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DOE OSTI2025

Reward Driven Workflows for Unsupervised Explainable Analysis of Phases and Ferroic Variants From Atomically Resolved Imaging Data

Rapid progress in aberration corrected electron microscopy necessitates development of robust methods for the identification of phases, ferroic variants, and other pertinent aspects of materials structure from imaging data. While unsupervised methods for clustering and classification are widely used for these tasks, their performance can be sensitive to hyperparameter selection in the analysis workflow. In this study, the effects of descriptors and hyperparameters are explored on the capability of unsupervised ML methods to distill local structural information, exemplified by the discovery of polarization and lattice distortion in Sm − dopped BiFeO 3 (BFO) thin films. It is demonstrated that a reward-driven approach can be used to optimize these key hyperparameters across the full workflow, where rewards are designed to reflect domain wall continuity and straightness, ensuring that the analysis aligns with the material's physical behavior. This approach allows the discovery of local descriptors that are best aligned with the specific physical behavior, providing insight into the fundamental physics of materials. The reward driven workflow is further extended to disentangle structural factors of variation via an optimized variational autoencoder (VAE). Lastly, the importance of well-defined rewards is explored as a quantifiable measure of the success of the workflow.

Barakati, Kamyar [University of Tennessee, Knoxvil↗

DOE OSTI2024

Leveraging generative AI for urban digital twins: a scoping review on the autonomous generation of urban data, scenarios, designs, and 3D city models for smart city advancement

The digital transformation of modern cities by integrating advanced information, communication, and computing technologies has marked the epoch of data-driven smart city applications for efficient and sustainable urban management. Despite their effectiveness, these applications often rely on massive amounts of high-dimensional and multi-domain data for monitoring and characterizing different urban sub-systems, presenting challenges in application areas that are limited by data quality and availability, as well as costly efforts for generating urban scenarios and design alternatives. As an emerging research area in deep learning, Generative Artificial Intelligence (GenAI) models have demonstrated their unique values in content generation. This paper aims to explore the innovative integration of GenAI techniques and urban digital twins to address challenges in the planning and management of built environments with focuses on various urban sub-systems, such as transportation, energy, water, and building and infrastructure. The survey starts with the introduction of cutting-edge generative AI models, such as the Generative Adversarial Networks (GAN), Variational Autoencoders (VAEs), Generative Pre-trained Transformer (GPT), followed by a scoping review of the existing urban science applications that leverage the intelligent and autonomous capability of these techniques to facilitate the research, operations, and management of critical urban subsystems, as well as the holistic planning and design of the built environment. Based on the review, we discuss potential opportunities and technical strategies that integrate GenAI models into the next-generation urban digital twins for more intelligent, scalable, and automated smart city development and management.

3D city modeling↗

DOE OSTI2026

Decoding the proton’s gluonic density with lattice QCD-informed machine learning

We present a first machine learning-based decoding of the gluonic structure of the proton from lattice QCD using a variational autoencoder inverse mapper (VAIM). Harnessing the power of generative AI, we predict the parton distribution function (PDF) of the gluon given information on the reduced pseudo-Ioffe-time distributions (RpITDs) as calculated from an ensemble with lattice spacing a ≈ 0.09 fm and a pion mass of M π ≈ 310 MeV. The resulting gluon PDF is consistent with phenomenological global fits within uncertainties, particularly in the intermediate-to-high-x region where lattice data are most constraining. A subsequent correlation analysis confirms that the VAIM learns a meaningful latent representation, highlighting the potential of generative AI to bridge lattice QCD and phenomenological extractions within a unified analysis framework.

