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DOE OSTI2025

The Effects of Compounded Model Size Reductions on Adversarial Robustness

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

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

DOE OSTI2024

High-Dimensional Bayesian Optimization via Semi-Supervised Learning with Optimized Unlabeled Data Sampling

We introduce a novel semi-supervised learning approach, named Teacher-Student Bayesian Optimization (TSBO ), integrating the teacher-student paradigm into BO to minimize expensive labeled data queries for the first time. TSBO incorporates a teacher model, an unlabeled data sampler, and a student model. The student is trained on unlabeled data locations generated by the sampler, with pseudo labels predicted by the teacher. The interplay between these three components implements a unique selective regularization to the teacher in the form of student feedback. This scheme enables the teacher to predict high-quality pseudo labels, enhancing the generalization of the GP surrogate model in the search space. To fully exploit TSBO , we propose two optimized unlabeled data samplers to construct effective student feedback that well aligns with the objective of Bayesian optimization. Furthermore, we quantify and leverage the uncertainty of the teacher-student model for the provision of reliable feedback to the teacher in the presence of risky pseudo-label predictions. TSBO demonstrates significantly improved sample-efficiency in several global optimization tasks under tight labeled data budgets. The implementation is available at https://github.com/reminiscenty/TSBO-Official.

Yin, Yuxuan↗

DOE OSTI2025

Transferable predictions of energetic and structural properties for refractory solid solution alloys across chemical compositions

We present a data-efficient approach to train graph neural networks (GNNs) on density functional theory (DFT) data for accurate and transferable predictions of energetic and structural properties of refractory solid solution alloys in the niobium-tantalum-vanadium (Nb-Ta-V) chemical space. We start by training the GNN model only on DFT data that describes refractory binary alloys niobium-tantalum (Nb-Ta), niobium-vanadium (Nb-V), and tantalum-vanadium (Ta-V) to predict formation enthalpy and root mean squared displacement. Once trained, the GNN predictions are tested on DFT data describing refractory ternary alloys Nb-Ta-V. While, unsurprisingly, direct transferability from binary to ternary is not sufficiently accurate, augmenting the training with only 1% of the available ternary data (uniformly distributed across the entire range of chemical compositions) improves significantly the quality of the GNN predictions. For comparison, we assess the transferability in the opposite direction by training GNN models on ternary Nb-Ta-V data and making predictions on binaries Nb-Ta, Nb-V, and Ta-V, which exhibits notably higher predictive errors. The proposed methodology, which favors transferability from lower-component to higher-component alloys, offers an efficient path towards avoiding the curse of dimensionality incurred when collecting DFT data for discovery and design of multi-component disordered alloys.

Density functional theory calculations↗

DOE OSTI2024

Domain-decomposition nonlinear manifold reduced order model

This software combines nonlinear-manifold reduced order models (NM-ROMs) with domain decomposition (DD) techniques. NM-ROMs, which utilize a shallow, sparse autoencoder trained with full order model (FOM) snapshot data, approximate the FOM state on a nonlinear manifold. These models offer advantages over linear-subspace ROMs (LS-ROMs) particularly in scenarios with slowly decaying Kolmogorov n-width. However, the training of NM-ROMs involves a number of parameters that scale with the size of the FOM, and storing high-dimensional FOM snapshots can significantly increase the cost of ROM training for extreme-scale problems. To mitigate these costs, the software employs DD to partition the FOM into smaller subdomains, computes NM-ROMs for each, and then integrates these to form a global NM-ROM. This strategy offers multiple benefits: it enables parallel training of subdomain NM-ROMs, reduces the number of parameters needed, decreases the dimensional requirements of subdomain FOM training data, and allows for customization to the unique characteristics of each FOM subdomain. The use of a shallow, sparse autoencoder architecture in each subdomain NM-ROM facilitates the application of hyper-reduction (HR), simplifying the nonlinear complexities and enhancing computational speed. This software marks the inaugural application of NM-ROM combined with HR to a DD problem. It features an algebraic DD reformulation of the FOM, training of NM-ROMs with HR for each subdomain, and employs a sequential quadratic programming (SQP) solver for the evaluation of the coupled global NMROM. The effectiveness of the DD NM-ROM with HR is numerically demonstrated on the 2D steady-state Burgers' equation, showing an order of magnitude improvement in accuracy over the DD LS-ROM with HR.

