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At least 1,315 records · Page 73

Using intrahost single nucleotide variant data to predict SARS-CoV-2 detection cycle threshold values

Over the last four years, each successive wave of the COVID-19 pandemic has been caused by variants with mutations that improve the transmissibility of the virus. Despite this, we still lack tools for predicting clinically important features of the virus. In this study, we show that it is possible to predict the PCR cycle threshold (Ct) values from clinical detection assays using sequence data. Ct values often correspond with patient viral load and the epidemiological trajectory of the pandemic. Using a collection of 36,335 high quality genomes, we built models from SARS-CoV-2 intrahost single nucleotide variant (iSNV) data, computing XGBoost models from the frequencies of A, T, G, C, insertions, and deletions at each position relative to the Wuhan-Hu-1 reference genome. Our best model had an R 2 of 0.604 [0.593–0.616, 95% confidence interval] and a Root Mean Square Error (RMSE) of 5.247 [5.156–5.337], demonstrating modest predictive power. Overall, we show that the results are stable relative to an external holdout set of genomes selected from SRA and are robust to patient status and the detection instruments that were used. This study highlights the importance of developing modeling strategies that can be applied to publicly available genome sequence data for use in disease prevention and control.

COVID19↗

"Sintering" Models and In-Situ Experiments: Data Assimilation for Microstructure Prediction in SLS Additive Manufacturing of Nylon Components

Selective laser sintering methods are workhorses for additively manufacturing polymer-based components. The ease of rapid prototyping also means it is easy to produce illicit components. It is necessary to have a data-calibrated in-situ physical model of the build process in order to predict expected and defective microstructure characteristics that inform component provenance. Toward this end, sintering models are calibrated and characteristics such as component defects are explored. This is accomplished by assimilating multiple data streams, imaging analysis, and computational model predictions in an adaptive Bayesian parameter estimation algorithm. From these data sources, along with a phase-field model, bulk porosity distributions are inferred. Model parameters are constrained to physically-relevant search directions by sensitivity analysis, and then matched to predictions using adaptive sampling. Using this feedback loop, data-constrained estimates of sintering model parameters along with uncertainty bounds are obtained.

3D printing, Additive Manufacturing, polymer, sint↗

LHC EFT WG note: SMEFT predictions, event reweighting, and simulation

This note provides a comprehensive overview of tools for predicting observables in the Standard Model effective field theory (SMEFT) at both tree level and one loop using event generators. We evaluate three primary methodologies–event reweighting, separate simulation of squared matrix elements, and full SMEFT process simulation–focusing on their statistical performance, computational efficiency, and potential biases. Each approach is assessed in terms of its accuracy, highlighting trade-offs between precision and resource demands. Practical insights into their applicability for high-energy physics analyses are offered, with particular attention to processes where SMEFT effects are significant. Additionally, we discuss the role of helicity in reweighting strategies and its impact on the quality of predictions. By comparing the methods across various LHC processes, this note provides guidance for selecting the most effective strategy for various SMEFT studies, ensuring robust predictions while optimizing computational resources.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Predicting Solar Plant Generation with Machine Learning Techniques

Accurately predicting power generation for PV sites is critical for prioritizing relevant operations & maintenance activities, thereby extending the lifetime of a system and improving profit margins. A number of factors influence power generation at PV sites, including local weather, shading and soiling losses, design of modules, DC mismatches, and degradation over time. Other external factors such as curtailment and grid outages can also have a notable impact on power generation. Machine learning techniques can be used to provide more accurate predictions of PV power production by accounting for important weather and climate information neglected by current industry methods. This article will cover the deficiencies of those methods and will show how machine learning can dramatically improve power generation predictions.

