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At least 1,603 records · Page 89

A Safety and Management Framework to Enable Automated Mobility Districts in Urban Areas

Automated mobility technology is beginning to emerge as a viable means to create sustainable and effective public mobility systems within denser urban environments. Automated mobility districts (AMDs) describe major urban districts or activity centers in which deployments of multiple automated vehicle (AV) transit and ride-hailing fleets are supported to meet public mobility needs. The authors put forward a framework to enable AMDs and their governing and management jurisdictional authorities to manage safety of AV operations based on lessons learned from the last century of automated guideway transit and roadway intersection traffic control systems. The essential concept is that of operational management and safety-critical control of multiple AV fleets using a “system-of-systems” approach to system safety analysis. The safety analysis would focus on safe passage of the AV fleet vehicles through complex roadway intersections and junctions, especially in the presence of other non-automated modes such as pedestrians and manually operated vehicles.

47 OTHER INSTRUMENTATION↗

Statistical relationships across epigenomes using large-scale hierarchical clustering

Recent advances in genomics and sequencing platforms have revolutionized our ability to create immense data sets, particularly for studying epigenetic regulation of gene expression. However, the avalanche of epigenomic data is difficult to parse for biological interpretation given nonlinear complex patterns and relationships. This attractive challenge in epigenomic data lends itself to machine learning for discerning infectivity and susceptibility. In this study, we explore over 3000 epigenomes of uninfected individuals and provide a framework to characterize the relationships among epigenetic modifiers, their modifiers, genetic loci, and specific immune cell types across all chromosomes using hierarchical clustering. Hierarchical clustering of epigenomic data revealed consistent epigenetic patterns across chromosomes, demonstrating that variation due to epigenetic modifiers is greater than variation between cell types. Gene Ontology and KEGG pathway analyses indicated significant enrichment of genes involved in chromatin remodeling, mRNA splicing, immune responses, and the regulation of microRNAs and snoRNAs. Epigenetic modifiers frequently formed biologically relevant clusters, including the cohesin complex, RNA Polymerase II transcription factors, and PRC2 complex members. These clustering behaviors remained consistent across all chromosomes, supported by entropy analysis and high Adjusted Rand Index scores, indicating robust cross-chromosomal similarity. Co-occurrence analysis further revealed specific sets of modifiers that consistently appeared together within clusters, reflecting shared biological functions and interactions. Validation using another dataset confirmed the reproducibility of these clustering patterns and modifier co-occurrence relationships, underscoring the reliability and generalizability of the methodology.

97 MATHEMATICS AND COMPUTING↗

Performance Characterization and Provenance of Distributed Task-based Workflows on HPC Platforms

Understanding performance and provenance of task-based workflows poses significant challenges, particularly in distributed configurations where resources are shared by multiple applications. Task-based workflow management systems further complicate performance predictability because of their dynamicity that subtly alters task execution order from run to run. In this paper we propose a layered characterization framework for performance and task provenance for Dask.distributed workflows running on high-performance computing (HPC) platforms. It collects data from jobs, the workflow management system, and the operating system to aid in understanding the performance of these workflows. Our approach encompasses three main contributions: first, an extension of Dask.distributed to capture high-fidelity task provenance using Mochi data services; second, the adaptation of the established HPC I/O characterization tool Darshan to gather high-fidelity I/O data, thereby enhancing the granularity of our analysis; and third, a framework to combine and process the collected data and provide helpful insights into performance characterization and reproducibility, alongside our lessons learned.

Dask↗

Large-Scale Materials Modeling at Quantum Accuracy: Ab Initio Simulations of Quasicrystals and Interacting Extended Defects in Metallic Alloys

Ab initio electronic-structure has remained dichotomous between achievable accuracy and length-scale. Quantum many-body (QMB) methods realize quantum accuracy but fail to scale. Density functional theory (DFT) scales favorably but remains far from quantum accuracy. We present a framework that breaks this dichotomy by use of three interconnected modules: (i) invDFT: a methodological advance in inverse DFT linking QMB methods to DFT; (ii) MLXC: a machine-learned density functional trained with invDFT data, commensurate with quantum accuracy; (iii) DFT-FE-MLXC: an adaptive higher-order spectral finite-element (FE) based DFT implementation that integrates MLXC with efficient solver strategies and HPC innovations in FE-specific dense linear algebra, mixed-precision algorithms, and asynchronous compute-communication. Furthermore, we demonstrate a paradigm shift in DFT that not only provides an accuracy commensurate with QMB methods in ground-state energies, but also attains an unprecedented performance of 659.7 PFLOPS (43.1% peak FP64 performance) on 619,124 electrons using 8,000 GPU nodes of Frontier supercomputer.

density functional theory↗

LivermorE Al Projector for Computed Tomography Tasks

With recent computed tomography (CT) efforts using Artificial Intelligence (AI) and Deep Learning (DL)techniques, there is a strong need for differentiable forward projection models that can be integrated into existing DL frameworks. We developed a pytorch-based package library providing differentiable forward and back projection functions and classes to facilitate forward and back propagation of CT operations in the training procedure. This forward projectors support three CT projection geometries: cone, parallel and modular beams. This package can be used with both CPU and GPU with CUDA.

