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DOE OSTI2020

Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes

Abstract Predicting the structure of multi‐protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage predefined structural features to distinguish accurate structural models from less accurate ones. This raises the question of whether it is possible to learn characteristics of accurate models directly from atomic coordinates of protein complexes, with no prior assumptions. Here we introduce a machine learning method that learns directly from the 3D positions of all atoms to identify accurate models of protein complexes, without using any precomputed physics‐inspired or statistical terms. Our neural network architecture combines multiple ingredients that together enable end‐to‐end learning from molecular structures containing tens of thousands of atoms: a point‐based representation of atoms, equivariance with respect to rotation and translation, local convolutions, and hierarchical subsampling operations. When used in combination with previously developed scoring functions, our network substantially improves the identification of accurate structural models among a large set of possible models. Our network can also be used to predict the accuracy of a given structural model in absolute terms. The architecture we present is readily applicable to other tasks involving learning on 3D structures of large atomic systems.

Eismann, Stephan↗

DOE OSTI2026

AnisONet: A deep neural operator-based anisotropic permeability upscaler from pore to Darcy scale

Directional permeability variations, which govern directional fluid flow in porous media with anisotropy, are important to accurately predict flow behavior, reactive transport, and fluid–solid interactions for various processes such as enhanced geothermal systems, energy storage devices, and biological systems. However, the intricate architecture of porous media makes it difficult to predict directional permeabilities. In this work, we present a novel machine learning (ML) framework, AnisONet, built upon an integration of a convolutional neural network, Swin transformer, and the deep operator network architecture, designed to predict anisotropic permeability and upscale predictions to larger spatial domains. First, AnisONet was evaluated with three classes of two-dimensional (2D) porous media, including synthetic circular and elliptical grains and natural sandstone grains from micro-computed tomography images. A lattice Boltzmann model (LBM) was used to calculate directional permeabilities at every 10° angle, producing 19 data points per image of porous media. AnisONet is then trained to predict permeability as a function of rotation angle. AnisONet showed strong predictive capability of directional permeability. Second, we tested our model for five upscaling cases with a large image size in the finite-element method (FEM) for 2D Darcy flow with various permeability tensor construction methods. Overall, upscaled permeability tensors in FEM simulations produce a reasonably good match with LBM results, highlighting the importance of selecting appropriate tensor formation strategies for accurate permeability upscaling. AnisONet, as a directional permeability estimator, could be further developed for more complex geometries, with the potential to develop a foundational ML model for various applications in porous media.

42 ENGINEERING↗

DOE OSTI2026

Topology-Informed Design Rules for Deconstructable Thermoset Copolymer Networks

Existing models of thermoset deconstruction facilitated by incorporating cleavable comonomers rely on a mean-field reverse gel point paradigm, which predicts network dissolution once cleavable bonds reach a critical stoichiometric threshold, but does not account for where those bonds reside within the network architecture. Using reactive coarse-grained molecular dynamics simulations coupled with graph-theoretic analysis, we extend this stoichiometric picture to show that deconstructability is governed by the curing-imprinted network topology rather than stoichiometry alone. This topological organization is hierarchical: at the local scale, the elastic effectiveness of cross-link junctions determines which cross-links constitute the load-bearing scaffold; at the mesoscale, the cross-linking rate kinetically templates that scaffold into topologically modular communities─densely cross-linked clusters connected by sparse bridging strands that sustain network connectivity. Using betweenness centrality to identify nodes that disproportionately lie on intercommunity shortest paths, we demonstrate that effective deconstruction of the network into macromolecular fragments requires cleavable comonomers to intercept these high-centrality bridging strands. We further find that under uniform, disassortative comonomer incorporation, this topological requirement provides a mechanistic basis for extending the reverse gel point to incorporate network topology. We also show that modularity imposes a fundamental limit on fragment uniformity that persists even when the centrality requirement is met. Finally, we demonstrate that chain stiffness provides a nearly independent lever to suppress mechanically redundant cross-links and raise the glass transition temperature without significantly altering the deconstruction outcome. Together, these findings reframe the thermoset design space around network topology and provide actionable guidelines for engineering thermoset copolymers with predictable deconstructability and targeted thermomechanical performance.