14 SOLAR ENERGY↗

New Predictive Capabilities for Nuclear Weapons in Composite Fires

The prevalence of flammable carbon-based composite airframe materials and their use in high-temperature nuclear weapon re-entry systems requires analysts to address the abnormal thermal environment hazards associated with composite material fires. These fires tend to burn very differently than conventional fuel fires, usually burning less intensely, but much longer. This could lead to challenges in understanding margins in classic safety themes. The technical challenges in modeling the phenomena associated with these new types of fires are considerable, but new models have been developed. Their predictions have been compared with well-documented measurements of a vertical porous burner fire, known as a "wall fire" (a "wall-fire" validation simulation is reflected in the figures below). These measurements were conducted at FMGlobal, a mutual insurance company with a strong fire risk management program, as part of an ongoing collaboration between Sandia and FMGlobal. To date, the "wall-fire" scenario has been set up and initial model assessments with grid refinement studies have been conducted focusing on mesh resolutions suitable for full weapon system simulations. This work will continue with further verification and validation tasks assessing the predictions of the new model. Future work will address specific aspects of the wall models that are lacking in their predictive ability.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Report on local data recovery approaches suitable for weather and climate prediction (Deliverable 1.3) (V.1.0)

Numerical weather and climate prediction rates as one of the scientific applications whose accuracy improvements greatly depend on the growth of the available computing power. As the number of cores in top computing facilities pushes into the millions, increasing average frequency of hardware and software failures forces users to review their algorithms and systems in order to protect simulations from breakdown. This report surveys approaches for fault-tolerance in numerical algorithms and system resilience in parallel simulations from the perspective of numerical weather and climate prediction systems. A selection of existing strategies is analyzed, featuring interpolation-restart and compressed checkpointing for the numerics, in-memory checkpointing, user-level failure mitigation-based and backup-based methods for the systems. Numerical examples showcase the performance of the techniques in addressing faults, with particular emphasis on iterative solvers for linear systems, a staple of atmospheric fluid flow solvers. The potential impact of these strategies is discussed in relation to current development of numerical weather prediction algorithms and systems towards the exascale. Trade-offs between performance, efficiency and effectiveness of resiliency strategies are analyzed and some recommendations outlined for future developments.

97 MATHEMATICS AND COMPUTING↗

Probabilistic predictions and uncertainty estimation for radiological and nuclear effects modeling

Better characterization of meteorological uncertainty is needed to predict the effects of radiological and nuclear releases in the atmosphere. Multi-physics ensembles of atmospheric simulations can estimate uncertainty of physical processes, but they are often limited for computational reasons. Because weather uncertainty is important for emergency response applications, but the conventional way of running multi-physics ensembles is infeasible, we have developed new machine learning-based methods that quickly estimate and identify key sources of meteorological uncertainty. Machine learning accelerates the analysis of weather uncertainty by iteratively learning about model physics options that affect plume predictions. We have demonstrated the power of machine learning by creating a large multi-physics weather and dispersion ensemble dataset containing 1,200 simulations for two hypothetical radiological release scenarios. By training on less than 10% of the ensemble, we can quickly and accurately predict different outcomes, including the mass of radiological material deposited and spatial distribution and extent of contaminated areas.

54 ENVIRONMENTAL SCIENCES↗

Disruption Prediction and Avoidance in High Beta Long Pulse KSTAR Plasmas

DoE Grant DE-SC0016409 (Disruption Prediction and Avoidance in High Beta Long Pulse KSTAR Plasmas) supported a collaboration among Columbia University, the Princeton Plasma Physics Laboratory (PPPL), and the Plasma Science and Fusion Center (PSFC) at MIT to conduct research on the KSTAR tokamak at the National Fusion Research Institute (NFRI) in Korea to improve predictive capability for disruptions in tokamaks. This initiative included upgrades to kinetic diagnostics at KSTAR whose measurements form the basis for the disruption prediction models. The major thrust of the PPPL and PSFC work was implementing a capability at KSTAR to allow partially-polarized background light seen by the KSTAR Motional Stark Effect (MSE) diagnostic to be compensated by ‘wavelength interpolation’ rather than the traditional ‘beam modulation’ technique. This objective was completed on time and on budget, and the MSE Background Polychromator is currently functioning at KSTAR. Primary responsibility for maintaining and operating the MSE-BP was transferred to Nova Photonics, Inc. in 2019.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Eject, crash, or survive: Using machine learning to predict orbital instability of exoplanetary systems