Gluon parton distribution function↗

DOE OSTI2025

Reduced Order Modeling conditioned on monitored features for response and error bounds estimation in engineered systems

Reduced Order Models (ROMs) form essential tools across engineering domains by virtue of their function as surrogates for computationally intensive digital twinning simulators. Although purely data-driven methods are available for ROM construction, schemes that allow to retain a portion of the physics tend to enhance the interpretability and generalization of ROMs. However, physics-based techniques can adversely scale when dealing with nonlinear systems that feature parametric dependencies. This study introduces a generative physics-based ROM that is suited for nonlinear systems with parametric dependencies and is additionally able to provide numerical error bounds associated with the respective estimates. A main contribution of this work is the conditioning of these parametric ROMs to features that can be derived from monitoring measurements, feasibly in an online fashion. This is contrary to most existing ROM schemes, which remain restricted to the prescription of the physics-based, and usually a priori unknown, system parameters. Our work utilizes conditional Variational Autoencoders to continuously map the required reduction bases to a feature vector extracted from limited output measurements, while additionally allowing for a probabilistic assessment of the ROM-estimated Quantities of Interest. An auxiliary task using a neural network-based parametrization of suitable probability distributions is introduced to re-establish the link with physical model parameters. We verify the proposed scheme on a series of simulated case studies incorporating effects of geometric and material nonlinearity under parametric dependencies related to system properties and input load characteristics.

Conditional VAEs↗

DOE OSTI2024

CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation

Molecular conformer generation (MCG) is an important task in cheminformatics and drug discovery. The ability to efficiently generate low-energy 3D structures can avoid expensive quantum mechanical simulations, leading to accelerated virtual screenings and enhanced structural exploration. Several generative models have been developed for MCG, but many struggle to consistently produce high-quality conformers for meaningful downstream applications. To address these issues, we introduce CoarsenConf, which coarse-grains molecular graphs based on torsional angles and integrates them into an SE(3)-equivariant hierarchical variational autoencoder. Through equivariant coarse-graining, we aggregate the fine-grained atomic coordinates of subgraphs connected via rotatable bonds, creating a variable-length coarse-grained latent representation. Our model uses a novel aggregated attention mechanism to restore fine-grained coordinates from the coarse-grained latent representation, enabling efficient generation of accurate conformers. Furthermore, we evaluate the chemical and biochemical quality of our generated conformers on multiple downstream applications, including property prediction and large-scale oracle-based protein docking. Overall, CoarsenConf generates more accurate conformer ensembles compared to prior generative models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Deciphering the Scattering of Mechanically Driven Polymers Using Deep Learning

Here, we present a deep learning approach for analyzing two-dimensional scattering data of semiflexible polymers under external forces. In our framework, scattering functions are compressed into a three-dimensional latent space using a Variational Autoencoder (VAE), and two converter networks establish a bidirectional mapping between the polymer parameters (bending modulus, stretching force, and steady shear) and the scattering functions. The training data are generated using off-lattice Monte Carlo simulations to avoid the orientational bias inherent in lattice models, ensuring robust sampling of polymer conformations. The feasibility of this bidirectional mapping is demonstrated by the organized distribution of polymer parameters in the latent space. By integrating the converter networks with the VAE, we obtain a generator that produces scattering functions from given polymer parameters and an inferrer that directly extracts polymer parameters from scattering data. While the generator can be utilized in a traditional least-squares fitting procedure, the inferrer produces comparable results in a single pass and operates 3 orders of magnitude faster. This approach offers a scalable automated tool for polymer scattering analysis and provides a promising foundation for extending the method to other scattering models, experimental validation, and the study of time-dependent scattering data.

Ding, Lijie [Oak Ridge National Laboratory (ORNL),↗

DOE OSTI2026

Accelerating Structure–Property Relationship Discovery with Multimodal Machine Learning and Self-Driving Microscopy

Microscopy combined with local spectroscopy is widely used to correlate nanoscale structure with functional properties in materials, but conventional measurements rely heavily on human-selected sampling locations and predefined targets, limiting data set diversity and the potential for discovery. Here, we present a framework that integrates autonomous microscopy with dual-novelty deep kernel learning (DN-DKL) for adaptive data acquisition and a dual variational autoencoder (VAE) for representation learning. DN-DKL actively guides the microscopy toward structurally and spectroscopically novel regions, enabling efficient collection of large spectral data sets. Dual-VAE embeds local structures and spectroscopic responses into a shared latent manifold that serves as a structure–property relationship map. We applied this framework for the investigation of halide perovskite films by using conductive atomic force microscopy. The results reveal distinct hysteresis behaviors that are linked to specific nanoscale structural motifs, including grain boundary junction points that show hysteresis under different bias conditions and asymmetric grain boundaries that suppress the charge transport. This framework establishes a general strategy that leverages the complementary strengths of self-driving microscopy, machine learning, and human expertise to accelerate scientific discovery in functional materials.

