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DOE OSTI2025

Leveraging unlabeled SEM datasets with self-supervised learning for enhanced particle segmentation

Scanning Electron Microscopes (SEMs) are widely used in experimental science laboratories, often requiring cumbersome and repetitive user analysis. Automating SEM image analysis processes is highly desirable to address this challenge. In particle sample analysis, Machine Learning (ML) has emerged as the most effective approach for particle segmentation. However, the time-intensive process of manually annotating thousands of SEM images limits the applicability of supervised learning approaches. Self-Supervised Learning (SSL) offers a promising alternative by enabling knowledge extraction from raw, unlabeled data. This study presents a framework for evaluating SSL techniques in SEM image analysis, focusing on novel methods leveraging the ConvNeXtV2 architecture for particle detection. A dataset comprising 25,000 SEM images is curated to benchmark these proposed SSL methods. The results demonstrate that ConvNeXtV2 models, with varying parameter counts, consistently outperform other techniques in particle detection across different length scales, achieving up to a 34% reduction in relative error compared to established SSL methods. Furthermore, an ablation study explores the relationship between dataset size and SSL performance, providing actionable insights for practitioners regarding model selection and resource efficiency. This research advances the integration of SSL into autonomous analysis pipelines and supports its application in accelerating materials science discovery.

Rettenberger, Luca↗

DOE OSTI2023

Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction

TRIMER, Transcription Regulation Integrated with MEtabolic Regulation, is a genome-scale modeling pipeline targeting at metabolic engineering applications. Using TRIMER, regulated metabolic reactions can be effectively predicted by integrative modeling of metabolic reactions with a Transcription Factor (TF)-gene regulatory network (TRN), which is modeled via a Bayesian network (BN). In this paper, we focus on sensitivity analysis of metabolic flux prediction for uncertainty quantification of BN structures for TRN modeling in TRIMER. We propose a computational strategy to construct the uncertainty class of TRN models based on the inferred regulatory order uncertainty given transcriptomic expression data. With that, we analyze the prediction sensitivity of the TRIMER pipeline for the metabolite yields of interest. The obtained sensitivity analyses can guide Optimal Experimental Design (OED) to help acquire new data that can enhance TRN modeling and achieve specific metabolic engineering objectives, including metabolite yield alterations. Here we have performed small- and large-scale simulated experiments, demonstrating the effectiveness of our developed sensitivity analysis strategy for BN structure learning to quantify the edge importance in terms of metabolic flux prediction uncertainty reduction and its potential to effectively guide OED.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Yield strength prediction of high-entropy alloys using machine learning

Yield strength at high temperature is an important parameter in the design and application of high entropy alloys (HEAs). However, the experimental measurement of yield strength at high temperature is quite costly, complicated, and time-consuming. Therefore, it is essential to identify and apply a robust method for the accurate prediction of yield strength at high temperature from the available experimental and simulation data. In this study, for the first time, a machine learning (ML) method based on the regression technique of random forest (RF) regressor is used to predict the yield strength of HEAs at the desired temperature. Further, the yield strengths of MoNbTaTiW and HfMoNbTaTiZr at 800 °C and 1200 °C, are predicted using the RF regressor model. We find that the results are consistent with the experimental reports, showing that the RF regressor model predicts the yield strength of HEAs at the desired temperatures with high accuracy.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Machine Learning-Guided Identification of PET Hydrolases from Natural Diversity

The enzymatic depolymerization of poly(ethylene terephthalate) (PET) is emerging as a leading chemical recycling technology for waste polyester. As part of this endeavor, new candidate enzymes identified from natural diversity can serve as useful starting points for enzyme evolution and engineering. In this study, we improved upon HMM searches by applying an iterative machine learning strategy to identify 400 putative PET-degrading enzymes (PET hydrolases) from naturally occurring homologs. Using high-throughput (HTP) experimental techniques, we successfully expressed and purified >200 enzyme candidates and assayed them for PET hydrolysis activity as a function of pH, temperature, and substrate crystallinity. From this library, we discovered 91 previously unknown PET hydrolases, 35 of which retain activity at pH 4.5 on crystalline material, which are conditions relevant to developing more efficient commercial processes. Notably, four enzymes showed equal to or higher activity than LCC-ICCG, a benchmark PET hydrolase, at this challenging condition in our screening assay, and 11 of which have pH optima <7. Using these data, we identified regions of PETases statistically correlated to activity at lower pH. We additionally investigated the effect of condition-specific activity data on trained machine learning predictors and found a precision (putative hit rate) improvement of up to 30% compared to a Hidden Markov Model alone. Our findings show that by pointing enzyme discovery toward conditions of interest with multiple rounds of experimental and machine learning, we can discover large sets of active enzymes and explore factors associated with activity at those conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Harnessing Machine Learning to Predict MoS 2 Solid Lubricant Performance

