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At least 145 records · Page 8

Hypothesis testing via AI: Generating physically interpretable models of scientific data with machine learning (Full Technical Report)

Deep learning has demonstrated an exceptional ability to solve complex tasks (an engineering success); however, it has done so at the expense of the ability to generate new knowledge (a scientific failure). We propose an alternative framework—entitled Deep Symbolic Regression (DSR)—in which artificial neural networks (NNs) rapidly generate hypotheses about physical relationships among inputs. This framework bypasses the need to interpret an NN altogether, while still leveraging the representational power of deep learning. The resulting models are tractable mathematical expressions, which are inherently and readily human interpretable and can provide insights into underlying physical phenomena. Further, we fold this methodology into the scientific process by allowing the scientist to directly integrate a priori knowledge and beliefs to accelerate learning. We demonstrate this methodology on symbolic regression—the problem of rediscovering underlying expressions describing a dataset—and achieve state-of-the-art performance across a wide variety of symbolic regression problems. Further, we generalize our DSR framework to apply to the more general class of symbolic optimization problems, in which one seeks to optimize a sequence of symbols or “tokens” under a black-box reward function. Examples of other symbolic optimization problems include neural architecture search and computational antibody design. Our generalized tool, Deep Symbolic Optimization (DSO), has been demonstrated on the task of learning symbolic control policies for reinforcement learning environments, and has been adopted as an enabling capability for computational antibody design.

97 MATHEMATICS AND COMPUTING↗

Machine Learned Hückel Theory: Interfacing Physics and Deep Neural Networks

The Hückel Hamiltonian is an incredibly simple tight-binding model known for its ability to capture qualitative physics phenomena arising from electron interactions in molecules and materials. Part of its simplicity arises from using only two types of empirically fit physics-motivated parameters: the first describes the orbital energies on each atom and the second describes electronic interactions and bonding between atoms. By replacing these empirical parameters with machine-learned dynamic values, we vastly increase the accuracy of the extended Hückel model. The dynamic values are generated with a deep neural network, which is trained to reproduce orbital energies and densities derived from density functional theory. The resulting model retains interpretability, while the deep neural network parameterization is smooth and accurate and reproduces insightful features of the original empirical parameterization. Altogether, this work shows the promise of utilizing machine learning to formulate simple, accurate, and dynamically parameterized physics models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Learning generative neural networks with physics knowledge

Deep generative neural networks have enabled modeling complex distributions, but incorporating physics knowledge into the neural networks is still challenging and is at the core of current physics-based machine learning research. To this end, we propose a physics generative neural network (PhysGNN), a new class of generative neural networks for learning unknown distributions in a physical system described by partial differential equations (PDE). PhysGNN couples PDE systems with generative neural networks. It is a fully differentiable model that allows back-propagation of gradients through both numerical PDE solvers and generative neural networks, and is trained by minimizing the discrete Wasserstein distance between generated and observed probability distributions of the PDE outputs using the stochastic gradient descent method. Moreover, PhysGNN does not require adversarial training like standard generative neural networks, which offers better stability than adversarial training. We show that PhysGNN can learn complex distributions in stochastic inverse problems, where conventional methods such as maximum likelihood estimation and momentum matching methods may be inapplicable when little knowledge is known about the form of unknown distributions or the physical model is too complex. Furthermore, our method allows physics-based generative neural network training for learning complex distributions in the context of differential equations.

97 MATHEMATICS AND COMPUTING↗

An open database of computed bulk ternary transition metal dichalcogenides

Abstract We present a dataset of structural relaxations of bulk ternary transition metal dichalcogenides (TMDs) computed via plane-wave density functional theory (DFT). We examined combinations of up to two chalcogenides with seven transition metals from groups 4–6 in octahedral (1T) or trigonal prismatic (2H) coordination. The full dataset consists of 672 unique stoichiometries, with a total of 50,337 individual configurations generated during structural relaxation. Our motivations for building this dataset are (1) to develop a training set for the generation of machine and deep learning models and (2) to obtain structural minima over a range of stoichiometries to support future electronic analyses. We provide the dataset as individual VASP xml files as well as all configurations encountered during relaxations collated into an ASE database with the corresponding total energy and atomic forces. In this report, we discuss the dataset in more detail and highlight interesting structural and electronic features of the relaxed structures.

