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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Machine learning at the Spallation Neutron Source accelerator and target

We describe the ongoing efforts to apply Machine Learning techniques to improve the performance of our accelerator and target. Specially, we are looking to minimize halo beam losses in the absence of a proper physics model, automatically detect and log anomalies in the target support systems such as cooling, and detect and prevent errant beam pulses in the linac. We also describe the infrastructure we use to acquire and stream data to the GPU cluster for training, our code development cycle, and edge computing for model inference. To minimize halo beam losses, we use a Reinforcement Learning technique tested on a virtual accelerator. The target anomaly detection is trained on archived data using incomplete physics models and is made part of the existing target reporting system. The errant beam prevention analyzes beam current and beam phase waveforms as well as accelerator configuration data to predict errant pulses. We also develop continual learning to adapt to changes in the accelerator.

Accelerator Physics↗
DOE OSTI2024

Demonstration and Evaluation of Explainable and Trustworthy Predictive Technology for Condition-based Maintenance

The domestic nuclear power plant (NPP) fleet has historically relied on labor-intensive and time-consuming predictive maintenance (PdM) programs, thus driving up operation and maintenance (O&M) costs to achieve high-capacity factors. Artificial intelligence (AI) and machine-learning (ML) can help simplify complex problems such as diagnosing equipment degradation to enable more effective decision-making efforts. The benefits of AI will be felt through more efficient plant O&M, improved work processes, and better integration of people and technology. Together, these benefits hold the promise to make nuclear power more sustainable by reducing O&M costs while improving employee engagement. While AI and ML technologies hold significant promise for the nuclear industry, there are challenges or barriers to their adoption. Explainability and trustworthiness of AI are two salient challenges that need to be addressed for wider deployment of these technologies in NPPs. This research focuses specifically on addressing the explainability and trustworthiness of AI technologies to advance the human, technical, and organization (HTO) readiness levels in adopting a risk-informed PdM strategy at commercial NPPs. In addition, this approach can be adapted to enhance the acceptability of AI in other nuclear applications with a few application-specific modifications. The technical approach ensuring wider adoption of AI technologies was developed by Idaho National Laboratory (INL)—in collaboration with Public Service Enterprise Group (PSEG), Nuclear, LLC—by utilizing the circulating water system (CWS) at two PSEG-owned plant sites for demonstration. Focused user studies were performed in collaboration with subject matter experts (SMEs) from PSEG and other nuclear domains to enhance human and organization readiness by building trust in AI-informed technologies. VIsualization for PrEdictive maintenance Recommendation (VIPER)—a Battelle Energy Alliance, LLC, copyrighted software—was developed and expanded to provide a user-centric visualization by incorporating inputs from the collaborating utility, human factors engineering guidelines, and data analysts. The VIPER software enables users, who may be unfamiliar with ML in general, to be interactively engaged by asking technical questions about PdM, work orders, diagnosis results and their confidence levels, the kind of data being used, and the types of ML algorithms employed. This interactive engagement enhances explainability and builds trust. One of the enabling accomplishments was the integration of large language models (LLMs), both text-based and vision-based, in the VIPER software.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Active oversight and quality control in standard Bayesian optimization for autonomous experiments

The fusion of experimental automation and machine learning has catalyzed a new era in materials research, prominently featuring Gaussian Process (GP) Bayesian Optimization (BO) driven autonomous experiments. Here we introduce a Dual-GP approach that enhances traditional GPBO by adding a secondary surrogate model to dynamically constrain the experimental space based on real-time assessments of the raw experimental data. This Dual-GP approach enhances the optimization efficiency of traditional GPBO by isolating more promising space for BO sampling and more valuable experimental data for primary GP training. We also incorporate a flexible, human-in-the-loop intervention method in the Dual-GP workflow to adjust for unanticipated results. We demonstrate the effectiveness of the Dual-GP model with synthetic model data and implement this approach in autonomous pulsed laser deposition experimental data. This Dual-GP approach has broad applicability in diverse GPBO-driven experimental settings, providing a more adaptable and precise framework for refining autonomous experimentation for more efficient optimization.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Loss Landscape Analysis for Reliable Quantized ML Models for Scientific Sensing