Kim, Hyojin↗

A Proposed Common Model of Multi-phase Strength and Equation of State for a Tri-laboratory Collaboration (Working Draft 1.1)

The proposed simple common model for multiphase strength and EoS (CMMP) is meant to be sufficiently simple that each of the collaborating labs can share in a common starting point. Another objective is to start with relatively simple assumptions, which will not necessarily capture details of the physical processes, and incrementally add complexity in order to identify the minimal-needed technical detail. Through this co-evolution of model and experiment, we will better learn the importance of various theoretical approximations and where to invest future resources in experiment and model development. This simple framework is based on pressure and temperature equilibrium of all co-existing phases combined with deviatoric stress averaging through a volume fraction weighted ow stress and a volume fraction weighted shear modulus. Implementations of the framework based on equilibrium phase fractions (i.e. instantaneous kinetic rate) and for finite rate transition kinetics are proposed.

36 MATERIALS SCIENCE↗

Hybrid learning techniques for scientific data reduction with performance guarantees

The research initiatives supported by the U.S. Department of Energy (DOE) Grant DE-SC0022265 are fundamentally aimed at pioneering advanced machine learning (ML) techniques for scientific data compression within high-performance computing (HPC) environments. This comprehensive body of work addresses the critical challenge posed by the exponential growth of data generated by scientific simulations in domains such as fusion energy, climate modeling, and computational fluid dynamics (CFD). A core objective is to develop compression algorithms that achieve substantial data reduction—often by orders of magnitude—while rigorously ensuring the fidelity of both the primary data (PD) and scientifically crucial derived quantities of interest (QoI). The methodologies deployed under this grant integrate sophisticated deep learning architectures, prominently featuring autoencoders, advanced generative models like conditional diffusion, and hybrid learning techniques. Key innovations include the development of Guaranteed Autoencoders (GAE) and the Guaranteed Conditional Diffusion with Tensor Correction (GCDTC) framework, which provide explicit, instance-level error bounds on reconstructed data. Furthermore, specialized strategies such as nonlinear constraint satisfaction are employed to preserve the integrity of QoI, a vital requirement for the trustworthiness of downstream scientific analyses. This research also focuses on the design and implementation of scalable, GPU-accelerated software pipelines that seamlessly integrate into existing HPC workflows, ensuring both computational efficiency and practical applicability. The CAESAR framework, for example, unifies foundation and generative models to create an adaptive and efficient compression solution for spatio-temporal scientific data. Collectively, these efforts represent a significant advancement in mitigating the scientific data deluge, enabling more effective data management, accelerated scientific discovery, and optimized utilization of HPC resources.

97 MATHEMATICS AND COMPUTING↗

A Nonlocal-Gradient Descent Method for Inverse Design in Nanophotonics

Local-gradient-based optimization approaches lack nonlocal exploration abilityrequired for escaping from local minima when searching non-convex landscapes.A directional Gaussian smoothing (DGS) approach was recently proposed in [29]and used to define a truly nonlocal gradient, referred to as the DGS gradient, inorder to enable nonlocal exploration in high-dimensional black-box optimization.Promising results show that replacing the traditional local gradient with the nonlocalDGS gradient can significantly improve the performance of gradient-based methodsin optimizing highly multi-modal loss functions. However, the current DGS methodis designed for unbounded and uncontrained optimization problems, making itinapplicable to real-world engineering optimization problems where the tuningparameters are often bounded and the loss function is usually constrained byphysical processes. In this work, we propose to extend to the DGS approachto the constrained inverse design framework in order to find better optima ofmulti-modal loss functions. A series of adaptive strategies for smoothing radiusand learning rate updating are developed to improve the computational efficiencyand robustness. Our methodology is demonstrated by an example of designing ananoscale wavelength demultiplexer, and shows superior performance compared tothe state-of-the-art approaches. By incorporating volume constraints, the optimizeddesign achieves an equivalently high performance but significantly reduces theamount of material usage.