Diaz, AlejandroN↗

DOE OSTI2024

Temporal dynamics of the multi-omic response to endurance exercise training

Regular exercise promotes whole-body health and prevents disease, but the underlying molecular mechanisms are incompletely understood. Here, the Molecular Transducers of Physical Activity Consortium profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome and immunome in whole blood, plasma and 18 solid tissues in male and female Rattus norvegicus over eight weeks of endurance exercise training. The resulting data compendium encompasses 9,466 assays across 19 tissues, 25 molecular platforms and 4 training time points. Thousands of shared and tissue-specific molecular alterations were identified, with sex differences found in multiple tissues. Temporal multi-omic and multi-tissue analyses revealed expansive biological insights into the adaptive responses to endurance training, including widespread regulation of immune, metabolic, stress response and mitochondrial pathways. Many changes were relevant to human health, including non-alcoholic fatty liver disease, inflammatory bowel disease, cardiovascular health and tissue injury and recovery. The data and analyses presented in this study will serve as valuable resources for understanding and exploring the multi-tissue molecular effects of endurance training and are provided in a public repository (https://motrpac-data.org/).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Neural Network‐Based Methods for Ocean Surface Wave Measurement Using Submarine Distributed Acoustic Sensing (DAS)

Two new data-driven models for estimating ocean surface waves from distributed acoustic sensing (DAS) submarine cable strain rate are developed using supervised machine learning on a 10-day data set collected offshore of Oliktok Point, Alaska. The new models were trained on target data from seafloor pressure moorings at three sites spaced evenly along 27.1 km of cable and were benchmarked against an empirical transfer function method previously used to estimate waves from DAS. A model which uses convolutional neural networks to transform 2-km frequency-wavenumber strain spectra to seafloor pressure spectra outperforms the benchmark in wave height prediction (RMSE of 0.15 vs. 0.41 m) and period prediction (0.29 vs. 0.37 s) when evaluated on a held-out test data set. When applied to a DAS data set collected on the same cable 2 years prior, the CNN-based model maintained similar significant wave height performance (RMSE = 0.23 m) relative to available satellite altimetry data. A two-hidden-layer, fully connected neural network which transforms 1-D strain spectra to seafloor pressure spectra also outperforms the benchmark in wave height prediction (RMSE of 0.19 vs. 0.41 m), but does not generalize as well to the prior data. Regression-based machine learning is useful for estimating waves from DAS data when the pressure-strain relationship varies temporally and spatially across different wave conditions. Models can be applied to DAS data to measure waves with higher spatial resolution and longer temporal coverage than traditional methods, which often measure waves only at a single point.

Davis, Jacob R. [Univ. of Washington, Seattle, WA ↗

DOE OSTI2024

Comparative Assessment of U-Net-Based Deep Learning Models for Segmenting Microfractures and Pore Spaces in Digital Rocks

Segmentation of high-resolution X-ray microcomputed tomography (µCT) images is crucial in digital rock physics (DRP), affecting the characterization and analysis of microscale phenomena in the porous media. The complexity of geological structures and nonideal scanning conditions pose significant challenges to conventional image segmentation approaches. Motivated by the recent increasing popularity of deep learning (DL) techniques in image processing, this work undertakes a comparative study of DL models, specifically U-Net and its variants, for segmenting multiple targets with distinguished features in digital rocks, including discrete fracture networks (DFNs), pore spaces, and solid rock. Particularly, DFNs have a smaller volumetric fraction over others, bringing in a substantial challenge of imbalanced segmentation. The primary focus is to evaluate the architecture and feature enhancement strategies of various DL models, including U-Net, attention U-Net, residual U-Net, U-Net++, and residual U-Net++. The models were designed as 2.5D, utilizing a central 2D image and its two adjacent upper and lower 2D images as input to provide a pseudo-3D context. In addition, because the ground truth of segmentation was unknown for real-world digital rocks, we created a benchmark data set following the inverse operations of segmentation. The data synthesis started from the label images (i.e., solid rock, pore spaces, and DFNs), followed by simulating partial volume blurring, adding random background noise, and introducing ring artifacts to mimic real raw X-ray µCT images. The data set, which included various rock types (i.e., sandstone and artificial data), scanning resolution, and magnitudes of noise and artifacts, was divided into training and testing data sets with a 90% and 10% ratio, respectively. Moreover, in addition to the conventional pixel-wise evaluation metrics, the physics-based metric of the lattice-Boltzmann method (LBM) simulated permeability provided more comprehensive assessments. The results demonstrated that the residual connections, nested architectures, and redesigned skip connections contribute to the model performance and give the residual U-Net++ the highest accuracy. The improvements were mainly on the boundaries and small targets, especially the DFNs, which dominate the interconnectivity and therefore affect the permeability greatly. This study also rigorously evaluated the efficiency and generalization of each model, demonstrating that the sophisticated architectures achieved excellent practicability and maintained robust performance on completely unseen data, ensuring their suitability for diverse and challenging DRP applications.