In this paper, we propose a method to perform empirical analysis of the loss landscape of machine learning (ML) models. The method is applied to two ML models for scientific sensing, which necessitates quantization to be deployed and are subject to noise and perturbations due to experimental conditions. Our method allows assessing the robustness of ML models to such effects as a function of quantization precision and under different regularization techniques -- two crucial concerns that remained underexplored so far. By investigating the interplay between performance, efficiency, and robustness by means of loss landscape analysis, we both established a strong correlation between gently-shaped landscapes and robustness to input and weight perturbations and observed other intriguing and non-obvious phenomena. Our method allows a systematic exploration of such trade-offs a priori, i.e., without training and testing multiple models, leading to more efficient development workflows. This work also highlights the importance of incorporating robustness into the Pareto optimization of ML models, enabling more reliable and adaptive scientific sensing systems.

Baldi, Tommaso [Pisa, Scuola Normale Superiore]↗
DOE OSTI2024

RuralAI in Tomato Farming: Integrated Sensor System, Distributed Computing, and Hierarchical Federated Learning for Crop Health Monitoring

Precision horticulture is evolving due to scalable sensor deployment and machine learning (ML) integration. These advancements boost the operational efficiency of individual farms, balancing the benefits of analytics with autonomy requirements. However, given concerns that affect wide geographic regions (e.g., climate change), there is a need to apply models that span farms. Federated learning (FL) has emerged as a potential solution. FL enables decentralized ML across different farms without sharing private data. Traditional FL assumes simple two-tier network topologies and, thus, falls short of operating on more complex networks found in real-world agricultural scenarios. Networks vary across crops and farms and encompass various sensor data modes, extending across jurisdictions. New hierarchical FL (HFL) approaches are needed for more efficient and context-sensitive model sharing, accommodating regulations across multiple jurisdictions. Here, we present the RuralAI architecture deployment for tomato crop monitoring, featuring sensor field units for soil, crop, and weather data collection. HFL with personalization is used to offer localized and adaptive insights. Model management, aggregation, and transfers are facilitated via a flexible approach, enabling seamless communication between local devices, edge nodes, and the cloud.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Converting sWeights to probabilities with density ratios

The use of machine learning approaches continues to have many benefits in experimental nuclear and particle physics. One common issue is generating training data which is sufficiently realistic to give reliable results. Here we advocate using real experimental data as the source of training data and demonstrate how one might subtract background contributions through the use of probabilistic weights which can be readily applied to training data. The sPlot formalism is a common tool used to isolate distributions from different sources. However, the negative sWeights produced by the sPlot technique can cause training problems and poor predictive power. This article demonstrates how density ratio estimation can be applied to convert sWeights to event probabilities, which we call drWeights. The drWeights can then be applied to produce the distributions of interest and are consistent with direct use of the sWeights. This article will also show how decision trees are particularly well suited to convert sWeights, with the benefit of fast prediction rates and adaptability to aspects of experimental data such as the data sample size and proportions of different event sources. We also show that a density ratio product approach in which the initial drWeights are reweighted by an additional converter gives substantially better results.

Glazier, Derek I. [Univ. of Glasgow, Scotland (Uni↗
DOE OSTI2024

Machine learning surrogate for charged particle beam dynamics with space charge based on a recurrent neural network with aleatoric uncertainty

In this work, we develop a machine learning (ML) model with aleatoric uncertainty for the low energy beam transport (LEBT) region of the LANSCE linear accelerator in which we model the transport of a space-charge-dominated 750 keV proton beam through a lattice of 22 quadrupole magnets. Our ML model is developed based on data generated by a Kapchinsky–Vladimirsky (KV) envelope model of beam transport. We show that a recurrent neural network can be used as a dynamical surrogate model for fast prediction of the LEBT beam envelope. Furthermore, we endow the model with the prediction of aleatoric uncertainty and compare three different approaches. We demonstrate that the ML-based uncertainty quantification models are well calibrated and produce good estimates of the regions where the model is less certain about its predictions. This ML framework is a necessary step in the development of a real-time virtual diagnostic tool with uncertainty quantification that can be integrated into more complex downstream tasks (e.g., adaptive control or learning flexible control policies via reinforcement learning) for improved efficiency in beam operations. In future work, we plan to expand on this preliminary study by considering more realistic envelope models that include longitudinal momentum spread and dispersive effects in bending magnets, as well as particle tracking codes with 3D space charge (such as and ). Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Dial