coarse-grained molecular dynamics↗

DOE OSTI2023

Efficient solutions of fermionic systems using artificial neural networks

In this study, we explore the similarities and differences between variational Monte Carlo techniques that employ conventional and artificial neural network representations of the ground-state wave function for fermionic systems. Our primary focus is on shallow neural network architectures, specifically the restricted Boltzmann machine, and we examine unsupervised learning algorithms that are appropriate for modeling complex many-body correlations. We assess the advantages and drawbacks of conventional and neural network wave functions by applying them to a range of circular quantum dot systems. Our findings, which include results for systems containing up to 90 electrons, emphasize the efficient implementation of these methods on both homogeneous and heterogeneous high-performance computing facilities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Strictly Enforcing Invertibility and Conservation in CNN-Based Super Resolution for Scientific Datasets

Abstract Recently, deep convolutional neural networks (CNNs) have revolutionized image “super resolution” (SR), dramatically outperforming past methods for enhancing image resolution. They could be a boon for the many scientific fields that involve imaging or any regularly gridded datasets: satellite remote sensing, radar meteorology, medical imaging, numerical modeling, and so on. Unfortunately, while SR-CNNs produce visually compelling results, they do not necessarily conserve physical quantities between their low-resolution inputs and high-resolution outputs when applied to scientific datasets. Here, a method for “downsampling enforcement” in SR-CNNs is proposed. A differentiable operator is derived that, when applied as the final transfer function of a CNN, ensures the high-resolution outputs exactly reproduce the low-resolution inputs under 2D-average downsampling while improving performance of the SR schemes. The method is demonstrated across seven modern CNN-based SR schemes on several benchmark image datasets, and applications to weather radar, satellite imager, and climate model data are shown. The approach improves training time and performance while ensuring physical consistency between the super-resolved and low-resolution data. Significance Statement Recent advancements in using deep learning to increase the resolution of images have substantial potential across the many scientific fields that use images and image-like data. Most image super-resolution research has focused on the visual quality of outputs, however, and is not necessarily well suited for use with scientific data where known physics constraints may need to be enforced. Here, we introduce a method to modify existing deep neural network architectures so that they strictly conserve physical quantities in the input field when “super resolving” scientific data and find that the method can improve performance across a wide range of datasets and neural networks. Integration of known physics and adherence to established physical constraints into deep neural networks will be a critical step before their potential can be fully realized in the physical sciences.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Efficient hybrid explicit-implicit learning for multiscale problems

Splitting method is a powerful method to handle application problems by splitting physics, scales, domain, and so on. Many splitting algorithms have been designed for efficient temporal discretization. Here, in this paper, our goal is to use temporal splitting concepts in designing machine learning algorithms and, at the same time, help splitting algorithms by incorporating data and speeding them up. We propose a machine learning assisted splitting scheme which improves the efficiency of the scheme meanwhile preserves the accuracy. We consider a recently introduced multiscale splitting algorithms, where the multiscale problem is solved on a coarse grid. To approximate the dynamics, only a few degrees of freedom are solved implicitly, while others explicitly. This splitting concept allows identifying degrees of freedom that need implicit treatment. In this paper, we use this splitting concept in machine learning and propose several strategies. First, the implicit part of the solution can be learned as it is more difficult to solve, while the explicit part can be computed. This provides a speed-up and data incorporation for splitting approaches. Secondly, one can design a hybrid neural network architecture because handling explicit parts requires much fewer communications among neurons and can be done efficiently. Thirdly, one can solve the coarse grid component via PDEs or other approximation methods and construct simpler neural networks for the explicit part of the solutions. We discuss these options and implement one of them by interpreting it as a machine translation task. This interpretation of the splitting scheme successfully enables us using the Transformer since it can perform model reduction for multiple time series and learn the connection between them. We also find that the splitting scheme is a great platform to predict the coarse solution with insufficient information of the target model: the target problem is partially given and we need to solve it through a known problem which approximates the target. Our machine learning model can incorporate and encode the given information from two different problems and then solve the target problems. We conduct four numerical examples and the results show that our method is stable and accurate.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Deep-Learning based Reconstruction of the Shower Maximum $X_{\mathrm{max}}$ using the Water-Cherenkov Detectors of the Pierre Auger Observatory

