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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↗

Shape restricted additive hazards models: Monotone, unimodal, and U‐shape hazard functions

We consider estimation of the semiparametric additive hazards model with an unspecified baseline hazard function where the effect of a continuous covariate has a specific shape but otherwise unspecified. Such estimation is particularly useful for a unimodal hazard function, where the hazard is monotone increasing and monotone decreasing with an unknown mode. A popular approach of the proportional hazards model is limited in such setting due to the complicated structure of the partial likelihood. Our model defines a quadratic loss function, and its simple structure allows a global Hessian matrix that does not involve parameters. Thus, once the global Hessian matrix is computed, a standard quadratic programming method can be applicable by profiling all possible locations of the mode. However, the quadratic programming method may be inefficient to handle a large global Hessian matrix in the profiling algorithm due to a large dimensionality, where the dimension of the global Hessian matrix and number of hypothetical modes are the same order as the sample size. We propose the quadratic pool adjacent violators algorithm to reduce computational costs. The proposed algorithm is extended to the model with a time‐dependent covariate with monotone or U‐shape hazard function. In simulation studies, our proposed method improves computational speed compared to the quadratic programming method, with bias and mean square error reductions. We analyze data from a recent cardiovascular study.

Mathematical & Computational Biology↗

Koopman-Based Approach to Nonintrusive Reduced Order Modeling: Application to Aerodynamic Shape Optimization and Uncertainty Propagation

A methodology for nonintrusive projection-based nonlinear model reduction originally presented by Renganathan et al. is further extended here toward parametric systems with a focus on application to aerospace design. Specifically, the method is extended to address static systems with parametric geometry (that deforms the mesh) in addition to parametric freestream boundary conditions. The main idea is to first perform a transformation on the governing equations such that it is lifted to a higher-dimensional but linear underdetermined system. This enables one to extract the system matrices easily as compared to that of the original nonlinear system. The underdetermined system is closed with a set of model-dependent nonlinear constraints upon which the model reduction is finally performed. The methodology is validated on the subsonic and transonic inviscid flows past the NACA0012 and the RAE2822 airfoils with parametrized shapes. The utility of the approach is further demonstrated by applying it to two common problems in aerospace design, namely, derivative-free global optimization and parametric uncertainty quantification with Monte Carlo sampling. Overall, the methodology is shown to achieve accuracy up to 5% and computational speedup of two to three orders of magnitude relative to the full order model. Comparison against another nonintrusive model reduction method revealed that the proposed approach is more robust, accurate, and retains the consistency between the state variables.

97 MATHEMATICS AND COMPUTING↗

Heterogeneity or illusion? Track the carbon Kuznets curve of global residential building operations

Residential buildings, the “last mile” sector in the global decarbonization, have become the most significant uncertain factor hindering carbon neutrality with increasing household energy demand. To track the operational carbon in buildings, this study investigates the carbon Kuznets curve (CKC) and the corresponding decoupling status of residential building operations at four emission scales by using the data of 30 countries from 2000 to 2019. The results show that (1) the CKC model can fit more than half of the samples. Most curves have an inverted U-shape, with 76% of emission per household and 82% of total emissions. (2) In the presence of the CKC, over four-fifths of global residential buildings peak regardless of any emission scale. The analysis denotes that the carbon emissions of developed countries reach their peaks earlier. In the total emissions, the samples’ peaking proportion is 20% and 25% with income per capita < 20,000 United States dollars (USD) and 20,000–40,000 USD, respectively. (3) The Tapio decoupling analysis and the threshold regression effectively verify the robustness and the heterogeneity of CKCs, respectively. Strong decoupling effects of CKCs in most countries are demonstrated at the scales of emission per floor space and the total emissions, and the heterogeneity proves the classic inverted U-shaped relationship between economy and emissions doesn’t exist in all emitters. Overall, this study tracks the historical carbon emission trajectories of residential building operations at a global scale, providing reference for different economies to simulate the dynamic of building carbon emissions along with the economic booming.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Multifrequency Analysis of Favored Models for the Messier 87* Accretion Flow