Bi, Sirui↗

Coolant Pump Predictive Data Analytics from Signatures Generated by the Recursive Short Time Fast Fourier Transform

Although a nuclear reactor is a hostile environment for sensors and signal transmissions, the reactor core is amenable to acoustic communication. An acoustic measurement infrastructure installed at the Advanced Test Reactor (ATR) nozzle trench area records acoustic signals that can capture reactor operating states. The distinct states produce unique signatures that can be identified and tracked using data processing and data analytics. The infrastructure relies on acoustic transmission through ATR in-pile structural components, piping, and coolant that transmit acoustically modified signals generated by the coolant pumps. This paper will discuss results from using the Recursive Short Time Fast Fourier Transform (RSTFFT) technique used to process acoustic signals and provide signatures that are identified and monitored by analytics. The RSTFFT is applied to ATR data to understand the vibration levels and signatures for different operating regimes as displayed by the spectrogram. The combination of coolant pumps for normal and high-power operation generate unique signatures. These acoustic signatures are used to develop machine learning approaches to automatically classify operating regimes. Two machine-learning models, Support Vector Machines and Linear Discriminant Analysis, were developed to classify two event classes. Class 1 is a normal steady-state operation, and Class 2 is any event that is due to start up, shut down, or other actions. Both types of machine learning models had over a 96% prediction accuracy for the two classes. These results lay the foundation for predictive analytic frameworks that can be leveraged by ATR to optimize operations and maintenance.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗

Plug & play directed evolution of proteins with gradient-based discrete MCMC

Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Reinforcement Learning of Structured Stabilizing Control for Linear Systems With Unknown State Matrix

This paper delves into designing feedback control gains for a continuous-time linear quadratic regulator (LQR) problem that is constrained to certain predefined structure with unknown state matrix. We bring forth the ideas from reinforcement learning (RL) in conjunction with sufficient stability and performance guarantees in order to design these structured gains using the trajectory measurements of states and controls. Here we first formulate a model-based framework using dynamic programming (DP) to embed the structural constraint to the LQR gain computation in the continuous-time setting, and then subsequently, formulate a policy iteration RL algorithm that can alleviate the requirement of known state matrix in conjunction with maintaining the feedback gain structure. The design enables a distributed learning control design which is necessary for many large-scale cyber-physical systems. Theoretical guarantees are provided for stability and convergence of the structured reinforcement learning (SRL) algorithm. We validate our theoretical results with numerical simulations on a multi-agent networked linear time-invariant (LTI) dynamic system.

42 ENGINEERING↗

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↗

Xanthos-Lake Model Source Code

This repository contains the source code for Xanthos-Lake, a lake-modeling extension of the Xanthos framework that introduces a coupled lake component comprising the Xanthos-Lake Snow and Ice Model (xLSIM) and the Xanthos-Lake Water Balance Model (xLWBM). xLSIM is a basin-aware machine-learning model for lake snow, ice, and thermal conditions. It predicts monthly lake ice thickness, snow depth, snow-cover fraction, mixing-layer temperature, and lake ice fraction from meteorological forcing and lake surface-area information. It uses sequence-based deep-learning architectures, including Transformer and hybrid Long Short-Term Memory–Transformer (LSTM–Transformer) models, together with seasonal encoding, multi-lake learning, physical masking, and basin-level cryospheric and non-cryospheric classification. The training workflow uses Ray for scalable execution and includes optional Ray Tune hyperparameter optimization. Model predictions, observations, diagnostics, and feature-importance outputs are written in NetCDF. xLWBM is the water-balance component of the new lake framework. It simulates monthly lake storage, surface area, evaporation, inflow, outflow, and lake–groundwater exchange. It combines physical water-balance equations with calibrated bathymetric relationships, weir-based outlet flow, modified Penman open-water evaporation, groundwater head relaxation, Penman–Monteith snow and ice sublimation, and snow, ice, and thermal conditions supplied by xLSIM. The model calibrates lake parameters against satellite-derived surface-area data, using evaporation-based calibration where surface-area data are unavailable, and supports small, medium, and large lake classes. For large lakes, xLWBM is integrated with the managed-routing workflow so that lake storage and outflow interact directly with downstream river routing and reservoir operations. Together, xLSIM and xLWBM provide Xanthos with a coupled lake-modeling capability. xLSIM supplies the snow, ice, and thermal conditions that affect lake evaporation and snow- and ice-related water exchanges, while xLWBM translates those conditions into dynamic lake storage, surface area, evaporation, and discharge. In return, xLWBM supplies evolving lake surface area to xLSIM. This coupling enables Xanthos to represent lakes as active hydrologic components within basin-scale water-availability and routing simulations.