58 GEOSCIENCES↗

DOE OSTI2026

DP-TwoLevel: two-stage gradient subspace learning for differentially private federated learning

Federated learning (FL) enables collaborative model training across distributed data sources without sharing raw data, but faces fundamental challenges in communication efficiency and privacy. Differentially private (DP) training mitigates information leakage but introduces noise that degrades model performance, especially in high-dimensional settings. We propose DP-TwoLevel, a hierarchical gradient projection method that improves utility under fixed DP constraints by exploiting low-dimensional structure in model updates. Our approach learns a two-level PCA-based representation of gradients and applies DP noise in a reduced-dimensional subspace, thereby lowering the effective noise magnitude while preserving dominant signal components. We evaluate the method across three datasets (MNIST, Fashion-MNIST, CIFAR-10) and three privacy regimes (ϵ∈0.5, 1.0, 2.0). Across nine experimental settings, DP-TwoLevel consistently outperforms DP-FedAvg, achieving an average accuracy improvement of 9.44%, with larger gains observed in lower ϵ(higher-noise) regimes (up to +22.31%). We further analyze scalability across models ranging from 100K to 1.49M parameters and identify a variance-based success criterion: performance remains strong when the projection preserves more than 75% of gradient variance, degrades in a marginal regime (65–75%), and fails below this threshold. Our results demonstrate that structure-aware dimensionality reduction can significantly improve the privacy–utility tradeoff in FL without modifying formal privacy guarantees. We also provide empirical evidence of scaling limitations for global projections and motivate per-layer extensions for larger models.

Kotevska, Olivera [ORNL] (ORCID:0000000316772243)↗

DOE OSTI2025

Development of Predictive Models for Advanced Reactor Autonomous Control

Advanced reactor designs including microreactors and small modular reactors will contribute to the clean production of cheap energy, and autonomous control for advanced reactors is an appealing option for reducing cost. However, there is a lack of industry experience applying autonomous control for advanced nuclear reactors. To accelerate the development and industry acceptance of autonomous control software for nuclear reactors, we aim to demonstrate autonomous control of the Purdue University research reactor (PUR-1) using INL-developed model predictive control (MPC) methods. To prepare for this demonstration, data-driven predictive models based on process data collected from PUR-1 have been developed and integrated with MPC and used to control a physics-based model of PUR-1. A data-driven dynamics model and a gated recurrent unit (GRU) network were both trained on process data from PUR-1. The dynamics model was shown to effectively control the reactor model with MPC when provided reactivity as a control variable but failed to control the model through the control rod positions. The GRU network produced more accurate predictions than the dynamics model when evaluated on operational data, and future work will include the evaluation of the GRU network in the controller.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Super Resolution for Renewable Energy Resource Data With Wind From Reanalysis Data (Sup3rWind) and Application to Ukraine [Slides]

In this work we present a novel deep learning-based downscaling method, using generative adversarial networks (GANs), for generating high-resolution wind resource data from ECMWF Reanalysis v5 data (ERA5). We show that by training a GAN model on ERA5, as opposed to coarsened high-resolution data, we achieve results that are competitive with conventional dynamical downscaling. This GAN-based downscaling method additionally reduces computational costs over dynamical downscaling by two orders of magnitude. All GANs are trained on data sampled from CONUS, selected to provide a diverse sampling of terrain conditions, and validated on observational data along with data held out from training. This cross-validation shows low error and high correlations with observations and excellent agreement with hold out data across physical distributions. Our approach is finally used to downscale 30km hourly ERA5 to 2-km 5-minute wind data, for January 2000 through December 2023, at multiple hub heights, over Ukraine, Moldova, and part of Romania. Comparisons against observational data from Meteorological Assimilation Data Ingest System (MADIS) and multiple wind farms show the same level of performance as for CONUS validation. This 24 year data record is the first member of the "super resolution for renewable energy resource data with wind from reanalysis data" dataset (Sup3rWind).