Physical vapor deposited (PVD) molybdenum disulfide (MoS 2 ) solid lubricant coatings are an exemplar material system for machine learning methods due to small changes in process variables often causing large variations in microstructure and mechanical/tribological properties. Here, in this work, a gradient boosted regression tree machine learning method is applied to an existing experimental data set containing process, microstructure, and property information to create deeper insights into the process-structure–property relationships for molybdenum disulfide (MoS 2 ) solid lubricant coatings. The optimized and cross-validated models show good predictive capabilities for density, reduced modulus, hardness, wear rate, and initial coefficients of friction. The contribution of individual deposition variables (i.e., argon pressure, deposition power, target conditioning) on coating properties is highlighted through feature importance. The process-property relationships established herein show linear and non-linear relationships and highlight the influence of uncontrolled deposition variables (i.e., target conditioning) on the tribological performance.

MoS2↗

DOE OSTI2026

Structure prediction of porous organic crystals

In this work, we explore the possibility of applying automated crystal structure prediction to reproduce the experimentally identified metastable porous polymorphs. Using our recently developed High-Throughput Organic Crystal Structure Prediction ( HTOCSP ) framework, we conducted a systematic study on five representative organic crystalline systems including hydrogen-bonded frameworks (HOFs), featured by the presence of significant porosity, in conjunction with different choices of energy models from classical, machine learning force fields, tight binding to density functional theory. Our results suggest that the current structure generation framework, with careful selection of symmetry conditions, is likely to generate rather complex and abundant metastable crystal candidates for porous crystals. In conjunction with the recent advance in universal machine learning force fields, it becomes possible to identify experimental structures as the energetically favorable candidates from a simple energy versus density analysis, thus paving the way for computational design of complex porous materials with the target systems prior to the experimental synthesis and characterization.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Prospects for Machine Learning and Pulse Shaping on the Scorpius Accelerator [Poster]

The Advanced Sources and Detectors (ASD) project aims to build Scorpius, a multi pulse linear induction accelerator capable of delivering a 1.4 kA electron beam at energies up to 24 MeV. One of the primary advancements of Scorpius is the use of solid state pulsed power (SSPP) to provide flexibility in pulse shaping by independently triggering 45 individual stages stacked in each of 984 line replaceable units (LRU), with 168 LRUs dedicated to the injector. By leveraging circuit modeling of each LRU stage, a machine learning model of the SSPP will be developed to allow for optimization of the pulse shape, including pulse flattening and reflection mitigation. Particle-in-cell simulations of Scorpius have, for example, demonstrated that reducing reflections during multi-pulse operation mitigates beam spill by preventing the production of off-energy electrons between pulses, thereby abating stimulated ion desorption from the wall and beam charge neutralization. This machine learning model will be validated and tuned with experimental data collected from the Scorpius injector and Integrated Test Stand

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

Machine Learning‐Guided Discovery of High‐Entropy Perovskite Oxide Electrocatalysts via Oxygen Vacancy Engineering

Abstract High‐entropy perovskite oxides (HEPOs) have recently emerged as multifunctional catalysts. However, the HEPOs’ structural and compositional complexity hinders the easy and accurate extrapolation of activity indicators, which are essential for establishing structure‐property correlations. Here, OxiGraphX, is introduced as a novel graph neural network (GNN) model designed to capture the complex relationships among structure, composition, and atomic chemical environments for accurate prediction of oxygen vacancy formation energies (OVFEs) in HEPOs. By integrating machine learning (ML), density functional theory (DFT), and experimental validation, this work demonstrates an efficient framework for rapidly and accurately screening HEPO electrocatalysts for oxygen evolution reaction (OER). The OxiGraphX predicts OVFEs with a precision exceeding existing data, enabling the identification of compositions of higher oxygen vacancy content (OVC) and, thus, higher catalytic activity. Furthermore, the model explores latent spaces that translate effectively into experimental domains, bridging computational predictions with real‐world applications. This approach accelerates the discovery of high‐performance HEPO catalysts while providing deeper insights into their catalytic mechanisms.

Chemistry↗

DOE OSTI2024

Anion-derived contact ion pairing as a unifying principle for electrolyte design

Enabling new electrochemical technologies requires systems that can operate under ever-more demanding conditions, and progress in energy storage applications reveals tantalizing opportunities to reimagine electrolyte design for performance at extreme potentials. Here, a common thread among these innovations is the formation of significant populations of contact ion pairs (CIPs) in the electrolyte, regardless of the specific cation chemistry or solvent system. The examples summarized in this review suggest that a set of general electrolyte design rules likely exists, where the purposeful selection of anion chemistry can yield CIP structures with tunable control over reaction thermodynamics, kinetics, and interphase chemistry. Identifying the relevant descriptors for high-performance, anion-derived CIP structures can be achieved utilizing a combined experimental and computational approach, aided by machine learning and artificial intelligence, to more rapidly survey the vast combinatorial space available and to enable a new generation of electrolytes for decarbonized electrochemical processes at scale.