Abstract The polarized images of the supermassive black hole Messier 87* (M87*) produced by the Event Horizon Telescope (EHT) provide a direct view of the near-horizon emission from a black hole accretion and jet system. The EHT theoretical analysis of the polarized M87* images compared thousands of snapshots from numerical models with a variety of spins, magnetization states, viewing inclinations, and electron energy distributions, and found a small subset consistent with the observed image. In this article, we examine two models favored by EHT analyses: a magnetically arrested disk with moderate retrograde spin and a magnetically arrested disk with high prograde spin. Both have electron distribution functions that lead to strong depolarization by cold electrons. We ray trace five snapshots from each model at 22, 43, 86, 230, 345, and 690 GHz to forecast future very long baseline interferometry (VLBI) observations and examine limitations in numerical models. We find that even at low frequencies where optical and Faraday rotation depths are large, approximately rotationally symmetric polarization persists, suggesting that shallow depths dominate the polarization signal. However, morphology and spectra suggest that the assumed thermal electron distribution is not adequate to describe emission from the jet. We find 86 GHz images show a ringlike shape determined by a combination of plasma and spacetime imprints, smaller in diameter than recent results from the Global mm-VLBI Array. We find that the photon ring becomes more apparent with increasing frequency, and is more apparent in the retrograde model, leading to large differences between models in asymmetry and polarization structure.

Astronomy & Astrophysics↗

Alignments between Galaxies and the Cosmic Web at z ~ 1–2 in the IllustrisTNG Simulations

Galaxy formation theories predict that galaxy shapes and angular momenta have nonrandom alignments with the cosmic web. This leads to so-called intrinsic alignment between pairs of galaxies, which is important to quantify as a nuisance parameter for weak lensing. We study galaxy–cosmic web alignment in the IllustrisTNG suite of hydrodynamical simulations at redshifts 1 and 2, finding that alignment trends are consistent with previous studies. However, we find that the magnitude of the spin alignment signal is ~2.4× weaker than seen in previous studies of the Horizon-AGN simulation, suggesting that this signal may have a significant dependence on subgrid physics. Based on IllustrisTNG, we then construct mock observational spectroscopic surveys that can probe shape–cosmic web alignment at z ~ 1–2, modeled on the low-z galaxy redshift and IGM tomography surveys on the upcoming Subaru Prime Focus Spectrograph Galaxy Evolution (PFS GE) survey. However, even over box sizes of L = 205 h -1 Mpc, we find that global anisotropies induce a sample variance in the 2D projected alignment signal that depend on the projected direction; this induces significant errors in the observed alignment. We predict a 5.3σ detection of IllustrisTNG's shape alignment signal at z ~ 1 from Subaru PFS GE, although a detection would be challenging at z ~ 2. However, a rough rescaling of the relative alignment signal strengths between the TNG and Horizon-AGN simulations suggests that PFS GE should be able to more easily constrain the latter's stronger signal.

79 ASTRONOMY AND ASTROPHYSICS↗

Drivers of Dry Day Sensitivity to Increased CO 2

Persistent precipitation deficits are among the most impactful consequences of global warming. Here we focus on changes in the annual number of dry days (NDD) and in the annual maximum length of dry spells due to a quadrupling of atmospheric CO 2 . We use atmosphere-only simulations to decompose the projected changes into additive contributions. A fast adjustment leads to a global increase in NDD despite notable regional exceptions (e.g., South Asia and Sahel). The effect of the uniform component of the surface ocean warming is model-dependent but shapes the regional distribution of the NDD response in each model. Finally, the ocean warming pattern also contributes to large uncertainties, likely through contrasting changes in large-scale circulation. Our results thus highlight the complexity of the NDD response, with policy-relevant practical implications for mitigation and adaptation strategies.

54 ENVIRONMENTAL SCIENCES↗

Virtual Power Plants: Pilots, Challenges, and Innovations Shaping Future Development

Virtual Power Plants (VPPs) aggregate distributed energy resources (DERs) to provide grid services traditionally delivered by centralized power plants. This article reviews the current state of VPP deployment, highlighting business models, compensation mechanisms, and global pilot projects. While VPPs offer benefits such as grid flexibility, resilience, and cost savings, challenges remain in communication infrastructure, regulatory frameworks, market access, and customer engagement. To address these, we propose a scalable, privacy-preserving hierarchical VPP architecture that coordinates with distribution utilities and preserves customer data. We also present the Integrated T&D Control Room of the Future as a key test bed for validating and accelerating VPP adoption. These innovations can help transition VPPs from pilot programs to integral components of a modern, reliable power grid.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Impacts of benchmarking choices on inferred model skill of the Arctic–Boreal terrestrial carbon cycle

