Recent studies have applied agent-based models to infer human-interpretable explanations of individual-scale behaviors that generate macro-scale patterns in complex social systems. Genetic programming has proven to be an ideal explainable AI tool for this purpose, where primitives may be expressed in an interpretable fashion and assembled into agent rules. Evolutionary model discovery (EMD) is a tool that combines genetic programming and random forest feature importance analysis, to infer individual-scale, human-interpretable explanations from agent-based models. We deploy EMD to investigate the cognitive biases behind the emergence of ideological polarization within a population. An agent-based model is developed to simulate a social network, where agents are able to create or sever links with one another, and update an internal ideological stance based on their neighbors' stances. Agent rules govern these actions and constitute of cognitive biases. A set of 7 cognitive biases are included as genetic program primitives in the search for rules that generate hyper-polarization among the population of agents. We find that heterogeneity in cognitive biases is more likely to generate polarized social networks. Highly polarized social networks are likely to emerge when individuals with confirmation bias are exposed to those with either attentional bias, egocentric bias, or cognitive dissonance.

Gunaratne, Chathika↗

DOE OSTI2024

Assessment of Machine Learning for Ultrasonic Nondestructive Evaluation of Alkali–Silica Reaction in Concrete

Alkali–silica reaction (ASR) is a type of material degradation in concrete structures that leads to concrete cracking and rebar corrosion, thereby reducing the material’s structural integrity and the overall structure’s lifetime and raising safety concerns. Ultrasonic nondestructive evaluation (NDE) has been proven to be a valuable technique for assessing concrete properties and monitoring ASR progression in concrete. However, the deployment and analysis of ultrasonic NDE and its data requires specialized expertise, often relying on the engineer’s subjective interpretation. With the surge in computational power, artificial intelligence (AI) and machine learning (ML) algorithms have become popular in automating NDE data analysis. Various industrial sectors are increasingly adopting ML algorithms for NDE data analysis with a growing emphasis on AI–assisted automation. Regulatory agencies are also preparing for this technological shift, anticipating corresponding revisions in standards. Thus, there is an urgent need to identify the capabilities and limitations of current ML technologies for the evaluation of concrete material properties and damage status. Furthermore, the effects of various factors on ML model performance must be thoroughly investigated. The study summarized herein evaluated the effectiveness of two ML models (i.e., support vector regression (SVR) and deep neural network (DNN)) in predicting concrete material damage induced by ASR based on the long-term ultrasonic monitoring data. Four distinct concrete specimens were cast with artificially induced ASR, and over a period exceeding 500 days, ultrasonic signals and expansion data were continuously collected. For the SVR model, wave velocity and 12 other wave features were extracted from the ultrasonic signals, with 6 out of 13 features selected as input for the model. Different combinations of training and testing datasets were designed to explore factors influencing prediction performance, including the range of data within training and testing sets, in addition to various signal preprocessing methodologies. These findings suggest the importance of using a training dataset with a broader data range compared with testing datasets for improved model performance alongside consistent signal preprocessing across datasets.

36 MATERIALS SCIENCE↗

DOE OSTI2025

White Paper: Scalable Digital Twin Capabilities for Aging and Surveillance of Engineered Systems

This white paper presents a multi-year initiative to develop practical, secure, and scalable digital twin capabilities for engineered systems in aging and surveillance contexts—an approach pioneered at the National Nuclear Security Administration (NNSA) Lawrence Livermore National Laboratory (LLNL) that maps directly onto the needs and ambitions of the Navy for ship- and fleet-level digital twins. LLNL’s work in building part- and process-level digital twins for advanced manufacturing, with a vision to scale up to entire factory floors and, ultimately, enterprise-wide digital twins, offers an adaptable pathway for the Navy as it seeks to modernize lifecycle management, readiness, and predictive maintenance across ships and fleets. For our application, we integrate physics-based modeling with automated data ingestion, processing, and AI-driven calibration, creating hybrid models that are both interpretable and data responsive. We modernized legacy workflows, established centralized data infrastructure, automated experimental pipelines, and demonstrated end-to-end coupling of accelerated aging data with finite element simulations via optimization and surrogate modeling. The result is a generalizable framework that supports part-level digital twins today and lays the groundwork for future system-level twins suitable for Navy applications.