36 MATERIALS SCIENCE↗

De novo design of small beta barrel proteins

Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy–based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.

59 BASIC BIOLOGICAL SCIENCES↗

Materials Characterization, Prediction and Control Project: Summary Report on Data Analytics Framework

This report summarizes the activities performed under the data analytics Vertex in the Materials Characterization, Prediction and Control Project funded under laboratory directed research and development at Pacific Northwest National Laboratory. The data analytics Vertex developed models for associating global or local process parameters, microstructural features, and performance properties of friction-stir-processed 316L stainless steel plates. Statistical, machine learning, and deep learning models, as well as generative artificial intelligence approaches, were used to develop the associations between the process-structure-property data streams. These associations formed the basis for predicting global properties of parts manufactured under different process envelopes, providing a basis for predicting performance using data driven as well as physics-informed and physics-constrained approaches. Additionally, the associations were used to predict local process parameters and microstructural features of the product, predictive relationships that have the potential to form the basis of a control framework that could eventually modulate a friction-stir process to maintain product quality.

316L stainless steel↗

LLMs for Mfg.—On the State of Large Language Models and Applications to Manufacturing

Additive Manufacturing (AM), referred to as 3D printing, has emerged as a key pillar of Industry 4.0 enabling layer-by-layer fabrication of intricate geometries from CAD models. In parallel, Large Language Models (LLMs), deep learning models for natural language generation trained on vast text corpora, have demonstrated unprecedented capabilities in understanding and generating human-like text. The convergence of these trends opens new opportunities at the intersection of AM and AI/ML, where LLMs can assist engineers and researchers in design, manufacture planning, and knowledge discovery. Recent academic work has begun to explore LLM applications in AM and adjacent fields, such as material science, mechanical engineering, and design for additive manufacturing. This exploration ranges from intelligent process planning to domain-specific knowledge retrieval. This survey provides a comprehensive review of current developments, focusing on peer-reviewed literature contributions that apply, adapt, and advance LLMs in general and domain-specific domains. We analyze state-of-the-art (SOTA) techniques, such as fine-tuning foundational models for specific domains, retrieval-augmented generation (RAG) pipelines, knowledge graph integration, and delve into the architectures and evaluation methods employed. The goal of this survey is to inform researchers and practitioners of the current capabilities and limitations of LLMs in general and in domain-specific applications, and to outline how these models are being tailored to meet the requirements of these applications.

36 MATERIALS SCIENCE↗

An Iterative Machine Learning Framework for Event Classification and Monte Carlo Tuning in SpinQuest

The E1039/SpinQuest experiment at Fermi National Accelerator Laboratory uses a 120~GeV proton beam from the Main Injector incident on transversely polarized proton and deuteron targets, using $NH_3$ and $ND_3$, respectively. In addition to measuring the Sivers asymmetry in Drell--Yan $pp$ and $pd$ scattering from sea quarks, SpinQuest will study transverse-spin effects, particularly the transverse single-spin asymmetry (TSSA) in $J/\psi$ production. The angular distributions from the $J/\psi$ decay could play an important role in understanding the gluon contribution to the proton spin structure. However, before extracting these angular distributions, it is necessary to isolate signal events originating from the target from events produced by other sources and from the combinatorial background. To effectively and accurately classify the target events, it is important to ensure that the simulated events are properly tuned to the experimental physics channels. We have introduced an iterative technique to match simulated and experimental events and to classify the physics channels using deep neural networks and a generative model based on normalizing flows.