17 WIND ENERGY↗

DOE OSTI2026

Transfer learning for analysis of collective and non-collective Thomson scattering spectra

Thomson scattering (TS) diagnostics provide reliable, minimally perturbative measurements of fundamental plasma parameters, such as electron density (⁠n e ) and electron temperature (⁠T e ⁠). Deep neural networks can provide accurate estimates of ⁠n e and T e when conventional fitting algorithms may fail, such as when TS spectra are dominated by noise, or when fast analysis is required for real-time operation. Although deep neural networks typically require large training sets, transfer learning can improve model performance on a target task with limited data by leveraging pre-trained models from related source tasks, where select hidden layers are further trained using target data. We present five architecturally diverse deep neural networks, pre-trained on synthetic TS data and adapted for experimentally measured TS data, to evaluate the efficacy of transfer learning in estimating n e and T e in both the collective and non-collective scattering regimes. We evaluate errors in n e and T e estimates as a function of training set size for models trained with and without transfer learning, and we observe decreases in model error from transfer learning when the training set contains ≲ 200 experimentally measured spectra.

Artificial neural networks↗

DOE OSTI2024

A fast and accurate domain decomposition nonlinear manifold reduced order model

Here, this paper integrates nonlinear-manifold reduced order models (NM-ROMs) with domain decomposition (DD). NM ROMs approximate the full order model (FOM) state in a nonlinear-manifold by training a shallow, sparse autoencoder using FOM snapshot data. These NM-ROMs can be advantageous over linear-subspace ROMs (LS-ROMs) for problems with slowly decaying Kolmogorov n-width. However, the number of NM-ROM parameters that need to be trained scales with the size of the FOM. Moreover, for “extreme-scale” problems, the storage of high-dimensional FOM snapshots alone can make ROM training expensive. To alleviate the training cost, this paper applies DD to the FOM, computes NM-ROMs on each subdomain, and couples them to obtain a global NM-ROM. This approach has several advantages: Subdomain NM-ROMs can be trained in parallel, involve fewer parameters to be trained than global NM-ROMs, require smaller subdomain FOM dimensional training data, and can be tailored to subdomain specific features of the FOM. The shallow, sparse architecture of the autoencoder used in each subdomain NM-ROM allows application of hyper-reduction (HR), reducing the complexity caused by nonlinearity and yielding computational speedup of the NM-ROM. This paper provides the first application of NM-ROM (with HR) to a DD problem. In particular, this paper details an algebraic DD reformulation of the FOM, training a NM-ROM with HR for each sub domain, and a sequential quadratic programming (SQP) solver to evaluate the coupled global NM-ROM. Theoretical convergence results for the SQP method and a priori and a posteriori error estimates for the DD NM-ROM with HR are provided. The proposed DD NM-ROM with HR approach is numerically compared to a DD LS-ROM with HR on the 2D steady-state Burgers’ equation, showing an order of magnitude improvement in accuracy of the proposed DD NM-ROM over the DD LS-ROM.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts

Antifungal drug resistance is a major challenge in fungal infection management. Numerous genomic changes are known to contribute to acquired drug resistance in clinical isolates of specific pathogens, but whether they broadly explain natural resistance across entire lineages is unknown. We leveraged genomic, ecological, and phenotypic trait data from naturally sampled strains from nearly all known species in subphylum Saccharomycotina to examine the evolution of resistance to eight antifungal drugs. The phylogenetic distribution of drug resistance varied by drug; fluconazole resistance was widespread, while 5-fluorocytosine resistance was rare, except in Lipomycetales. A random forest algorithm trained on genomic data predicted drug-resistant yeasts with 54–75% accuracy. Fluconazole resistance was consistently predicted with the highest accuracy (75.2%). Furthermore, fluconazole resistance prediction accuracy was similar between models trained on genome-wide variation in the presence and number of InterPro protein annotations across Saccharomycotina (75.2%) and those trained on amino acid sequence alignment data of Erg11, a protein known to be involved in fluconazole resistance (74.3-74.9%). Interestingly, the top Erg11 residues for predicting fluconazole resistance across Saccharomycotina do not overlap with, are not spatially close to, and are less conserved than those previously linked to resistance in clinical isolates of Candida albicans. In silico deep mutational scanning of the C. albicans Erg11 protein reveals that amino acid variants implicated in clinical cases of resistance are almost universally destabilizing while variants in our most informative residues are energetically more neutral, explaining why the latter are much more common than the former in natural populations. Importantly, previous experimental analyses of C. albicans Erg11 have shown that amino acid variation in our most informative residues, despite having never been directly implicated in clinical cases, can directly contribute to resistance. Our results suggest that studies of natural resistance in yeast species never encountered in the clinic will yield a fuller understanding of antifungal drug resistance.