Astronomers throughout history, including titans like Kepler and Newton, have tackled planetary dynamics and orbital instability. Despite strides taken in research, understanding the evolution of planetary orbits remains an intricate, computationally expensive, and analytically unsolved problem. I apply machine learning classification methods to numerical simulations of planetary systems in order to predict the long-term fate of the planet - whether the planet remains in a stable orbit or not. My method uses the first 41.1 years (≤ 500 orbits) of data from a planet’s simulation to calculate 17 dynamically-motivated metrics; I trained my classifier on these features to predict a planet’s stability after 107 years. At 84.33%, my classifier was comparable in accuracy to pre-existing literature, despite using significantly less computational power than most other methods. In my research, I found that the standard deviation of eccentricity, mass ratios for neighboring planets, and semi-major axis ratio with the outer planet neighbor to be the most predictive features of instability. I propose reasons for the importance of these features, their role in planetary dynamics, as well as possible explanations for why some planets were misclassified. By understanding the important metrics of instability and reasons for misclassification, we can begin to understand more about system architectures, orbital motion and dynamics, and the formation and evolution of the exoplanetary systems. This is applicable in our own Solar System, and with exoplanet discovery missions such as TESS, this research becomes especially relevant in understanding the new exoplanetary systems we discover.

79 ASTRONOMY AND ASTROPHYSICS↗

Eject, crash, or survive: Using machine learning to predict orbital instability of exoplanetary systems

Astronomers throughout history, including titans like Kepler and Newton, have tackled planetary dynamics and orbital instability. Despite strides taken in research, understanding the evolution of planetary orbits remains an intricate, computationally expensive, and analytically unsolved problem. I apply machine learning classification methods to numerical simulations of planetary systems in order to predict the long-term fate of the planet - whether the planet remains in a stable orbit or not. My method uses the first 41.1 years (≤ 500 orbits) of data from a planet’s simulation to calculate 17 dynamically-motivated metrics; I trained my classifier on these features to predict a planet’s stability after 107 years. At 84.33%, my classifier was comparable in accuracy to pre-existing literature, despite using significantly less computational power than most other methods. In my research, I found that the standard deviation of eccentricity, mass ratios for neighboring planets, and semi-major axis ratio with the outer planet neighbor to be the most predictive features of instability. I propose reasons for the importance of these features, their role in planetary dynamics, as well as possible explanations for why some planets were misclassified. By understanding the important metrics of instability and reasons for misclassification, we can begin to understand more about system architectures, orbital motion and dynamics, and the formation and evolution of the exoplanetary systems. This is applicable in our own Solar System, and with exoplanet discovery missions such as TESS, this research becomes especially relevant in understanding the new exoplanetary systems we discover.

79 ASTRONOMY AND ASTROPHYSICS↗

A Spatiotemporal Sequence Forecasting Platform to Advance the Prediction of Changing Spatiotemporal Patterns of CO 2 Concentration by Incorporating Human Activity and Hydrological Extremes

Focal Areas (2): Predictive modeling using AI techniques and AI-derived model components. It describes the use of AI and other tools to design a prediction system comprising a hierarchy of models. Specifically, this white paper focuses on the development of a collaborative deep learning platform for evaluating and predicting spatiotemporal relationships between the hydrological and carbon cycles and includes capabilities for considering biogenic and anthropogenic inputs to these systems.

54 ENVIRONMENTAL SCIENCES↗

Advancing the Predictability of Water Cycle Phenomena via the Application of AI to Model Ensemble Simulations and Observations

AI has the power to identify new pathways to extended predictability of the water cycle via its application to model ensembles together with accompanying observations. We discuss both scientific and technological aspects of this challenge, and address the parts of the MODEX approach involving “Model simulations, evaluation, analysis, and benchmarking” and “Identification of key knowledge gaps”. The widespread incorporation of AI into model analysis will significantly advance Earth system predictability and our predictive capabilities.