atomic force microscopy↗

DOE OSTI2025

Emulation With Uncertainty Quantification of Regional Sea‐Level Change Caused by the Antarctic Ice Sheet

Abstract Projecting regional sea‐level change under various climate‐change scenarios typically involves running forward simulations of the Earth's gravitational, rotational and deformational (GRD) response to ice‐mass change, which requires substantial computational cost if applied to probabilistic frameworks requiring thousands to millions of samples. Here we build emulators of regional sea‐level change at 27 coastal locations, due to the GRD effects associated with future Antarctic Ice Sheet mass change over the 21st century. The emulators are evaluated against a numerical sea‐level model applied to an ensemble of ice‐sheet model simulations of the Antarctic Ice Sheet through 2100. We build a physics‐based emulator using a recent sensitivity kernel approach and compare it to machine learning based emulators (neural network and conditional variational autoencoder methods). In order to quantify uncertainty, we derive well‐calibrated prediction intervals for regional sea‐level change via split‐conformal inference and linear regression, and show that Monte Carlo dropout does not yield well‐calibrated uncertainties in this instance. We also demonstrate substantial gains in computational efficiency using both the physics‐based emulator and neural networks in comparison to the numerical model for the complete regional sea‐level solution. Overall, we find the physics‐based emulator modestly outperforms the machine learning emulators for this problem.

58 GEOSCIENCES↗

DOE OSTI2026

Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy

T cell states are prognostic in different cancer types. Recent technologies enable joint profiling of T cell RNA and T cell receptor (TCR) sequences at single-cell resolution. Here we present the TCR-RNA Integrating Model (TRIM), a multi-modal variational autoencoder framework that integrates RNA-TCR data and predicts T cell clonality and transcriptional states. TRIM learns a shared representation of the data conditioned on patient, tissue source, and treatment timepoint. We applied TRIM to three independent datasets that included T cells collected before and after checkpoint inhibitor treatment, sourced either from blood and tumor biopsies in patients with head and neck squamous cell carcinoma and colorectal cancer, or from tumor and adjacent tissue in a pan-cancer dataset. In all settings, TRIM accurately predicted intra-tumor T cell clonal expansion and transcriptional status based on T cells from blood or normal tissue before treatment, demonstrating its utility in modeling multimodal T cell data and predicting T cell response to treatment and disease progression.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Inverse mapping of properties to composition through generative modeling for designing molten salts

Generative modeling (GM) has been increasingly used for the inverse design and optimization of materials, yet its application to molten salt mixtures remains unexplored despite how a successful approach to the inverse design of molten salts would contribute to efficiently exploiting their customizability and unlocking their advantages in applications, such as energy production and energy storage. This work presents a workflow for the inverse design of molten salts with targeted density values, addressing the challenge of representing these complex mixtures in GM. A dataset of critically evaluated molten salt densities is used to train a variational autoencoder coupled with a predictive deep neural network, which then can be used to generate new molten salt compositions with desired density values. The effectiveness of the approach is demonstrated by designing mixtures with distinct densities and validating the predicted values using ab initio molecular dynamics simulations.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

Conditioned quantum-assisted deep generative surrogate for particle-calorimeter interactions

Particle collisions at accelerators like the Large Hadron Collider (LHC), recorded by experiments such as ATLAS and CMS, enable precise standard model measurements and searches for new phenomena. Simulating these collisions significantly influences experiment design and analysis but incurs immense computational costs, projected at millions of CPU-years annually during the high luminosity LHC (HL-LHC) phase. Currently, simulating a single event with Geant4 consumes around 1000 CPU seconds, with calorimeter simulations especially demanding. To address this, we propose a conditioned quantum-assisted generative model, integrating a conditioned variational autoencoder (VAE) and a conditioned restricted Boltzmann machine (RBM). Our RBM architecture is tailored for D-Wave’s Pegasus-structured advantage quantum annealer for sampling, leveraging the flux bias for conditioning. This approach combines classical RBMs as universal approximators for discrete distributions with quantum annealing’s speed and scalability. We also introduce an adaptive method for efficiently estimating effective inverse temperature, and validate our framework on Dataset 2 of CaloChallenge.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Co-orchestration of multiple instruments to uncover structure–property relationships in combinatorial libraries