Harrison, Marie-Claire [Vanderbilt Univ., Nashvill↗

DOE OSTI2026

ML-based Micro-CT SOFC Microstructure Models (from Kent 2026 Microstructural Augmentation paper)

Overview -------------------------- This repository contains datasets from the manuscript **"Enhanced Generalizability to Deep-Learning Quantification of 3D Microstructural Characteristics through Microstructurally Aware Augmentation of Scarce Data"** (*William F. Kent, Rochan Bajpai, Rachel C. Kurchin, William K. Epting, Harry W. Abernathy, Paul A. Salvador. Submitted 2026*). The methods are also described in the dissertation **Data Intensive Analysis of Solid Oxide Cell Microstructures** (*Doctoral dissertation, Carnegie Mellon University, 2025*). The datasets here are trained convolutional neural network (CNN) models for predicting key microstructural properties of solid oxide cell (SOC) electrodes from low-res, 2-channel 3D images, as well as some helpful code. The parameters for input images are provided in the paper. Sample data is provided in the file `Combined_anode_aug_dual_1k_examples` - that particular data was used to train `anode_all_aug.pth` and will work most accurately with that model. Please familiarize yourself with all caveats on accuracy and applicability, as detailed in the associated paper. Usage -------------------------- The basic usage is as follows, assuming `model_fn` is the path to the .pth file, and `X` is 2-channel input image(s) of the proper dimensions (either one image of shape `[2,12,24,24]`, or a batch of N input images of shape `[N,2,12,24,24]`): from CNN_inferencer import load_model_for_inference model = load_model_for_inference(model_fn) y_predicted = model(X) The model object automatically handles input scaling and output de-scaling based on the way the models were trained - in other words, pass in a 2-channel micro-CT image, and it will output microstructural property values in real units. ## Other model object attributes Note that model has useful attributes other than its forward pass model(X). * `model.output_descaler` - returns the output descaler object. Model does the de-scaling when generating inferences, but you may want to re-use this de-scaler on other values to e.g. compare predictions to ground truth from already-scaled training data. * `model.prop_names` - Gives the property names of the predicted y values, in order. Only exists if there's an output scaler as part of the model object, which there will be in the models provided here. ## Usage with sample data Here is a short script to use with the included sample data. from CNN_inferencer import display_predictions, load_model_for_inference, calculate_mape, parity_plot import h5py import numpy as np model_fn = 'anode_all_aug.pth' data_fn = 'Combined_anode_aug_dual_1k_examples.h5' N_samples = 200 figure_outdir = '.' model = load_model_for_inference(model_fn) with h5py.File(data_fn,'r') as f: XX = f['X'] #These are the 2-channel 3D images yy = f['y'] #These are the ground-truth microstructural properties, but they have been scaled for training - need to de-scale below N = XX.shape[0] #How many images total in the input data file #Run inferences on N_samples random samples from XX. #Run in a batch, much more efficient than one at a time. ii = np.random.choice(N,N_samples,replace=False) ii.sort() y_pred = model(XX[ii]) #Get the original/true (but normalized/scaled) values from the training dataset... #Because they were normalized, they are not in real units yet. So let's also de-scale them using model.output_scaler. y_true = model.output_scaler.transform(yy[ii]) #Let's display actual values for just 5 random ones for i in np.random.choice(N_samples,5,replace=False): display_predictions(y_true[i], y_pred[i], model.prop_names) #Make parity plots for each property (ground truth vs predicted values) #Also label each plot with the mean abs. percent error (MAPE) of the predicted values for i,key in enumerate(model.prop_names): mape = calculate_mape(y_true[:,i], y_pred[:,i]) parity_plot(y_true[:,i], y_pred[:,i], figure_outdir, key, extra_title=f' ({mape:.2f}% MAPE)')

3D microstructure↗

DOE OSTI2025

BULKI-Store v0.3.2

BULKI-Store is a distributed object storage system optimized for high-performance computing environments. Built with a Rust core and Python bindings, it efficiently manages scientific and machine learning datasets across HPC clusters. The system employs a client-server architecture with MPI integration, enabling seamless scaling on supercomputers like Perlmutter. BULKI-Store's object-oriented approach provides intuitive data organization with rich metadata support, contrasting with traditional file-based solutions. Key optimizations include selective checkpoint loading, unified checkpoint files, and object chunking for large data transfers. For machine learning workloads, BULKI-Store offers advantages through fine-grained access patterns, dynamic data sharing between training instances, and reduced memory pressure. Memory management features include strategic Python GC calls, minimized data copies, and batch processing capabilities. The system leverages Rayon's thread pool for asynchronous data prefetching and supports multiple CPU architectures (ARM64, x86, AMD, RISC-V). By combining performance optimizations with developer-friendly APIs, BULKI-Store addresses the complex data management challenges of modern HPC applications while maintaining compatibility across heterogeneous computing environments.