The atmospheric depth of the air shower maximum X max is an observable commonly used for the determination of the nuclear mass composition of ultra-high energy cosmic rays. Direct measurements of X max are performed using observations of the longitudinal shower development with fluorescence telescopes. At the same time, several methods have been proposed for an indirect estimation of X max from the characteristics of the shower particles registered with surface detector arrays. In this paper, we present a deep neural network (DNN) for the estimation of X max . The reconstruction relies on the signals induced by shower particles in the ground based water-Cherenkov detectors of the Pierre Auger Observatory. The network architecture features recurrent long short-term memory layers to process the temporal structure of signals and hexagonal convolutions to exploit the symmetry of the surface detector array. We evaluate the performance of the network using air showers simulated with three different hadronic interaction models. Thereafter, we account for long-term detector effects and calibrate the reconstructed X max using fluorescence measurements. Finally, we show that the event-by-event resolution in the reconstruction of the shower maximum improves with increasing shower energy and reaches less than 25 g/cm 2 at energies above 2 × 10 19 eV.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Quantum/AI Topology-Aware Latency-Adaptive HPC Workflow Scheduling Optimization

The growing demand for more powerful high-performance computing (HPC) systems has led to a steady rise in energy consumption by supercomputing worldwide. This study is focused on comparing our Application-Topology Mapper (ATMapper) to the popular Simple Linux Utility for Resource Management (SLURM) for the purpose of exploring methods that can further optimize job-scheduling within HPC systems. ATMapper is an Artificial-Intelligence based approach to job-scheduling that is currently being enhanced with quantum annealing (QA) to generate optimal schedules faster. We are applying QA to speedup our ATMapper process to achieve higher computing efficiency, thereby reducing HPC energy consumption. Here, we examine how four job-scheduling approaches perform in processor node assignment when using an example network architecture of 4 interconnected nodes. Using a specialized script, we are assessing the schedule of a computation flow with 11 interdependent tasks. The data movements among nodes were tracked to count for the number of interactions (network hops) between nodes needed to complete the tasks. The total number of hops and the job completion time were then used to quantify the efficiency of the different mapping approaches. In addition to SLURM, we also compare our ATMapper to the QA-enabled LBNL TIGER and the D-Wave Distributed Computing processor assignment approaches. The preliminary results showed that our topology-aware, latency-adaptive ATMapper is significantly more efficient when compared to the other scheduling approaches due to its load-imbalance network allocation. The scheduler displayed a computing efficiency of 53% by performing significantly fewer network hops than its alternatives. By reducing the number of hops, ATMapper was able to perform all 11 tasks by using only 3 nodes out of given 4. This research indicates the potential to use QA/AI for HPC job-scheduling. Later, we will test a SLURM simulator program to draw further comparisons on the effectiveness of ATMapper's scheduling approach. The results of this comparison will serve as a baseline for later improving SLURM's performance using a QA-enhanced ATMapper approach.