A key step in almost all scientific endeavors is answering the question: Given this data I already collected, what new data do I expect will yield the most useful information toward my scientific objective? The area of (sequential) experimental design has long been investigating answers to this question, but in recent years techniques from the machine learning subfield of active learning are increasingly applied. Researchers need a simple software tool for active learning applied to experimental design that can easily integrate into their existing workflows. This computer code, Dial, provides a microservice in ORNL's INTERSECT ecosystem for active learning applied to experimental design. By being part of the INTERSECT ecosystem, Dial is simple to integrate into any INTERSECT-based workflow. Dial provides multiple backend options, where a backend is an implementation of a specific active learning method. Users can select the backend that performs best for their application. Developers can also add new backends as needed. At its core, Dial receives a set of pre-existing measurements and input parameter bounds and then recommends one or more new sets of parameters to measure. Dial also includes interfaces to other microservices in the INTERSECT ecosystem so that it can be incorporated into INTERSECT campaigns. Dial provides a simple, yet powerful interface to convert automated INTERSECT workflows into autonomous workflows that adapt based on the results that are obtained. A shared microservice for active learning prevents duplicated effort by each application team implementing its own adaptive design of experiments tool.

Drane, Lance [Oak Ridge National Laboratory (ORNL)↗
DOE OSTI2026

Learned adaptive properties for mitigation of weight perturbations in embedded spiking networks

Recent years have seen an increased importance of neural network inference in edge-based scenarios, which impose size and power constraints requiring novel computing devices. These same edge scenarios may require operating over long periods of time, or exposure to extreme environments, resulting in a drift of neural network weights that cause degraded performance. In searching for ways to develop neural network approaches that perform robustly under these conditions, we propose a biologically-inspired mechanism for the dynamic adaptation of within-neuron parameters that is guided by a global context signal carrying information about perturbations and variability in incoming stimuli. Specifically, we demonstrate that adaptive voltage thresholds or neuronal time constants, when informed by a global context signal, can enable network-level mechanisms to recover from perturbed synaptic weights. Consistent with prior literature, the context-modulated approach is effective for recurrent, but not feedforward networks, by modulating network level dynamics. We demonstrate this approach successfully recovers performance in image classification tasks and spatiotemporal tracking tasks under idealized and Gaussian noise as well as for realistic perturbations from a memristive device when exposed to ionizing radiation. Finally, we discuss how this approach enables the design of robust and energy-efficient neuromorphic systems that perform well, even in resource-constrained scenarios with extreme environments such as edge processing.

context modulation↗
DOE OSTI2025

Implementation of disruptive designs for gas turbine components using direct energy deposition additive manufacturing

This research aims to develop a framework for establishing the correlation between in-situ monitoring data, process parameters, and microstructure evolution in blown-powder laser-directed energy deposition (DED) additive manufacturing (AM). To achieve this, a comprehensive manufacturing framework has been developed, spanning from in-situ data acquisition, melt-pool simulation, microstructure modeling, and statistical microstructure quantification. A machine learning-based surrogate model is constructed to predict melt pool geometry directly from in-situ coaxial camera data. The surrogate model is trained using outputs from a high-fidelity melt pool simulation, which provides accurate melt pool dimension data under varying process conditions. The predicted melt pool geometry is then used as input to a microstructure model to predict microstructural features. To rigorously compare and analyze microstructures, the project introduces statistical metrics that quantify differences based on key features such as morphology and texture. Microstructures are represented using advanced statistical descriptors including angular chord length distribution, two-point spatial statistics, orientation distribution function, and global spherical harmonic. These representations are used to compute four distinct “dissimilarity scores” that quantitatively capture differences in texture and morphology. This framework is demonstrated to enable automated calibration of simulation parameters by minimizing discrepancies between simulated and target microstructures. The technology developed in this project enables direct correlation between in-situ monitoring data and resulting microstructure, paving the way for adaptive microstructure control in metal AM. This capability strengthens the connection between process parameters and final material properties, facilitating more precise and reliable material design.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Constructing a High‐Resolution Aftershock Catalog for the 2017 Mw 8.2 Tehuantepec Earthquake Sequence Using a Machine Learning–Based Workflow