36 MATERIALS SCIENCE↗

DOE OSTI2026

A human-in-the-loop explanation framework for morphologically transparent AI predictions from whole-slide images

Deep learning models enable the prediction of clinical endpoints from whole-slide images (WSIs), but many such models function as “black boxes”, lacking transparency about whether and which histomorphological patterns drive their predictions, hindering interpretability and clinical adoption. Here we propose a human-in-the-loop explanation framework, MorphoXAI, which provides both local and global interpretability for deep learning models by incorporating human-expert interpretations. At the global level, it reveals the histomorphological patterns on which the model consistently relies to distinguish between classes of WSIs, as well as the patterns associated with confusion between classes. At the local level, it indicates which of these patterns are used in the prediction of an individual WSI and which regions within the slide correspond to such patterns. We validated our method across multiple deep learning–based WSI analysis tasks spanning different tissue types. The results show that our framework generates explanations that accurately reflect the histomorphology underlying the model’s predictions at both global and local levels. For interpretability and clinical utility in diagnostic contexts, human evaluation results showed that our explanations were easy to interpret, rich in diagnostic features, and directly helpful for diagnostic decision-making, thereby enhancing pathologist-AI collaboration. Our work highlights that unifying global and local explanations and grounding them in expert-interpreted morphology enhances the interpretability and verifiability of deep learning models, thereby facilitating the transparent deployment of such models in clinical practice.

Lou, Peiliang↗

DOE OSTI2024

Integrating multi-modal remote sensing, deep learning, and attention mechanisms for yield prediction in plant breeding experiments

In both plant breeding and crop management, interpretability plays a crucial role in instilling trust in AI-driven approaches and enabling the provision of actionable insights. The primary objective of this research is to explore and evaluate the potential contributions of deep learning network architectures that employ stacked LSTM for end-of-season maize grain yield prediction. A secondary aim is to expand the capabilities of these networks by adapting them to better accommodate and leverage the multi-modality properties of remote sensing data. In this study, a multi-modal deep learning architecture that assimilates inputs from heterogeneous data streams, including high-resolution hyperspectral imagery, LiDAR point clouds, and environmental data, is proposed to forecast maize crop yields. The architecture includes attention mechanisms that assign varying levels of importance to different modalities and temporal features that, reflect the dynamics of plant growth and environmental interactions. The interpretability of the attention weights is investigated in multi-modal networks that seek to both improve predictions and attribute crop yield outcomes to genetic and environmental variables. This approach also contributes to increased interpretability of the model's predictions. The temporal attention weight distributions highlighted relevant factors and critical growth stages that contribute to the predictions. The results of this study affirm that the attention weights are consistent with recognized biological growth stages, thereby substantiating the network's capability to learn biologically interpretable features. Accuracies of the model's predictions of yield ranged from 0.82-0.93 R 2 ref in this genetics-focused study, further highlighting the potential of attention-based models. Further, this research facilitates understanding of how multi-modality remote sensing aligns with the physiological stages of maize. The proposed architecture shows promise in improving predictions and offering interpretable insights into the factors affecting maize crop yields, while demonstrating the impact of data collection by different modalities through the growing season. By identifying relevant factors and critical growth stages, the model's attention weights provide valuable information that can be used in both plant breeding and crop management. The consistency of attention weights with biological growth stages reinforces the potential of deep learning networks in agricultural applications, particularly in leveraging remote sensing data for yield prediction. To the best of our knowledge, this is the first study that investigates the use of hyperspectral and LiDAR UAV time series data for explaining/interpreting plant growth stages within deep learning networks and forecasting plot-level maize grain yield using late fusion modalities with attention mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A primer on artificial intelligence in plant digital phenomics: embarking on the data to insights journey