Abstract Land surface models require continuous validation against observations to improve and reduce simulation uncertainty. However, inferred model performance can be heavily influenced by subjective choices made in the selection and application of observational data products. A key area often misrepresented by models is the Arctic–Boreal region, which is a potential tipping point region in Earth’s climate system due to large permafrost carbon stocks that are vulnerable to release with climate warming. We use the International Land Model Benchmarking (ILAMB) framework to evaluate how the model skill of TRENDY-v9 models varies based on the choice of observational-based benchmark and how benchmarks are applied in model evaluation. This analysis uses global datasets integrated into ILAMB and new, regionally-specific observational products from the Arctic–Boreal Vulnerability Experiment. Our results cover the overall time period of 1979–2019 and show that model scores can vary substantially depending on the data product applied, with higher model scores indicating better model performance against observations. The lowest model scores occur when benchmarked against regional, compared to global, datasets. We also evaluate observed and modeled functional relationships between ecosystem respiration and air temperature and between gross primary production and precipitation. Here, we find that the magnitude and shape of the responses are strongly impacted by the choice of observational dataset and the approach used to construct the functional relationship benchmark. These results suggest that model evaluation studies could conclude a false sense of model skill if only using a single benchmark data product or if not applying regional data products when performing a regional model analysis. Collectively, our findings highlight the influence of benchmarking choices on model evaluation and point to the need for benchmarking guidelines when assessing model skill.

Poe, Jeralyn (ORCID:0000000318495278)↗

Epistasis and evolution: recent advances and an outlook for prediction

As organisms evolve, the effects of mutations change as a result of epistatic interactions with other mutations accumulated along the line of descent. This can lead to shifts in adaptability or robustness that ultimately shape subsequent evolution. Here, we review recent advances in measuring, modeling, and predicting epistasis along evolutionary trajectories, both in microbial cells and single proteins. We focus on simple patterns of global epistasis that emerge in this data, in which the effects of mutations can be predicted by a small number of variables. The emergence of these patterns offers promise for efforts to model epistasis and predict evolution.

59 BASIC BIOLOGICAL SCIENCES↗

LANL Weapons Physics Directorate: Mission Scope and Opportunities [Slides]

The Weapons Physics Directorate stewards a number of critical capabilities to meet the LANL mission. To execute our mission, ALDX develops and applies cutting-edge theory, computational models and multi-physics simulation codes, and designs, executes, and analyzes complex experiments. Our mission is to sustain the current stockpile, provide future stockpile options, and help shape a globalized nuclear world.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Modeling and Characterization of Surface Discharges in Insulating Material for Spacers: Electrode Shape, Discharge Mode, and Revision of the Creepage Concept

In the design of MV AC and DC spacers, the predominant factors are surface and interface conditions. Design is generally carried out on specifications and standards which are based on long-term experience and lab testing. However, the diffusion of power electronics with a trend to increase electric field, switching frequency, and rise time to achieve higher power density calls for an innovative, global approach to optimized insulation system design. A new methodology, based on field simulation, discharge modeling, and partial discharge inception measurements, called the three-leg approach, can form the basis to optimize insulation design for any type of supply voltage waveform. This paper focuses on the influence of the type of electrode on the inception and phenomenology of surface discharges and, as a consequence, on the interpretation of the results used for application of the three-leg approach. It is demonstrated that a typical electrode system used for insulating material testing can generate both gas and surface discharges at the triple point, when the electrodes have a smooth profile that is used to avoid corona or flashover. Hence, testing partial discharge may not provide a straightforward indication of the surface discharge inception and, thus, be partially misleading for insulation design. Another takeover is that such analysis must benefit from PD testing tools endowed with analytics able to provide automatic identification of the type of defect generating PD, i.e., internal, surface, and corona, since design and remedy actions can be taken, and adequate insulating materials developed, only knowing the type of source generating PD. Hence, testing partial discharge may not provide a straightforward indication of surface discharge inception and, thus, be partially misleading for insulation design. In addition to the importance of the three-leg approach to favor reliable and optimized design of insulation systems, there is a clear need to have a PD testing tool endowed with analytics. It should preferably be able to provide automatic identification of the type of defect generating PD, i.e., internal, surface, and corona.