electrochemistry↗

DOE OSTI2024

Analysis of biokinetic parameters reveals patterns in mercury accumulation across aquatic species

Mercury (Hg) is a potent neurotoxicant and poses a risk to human health through the ingestion of Hg-contaminated fish. Mercury, especially in its organic form methylmercury (MeHg), biomagnifies up food chains such that even small aqueous concentrations of Hg can result in significant concentrations of total Hg in fish. Understanding the ecological and human health risks associated with Hg and MeHg exposure requires an understanding of the factors that affect its bioaccumulation in aquatic species. We compiled estimates of three biokinetic parameters: uptake rate (k u ), assimilation efficiency (AE), and efflux rate (k e ). These parameters describe contaminant uptake from aqueous (k u ) and dietary (AE) exposure and the rate of excretion (k e ). We found parameter values for 38 and 34 different species of fish and aquatic invertebrates, respectively, and collected 502 parameter values in total. Here, we used a machine learning technique to establish the relationships between experimental and physiological variables and these parameter values. We found differences in which variables were associated with biokinetic parameter values for fish and aquatic invertebrates. The form of Hg was the most impactful variable, influencing values of all parameters except k u for invertebrates, for which aqueous exposure time was the only significant predicator variable. The parameter k e were the only values significantly influenced by more than one variable, with water type (freshwater, brackish, or marine), organism weight, and form of Hg significantly impacting parameter values for fish and/or invertebrates. To our knowledge, this study represents the most extensive review of biokinetic parameters of Hg and MeHg accumulation in aquatic organisms. Environmental parameters found to significantly impact Hg and MeHg bioaccumulation in past studies were not identified as important in our analyses across aquatic ecosystems and species. Our dataset and analysis reveal novel patterns that may help us better understand and manage Hg bioaccumulation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Perovskite neural trees

Trees are used by animals, humans and machines to classify information and make decisions. Natural tree structures displayed by synapses of the brain involves potentiation and depression capable of branching and is essential for survival and learning. Demonstration of such features in synthetic matter is challenging due to the need to host a complex energy landscape capable of learning, memory and electrical interrogation. We report experimental realization of tree-like conductance states at room temperature in strongly correlated perovskite nickelates by modulating proton distribution under high speed electric pulses. This demonstration represents physical realization of ultrametric trees, a concept from number theory applied to the study of spin glasses in physics that inspired early neural network theory dating almost forty years ago. We apply the tree-like memory features in spiking neural networks to demonstrate high fidelity object recognition, and in future can open new directions for neuromorphic computing and artificial intelligence.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Spatial arrangement of dynamic surface species from solid-state NMR and machine learning-accelerated MD simulations

Here, the surface arrangement of motional organic functionalities is explored by experimental dipolar coupling measurements and the prediction of motionally-averaged coupling constant from molecular dynamics simulations. The use of machine learning potentials was key to reaching the timescale required. The distance between dynamic surface species are important in cooperative heterogeneous catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Quantum error mitigation by hidden inverses protocol in superconducting quantum devices

We present a method to improve the convergence of variational algorithms based on hidden inverses (HIs) to mitigate coherent errors. In the context of error mitigation, this means replacing the hardware implementation of certain Hermitian gates with their inverses. Doing so results in noise cancellation and a more resilient quantum circuit. This approach improves performance in a variety of two-qubit error models where the noise operator also inverts with the gate inversion. We apply the mitigation scheme on superconducting quantum processors running the variational quantum eigensolver (VQE) algorithm to find the H 2 ground-state energy. When implemented on superconducting hardware we find that the mitigation scheme effectively reduces the energy fluctuations in the parameter learning path in VQE, reducing the number of iterations for a converged value. We also provide a detailed numerical simulation of VQE performance under different noise models and explore how HIs and randomized compiling affect the underlying loss landscape of the learning problem. These simulations help explain our experimental hardware outcomes, helping to connect lower-level gate performance to application-specific behavior in contrast to metrics like fidelity which often do not provide an intuitive insight into observed high level performance.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Optimal adjustment sets for causal query estimation in partially observed biomolecular networks