Hossain, Forhad [Virginia U. (main)] (ORCID:000000↗

Transfer learning of neural surrogates on multifidelity groundwater simulations

Multifidelity data used in the paper published in Advances in Water Resources 206 (2025) 105140, https://doi.org/10.1016/j.advwatres.2025.105140 The code used to process the data is openly available on GitHub at https://github.com/Model-Reduction-and-UQ-Group/Transfer_Learning_K_reconstruction Computationally inexpensive surrogates of process-based models, such as deep neural networks, enable ensemble-based computations used in risk assessment, data assimilation, etc. However, generation of large datasets required to train a neural network can be as expensive as the ensemble simulations themselves. We ameliorate this challenge by using data from multifidelity (MF) groundwater simulations and transfer learning (TL) to reduce data generation costs while maintaining model accuracy. As a computational example, we train a deep convolutional neural network (CNN) to reconstruct permeability fields from saturation maps derived from a multiphase flow model. Starting with very low- and low-fidelity data generated on increasingly coarse meshes, we pretrain the CNN, followed by output-layer training and fine-tuning using only a limited number of high-fidelity samples. We demonstrate the surrogate’s robustness when interpreting low-quality inputs—such as interpolated maps or data affected by noise—which has strong implications for the applicability in practical hydrogeological scenarios. This multilevel MF-TL strategy achieves a favorable trade-off between computational efficiency and predictive accuracy, significantly outperforming high-fidelity-only approaches under the same computational budget.

Chiofalo, Alessia [University of Bologna] (ORCID:0↗

Time-lapse seismic data inversion for estimating reservoir parameters using deep learning

Geologic carbon sequestration involves the injection of captured carbon dioxide ([Formula: see text]) into subsurface formations for long-term storage. The movement and fate of the injected [Formula: see text] plume is of great concern to regulators because monitoring helps to identify potential leakage zones and determines the possibility of safe long-term storage. To address this concern, we design a deep-learning framework for [Formula: see text] saturation monitoring to determine the geologic controls on the storage of the injected [Formula: see text]. We use different combinations of porosities and permeabilities for a given reservoir to generate saturation and velocity models. We train the deep-learning model with a few time-lapse seismic images and their corresponding changes in saturation values for a particular [Formula: see text] injection site. The deep-learning model learns the mapping from the change in the time-lapse seismic response to the change in [Formula: see text] saturation during the training phase. We then apply the trained model to data sets comprising different time-lapse seismic image slices (corresponding to different time instances) generated using different porosity and permeability distributions that are not part of the training to estimate the [Formula: see text] saturation values along with the plume extent. Our algorithm provides a deep-learning assisted framework for the direct estimation of [Formula: see text] saturation values and plume migration in heterogeneous formations using the time-lapse seismic data. Our method improves the efficiency of time-lapse inversion by streamlining the large number of intermediate steps in the conventional time-lapse inversion workflow. This method also helps to incorporate the geologic uncertainty for a given reservoir by accounting for the statistical distribution of porosity and permeability during the training phase. Tests on different examples verify the effectiveness of our approach.

Geochemistry & Geophysics↗

TOUGH2-seed: A coupled fluid flow and mechanical-stochastic approach to model injection-induced seismicity

Understanding the injection-induced triggering mechanism is a fundamental step towards controlling the seismicity generated by deep underground exploitation. Here we propose a modeling approach based on coupling the TOUGH2 simulator with a geomechanical-stochastic model. Additionally, the hydro-mechanical-stochastic model provides a good representation of different mechanisms influencing each other during and after the injection phase. Each mechanism affects the induced seismicity in a different way and at different times during the reservoir stimulation, confirming that a complex interaction is in place, and that more sophisticated and physics-based approaches coupled with statistical model are required to explain such a complex interaction. In addition to previous statistical and hybrid models, our approach accounts for a full 3D formulation of both stresses and fluid flow, further including all the TOUGH2 capabilities. Furthermore, it includes interactions between triggered seismic events through calculation of static stress transfer. Here, in this work, we present the main capabilities of TOUGH2-SEED and apply the model to the Basel EGS case, successfully reproducing the injection pressure as well as the evolution of the seismicity.

58 GEOSCIENCES↗

Non-Blind Deblurring for Fluorescence: A Deformable Latent Space Approach with Kernel Parameterization