36 MATERIALS SCIENCE↗

Response of Graphite to Dynamic Loading and Hypervelocity Jet Impacts

The compressive strengths of three varieties of high purity graphite, PCEA, NBG-18, and NBG-25, as well as the depth of penetration of small-scale charges into these materials was experimentally determined. These grades are similar in density, ranging from 1.80 – 1.85 g/cc, and nominal apparent porosity, ranging from 18% to 20%, but provide a wide range in maximum grain or particle size from 10s to 1000s of µm. Two very different manufacturing methods are also represented; PCEA is extruded while NBG-18 and NBG-25 are iso-molded. The quasistatic and dynamic strengths of each grade were determined on a load frame and split-Hopkinson pressure bar, respectively. The depth of penetration (DOP) of two small-scale shaped charges, the Teledyne RP-1 and RP-4, was determined against graphite. The global response of the RP-4 impacts was markedly different as the PCEA samples remained intact while all the NBG-25 samples split into 2 or 3 pieces after the jet penetration had completed. However, for all tests, the trusted DOPs fell within 2 cm. Preliminary hydrocode modeling of the penetration events used existing models that were not designed for graphite. The results can be tuned to reasonably reproduce the DOP, but the wound channel geometry is not reproduced well. A model designed for graphite would need to represent graphite’s non-linear and energy dissipation characteristics.

36 MATERIALS SCIENCE↗

The Dependence of Mean Climate State on Shortwave Absorption by Water Vapor

Abstract State-of-the-art climate models exhibit significant spread in the climatological value of atmospheric shortwave absorption (SWA). This study investigates both the possible causes and climatic impacts of this SWA intermodel spread. The intermodel spread of global-mean SWA largely originates from the intermodel difference in water vapor shortwave absorptivity. Hence, we alter the water vapor shortwave absorptivity in the Community Earth System Model, version 1, with the Community Atmosphere Model, version 4 (CESM1-CAM4). Increasing the water vapor shortwave absorptivity leads to a reduction in global-mean precipitation and a La Niña–like cooling over the tropical Pacific. The global-mean atmospheric energy budget suggests that the precipitation is suppressed as a way to compensate for the increased SWA. The precipitation reduction is driven by the weakened surface winds, stabilized planetary boundary layer, and surface cooling. The La Niña–like cooling over the tropical Pacific is attributed to the zonal asymmetry of climatological evaporative damping efficiency and the low cloud enhancement over the eastern basin. Complementary fixed SSTs simulations suggest that the latter is more fundamental and that it primarily arises from atmospheric processes. Consistent with our experiments, the CMIP5/6 models with a higher global-mean SWA tend to produce tropical Pacific toward a more La Niña–like mean state, highlighting the possible role of water vapor shortwave absorptivity for shaping the mean-state climate patterns.

Kim, Hanjun↗

Climate Impact of Primary Plastic Production

Plastics show the strongest production growth of all bulk materials over the last decade. The industry’s current growth trajectory is exponential and plastic production is expected to double or triple by 2050. The rapidly increasing production of plastics and the continued reliance on fossil fuels for production, have contributed to numerous environmental problems and health harms. As a result, plastic pollution has become an increasing threat to natural ecosystems, human health and climate. However, there is a lack of granularity on the contribution of the primary plastics specifically to greenhouse gas (GHG) emissions and their impact on the remaining global carbon budget needed to stay below a 1.5°C or 2°C global average temperature rise. In this report, we explore the contribution of primary plastic production to climate change disaggregated by polymer and technology. To this end, we have developed comprehensive bottom-up modeling of GHG emissions from global primary plastic production, with a special focus on polymer value chains. We have analyzed the results under various growth scenarios in the context of carbon budgets compatible with a 1.5°C global trajectory. Modeling includes the material flows of all production stages, processes and technologies used in primary plastic production value chains, including from the extraction of fossil fuels required for production to shaping the final product. We specifically focus on nine major types of fossil fuelbased plastic polymers that are produced and consumed in large quantities: three types of polyethylene (PE) – low-density (LDPE), linear low-density (LLDPE), and high-density (HDPE) – as well as polypropylene (PP); polyethylene terephthalate (PET); polyvinyl chloride (PVC); polystyrene (PS) and other key styrene-based plastics such as styrene acrylonitrile (SAN) and acrylonitrile butadiene styrene (ABS), and polyurethane (PU). Together these account for about 80% of plastics production.

