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852 records · Page 48

scPlantAnnotate: an accurate and robust transformer-based model for plant cell type annotation

Accurate cell type annotation remains a major bottleneck in plant single-cell RNA sequencing (scRNA-seq), where existing tools are often adapted from animal studies and perform sub-optimally on plant data. The lack of plant-specific computational frameworks limits the construction of plant cell atlases and downstream biological discovery. We develop and evaluate scPlantAnnotate, a Transformer-based reference annotation framework tailored for plant scRNA-seq data, and benchmark it against state-of-the-art deep learning and conventional methods across multiple plant species. Species-specific scPlantAnnotate models were trained using curated datasets from Arabidopsis thaliana, Zea mays, Oryza sativa, and Glycine max. We compared scPlantAnnotate with leading baselines under both standard random-split evaluation and a more stringent leave-one-dataset-out setting, which tests robustness to completely unseen datasets and tissue types. scPlantAnnotate consistently outperforms existing approaches across all four species under random-split evaluation. In the leave-one-dataset-out setting for A. thaliana, where performance drops markedly for all methods due to strong batch effects and dataset heterogeneity, scPlantAnnotate nonetheless achieves the highest Accuracy, Macro-F1, Balanced Accuracy, and Macro-AUROC on average and ranks first on most held-out datasets. These results demonstrate improved robustness to dataset shifts, a critical yet underexplored challenge in plant scRNA-seq analysis. A freely accessible web server enables users to annotate their own datasets using pretrained models. scPlantAnnotate provides a plant-specific, Transformer-based framework for single-cell annotation that delivers state-of-the-art performance and enhanced robustness to unseen datasets. By addressing limitations of existing tools and enabling scalable reference-based annotation, scPlantAnnotate supports the development of comprehensive plant cell atlases and facilitates broader use of single-cell genomics in plant biology.

Bioinformatics↗

Hydrogen Detection Strategies to Support H2@SCALE - The NREL Sensor Laboratory

Hydrogen represents a major pathway to decarbonize and stabilize the national and international energy industry and select manufacturing markets. To facilitate the development of hydrogen markets, the US Department of Energy initiated H2@Scale to bring together stakeholders to advance affordable hydrogen production, transport, storage, and utilization to increase revenue opportunities in multiple energy sectors. One major impediment to hydrogen implementation is cost. To expedite the use of hydrogen in energy and other markets, the United States announced in 2021 the Hydrogen Shot, which seeks to reduce the cost of clean hydrogen by 80% to $1 per 1 kilogram in 1 decade ("1 1 1"). As the cost of hydrogen drops, new applications will emerge that will require unique configurations of existing equipment and infrastructure, and eventually lead to advances in the generation and utilization of hydrogen. As the hydrogen economy expands, sensors and detection methods will need to adapt to changing infrastructure demands to address the primary targets of health & safety, emissions monitoring, and process control. The NREL Sensor Laboratory is playing a pivotal role in advancing the use of hydrogen sensors and detection methodologies in each of these categories to support DOE's mission for safe and efficient utilization in emerging markets. Health & safety monitors are required to ensure that operators and facilities can react to unintended hydrogen releases, either as GH2, LH2, or as a constituent of blends (e.g., natural gas or ammonia). Current detection methodologies focus on safety applications to detect near its lower flammable limit (4 vol %), and typically include point sensors in applications such as fixed or mobile detectors (e.g., personal gas monitors). Methodologies amenable for area detection include acoustic, emerging optical imaging methods, and flame detectors. Comparable detection strategies can be utilized for emissions monitoring and quantization, however few methods can simultaneously cover both low (emissions) and high (health & safety) levels. Deployment of emission level detectors will be required to 1) reduce product loss through small but potentially significant leaks from an environmental or cost perspective, 2) reduce downtime of high demand systems by early identification of eminent system failures (leaks through pump or compressor seals indicative of impending failure), and 3) address potential emission monitoring requirements that may be set by regulating bodies. The first two points should be adopted by industry to reduce the cost-of-goods-sold. The third main category for hydrogen detection relates to process control and may be advantageous for many existing applications. Two main applications are emerging. For example, the purity requirements for hydrogen that is dispensed from refueling systems for hydrogen fuel cell electric vehicles (FCEV) is rigorously regulated by the Standard SAE J2719, which prescribes maximum allowable levels of multiple impurities in the hydrogen fuel and must be verified by a regulatory body. Hydrogen contaminant detectors (HCD) integrated to the fueling station can assure this compliance. HCDs must be able operate in 100% H2 backgrounds and be able to distinguish between multiple contaminants at low ppm to low ppb levels. Secondly, as a strategy to decarbonize the natural gas grid, there are proposals to blend hydrogen with natural gas. This blending will affect transport applications (pipeline infrastructure), stationary combustion systems (turbines), and consumer and commercial appliances. In the short-term, hydrogen levels up to 20% are proposed. Variations in the hydrogen level can have dramatic impact on the combustion process and on the potential response of safety sensors. These mixtures may be regulated so that the concentration at a delivery point must be monitored with high precision. However, routine maintenance may introduce background gases such as ambient air (with water) or maintenance gases (introduced with welding processes or adhesive outgassing.) Therefore, the detection methodology must be robust enough to recover or respond to various contaminants. Several reviews can be found in literature addressing sensing and detection technologies, including their limitations and applications. However, for most applications, limitations can be alleviated by combining various detection techniques either through system integration or implementation of machine learning methods (artificial intelligence). In this presentation, we will discuss several applications, highlight their current approach for hydrogen detection, and suggest detection strategies to supplement their limitations.