Abstract Causal query estimation in biomolecular networks commonly selects a ‘valid adjustment set’, i.e. a subset of network variables that eliminates the bias of the estimator. A same query may have multiple valid adjustment sets, each with a different variance. When networks are partially observed, current methods use graph-based criteria to find an adjustment set that minimizes asymptotic variance. Unfortunately, many models that share the same graph topology, and therefore same functional dependencies, may differ in the processes that generate the observational data. In these cases, the topology-based criteria fail to distinguish the variances of the adjustment sets. This deficiency can lead to sub-optimal adjustment sets, and to miss-characterization of the effect of the intervention. We propose an approach for deriving ‘optimal adjustment sets’ that takes into account the nature of the data, bias and finite-sample variance of the estimator, and cost. It empirically learns the data generating processes from historical experimental data, and characterizes the properties of the estimators by simulation. We demonstrate the utility of the proposed approach in four biomolecular Case studies with different topologies and different data generation processes. The implementation and reproducible Case studies are at https://github.com/srtaheri/OptimalAdjustmentSet.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Implementing two-qubit gates at the quantum speed limit

The speed of elementary quantum gates, particularly two-qubit gates, ultimately sets the limit on the speed at which quantum circuits can operate. In this work, we experimentally demonstrate commonly used two-qubit gates at nearly the fastest possible speed allowed by the physical interaction strength between two superconducting transmon qubits. We achieve this quantum speed limit by implementing experimental gates designed using a machine-learning-inspired optimal control method. Importantly, our method only requires the single-qubit drive strength to be moderately larger than the interaction strength to achieve an arbitrary two-qubit gate close to its analytical speed limit with high fidelity. Thus the method is applicable to a variety of platforms, including those with comparable single-qubit and two-qubit gate speeds, or those with always-on interactions. We expect our method to offer significant speedups for non-native two-qubit gates that are typically achieved with a long sequence of single-qubit and native two-qubit gates.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Attention to quantum complexity

The imminent era of error-corrected quantum computing demands robust methods to characterize quantum state complexity from limited, noisy measurements. We introduce the Quantum Attention Network (QuAN), a classical artificial intelligence (AI) framework leveraging attention mechanisms tailored for learning quantum complexity. Inspired by large language models, QuAN treats measurement snapshots as tokens while respecting permutation invariance. Combined with our parameter-efficient miniset self-attention block, this enables QuAN to access high-order moments of bit-string distributions and preferentially attend to less noisy snapshots. We test QuAN across three quantum simulation settings: driven hard-core Bose-Hubbard model, random quantum circuits, and toric code under coherent and incoherent noise. QuAN directly learns entanglement and state complexity growth from experimental computational basis measurements, including complexity growth in random circuits from noisy data. In regimes inaccessible to existing theory, QuAN unveils the complete phase diagram for noisy toric code data as a function of both noise types, highlighting AI’s transformative potential for assisting quantum hardware.

Kim, Hyejin [Cornell Univ., Ithaca, NY (United Sta↗

DOE OSTI2022

Defect identification in simulated Bragg coherent diffraction imaging by automated AI

X-ray Bragg coherent diffraction imaging is a powerful technique for operando and in situ materials characterization and provides a unique means of quantifying the influence of one-dimensional (1D) and two-dimensional (2D) material defects on material response. However, obtaining full images from raw x-ray diffraction data is nontrivial and computationally intensive, precluding real-time experimental feedback. Here, we present a machine learning approach to identify the presence of crystalline line defects (edge and screw) in samples from the raw, 2D, coherent diffraction data without the need for image reconstruction through iterative phase retrieval. Further, we compare different approaches to designing neural networks for this application and demonstrate the potential of automated ML (autoML) approaches.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Evaluating Production Implications of Pressure Maintenance in Unconventional Oil and Gas Wells using a Machine Learning Modeling Approach: Case Study in the Permian Basin

This study implements the proprietary machine learning-based model (model) developed under the 2022 study titled “Evaluating the Impact of Proprietary Oil & Gas Data on Machine Learning Model Performance Using a Quasi-Experimental Analytical Approach” for forecasting unconventional oil and gas production using well data from the Permian Basin. The model, developed using an exclusive dataset that includes time series production data from an operator in the Permian Basin, is designed to jointly predict daily oil, gas, and water production for horizontal wells as a function of bottomhole pressure drawdown, spatial placement across the study domain, and well-completion attributes. In this study, the model was explicitly applied to explore its utility to evaluate the impact of varying drawdown strategies on the production forecast of a well in the Permian Basin dataset. Managing pressure drawdown has been identified as a way to improve estimated ultimate recovery (EUR) from unconventional shale wells due to the stress-dependent nature of fractures in shale reservoirs. Research has shown that applying a lower pressure drawdown helps to maintain the reservoir conductivity, resulting in higher productivity over the life of a well. Historic bottomhole pressure data from the well over time was used as a benchmark from which to set more and less aggressive pressure decline rates as bounding modeling cases. All pressure decline rates/strategies were forecasted over 5 years, and the model was used to generate oil, water, and gas prediction over the same timeframe. This report presents the results from the production forecast and discusses potential operational and economic implications, with contrasting perspectives between well productivity and profitability given typical oil and gas economics and the volatility in the oil and gas market.

02 PETROLEUM↗