We report N\non-blind deblurring (NBD) is a modeling method of the image deblurring problem in computer vision, where the blurring kernel is known or can be externally estimated. In this paper, we attempt to solve a parametric NBD problem, inspired by the simultaneous acquisition of ptychography and fluorescent imaging (FI). Ptychography is an imaging method that favors larger probes, i.e. convolutional kernels, while FI relies on a small probe for high resolution. Also, the kernel can be solved during ptychographic reconstruction. With Ptycho-FI using the same larger kernel, we can perform NBD on the blurred fluorescent images to achieve high-resolution FI, and thus speed up the experiments. To this end, we design a deep latent space deformation network that is directly parameterized by the kernel. The network consists of three components: encoder, deformer, and decoder, where the deformer is specifically meant to rectify the latent space representations of blurred images to a standard latent space, regardless of the kernel. The deformation network is trained with a two-stage training scheme. We conduct extensive experiments to confirm that our parametric model can adapt to drastically different blurring kernels and perform robust deblurring.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

RockFlow: Fast Generation of Synthetic Source Rock Images Using Generative Flow Models

Image-based evaluation methods are a valuable tool for source rock characterization. The time and resources needed to obtain images has spurred development of machine-learning generative models to create synthetic images of pore structure and rock fabric from limited image data. While generative models have shown success, existing methods for generating 3D volumes from 2D training images are restricted to binary images and grayscale volume generation requires 3D training data. Shale characterization relies on 2D imaging techniques such as scanning electron microscopy (SEM), and grayscale values carry important information about porosity, kerogen content, and mineral composition of the shale. Here, we introduce RockFlow, a method based on generative flow models that creates grayscale volumes from 2D training data. We apply RockFlow to baseline binary micro-CT image volumes and compare performance to a previously proposed model. We also show the extension of our model to 2D grayscale data by generating grayscale image volumes from 2D SEM and dual modality nanoscale shale images. The results show that our method underestimates the porosity and surface area on the binary baseline datasets but is able to generate realistic grayscale image volumes for shales. With improved binary data preprocessing, we believe that our model is capable of generating synthetic porous media volumes for a very broad class of rocks from shale to carbonates to sandstone.

58 GEOSCIENCES↗

Predicting CO 2 Plume Migration in Heterogeneous Formations Using Conditional Deep Convolutional Generative Adversarial Network

Numerical simulation of flow and transport in heterogeneous formations has long been studied, especially for uncertainty quantification and risk assessment. The high computational cost associated with running large-scale numerical simulations in a Monte Carlo sense has motivated the development of surrogate models, which aim to capture the important input-output relations of physics-based models but require only a fraction of the cost of full model runs. In this work, we formulate a conditional deep convolutional generative adversarial network (cDC-GAN) surrogate model to learn the dynamic functional mappings in multiphase models. The cDC-GAN belongs to a class of semisupervised learning methods that can be used to learn the data generation processes. Like the original GAN, a main strength of the cDC-GAN is that it includes a self-training scheme for improving the quality of generative modeling in a game theoretic framework, without requiring extensive statistical knowledge and assumptions on input data distributions. In particular, our cDC-GAN model is designed to learn cross-domain mappings between high-dimensional input (e.g., permeability) and output (e.g., phase saturations) pairs, with the ability to incorporate conditioning information (e.g., prediction time). As a use case, we demonstrate the performance of cDC-GAN for predicting the migration of carbon dioxide (CO 2 ) plume in heterogeneous carbon storage reservoirs, which has both numerical and practical significance because of the safe storage requirements now mandated in many countries. Results show that cDC-GAN achieves high accuracy in predicting the spatial and temporal evolution patterns of the injected CO 2 plume, as compared to the original results obtained using a compositional reservoir simulator. The performance of cDC-GAN models, trained using the same number of training samples, stays relatively robust when the level of spatial heterogeneity is increased. Our cDC-GAN is pattern based and is not limited by the underlying physics. Thus, it provides a general framework for developing surrogate models, and for conducting uncertainty analyses for a wide range of physics-based models used in both groundwater and subsurface energy exploration applications.