ENERGY STORAGE,HYDROGEN↗

Data-driven cyber attack detection and mitigation for decentralized wide-area protection and control in smart grids

Modern power systems have already evolved into complicated cyber physical systems (CPS), often referred to as smart grids, due to the continuous expansion of the electrical infrastructure, the augmentation of the number of heterogeneous system components and players, and the consequential application of a diversity of information and telecommunication technologies to facilitate the Wide Area Monitoring, Protection and Control (WAMPAC) of the day-to-day power system operation. Because of the reliance on cyber technologies, WAMPAC, among other critical functions, is prone to various malicious cyber attacks. Successful cyber attacks, especially those sabotage the operation of Bulk Electric System (BES), can cause great financial losses and social panics. Application of conventional IT security solutions is indispensable, but it often turns out to be insufficient to mitigate sophisticated attacks that deploy zero-day vulnerabilities or social engineering tactics. To further improve the resilience of the operation of smart grids when facing cyber attacks, it is desirable to make the WAMPAC functions per se capable of detecting various anomalies automatically, carrying out adaptive activity adjustments in time and thus staying unimpaired even under attack. Most of the existing research efforts attempt to achieve this by adding novel functional modules, such as model-based anomaly detectors, to the legacy centralized WAMPAC functions. In contrast, this dissertation investigates the application of data-driven algorithms in cyber attack detection and mitigation within a decentralized architecture aiming at improving the situational awareness and self-adaptiveness of WAMPAC. First part of the research focuses on the decentralization of System Integrity Protection Scheme (SIPS) with Multi-Agent System (MAS), within which the data-driven anomaly detection and optimal adaptive load shedding are further explored. An algorithm named as Support Vector Machine embedded Layered Decision Tree (SVMLDT) is proposed for the anomaly detection, which provides satisfactory detection accuracy as well as decision-making interpretability. The adaptive load shedding is carried out by every agent individually with dynamic programming. The load shedding relies on the load profile propagation among peer agents and the attack adaptiveness is accomplished by maintaining the historical mean of load shedding proportion. Load shedding only takes place after the consensus pertaining to the anomaly detection is achieved among all interconnected agents and it serves the purpose of mitigating certain cyber attacks. The attack resilience of the decentralized SIPS is evaluated using IEEE 39 bus model. It is shown that, unlike the traditional centralized SIPS, the proposed solution is able to carry out the remedial actions under most Denial of Service (DoS) attacks. The second part investigates the clustering based anomalous behavior detection and peer-assisted mitigation for power system generation control. To reduce the dimensionality of the data, three metrics are designed to interpret the behavior conformity of generator within the same balancing area. Semi-supervised K-means clustering and a density sensitive clustering algorithm based on Hierarchical DBSCAN (HDBSCAN) are both applied in clustering in the 3D feature space. Aiming to mitigate the cyber attacks targeting the generation control commands, a peer-assisted strategy is proposed. When the control commands from control center is detected as anomalous, i.e. either missing or the payload of which have been manipulated, the generating unit utilizes the peer data to infer and estimate a new generation adjustment value as replacement. Linear regression is utilized to obtain the relation of control values received by different generating units, Moving Target Defense (MTD) is adopted during the peer selection and 1-dimensional clustering is performed with the inferred control values, which are followed by the final control value estimation. The mitigation strategy proposed requires that generating units can communicate with each other in a peer-to-peer manner. Evaluation results suggest the efficacy of the proposed solution in counteracting data availability and data integrity attacks targeting the generation controls. However, the strategy stays effective only if less than half of the generating units are compromised and it is not able to mitigate cyber attacks targeting the measurements involved in the generation control.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Digitalization mapping and assessment process supporting ION strategic transformation activities