The rapid growth of automated and autonomous instrumentation brings forth opportunities for the co-orchestration of multimodal tools that are equipped with multiple sequential detection methods or several characterization techniques to explore identical samples. This is exemplified by combinatorial libraries that can be explored in multiple locations via multiple tools simultaneously or downstream characterization in automated synthesis systems. In co-orchestration approaches, information gained in one modality should accelerate the discovery of other modalities. Correspondingly, an orchestrating agent should select the measurement modality based on the anticipated knowledge gain and measurement cost. Herein, we propose and implement a co-orchestration approach for conducting measurements with complex observables, such as spectra or images. The method relies on combining dimensionality reduction by variational autoencoders with representation learning for control over the latent space structure and integration into an iterative workflow via multi-task Gaussian Processes (GPs). This approach further allows for the native incorporation of the system's physics via a probabilistic model as a mean function of the GPs. We illustrate this method for different modes of piezoresponse force microscopy and micro-Raman spectroscopy on a combinatorial Sm-BiFeO3 library. However, the proposed framework is general and can be extended to multiple measurement modalities and arbitrary dimensionality of the measured signals.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Generative AI for design of nanoporous materials: review and future prospects

Generative artificial intelligence (AI) is emerging as a powerful tool for advancing the design of nanoporous materials such as metal–organic frameworks, covalent–organic frameworks, and zeolites. These materials have potential application in important areas such as carbon capture, catalysis, gas storage, chemical separation, and drug delivery due to their modular, tunable structures, and their performance in these areas depends on precise control over their structure, chemical functionalities, and properties. Herein, we provide a review of generative AI algorithms that are emerging as powerful tools for the design of nanoporous materials, namely generative adversarial networks, variational autoencoders, diffusion models, genetic algorithms, reinforcement learning, and large language models. Some models are particularly good at generating diverse and high-quality designs, while others excel at exploring large design spaces or optimizing materials with desired properties. Certain algorithms also allow for efficient transitions between different designs, and some offer versatility in generating materials based on textual input. We discuss the advantages, limitations, and applications of these algorithms in porous material design and emphasize the future potential of integrating AI with experimental workflows to accelerate the development and validation of AI-generated materials.

36 MATERIALS SCIENCE↗

DOE OSTI2025

CaloChallenge 2022: a community challenge for fast calorimeter simulation

Here, we present the results of the ‘Fast Calorimeter Simulation Challenge 2022’—the CaloChallenge. We study state-of-the-art generative models on four calorimeter shower datasets of increasing dimensionality, ranging from a few hundred voxels to a few tens of thousand voxels. The 31 individual submissions span a wide range of current popular generative architectures, including variational autoencoders (VAEs), generative adversarial networks (GANs), normalizing flows, diffusion models, and models based on conditional flow matching. We compare all submissions in terms of quality of generated calorimeter showers, as well as shower generation time and model size. To assess the quality we use a broad range of different metrics including differences in one-dimensional histograms of observables, KPD/FPD scores, AUCs of binary classifiers, and the log-posterior of a multiclass classifier. The results of the CaloChallenge provide the most complete and comprehensive survey of cutting-edge approaches to calorimeter fast simulation to date. In addition, our work provides a uniquely detailed perspective on the important problem of how to evaluate generative models. As such, the results presented here should be applicable for other domains that use generative AI and require fast and faithful generation of samples in a large phase space.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Masked Particle Modeling on Sets: Towards Self-Supervised High Energy Physics Foundation Models

Abstract We propose masked particle modeling (MPM) as a self-supervised method for learning generic, transferable, and reusable representations on unordered sets of inputs for use in high energy physics (HEP) scientific data. This work provides a novel scheme to perform masked modeling based pre-training to learn permutation invariant functions on sets. More generally, this work provides a step towards building large foundation models for HEP that can be generically pre-trained with self-supervised learning and later fine-tuned for a variety of down-stream tasks. In MPM, particles in a set are masked and the training objective is to recover their identity, as defined by a discretized token representation of a pre-trained vector quantized variational autoencoder. We study the efficacy of the method in samples of high energy jets at collider physics experiments, including studies on the impact of discretization, permutation invariance, and ordering. We also study the fine-tuning capability of the model, showing that it can be adapted to tasks such as supervised and weakly supervised jet classification, and that the model can transfer efficiently with small fine-tuning data sets to new classes and new data domains.