Zhang, Wei [Lawrence Berkeley National Laboratory ↗

DOE OSTI2025

SOC Microstructural Property Estimator

This pre-trained ML model is a tool that uses basic compositional parameters for porous solid oxide cell (SOC) electrodes - the phase fractions and mean particle/pore diameters – as inputs and uses them to estimate additional electrochemical performance parameters: active (i.e., connected) TPB density, all tortuosity factors, and phase pair specific interfacial areas. The electrode is assumed to be composed of two solid phases and a pore phase. The property calculations are performed using neural network regression models trained on a large bank of synthetic electrode microstructural data that NETL has generated using the program DREAM3D (that bank is also hosted on EDX: https://edx.netl.doe.gov/dataset/soc-synthetic-microstructure-bank). This means the generated parameters are based on training from actual measured properties from 3D microstructures, not estimated from geometric simplifications. This tool was developed and is intended to replace percolation theory calculations in models that use hypothetical electrode properties. An example use case would be running SOC performance simulations across a parametric sweep of electrode designs (e.g., varying phase fractions and particle sizes) and assessing how it impacts the electrochemical performance of the SOC. Within the parameter space of the training data (statistics of that parameter space is provided in the readme file), this model achieves sub-5% mean absolute percent errors, an order of magnitude less error than percolation theory across the same parameter space. However, be aware that this tool was developed with parametric simulations in mind, and users are encouraged to assess accuracy for their own specific use case rather than taking accuracy metrics at face value. More info, including a usage guide, is in the included readme file. This tool should be cited with the DOI number provided.

Electrode Microstructure↗

DOE OSTI2024

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net

Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step in the cryo-EM-based structure determination. However, existing methods trained on a limited amount of cryo-EM data still cannot accurately pick protein particles from noisy cryo-EM images. The general foundational artificial intelligence–based image segmentation model such as Meta’s Segment Anything Model (SAM) cannot segment protein particles well because their training data do not include cryo-EM images. Here, we present a novel approach (CryoSegNet) of integrating an attention-gated U-shape network (U-Net) specially designed and trained for cryo-EM particle picking and the SAM. The U-Net is first trained on a large cryo-EM image dataset and then used to generate input from original cryo-EM images for SAM to make particle pickings. CryoSegNet shows both high precision and recall in segmenting protein particles from cryo-EM micrographs, irrespective of protein type, shape and size. On several independent datasets of various protein types, CryoSegNet outperforms two top machine learning particle pickers crYOLO and Topaz as well as SAM itself. The average resolution of density maps reconstructed from the particles picked by CryoSegNet is 3.33 Å, 7% better than 3.58 Å of Topaz and 14% better than 3.87 Å of crYOLO. It is publicly available at https://github.com/jianlin-cheng/CryoSegNet

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Transferring predictions of formation energy across lattices of increasing size*

In this study, we show the transferability of graph convolutional neural network (GCNN) predictions of the formation energy of the nickel-platinum solid solution alloy across atomic structures of increasing sizes. The original dataset was generated with the large-scale atomic/molecular massively parallel simulator using the second nearest-neighbor modified embedded-atom method empirical interatomic potential. Geometry optimization was performed on the initially randomly generated face centered cubic crystal structures and the formation energy has been calculated at each step of the geometry optimization, with configurations spanning the whole compositional range. Using data from various steps of the geometry optimization, we first trained our open-source, scalable implementation of GCNN called HydraGNN on a lattice of 256 atoms, which accounts well for the short-range interactions. Using this data, we predicted the formation energy for lattices of 864 atoms and 2048 atoms, which resulted in lower-than-expected accuracy due to the long-range interactions present in these larger lattices. We accounted for the long-range interactions by including a small amount of training data representative for those two larger sizes, whereupon the predictions of HydraGNN scaled linearly with the size of the lattice. Therefore, our strategy ensured scalability while reducing significantly the computational cost of training on larger lattice sizes.

36 MATERIALS SCIENCE↗