The existing fleet of commercial nuclear power plants (NPPs) are an important asset in the nation’s portfolio of electrical generating resources. Their continued safe and reliable operation are critical to providing a large source of carbon-free electricity to power the nation’s economy. The United States Department of Energy’s (DOE) Light Water Reactor Sustainability (LWRS) Program develops the scientific bases, methods, and tools, for the continued safe and economical operation of the nation's commercial NPPs. The Plant Modernization Pathway within LWRS Program focuses on providing guidance to industry on the full-scale implementation of modernization solutions for NPPs that significantly reduce the technical and financial risks associated with modernization. This research is focused on helping the nuclear industry understand how to digitize and digitalize their NPPs so that they can design their modernization solutions to be scalable, sustainable, and integrated both laterally and horizontally within their organization. That is, this research creates a digital transformation in NPPs by reshaping cultural mindsets and by identifying business efficiencies. In partnership with industry, and using four previously established guiding principles for digitalization, this research supported NPP modernization through assessing readiness for digitalization as a means to achieve integrated operations for nuclear. Specifically, this research created an assessment to review an entire organization’s work processes to gather information about the digitalization health of the plant. The assessment tools were administered to plant employees, and the results were used to develop a digitalization plan. The survey assessment identified the optimal candidate processes that would most benefit from a digitalization initiative which were revealed through analytical frameworks. One analysis calculated mean digitalization health indicator scores for all endorsed activities which allowed the researchers to rank and color code the results for easy identification. Individual health indicator scores are also provided, should our industry partner wish to understand these findings according to their own organizational priorities, business considerations and desired end-state. The results were also analyzed from the perspective that organizations are comprised of different types of innovators (e.g., generators, optimizers, conceptualizers, and implementers), which differentially affects the organization’s ability to comprehend and adapt to change (i.e., opportunities to innovate). Understanding the relative composition of innovator types at an NPP allows them to gather insights into the strengths and weaknesses they have in innovating how work is performed. For the utility that partnered with this research team, the results showed that implementers make up the largest portion of respondents and conceptualizers the smallest portion. Knowing the proportion of innovator types gave this organization insights on how they can effectively implement their innovation solutions. Additionally, the results were analyzed from a technical, economic, and risk perspective to identify and quantify work reduction opportunities (WROs). Recognizing that not all cost-saving opportunities are the same, a Technical, Economic and Risk Assessment (TERA) was performed to evaluate WROs to identify areas of greatest potential and lowest risk. The key results from TERA included a digitalization opportunity score for each activity, and a calculation of potential cost savings. These two outputs formed the bases for calculating a priority index and rank for the activities/processes assessed. From the prioritization calculations, TERA can then help the utility 1) decide what digitalization priorities to invest money in implementing and then 2) calculates how much should be invested in the digitalization initiatives selected to achieve cost savings and/or an acceptable return on investment. Last, onsite interviews revealed several inefficiencies in the standard work processes that occur cross-departmentally that are due to the absence of digitized and digitalized processes. Examples of these include time spent scanning paper documents and then uploading the documents electronically, obtaining signatures, and searching for desired information. This represents a digital but not digitalized process. Over 15 opportunities to improve work processes were identified through this multi-method digitalization assessment. The various analytical assessments used (e.g., TERA, digitalization health indicator scores), as well as discussions with the utility partner, corroborated that all the opportunities identified had a strong potential to make work processes more efficient and to improve overall performance of the NPP.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