Heinrich, Lukas (ORCID:0000000240487584)↗

DOE OSTI2026

Crystal generation using the fully differentiable pipeline and latent space optimization

We present a materials generation framework that couples a symmetry-conditioned variational autoencoder with a differentiable SO(3) power spectrum objective to steer candidates toward a specified local environment under the crystallographic constraints. In particular, we implement a fully differentiable pipeline that performs batch-wise optimization on both direct and latent crystallographic representations. Using the GPU acceleration, the implementation achieves about fivefold speed compared to our previous CPU workflow, while yielding comparable outcomes. In addition, we introduce the optimization strategy that alternatively performs optimization on the direct and latent crystal representations. This dual-level relaxation approach can effectively escape local minima defined by different objective gradients, thus increasing the success rate of generating complex structures satisfying the target local environments. This framework can be extended to systems consisting of multi-components and multi-environments, providing a scalable route to generate material structures with the target local environment.

conditional VAE↗

DOE OSTI2025

Learning nuclear cross sections across the chart of nuclides with graph neural networks

We explore the use of deep learning techniques to learn how nuclear cross sections change as we add or remove protons and neutrons. As a proof of principle, we focus on the neutron-induced reactions in the fast energy regime. Our approach follows a two-stage learning framework. First, we apply representation learning to encode cross section data into a latent space using either variational autoencoders (VAEs) or implicit neural representations (INRs). Then, we train graph neural networks (GNNs) on the resulting embeddings to predict missing values across the nuclear chart by leveraging the topological structure of neighboring isotopes. We demonstrate accurate cross section predictions within a 9 × 9 block of missing nuclei. We also find that the optimal GNN training strategy depends on the type of latent representation used, with VAE embeddings performing best under end-to-end optimization in the original space, while INR embeddings achieve better results when the GNN is trained only in the latent space. Furthermore, using clustering algorithms, we map groups of latent vectors into regions of the nuclear chart and show that VAEs and INRs can discover some of the neutron magic numbers. These findings suggest that deep-learning models based on the representation encoding of cross sections combined with graph neural networks hold significant potential in augmenting nuclear theory models, e.g., by providing reliable estimates of covariances of cross sections, including cross-material covariances.

Machine learning↗

DOE OSTI2024

Effectiveness of denoising diffusion probabilistic models for fast and high-fidelity whole-event simulation in high-energy heavy-ion experiments

Artificial intelligence (AI) generative models, such as generative adversarial networks (GANs), variational autoencoders, and normalizing flows, have been widely used and studied as efficient alternatives for traditional scientific simulations. However, they have several drawbacks, including training instability and inability to cover the entire data distribution, especially for regions where data are rare. This is particularly challenging for whole-event, full-detector simulations in high-energy heavy-ion experiments, such as sPHENIX at the Relativistic Heavy Ion Collider and Large Hadron Collider experiments, where thousands of particles are produced per event and interact with the detector. This work investigates the effectiveness of denoising diffusion probabilistic models (DDPMs) as an AI-based generative surrogate model for the sPHENIX experiment that includes the heavy-ion event generation and response of the entire calorimeter stack. DDPM performance in sPHENIX simulation data is compared with a popular rival, GANs. Results show that both DDPMs and GANs can reproduce the data distribution where the examples are abundant (low-to-medium calorimeter energies). Nonetheless, DDPMs significantly outperform GANs, especially in high-energy regions where data are rare. Additionally, DDPMs exhibit superior stability compared to GANs. The results are consistent between both central and peripheral centrality heavy-ion collision events. Moreover, DDPMs offer a substantial speedup of approximately a factor of 100 compared to the traditional Geant4 simulation method.

42 ENGINEERING↗