Caraveo, Braulio [University of Huston - Clear Lak↗

DOE OSTI2021

Correspondence of NNGP Kernel and the Matérn Kernel

Kernels representing limiting cases of neural network architectures have recently gained popularity. However, the application and performance of these new kernels compared to existing options, such as the Matérn kernel, is not well studied. We take a practical approach to explore the neural network Gaussian process (NNGP) kernel and its application to data in Gaussian process regression. We first demonstrate the necessity of normalization to produce valid NNGP kernels and explore related numerical challenges. We further demonstrate that the predictions from this model are quite inflexible, and therefore do not vary much over the valid hyperparameter sets. We then demonstrate a surprising result that the predictions given from the NNGP kernel correspond closely to those given by the Matérn kernel under specific circumstances, which suggests a deep similarity between overparameterized deep neural networks and the Matérn kernel. Finally, we demonstrate the performance of the NNGP kernel as compared to the Matérn kernel on three benchmark data cases, and we conclude that for its flexibility and practical performance, the Matérn kernel is preferred to the novel NNGP in practical applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Empirically-calibrated H100 node power models for accurate AI training energy estimation

Accurately quantifying the energy use of artificial intelligence (AI) training is critical for infrastructure planning, carbon accounting, and sustainable data center operation, but few studies have directly measured the power consumption of production workloads on contemporary hardware. By combining empirical measurements from Brookhaven National Laboratory during AI training on 8-graphics-processing-unit H100 systems with open-source benchmarking data, we develop statistical models relating computational intensity to node-level power consumption. We measure the gap between manufacturer-rated thermal design power (TDP) and actual power demand during AI training. Our analysis reveals that even computationally intensive workloads operate at only 76% of the 10.2 kW TDP rating. Our architecture-specific model, calibrated to floating-point operations, predicts energy consumption with 11.4% mean absolute percentage error, significantly outperforming TDP-based approaches (27%–37% error). We identified distinct power signatures between transformer and convolutional neural network architectures, with transformers showing characteristic fluctuations that may impact grid stability. These results provide a measurement-grounded basis for improving AI training energy estimates, enabling more reliable infrastructure sizing, cost projections, and environmental impact assessments.

Newkirk, Alex C↗

DOE OSTI2021

Archparse

Archparse is a Python package that holds the purpose and capability of converting the contents of a text file to a functioning neural network based on the Tensorflow 2.X framework. This is able to be done with minimal written Python code and next to no knowledge of how to build models with Tensorflow directly. More specifically Archparse parses a text file with extension ".arch" which contains neural network architecture information that corresponds to either the Tensorflow 2.X API or custom code written with the Tensorflow 2.X API. Included in the initial version is the capacity to easily produce sequential autoencoders and sequential neural networks.

Vander Wal, MichaelD.↗

DOE OSTI2022

Training neural networks using Metropolis Monte Carlo and an adaptive variant

Abstract We examine the zero-temperature Metropolis Monte Carlo (MC) algorithm as a tool for training a neural network by minimizing a loss function. We find that, as expected on theoretical grounds and shown empirically by other authors, Metropolis MC can train a neural net with an accuracy comparable to that of gradient descent (GD), if not necessarily as quickly. The Metropolis algorithm does not fail automatically when the number of parameters of a neural network is large. It can fail when a neural network’s structure or neuron activations are strongly heterogenous, and we introduce an adaptive Monte Carlo algorithm (aMC) to overcome these limitations. The intrinsic stochasticity and numerical stability of the MC method allow aMC to train deep neural networks and recurrent neural networks in which the gradient is too small or too large to allow training by GD. MC methods offer a complement to gradient-based methods for training neural networks, allowing access to a distinct set of network architectures and principles.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Data-driven recovery of hidden physics in reduced order modeling of fluid flows