MPEX AI Digital Twins

All magnetically confined plasma fusion power plant concepts (Tokamak, Spherical Tokamak, Stellarator, Mirror, ...) must exhaust the heat and plasma from the core confinement region to the material walls. The primary channel for this exhaust is through a plasma divertor which directs plasma along open magnetic field lines to a material target. The Material Plasma Exposure eXperiment (MPEX) illustrated in Figure 1, is a high-power, steady-state linear plasma device designed to produce the plasma material interaction (PMI) conditions of the divertor of future magnetic confinement fusion power plants: energy flux 20MW/m 2 , ion fluence 1031/m 2 , pulse duration 106 sec. These goals of plasma exposure in MPEX are well beyond those achieved in magnetic fusion experimental devices. Successfully achieving these high power steady state conditions for long pulses requires operational control of the heating and particle sources and the plasma flux to the walls and target. The MPEX AI Hot Spot Controller, proposed in this project, will help achieve the operational milestones of MPEX. The MPEX device will begin commissioning at the end of FY26. A smaller proto-MPEX was operated for 14,666 plasma discharges and will resume operation in September of 2025 as proto-MPEX-lite, with reduced capability, to test a new window for the Helicon plasma source. The proto-MPEX data has undergone surrogate modeling with machine learning methods (R. Archibald, 2022 IEEE International Conference on Big Data). This proto-MPEX data will be used to begin development of the AI digital twins described in this white paper. The scientific mission of MPEX is to qualify materials of different composition for use in the high energy and plasma flux conditions of a fusion power plant. The materials exposed in MPEX will in some cases be exposed to high neutron fluxes at other ORNL facilities to measure the changes to their PMI properties. The targets exposed in MPEX will be transported under vacuum to a Surface Analysis Station (SAS). The SAS will be equipped with the following diagnostics: Focused Ion Beam (FIB) for trench milling, 100-400 angstrom resolution scanning electron microscope (SEM), surface mapping x-ray spectrometer, high resolution camera, and a future upgrade to a laser induced breakdown spectroscopy quadruple mass spectrometer (LIBS-QMS). The MPEX experiments will generate diverse pre- and post-exposure measurement data of detailed material properties down to the crystal grain level in 3D for post-exposure assessment of PMI damage (e.g. cracking, melting, erosion and redeposition of the material). Physics models for the PMI, and how the material composition and manufacturing impact its performance under high energy plasma exposure, need to be validated with MPEX data to guide the selection of new candidate materials. Our vision for the MPEX AI Digital Twins project is to supply experimental and physics model simulation data to train Artificial Intelligence (AI) models for data processing, analysis, operational control, PMI and materials simulation to maximize the scientific output of the MPEX device. Ultimately, an AI digital twin of MPEX material assessment metrics for tested and synthetic material types with simulated PMI will be trained by the AI Modeling Teams on the experimental and physics simulation data submitted to the American Science Cloud by this project. A purely empirical search for the best material is inefficient given the finite number of samples that can be tested on MPEX. In order to expand the material properties database for training the MPEX Material Assessment AI Digital Twin, and to gain physics understanding of the PMI processes, physics models of the material properties and PMI processes are required. The physics simulations provide detailed simulation data, like impact angles for plasma ions, sputtering yields, transport of the ionized sputtered target material in the plasma, and redeposition locations. This simulation data expands the measurement data for deeper physics understanding. The experimental data is essential to validate the PMI and material structure simulation models. The validated models can then be used to generate new simulation data of MPEX material assessments for synthetic material compositions that have not been exposed in MPEX. These predictive simulations, plus the whole experimental dataset, will be used to train the MPEX Material Assessment AI Digital Twin allowing a rapid generative AI search for new materials with reduced PMI damage by interpolating the domain of the training set. These new optimum materials can be simulated with the physics codes and/or tested in MPEX. The ability of AI neural networks to interpolate multi-dimensional parameter spaces and generate virtual data is exploited for a more efficient search for optimum materials. The advent of the Transformational AI Models Consortium (TAIMC) is an opportunity to engage with state of the art private and public AI developers to achieve the goals of the AI digital twins and AI accelerated physics models proposed in this project. Our partners at ORNL from the Advance Scientific Computing Research (ASCR) organization will collaborate in accelerating the integrated plasma material interaction simulation framework. This simulation framework will provide a platform for generating simulation data across a range of physical fidelities, including hybrid methods that produce multi-fidelity results. This data will be leveraged for AI model development, both for generation of surrogates and the automation of simulation campaigns. A part of the research below will include collaborative efforts with the TAIMC to (i) adapt data storage approaches to ensure AI-readiness, (ii) provide a protypical exemplar to inform and exercise constructed workflows, and (iii) generate and share data, using the TAIMC unified AI data standard, for foundational models that will be trained from multiple sources across the DOE complex. We will also collaborate with the TAIMC, as well as the planned AI modeling teams, to develop approaches for reducing the cost of data generation. These include tailored multi-fidelity approaches as well as fine-tuning strategies to augment general, large-scale foundational models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Modeling Mesoscale Processes of Scalable Synthesis (Final Report)