54 ENVIRONMENTAL SCIENCES↗

Surfactant-Specific AI-Driven Molecular Design: Integrating Generative Models, Predictive Modeling, and Reinforcement Learning for Tailored Surfactant Synthesis

Molecular design is a critical aspect of various scientific and industrial fields, where the properties of molecules hold significant importance. In this study, a 3-fold methodology design is presented that leverages the power of generative artificial intelligence (AI), predictive modeling, and reinforcement learning to create tailored molecules with desired properties. This model synergistically combines deep learning techniques with Self-Referencing Embedded Strings (SELFIES) molecular representation to build a generative model that generates valid molecules and a graphical neural network model that accurately forecasts molecular properties. The Variational Autoencoder (VAE) coupled with reinforcement learning helps refine molecule generation based on targeted attributes. Data from an experimental study involving surfactants were used to test the framework. A validation of the structural integrity of the molecules generated was conducted, and Tanimoto similarities were used to quantify the similarity and diversity between the original and generated molecular structures. Also, saliency maps for the generated surfactants were produced to identify the features explaining the property values. Lastly, molecular dynamics simulations were used to validate the stability of the generated molecules. The results showed that the proposed framework can effectively produce valid molecules within the set property threshold value.

36 MATERIALS SCIENCE↗

Hybrid learning techniques for scientific data reduction with performance guarantees

The research initiatives supported by the U.S. Department of Energy (DOE) Grant DE-SC0022265 are fundamentally aimed at pioneering advanced machine learning (ML) techniques for scientific data compression within high-performance computing (HPC) environments. This comprehensive body of work addresses the critical challenge posed by the exponential growth of data generated by scientific simulations in domains such as fusion energy, climate modeling, and computational fluid dynamics (CFD). A core objective is to develop compression algorithms that achieve substantial data reduction—often by orders of magnitude—while rigorously ensuring the fidelity of both the primary data (PD) and scientifically crucial derived quantities of interest (QoI). The methodologies deployed under this grant integrate sophisticated deep learning architectures, prominently featuring autoencoders, advanced generative models like conditional diffusion, and hybrid learning techniques. Key innovations include the development of Guaranteed Autoencoders (GAE) and the Guaranteed Conditional Diffusion with Tensor Correction (GCDTC) framework, which provide explicit, instance-level error bounds on reconstructed data. Furthermore, specialized strategies such as nonlinear constraint satisfaction are employed to preserve the integrity of QoI, a vital requirement for the trustworthiness of downstream scientific analyses. This research also focuses on the design and implementation of scalable, GPU-accelerated software pipelines that seamlessly integrate into existing HPC workflows, ensuring both computational efficiency and practical applicability. The CAESAR framework, for example, unifies foundation and generative models to create an adaptive and efficient compression solution for spatio-temporal scientific data. Collectively, these efforts represent a significant advancement in mitigating the scientific data deluge, enabling more effective data management, accelerated scientific discovery, and optimized utilization of HPC resources.

97 MATHEMATICS AND COMPUTING↗

Final report- UFL - RAPIDS2: A SciDAC Institute for Computer Science, Data, and Artificial Intelligence

The research initiatives supported by the U.S. Department of Energy (DOE) Grant DE-SC0022265 are fundamentally aimed at pioneering advanced machine learning (ML) techniques for scientific data compression within high-performance computing (HPC) environments. This comprehensive body of work addresses the critical challenge posed by the exponential growth of data generated by scientific simulations in domains such as fusion energy, climate modeling, and computational fluid dynamics (CFD). A core objective is to develop compression algorithms that achieve substantial data reduction—often by orders of magnitude—while rigorously ensuring the fidelity of both the primary data (PD) and scientifically crucial derived quantities of interest (QoI). The methodologies deployed under this grant integrate sophisticated deep learning architectures, prominently featuring autoencoders, advanced generative models like conditional diffusion, and hybrid learning techniques. Key innovations include the development of Guaranteed Autoencoders (GAE) and the Guaranteed Conditional Diffusion with Tensor Correction (GCDTC) framework, which provide explicit, instance-level error bounds on reconstructed data. Furthermore, specialized strategies such as nonlinear constraint satisfaction are employed to preserve the integrity of QoI, a vital requirement for the trustworthiness of downstream scientific analyses. This research also focuses on the design and implementation of scalable, GPU-accelerated software pipelines that seamlessly integrate into existing HPC workflows, ensuring both computational efficiency and practical applicability. The CAESAR framework, for example, unifies foundation and generative models to create an adaptive and efficient compression solution for spatio-temporal scientific data. Collectively, these efforts represent a significant advancement in mitigating the scientific data deluge, enabling more effective data management, accelerated scientific discovery, and optimized utilization of HPC resources.

97 MATHEMATICS AND COMPUTING↗