In this article, we introduce a modular hybrid analysis and modeling (HAM) approach to account for hidden physics in reduced order modeling (ROM) of parameterized systems relevant to fluid dynamics. The hybrid ROM framework is based on using first principles to model the known physics in conjunction with utilizing the data-driven machine learning tools to model the remaining residual that is hidden in data. This framework employs proper orthogonal decomposition as a compression tool to construct orthonormal bases and Galerkin projection (GP) as a model to build the dynamical core of the system. Our proposed methodology hence compensates structural or epistemic uncertainties in models and utilizes the observed data snapshots to compute true modal coefficients spanned by these bases. The GP model is then corrected at every time step with a data-driven rectification using a long short-term memory (LSTM) neural network architecture to incorporate hidden physics. A Grassmannian manifold approach is also adopted for interpolating basis functions to unseen parametric conditions. The control parameter governing the system's behavior is thus implicitly considered through true modal coefficients as input features to the LSTM network. The effectiveness of the HAM approach is then discussed through illustrative examples that are generated synthetically to take hidden physics into account. Furthermore, our approach thus provides insights addressing a fundamental limitation of the physics-based models when the governing equations are incomplete to represent underlying physical processes.

42 ENGINEERING↗

DOE OSTI2020

Deep transfer learning for star cluster classification: I. application to the PHANGS– HST survey

ABSTRACT We present the results of a proof-of-concept experiment that demonstrates that deep learning can successfully be used for production-scale classification of compact star clusters detected in Hubble Space Telescope(HST) ultraviolet-optical imaging of nearby spiral galaxies ($D\lesssim 20\, \textrm{Mpc}$) in the Physics at High Angular Resolution in Nearby GalaxieS (PHANGS)–HST survey. Given the relatively small nature of existing, human-labelled star cluster samples, we transfer the knowledge of state-of-the-art neural network models for real-object recognition to classify star clusters candidates into four morphological classes. We perform a series of experiments to determine the dependence of classification performance on neural network architecture (ResNet18 and VGG19-BN), training data sets curated by either a single expert or three astronomers, and the size of the images used for training. We find that the overall classification accuracies are not significantly affected by these choices. The networks are used to classify star cluster candidates in the PHANGS–HST galaxy NGC 1559, which was not included in the training samples. The resulting prediction accuracies are 70 per cent, 40 per cent, 40–50 per cent, and 50–70 per cent for class 1, 2, 3 star clusters, and class 4 non-clusters, respectively. This performance is competitive with consistency achieved in previously published human and automated quantitative classification of star cluster candidate samples (70–80 per cent, 40–50 per cent, 40–50 per cent, and 60–70 per cent). The methods introduced herein lay the foundations to automate classification for star clusters at scale, and exhibit the need to prepare a standardized data set of human-labelled star cluster classifications, agreed upon by a full range of experts in the field, to further improve the performance of the networks introduced in this study.

Wei, Wei↗

DOE OSTI2022

Robust and scalable uncertainty estimation with conformal prediction for machine-learned interatomic potentials

Abstract Uncertainty quantification (UQ) is important to machine learning (ML) force fields to assess the level of confidence during prediction, as ML models are not inherently physical and can therefore yield catastrophically incorrect predictions. Established a-posteriori UQ methods, including ensemble methods, the dropout method, the delta method, and various heuristic distance metrics, have limitations such as being computationally challenging for large models due to model re-training. In addition, the uncertainty estimates are often not rigorously calibrated. In this work, we propose combining the distribution-free UQ method, known as conformal prediction (CP), with the distances in the neural network’s latent space to estimate the uncertainty of energies predicted by neural network force fields. We evaluate this method (CP+latent) along with other UQ methods on two essential aspects, calibration, and sharpness, and find this method to be both calibrated and sharp under the assumption of independent and identically-distributed (i.i.d.) data. We show that the method is relatively insensitive to hyperparameters selected, and test the limitations of the method when the i.i.d. assumption is violated. Finally, we demonstrate that this method can be readily applied to trained neural network force fields with traditional and graph neural network architectures to obtain estimates of uncertainty with low computational costs on a training dataset of 1 million images to showcase its scalability and portability. Incorporating the CP method with latent distances offers a calibrated, sharp and efficient strategy to estimate the uncertainty of neural network force fields. In addition, the CP approach can also function as a promising strategy for calibrating uncertainty estimated by other approaches.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

Deep learning models for interpretation of point of care ultrasound in military working dogs