Artificial intelligence (AI) has emerged as a fundamental component of global agricultural research that is poised to impact on many aspects of plant science. In digital phenomics, AI is capable of learning intricate structure and patterns in large datasets. We provide a perspective and primer on AI applications to phenome research. We propose a novel human-centric explainable AI (X-AI) system architecture consisting of data architecture, technology infrastructure, and AI architecture design. We clarify the difference between post hoc models and 'interpretable by design' models. We include guidance for effectively using an interpretable by design model in phenomic analysis. We also provide directions to sources of tools and resources for making data analytics increasingly accessible. In conclusion, this primer is accompanied by an interactive online tutorial.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Interpretable Deep Learning for the Earth System with Fractal Nets

Focal Area 3: Explainable AI Our confidence in the projections made by Earth System Models (ESMs) depends on understanding them to be, in some important respects, faithful representations of the Earth system. Here we present an “explainable Artificial Intelligence (AI)” method that allows us to uncover the dynamical structure of the observed and modeled Earth system, discover hidden links across wide spatiotemporal scales, target model development efforts at poorly-represented dynamics, and optimize observed or modeled data collection to maximize predictive information. Science Challenge: Dynamical system science for the Earth system poses unique challenges given the large degree of internal climate variability. Thus, tools that help us understand how ESMs succeed and fail at representing these dynamics are crucial, particularly in relation to the observed system. Furthermore, the computational and memory constraints on ESM data output motivate in situ analysis of ESM dynamics, including automatic detection of dynamical shifts. Also, of key importance are procedures that leverage ESMs to optimize observational campaigns for improving process representation, reducing structural uncertainty and improving model skill.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Artificial intelligence to unlock real-world evidence in clinical oncology: A primer on recent advances

Purpose: Real world evidence is crucial to understanding the diffusion of new oncologic therapies, monitoring cancer outcomes, and detecting unexpected toxicities. In practice, real world evidence is challenging to collect rapidly and comprehensively, often requiring expensive and time-consuming manual case-finding and annotation of clinical text. In this Review, we summarise recent developments in the use of artificial intelligence to collect and analyze real world evidence in oncology. Methods: We performed a narrative review of the major current trends and recent literature in artificial intelligence applications in oncology. Results: Artificial intelligence (AI) approaches are increasingly used to efficiently phenotype patients and tumors at large scale. These tools also may provide novel biological insights and improve risk prediction through multimodal integration of radiographic, pathological, and genomic datasets. Custom language processing pipelines and large language models hold great promise for clinical prediction and phenotyping. Conclusions: Despite rapid advances, continued progress in computation, generalizability, interpretability, and reliability as well as prospective validation are needed to integrate AI approaches into routine clinical care and real-time monitoring of novel therapies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

FAIR AI models in high energy physics

Abstract The findable, accessible, interoperable, and reusable (FAIR) data principles provide a framework for examining, evaluating, and improving how data is shared to facilitate scientific discovery. Generalizing these principles to research software and other digital products is an active area of research. Machine learning models—algorithms that have been trained on data without being explicitly programmed—and more generally, artificial intelligence (AI) models, are an important target for this because of the ever-increasing pace with which AI is transforming scientific domains, such as experimental high energy physics (HEP). In this paper, we propose a practical definition of FAIR principles for AI models in HEP and describe a template for the application of these principles. We demonstrate the template’s use with an example AI model applied to HEP, in which a graph neural network is used to identify Higgs bosons decaying to two bottom quarks. We report on the robustness of this FAIR AI model, its portability across hardware architectures and software frameworks, and its interpretability.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Vision Foundation Models in Remote Sensing: A survey