The main objective of the center is to develop tools that can help for the understanding of equilibrium and non-equilibrium properties of nanoparticles in aqueous electrolytes. To achieve this goal, we need to develop new computational methodologies that can integrate molecular level description such as the electronic structure analysis to mesoscale description such as generalized hydrodynamics. The challenge is to develop systematic coarse graining techniques that can adaptively choose the level of description needed for the particular task. For example, if bonding breaking is involved, then one should use appropriate models from quantum mechanics to accurately model the time scale and molecular mechanism for the breaking process. However, to model transport process or the process of self-assembly, much less detailed models can be used. There are two main components to this task. One is to develop accurate models that bridge different levels of description. The classical example is the QM/MM model that bridges quantum mechanics and molecular mechanics for studying chemical reactions of large molecules. This work was awarded the Nobel prize this year. For our purpose, we also need to develop methods that bridge molecular and continuum levels of description. Another main task is to develop systematic coarse-graining methods that can give rise to accurate mesoscale and macroscale models, starting from more detailed models at the atomic or molecular scale. None of these ideas are new. By now they have been fashionable topics for quite some time. But neither problem is satisfactorily resolved. The main problem is that uncontrolled approximations are used. As a result, we have very little idea about the validity and accuracy of these models. The main purpose of the center is to exploit the Mori-Zwanzig formalism to achieve the goals stated above. The Mori-Zwanzig formalism is a general tool for eliminating degrees of freedom from existing models. What is attractive about this formalism is its generality. The flip side is that it is also somewhat of a tautology. In order to make it a practical tool, one has to make approximations and this is where the trouble comes. Instead of focusing on Mori-Zwanzig formalism, the PI proposes to study the closely related renormalization group formalism (RG). Like Mori-Zwanzig, RG is a general strategy for eliminating small scale degrees of freedom in a model. Unlike Mori-Zwanzig, RG has the advantage that at least for some problems, one can write a PDE (partial differential equation) type of model for the exact RG flow, without any approximation. This gives us a solid starting point for discussing and analyzing approximations. The PI studied approximate RG flows for turbulent diffusion and related problems. However, extending it to more practical problems proved to be hard. The second line that the PI has pursued is to develop special numerical algorithms for studying particularly important events for dynamics processes in meso-scale systems. The PI succeeded in doing so for the problem of understanding phase transition in metallic systems.

97 MATHEMATICS AND COMPUTING↗