Introduction: Military working dogs (MWDs) are essential for military operations in a wide range of missions. With this pivotal role, MWDs can become casualties requiring specialized veterinary care that may not always be available far forward on the battlefield. Some injuries such as pneumothorax, hemothorax, or abdominal hemorrhage can be diagnosed using point of care ultrasound (POCUS) such as the Global FAST® exam. This presents a unique opportunity for artificial intelligence (AI) to aid in the interpretation of ultrasound images. In this article, deep learning classification neural networks were developed for POCUS assessment in MWDs. Methods: Images were collected in five MWDs under general anesthesia or deep sedation for all scan points in the Global FAST® exam. For representative injuries, a cadaver model was used from which positive and negative injury images were captured. A total of 327 ultrasound clips were captured and split across scan points for training three different AI network architectures: MobileNetV2, DarkNet-19, and ShrapML. Gradient class activation mapping (GradCAM) overlays were generated for representative images to better explain AI predictions. Results: Performance of AI models reached over 82% accuracy for all scan points. The model with the highest performance was trained with the MobileNetV2 network for the cystocolic scan point achieving 99.8% accuracy. Across all trained networks the diaphragmatic hepatorenal scan point had the best overall performance. However, GradCAM overlays showed that the models with highest accuracy, like MobileNetV2, were not always identifying relevant features. Conversely, the GradCAM heatmaps for ShrapML show general agreement with regions most indicative of fluid accumulation. Discussion: Overall, the AI models developed can automate POCUS predictions in MWDs. Preliminarily, ShrapML had the strongest performance and prediction rate paired with accurately tracking fluid accumulation sites, making it the most suitable option for eventual real-time deployment with ultrasound systems. Further integration of this technology with imaging technologies will expand use of POCUS-based triage of MWDs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Understanding important features of deep learning models for segmentation of high-resolution transmission electron microscopy images

Cutting edge deep learning techniques allow for image segmentation with great speed and accuracy. However, application to problems in materials science is often difficult since these complex models may have difficultly learning meaningful image features that would enable extension to new datasets. In situ electron microscopy provides a clear platform for utilizing automated image analysis. In this work, we consider the case of studying coarsening dynamics in supported nanoparticles, which is important for understanding, for example, the degradation of industrial catalysts. By systematically studying dataset preparation, neural network architecture, and accuracy evaluation, we describe important considerations in applying deep learning to physical applications, where generalizable and convincing models are required. With a focus on unique challenges that arise in high-resolution images, we propose methods for optimizing performance of image segmentation using convolutional neural networks, critically examining the application of complex deep learning models in favor of motivating intentional process design.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Theory for Equivariant Quantum Neural Networks

Quantum neural network architectures that have little to no inductive biases are known to face trainability and generalization issues. Inspired by a similar problem, recent breakthroughs in machine learning address this challenge by creating models encoding the symmetries of the learning task. This is materialized through the usage of equivariant neural networks the action of which commutes with that of the symmetry. In this work, we import these ideas to the quantum realm by presenting a comprehensive theoretical framework to design equivariant quantum neural networks (EQNNs) for essentially any relevant symmetry group. We develop multiple methods to construct equivariant layers for EQNNs and analyze their advantages and drawbacks. Our methods can find unitary or general equivariant quantum channels efficiently even when the symmetry group is exponentially large or continuous. As a special implementation, we show how standard quantum convolutional neural networks (QCNNs) can be generalized to group-equivariant QCNNs where both the convolution and pooling layers are equivariant to the symmetry group. We then numerically demonstrate the effectiveness of a S U ( 2 ) -equivariant QCNN over symmetry-agnostic QCNN on a classification task of phases of matter in the bond-alternating Heisenberg model. Our framework can be readily applied to virtually all areas of quantum machine learning. Lastly, we discuss about how symmetry-informed models such as EQNNs provide hopes to alleviate central challenges such as barren plateaus, poor local minima, and sample complexity. Published by the American Physical Society 2024

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