Artificial intelligence (AI) technologies have profoundly transformed the field of remote sensing (RS), revolutionizing data collection, processing, and analysis. Traditionally reliant on manual interpretation and task-specific models, RS research has been significantly enhanced by the advent of foundation models (FMs)—large-scale pretrained AI models capable of performing a wide array of tasks with unprecedented accuracy and efficiency. This article provides a comprehensive survey of FMs in the RS domain. We categorize these models based on their architectures, pretraining datasets, and methodologies. Through detailed performance comparisons, we highlight emerging trends and the significant advancements achieved by those FMs. Additionally, we discuss technical challenges, practical implications, and future research directions, addressing the need for high-quality data, computational resources, and improved model generalization. Our research also finds that pretraining methods, particularly self-supervised learning (SSL) techniques like contrastive learning (CL) and masked autoencoders (MAEs), remarkably enhance the performance and robustness of FMs. This survey aims to serve as a resource for researchers and practitioners by providing a panorama of advances and promising pathways for the continued development and application of FMs in RS.

data models↗

DOE OSTI2025

Synthetic Scientific Image Generation with VAE, GAN, and Diffusion Model Architectures

Generative AI (genAI) has emerged as a powerful tool for synthesizing diverse and complex image data, offering new possibilities for scientific imaging applications. This review presents a comprehensive comparative analysis of leading generative architectures, ranging from Variational Autoencoders (VAEs) to Generative Adversarial Networks (GANs) on through to Diffusion Models, in the context of scientific image synthesis. We examine each model's foundational principles, recent architectural advancements, and practical trade-offs. Our evaluation, conducted on domain-specific datasets including microCT scans of rocks and composite fibers, as well as high-resolution images of plant roots, integrates both quantitative metrics (SSIM, LPIPS, FID, CLIPScore) and expert-driven qualitative assessments. Results show that GANs, particularly StyleGAN, produce images with high perceptual quality and structural coherence. Diffusion-based models for inpainting and image variation, such as DALL-E 2, delivered high realism and semantic alignment but generally struggled in balancing visual fidelity with scientific accuracy. Importantly, our findings reveal limitations of standard quantitative metrics in capturing scientific relevance, underscoring the need for domain-expert validation. We conclude by discussing key challenges such as model interpretability, computational cost, and verification protocols, and discuss future directions where generative AI can drive innovation in data augmentation, simulation, and hypothesis generation in scientific research.

Generative Adversarial Networks↗

DOE OSTI2023

Explainable AI (XAI)-driven vibration sensing scheme for surface quality monitoring in a smart surface grinding process

Local Interpretable and Model-agnostic Explanation (LIME), an explainable artificial intelligence (XAI) approach is adapted to identify the globally important time-frequency bands for predicting average surface roughness (Ra) in a smart grinding process. The smart grinding setup consisted of a Supertech CNC precision surface grinding machine, instrumented with a Dytran piezoelectric accelerometer attached to the tailstock quill along the tangential direction (Y-axis). For every grinding pass, vibration signatures were captured, and the ground truth surface roughness values were recorded using a Mahr Marsurf M300C portable surface roughness profilometer. The roughness values ranged from 0.06 to 0.14 microns over the complete set of experiments. Time-frequency domain spectrogram frames were extracted for each of the vibration signals collected during the grinding process. Convolutional Neural Networks (CNNs) were modeled to predict the surface roughness based on these spectrogram frames and their image augmentations. The best CNN model was able to predict the roughness values with an overall R2-score of 0.95, training R2-score of 0.99, and testing R2-score of 0.81 with only 80 sets of vibration signals corresponding to 4 experiments with 20 trials each. Although the data size is not large enough to guarantee such performance metrics in real-world scenarios, one can extract statistically consistent explanations underlying the relationships these complex deep learning models capture. Further, the LIME methodology was implemented on the developed surface roughness CNN model to identify the important time-frequency bands (i.e., the superpixels of a spectrogram) influencing the predictions. Based on the identified important regions on the spectrogram frames, the corresponding frequency characteristics were determined that influence the surface roughness predictions. The important frequency range based on LIME results was approximately 11.7 to 19.1 kHz. The power of XAI was demonstrated by cutting down the sampling rate from 160 kHz to 30, 20, 10, and 5 kHz based on the important frequency range and considering Nyquist criteria. Separate CNN models were developed for these ranges by only extracting time-frequency contents below their corresponding Nyquist cut-offs. A proper data acquisition strategy is proposed by comparing the model performances to argue the selection of a sufficient sampling rate to capture the grinding process successfully and robustly.