54 ENVIRONMENTAL SCIENCES↗

Autonomous reinforcement learning agents for improving predictions and observations of extreme climate events

Primary Focus Area: This proposal addresses focus area 2, “Predictive modeling through the use of AI techniques.” Science Challenge: Extreme climate events associated with severe weather, coastal and inland flooding, droughts, heat waves and wildfires are expected to increase in frequency and severity in the future. Due to the complexity and chaotic behavior of the climate system, accurately predicting and observing extreme climate events requires a tremendous amount of human intervention to run predictive climate simulations and deploy measurement systems. Extreme events often unfold very quickly, leaving little time to iterate on simulations or re-position instruments. Through reinforcement learning, autonomous AI agents can be designed to make real-time decisions to characterize extreme climate events more efficiently through adaptive models and targeted observations.

54 ENVIRONMENTAL SCIENCES↗

Co-Evolving Climate Models under Uncertainty to Improve Predictive Skill

Focal Area: Predictive modeling through the use of AI techniques and AI-derived model components; the use of AI and other tools to design a prediction system comprising of a hierarchy of models Science Challenge: Advances in modeling of climate and improved observational capabilities have led to great improvements in understanding large-scale historical climate effects. It however remains a challenge to reliably predict the risk of fine-scale regional climate events on human systems even as such risks are on the rise because warmer and wetter climates are more prone to hydrometeorological extremes,

54 ENVIRONMENTAL SCIENCES↗

Combining artificial intelligence, Earth observations, and climate models to improve predictability of ice-biogeochemistry interactions

Focal Area: Predictive Modeling. We describe how artificial intelligence (AI) can be combined with state-of-the-science Earth system models to better predict future regional climate responses. To demonstrate, we describe a case study in biogeochemical interactions with sea ice. Science Challenge: Biogeochemical models are poorly constrained for high latitude systems. Machine learning methods and edge computing can be combined with Earth system models, such as the Energy Exascale Earth System Model (E3SM), to gain insight into ice-biogeochemical interactions and improve sea ice extent prediction.

54 ENVIRONMENTAL SCIENCES↗

Event-scale predictions of water and nitrogen exports in coastal watersheds

Focal Area(s): The purpose of this white paper is to call for the improvement of the predictability and explainability of the magnitude and timing of water and nutrient exports in coastal watersheds. In this regard, hybrid machine learning approaches and process-based numerical models provide new opportunities to maximize predictability, emulate process-based model components, and explicitly address model uncertainty associated with event-scale predictions in coastal watersheds.

54 ENVIRONMENTAL SCIENCES↗

Subseasonal-to-seasonal Prediction of Atmospheric Rivers in the Western United States

Atmospheric rivers (ARs) account for a large portion of winter total precipitation (especially heavy precipitation) in the coastal states of western US (Dettinger et al., 2011; Rutz et al., 2014), but accurate subseasonal-to-seasonal predictions of ARs remain challenging. The challenge stems from relatively short observational records, the interactions of different climate modes and their nonlinear impacts on ARs, and uncertainties in AR activity due to AR detection methods (Huang et al., 2021). Important sources of AR prediction skill include different climate modes, such as the El Niño/Southern Oscillation (ENSO), Madden–Julian oscillation (MJO), and quasi-biennial oscillation (QBO) (DeFlorio et al., 2018, 2019; Mundhenk et al., 2018). Nevertheless, a lack of consensus on climate mode–AR relationship limits the subseasonal-to-seasonal predictive skills on ARs.

54 ENVIRONMENTAL SCIENCES↗

Toward Hybrid Physics-Machine Learning to improve Land Surface Model predictions

A critical challenge for Land Surface Models (LSMs) is to simulate processes at the surface and the subsurface and their feedbacks to the atmosphere. Even using the same climate forcings, different LSMs predict different surface fluxes and soil moisture conditions due to differences in the formulations of individual processes, parameterizations, and representation of spatial heterogeneity. Ultimately, these differences contribute to the LSM prediction errors and uncertainty. This research seeks to address this challenge by coupling physics-based modeling with state-of-the-art machine learning (ML) techniques to describe complex physical and biogeochemical processes and narrow the gap between model predictions and observations.

58 GEOSCIENCES↗