Machine Learning↗

Operator learning for predicting multiscale bubble growth dynamics

We report simulating and predicting multiscale problems that couple multiple physics and dynamics across many orders of spatiotemporal scales is a great challenge that has not been investigated systematically by deep neural networks (DNNs). Herein, we develop a framework based on operator regression, the so-called deep operator network (DeepONet), with the long-term objective to simplify multiscale modeling by avoiding the fragile and time-consuming “hand-shaking” interface algorithms for stitching together heterogeneous descriptions of multiscale phenomena. To this end, as a first step, we investigate if a DeepONet can learn the dynamics of different scale regimes, one at the deterministic macroscale and the other at the stochastic microscale regime with inherent thermal fluctuations. Specifically, we test the effectiveness and accuracy of the DeepONet in predicting multirate bubble growth dynamics, which is described by a Rayleigh–Plesset (R–P) equation at the macroscale and modeled as a stochastic nucleation and cavitation process at the microscale by dissipative particle dynamics (DPD). First, we generate data using the R–P equation for multirate bubble growth dynamics caused by randomly time-varying liquid pressures drawn from Gaussian random fields (GRFs). Our results show that properly trained DeepONets can accurately predict the macroscale bubble growth dynamics and can outperform long short-term memory networks. We also demonstrate that the DeepONet can extrapolate accurately outside the input distribution using only very few new measurements. Subsequently, we train the DeepONet with DPD data corresponding to stochastic bubble growth dynamics. Although the DPD data are noisy and we only collect sparse data points on the trajectories, the trained DeepONet model is able to predict accurately the mean bubble dynamics for time-varying GRF pressures. Taken together, our findings demonstrate that DeepONets can be employed to unify the macroscale and microscale models of the multirate bubble growth problem, hence providing new insight into the role of operator regression via DNNs in tackling realistic multiscale problems and in simplifying modeling with heterogeneous descriptions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Consensus Equilibrium for Subsurface Delineation

Heterogeneity and insufficient site characterization limit our knowledge of the subsurface. Inversion techniques, which minimize the mismatch between observations and model predictions, have become an essential tool of subsurface characterization. Most optimization-based approaches fail to incorporate various implicit priors and capture the geological complexity. We overcome these limitations by deploying the plug-and-play and consensus equilibrium (CE) strategies, which provide a flexible framework for image reconstruction. Our CE methodology for spatial delineation of geologic formations consists of an image denoiser and a variational auto-encoder (deep learning-based emulator). The former ameliorates the reconstruction noise, yielding well-defined geological structures; its mathematical equivalence with the proximal operator allows the deployment of advanced denoisers (e.g., CNN-based denoiser) that do not correspond to a regularization objective. The latter defines a geology prior that imposes a geological constraint, for example, continuity and shape of geological features, onto the reconstructed image. Here, we conduct a series of numerical experiments dealing with transient two-dimensional flow driven by a pumping well and natural hydraulic head gradient. They demonstrate the CE framework's ability to delineate, both probabilistically and deterministically, complex subsurface environments with sufficient quality.

42 ENGINEERING↗

Reinforcement Learning for Intentional Islanding in Resilient Power Transmission Systems

Intentional islanding is the process of identifying and deliberately decomposing the transmission network to form self-sustained islands from an endangered network during disruptions to improve resilience and security. Most existing intentional islanding models are offline resilience decision tools and hence do not provide outage responses in a timely manner. In this paper, a reinforcement learning (RL) based model for intentional islanding is developed, which offers real-time switching control, online deployability, and adaptability to varying system conditions. The intentional islanding process is formulated as a Markov decision process, where the optimal transmission switching policy is learned using the RL approach. The control policy is learned over an environment that encompasses a Power System Simulator for Engineering (PSS/E) model of the transmission network, facilitated by an interface to the standard openAI Gym framework. The proposed RL-based methodology aims to form stable and self-sustainable islands by ensuring voltage stability while reducing the power mismatch in the formed islands. A proximal policy optimization algorithm is designed, which is suitable for controlling the on/off status of the switches with multi-layer perceptron as value and actor networks. The effectiveness of the proposed framework in the self-recovery of the grid by island formation is applied on the modified IEEE 39-bus test network and validated by dynamic simulations.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Crystal Orientation and Defect Mapping in Electron-Beam-Sensitive Zeolites with Near-Axis Transmission Kikuchi Diffraction

Porous materials are vital in catalysis, energy conversion, and environmental remediation. Understanding structural heterogeneity in zeolites is key to linking synthesis, framework intergrowths, and catalytic performance, yet current methods for phase identification and spatial mapping lack sufficient resolution or throughput. We present a high-throughput approach using near-axis transmission Kikuchi diffraction in a scanning electron microscope, achieving high phase and spatial resolution for electron-beam-sensitive zeolites, including ZSM-5 and, for the first time, Zeolite A. Here, this method enables direct visualization of intergrowth features that critically affect catalytic and adsorption behavior, bridging the gap between ensemble-averaged X-ray diffraction and high-resolution but low-throughput transmission electron microscopy. Combining nanoscale mapping with statistical sampling is highly suited for machine-learning pipelines guiding new structure function understanding and could be extended to other beam-sensitive porous materials such as metal–organic or covalent–organic frameworks.

crystallography↗