42 ENGINEERING↗

DOE OSTI2023

Reprint of: Explainable AI (XAI)-driven vibration sensing scheme for surface quality monitoring in a smart surface grinding process

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Generative AI in Supply Chain Management: Applications, Challenges, and Future Directions

Supply chain management (SCM) is undergoing rapid transformation due to increasing global complexity, demand volatility, and operational disruptions. Generative Artificial Intelligence (GenAI) has emerged as a powerful paradigm capable of synthesizing data, simulating operational scenarios, and enabling adaptive decision-making across supply chain networks. This paper presents a survey of GenAI’s role in SCM, focusing on its applications in predictive analytics, autonomous logistics, and fraud detection. Unlike traditional AI systems that rely primarily on predictive analytics, GenAI models, including large language models, generative adversarial networks, and diffusion-based architectures, enable the creation of synthetic supply chain scenarios and autonomous optimization strategies. This survey provides (1) a taxonomy of GenAI techniques for supply chain applications, (2) a comparative analysis of generative AI approaches with traditional machine learning, reinforcement learning, and blockchain-based methods, and (3) a discussion of key challenges such as data privacy, interpretability, and integration with legacy enterprise systems. Furthermore, we outline open research problems and propose directions for future research toward autonomous, resilient, and sustainable AI-driven supply chains.

15 - GEOTHERMAL ENERGY↗

DOE OSTI2025

Computer Vision Pipeline for Image Analysis for Freeze‐Fracture Electron Microscopy: Rosette Cellulose Synthase Complexes Case

In materials science, plant biology, agriculture, and environmental research, the automated analysis of high-magnification, complex microscopy images, such as those generated by freeze-fracture electron microscopy (FF-TEM), remains a critical challenge that limits the scalability of data interpretation. We present a deep learning computer vision pipeline for high-throughput detection and morphological characterization analysis of cellulose synthase complexes (CSCs, or rosettes) in FF-TEM images. The pipeline integrates preprocessing, detection, human-in-the-loop verification, and semantic segmentation to quantify features such as rosette diameter and inter-lobe spacing. The approach was trained and tested on a curated dataset of high-resolution FF-TEM micrographs of Physcomitrium patens, expanded via strategic tiling and augmentation to over 650 images. We compare YOLOv8 and YOLOv9 architectures and demonstrate that YOLOv9 achieves superior performance in both localization accuracy (mAP50-95 = 0.854) and inference speed. The resulting distributions revealed biological variability consistent with prior manual studies, validating the approach for high-throughput applications. Our results show that the pipeline achieves human-expert level accuracy while dramatically reducing analysis time, enabling scalable, reproducible structural characterization of intramembrane protein complexes. The pipeline is broadly applicable to other domains requiring precise interpretation of complex microscopy data and establishes a foundation for future artificial intelligence (AI)-assisted workflows in biological imaging.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Benchmarking universal machine learning interatomic potentials for rapid analysis of inelastic neutron scattering data

The accurate calculation of phonons and vibrational spectra remains a significant challenge, requiring highly precise evaluations of interatomic forces. Traditional methods based on the quantum description of the electronic structure, while widely used, are computationally expensive and demand substantial expertise. Emerging universal machine learning interatomic potentials (uMLIPs) offer a transformative alternative by employing pre-trained neural network surrogates to predict interatomic forces directly from atomic coordinates. This approach dramatically reduces computation time and minimizes the need for technical knowledge. In this paper, we produce a phonon database comprising nearly 5000 inorganic crystals to benchmark the performance of several leading uMLIPs. We further assess these models in real-world applications by using them to analyze experimental inelastic neutron scattering data collected on a variety of materials. Through detailed comparisons, we identify the strengths and limitations of these uMLIPs, providing insights into their accuracy and suitability for fast calculations of phonons and related properties, as well as the potential for real-time interpretation of neutron scattering spectra. Our findings highlight how the rapid advancement of AI in science is revolutionizing experimental research and data analysis.

inelastic neutron scattering↗