The 8 September 2017 Mw 8.2 Tehuantepec earthquake was the largest instrumentally recorded normal‐faulting earthquake in Mexico. The mainshock occurred offshore within the Tehuantepec seismic gap, generating >30,000 aftershocks in the following year. We applied an open‐source, machine learning (ML)–assisted workflow to construct a high‐resolution aftershock catalog using data from temporary and permanent seismic networks in southern Mexico. The workflow integrates PhaseNet for phase detection; GaMMA for phase association; and VELEST, HypoInverse, and HypoDD for velocity modeling and relocation. We processed seven months of continuous waveform data from 29 broadband stations, including a temporary rapid‐response deployment that improved station coverage of the offshore rupture zone. To evaluate performance, we compared our results against analyst‐reviewed picks and event locations from the Servicio Sismológico Nacional catalog. The resulting catalog contains 11,374 relocated earthquakes and represents the most comprehensive published dataset for this sequence, incorporating the first full use of the temporary network. Relocated hypocenters show improved depth control and align well with the Slab2.0 subduction geometry, revealing clearer separation between offshore slab events and onshore crustal seismicity. This study demonstrates that combining ML‐based detection with established methods provides a scalable and reproducible approach for constructing high‐quality earthquake catalogs in tectonically complex environments and offers practical guidance for adapting similar workflows to other earthquake sequences.

Garcia, Marc [The University of Texas at El Paso, ↗
DOE OSTI2026

Predicting Adaptively Chosen Observables in Quantum Systems

Recent advances have demonstrated that 𝒪⁡(log 𝑀) measurements suffice to predict 𝑀 properties of arbitrarily large quantum many-body systems. However, these remarkable findings assume that the properties to be predicted are chosen independently of the data. This assumption can be violated in practice, where scientists adaptively select properties after looking at previous predictions. This work investigates the adaptive setting for three classes of observables: local, Pauli, and bounded-Frobenius-norm observables. We prove that Ω⁡(√𝑀) samples of an arbitrarily large unknown quantum state are necessary to predict expectation values of 𝑀 adaptively chosen local and Pauli observables, where the system size scales exponentially and polynomially in 𝑀, respectively. We also present computationally efficient algorithms that achieve this information-theoretic lower bound. In contrast, for bounded-Frobenius-norm observables, we devise an algorithm requiring only 𝒪⁡(log 𝑀) samples, independent of system size. These results highlight the potential pitfalls of adaptivity in analyzing data from quantum experiments and provide algorithmic tools to safeguard against erroneous predictions in quantum experiments.

Machine learning↗
DOE OSTI2025

Computationally efficient models for aqueous organic redox flow batteries

The rising usage of intermittent energy has garnered the need for large scale energy storage systems. Redox flow batteries (RFB) based energy storage system shows promising potential. Numerical simulations and machine learning approaches have been widely used to study RFB performance. The development of autonomous material discovery framework and digital twin of energy storage system usually needs to query cell performance through fast response models. In this study, two computationally efficient models are introduced: a physics-based analytical flow battery model (EZBattery), and a machine learning operator model (Deep Operator Network, denoted by DeepONet). Both models can provide cell performance near instantly, and prediction accuracy was systematically examined on an application of evaluating the performances of a 780 cm 2 aqueous organic redox flow battery (AORFB), using potential anolyte candidates in dihydroxyphenazine (DHP)-based family of organic materials. A validated computationally expansive 3-dimensional multi-physics finite element model by COMSOL was used as the ground truth and provided the training data set for the DeepONet. 1280 samples were generated with 10 properties to mimic the different possible anolyte candidates, and the cell performances were evaluated under 10 different combined operating conditions. The accuracy comparisons for the two computationally efficient models show that both models can provide comparable accuracy in predicting cell charging/discharging voltage curves. DeepONet can provide slightly higher overall accuracy than EZBattery with faster calculation speed, but highly relies on the training dataset. EZBattery does not need a training dataset and can provide interpretable physics-based explanations of the results, while being more flexible to adjust to adapt any different cell designs, flow battery architectures, and electrolyte materials.