54 ENVIRONMENTAL SCIENCES↗

Climate Impact of Primary Plastic Production

Plastics show the strongest production growth of all bulk materials over the last decade. The industry’s current growth trajectory is exponential and plastic production is expected to double or triple by 2050. The rapidly increasing production of plastics and the continued reliance on fossil fuels for production, have contributed to numerous environmental problems and health harms. As a result, plastic pollution has become an increasing threat to natural ecosystems, human health and climate. However, there is a lack of granularity on the contribution of the primary plastics specifically to greenhouse gas (GHG) emissions and their impact on the remaining global carbon budget needed to stay below a 1.5°C or 2°C global average temperature rise. In this report, we explore the contribution of primary plastic production to climate change disaggregated by polymer and technology. To this end, we have developed comprehensive bottom-up modeling of GHG emissions from global primary plastic production, with a special focus on polymer value chains. We have analyzed the results under various growth scenarios in the context of carbon budgets compatible with a 1.5°C global trajectory. Modeling includes the material flows of all production stages, processes and technologies used in primary plastic production value chains, including from the extraction of fossil fuels required for production to shaping the final product. We specifically focus on nine major types of fossil fuel-based plastic polymers that are produced and consumed in large quantities: three types of polyethylene (PE) – low-density (LDPE), linear low-density (LLDPE), and high-density (HDPE) – as well as polypropylene (PP); polyethylene terephthalate (PET); polyvinyl chloride (PVC); polystyrene (PS) and other key styrene-based plastics such as styrene acrylonitrile (SAN) and acrylonitrile butadiene styrene (ABS), and polyurethane (PU). Together these account for about 80% of plastics production.

54 ENVIRONMENTAL SCIENCES↗

Intercomparison of Thermal Regime Algorithms in 1-D Lake Models

Lakes are an important component of the global weather and climate system, but the modeling of their thermal regimes has shown large uncertainties due to the highly diverse lake properties and model configurations. Here we evaluate the algorithms of four key lake thermal processes including turbulent heat fluxes, wind-driven mixing, light extinction, and snow density, using a highly diverse lake dataset provided by the Inter-sectoral Impact Model Intercomparison Project (ISIMIP) 2a lake sector. Algorithm codes are configured and run separately within the same parent model to rule out any interference from factors apart from the algorithms examined. Evaluations are based on both simulation accuracy and recalibration complexity for application to global lakes. For turbulent heat fluxes, the non-Monin-Obukhov similarity (MOS) based, more simplified algorithms perform better in predicting lake epilimnion temperatures and achieve high convergence in the values of the calibrated parameters. For wind-driven mixing, a two-algorithm strategy considering lake shape and season is suggested with the regular mixing algorithm used for spring and earlier summer and the mixing-enhanced algorithm for summer steady stratification and fall overturn periods. There are no evident differences in the simulated thermocline depths using different light extinction algorithms or the observation. Finally, for lake ice phenology, a constant snow density at around 110 kg m-3 is found to be sufficient for most northern lakes while the Arctic lakes require a higher value. Our study provides highly practical guides for improving 1-D lake models and feasible parameterization strategies to better simulate global lake thermal regimes.

58 GEOSCIENCES↗

Parallel projection—An improved return mapping algorithm for finite element modeling of shape memory alloys

Here, we present a novel finite element analysis of inelastic structures containing Shape Memory Alloys (SMAs). Phenomenological constitutive models for SMAs lead to material nonlinearities, that require substantial computational effort to resolve. Finite element analysis methods, which rely on Gauss quadrature integration schemes, must solve two sets of coupled differential equations: one at the global level and the other at the local, i.e. Gauss point level. In contrast to the conventional return mapping algorithm, which solves these two sets of coupled differential equations separately using a nested Newton procedure, we propose a scheme to solve the local and global differential equations simultaneously. In the process we also derive closed-form expressions used to update the internal/constitutive state variables, and unify the popular closest-point and cutting plane methods with our formulas. Numerical testing indicates that our method allows for larger thermomechanical loading steps and provides increased computational efficiency, over the standard return mapping algorithm.

42 ENGINEERING↗