Analytical model↗
DOE OSTI2024

Multi-Source Machine Learning and Thermoplastics Enhanced Aerostructure Manufacturing (mTEAM)

RTX Technology Research Center (RTRC), together with Collins Aerospace (Collins) and Oak Ridge National Laboratory (ORNL) has developed an Artificial Intelligence (AI) / Machine Learning (ML) guided solution to advance the manufacturing and assembly of high performance and lightweight thermoplastic composite (TPC) aerospace products. The solution aims to lower risk, cost and lead time for induction heating based welding and consolidation processes for TPC structure. The cost and lead time of part and material specific process development for induction welding (IW) and induction consolidation will be reduced by replacing traditional empirical methods with optimization methods that merge AI/ML and physics-based process simulations and process experiments with sensing and controls. TPC-IW process development is empirical in nature, and uncertainties in material & process behavior exist near & far from the induction coil. Physics-based simulations can be leveraged directly for process optimization but can be too computationally expensive to run in high fidelity and real time to do robust process optimization. The key impact of successful TPC induction consolidation and welding is cost & lead time reduction for part & material specific consolidation and welding recipes. This is an enabler for more rapid deployment of TPC structures via joining assembly, which can reduce energy & cost intensive usage of autoclaves & ovens. The solution aimed to advance the U.S. Department of Energy’s interests in using thermoplastics and automation in composite manufacturing for improvement of products for existing markets via increased production speeds, reduced costs, and lowered use of energy. Welded TPC structures can offer significant weight & energy savings for high-value commercial aerospace & industrial applications compared to metal & thermoset composite structures assembled by mechanical fastening and/or adhesive bonding. The project was organized into two Budget Periods. Budget Period 1 (BP1) was 15 months and its goal was to perform ML process optimization framework development & deployment on lab-coupon aerostructure components. A Go/No-Go Review was performed at the end of BP1 to verify fulfilment of key tasks & milestones to justify a Go Decision to move into the next Budget Period. Budget Period 2 (BP2) was 12 months and its goal was the deployment of the ML framework for ML process optimization of pilot industrial scale aerostructure components. The overall project aim was to develop & demonstrate ML-enhanced modeling framework that learns process-property mapping from multiple data sources at different fidelities. During BP1, the team accomplished key tasks & milestones to demonstrate the concept of multi-source ML for TPC aerostructure consolidation and assembly. First, the team completed documentation of induction based TPC heating requirements including baseline metrics to compare measured results against. Next the team completed demonstration of data generation from physics-based simulations for ML surrogate model generation and demonstrated the integration of physics-based simulation data into multi-source AI/ML algorithms. In parallel, the team established the lab-coupon scale induction welding system and completed a process to label and reduce generated data from physics-based simulation and experiments for ML surrogate models to enable multi-source ML model training & testing. To complete BP1, the team integrated physics-based simulation data and experimental data into multi-source ML algorithms. This was based on the team completing ML deployment of the induction welding on a lab system at RTRC and AI/ML deployment on existing induction welding line at Collins. ORNL visited both Collins and RTRC sites to witness the TPC induction welding process. Then, ORNL designed and constructed a new version of their vision-based sensing system better adapted to acquire process signals of the TPC induction welding process for process anomaly and defect detection. In BP2, the team accomplished key tasks & milestones to scale up multi-source ML for TPC aerostructure consolidation and assembly from the lab-coupon scale to the pilot-industrial scale. In BP2, the team demonstrated real time anomaly & defect detection via experiments performed by ORNL & RTRC. The team completed ML-optimization heating trials for TPC induction consolidation at Collins, and the team confirmed pilot industrial scale experimental data from Collins was compatible with the developed ML pipeline from RTRC. The team completed sub-element scale ML process optimization demonstration at RTRC, where the team leveraged RTRC’s robotic TPC welding setup to de-risk the ML process optimization by performing ML analysis of recorded temperatures to account for complex part features. Then, the team applied its ML-derived control strategies and ML process optimization framework at Collins to the pilot-industrial scale on a demo skin-stiffener part representative of a nacelle aerostructure fan cowl section. The key innovation is the AI/ML framework enabling effective process development of high performance, lightweight, energy efficient TPCs for composite aircraft structures.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Reinforcement Learning as a Parsimonious Alternative to Prediction Cascades: A Case Study on Image Segmentation

Deep learning architectures have achieved state-of-the-art (SOTA) performance on computer vision tasks such as object detection and image segmentation. This may be attributed to the use of over-parameterized, monolithic deep learning architectures executed on large datasets. Although such large architectures lead to increased accuracy, this is usually accompanied by a larger increase in computation and memory requirements during inference. While this is a non-issue in traditional machine learning (ML) pipelines, the recent confluence of machine learning and fields like the Internet of Things (IoT) has rendered such large architectures infeasible for execution in low-resource settings. For some datasets, large monolithic pipelines may be overkill for simpler inputs. To address this problem, previous efforts have proposed decision cascades where inputs are passed through models of increasing complexity until the desired performance is achieved. However, we argue that cascaded prediction leads to sub-optimal throughput and increased computational cost due to wasteful intermediate computations. To address this, we propose PaSeR (Parsimonious Segmentation with Reinforcement Learning) a non-cascading, cost-aware learning pipeline as an efficient alternative to cascaded decision architectures. Through experimental evaluation on both real-world and standard datasets, we demonstrate that PaSeR achieves better accuracy while minimizing computational cost relative to cascaded models. Further, we introduce a new metric IoU/GigaFlop to evaluate the balance between cost and performance. On the real-world task of battery material phase segmentation, PaSeR yields 179% improvement over SOTA MatPhase model and a 196% improvement over IDK Cascades under the IoU/GigaFlop metric. We also demonstrate PaSeR’s adaptability to complementary models trained on a noisy MNIST dataset, where it outperforms all baselines on IoU/GigaFlop by an average of 44%.

Srikshan, Bharat↗
DOE OSTI2025

Joint Modeling of Quasar Variability and Accretion Disk Reprocessing Using Latent Stochastic Differential Equations

Quasars are bright active galactic nuclei powered by the accretion of matter around supermassive black holes at the center of galaxies. Their stochastic brightness variability depends on the physical properties of the accretion disk and black hole. The upcoming Rubin Observatory Legacy Survey of Space and Time (LSST) is expected to observe tens of millions of quasars, so there is a need for efficient techniques like machine learning that can handle the large volume of data. Quasar variability is believed to be driven by an X-ray corona, which is reprocessed by the accretion disk and emitted as UV/optical variability. We are the first to introduce an auto-differentiable simulation of the accretion disk and reprocessing. We use the simulation as a direct component of our neural network to jointly model the driving variability and reprocessing, trained with supervised learning on simulated LSST-like 10 yr quasar light curves. We encode the light curves using a transformer encoder, and the driving variability is reconstructed using latent stochastic differential equations, a physically motivated generative deep learning method that can model continuous-time stochastic dynamics. By embedding the physical processes of the driving signal and reprocessing into our network, we achieve a model that is more robust and interpretable. We demonstrate that our model outperforms a Gaussian process regression baseline and can infer accretion disk parameters and time delays between wave bands, even for out-of-distribution driving signals. Our approach provides a powerful framework that can be adapted to solve other inverse problems in multivariate time series.

Fagin, Joshua [City Univ. of New York (CUNY), NY (↗
DOE OSTI2024

Uncovering obscured phonon dynamics from powder inelastic neutron scattering using machine learning

The study of phonon dynamics is pivotal for understanding material properties, yet it faces challenges due to the irreversible information loss inherent in powder inelastic neutron scattering spectra and the limitations of traditional analysis methods. In this study, we present a machine learning framework designed to reveal obscured phonon dynamics from powder spectra. Using a variational autoencoder, we obtain a disentangled latent representation of spectra and successfully extract force constants for reconstructing phonon dispersions. Notably, our model demonstrates effective applicability to experimental data even when trained exclusively on physics-based simulations. The fine-tuning with experimental spectra further mitigates issues arising from domain shift. Analysis of latent space underscores the model’s versatility and generalizability, affirming its suitability for complex system applications. Furthermore, our framework’s two-stage design is promising for developing a universal pre-trained feature extractor. This approach has the potential to revolutionize neutron measurements of phonon dynamics, offering researchers a potent tool to decipher intricate spectra and gain valuable insights into the intrinsic physics of materials.

domain adaptation↗
DOE OSTI2025

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning

The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.

Artificial intelligence↗