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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Modeling Hydrodynamic Instabilities, Shocks, and Radiation Waves in High Energy Density Experiments [Dissertation]

This thesis presents the computational design, modeling, and analysis of three experiments in high-energy density physics (HEDP), all of them concerning fundamental radiation flows. The first experiment is a laboratory astrophysics experiment to investigate the role of the Kelvin-Helmholtz instability (KHI) in the process of galactic filaments supplying gas to galactic halos. The achieved goal was to provide a first study in which the role of the instability is maximal and predict behavior in future iterations of an experiment accessing a more radiative regime where the role of the instability is stifled. This experiment would help answer how certain galaxies are able to grow so rapidly and produce many stars as the KHI limits this process. The second experiment, COAX, is a radiation flow experiment with a novel spectroscopy diagnostic configuration, designed to spatially measure the temperature of a radiation wave as it travels down a doped foam. A key result of this work was the development of a synthetic spectroscopy application and application of modern spectroscopy comparison techniques to provide our first temperature reconstructions from the experimental data. This experimental platform serves as the launching ground for a number of new experiments that vary the basic premise and thus is foundational to our ongoing research. The final experiment is a full integration of modeling, design, and theoretical development for the Radishock experiment. This experimental platform studies the head-on collision of a radiation wave with a counter-propagating shock, and like COAX, uses spectroscopy to diagnose and detect the interaction. My research analyzes the successful shots, indicating aspects of successful detections and suggests improvements to future iterations of the design.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

CR-39 nuclear track detector response to inertial confinement fusion relevant ions

The detection properties of CR-39 were investigated for protons, deuterons, and tritons of various energies. Two models for the relationship between the track diameter and particle energy are presented and demonstrated to match experimental data for all three species. Data demonstrate that CR-39 has 100% efficiency for protons between 1 MeV and 4 MeV, deuterons between 1 MeV and 12.2 MeV, and tritons between 1 MeV and 10 MeV. The true upper bounds for deuterons and tritons exceed what could be measured in data. Simulations were developed to further explore the properties of CR-39 and suggest that the diameter–energy relationship of alpha particles cannot be captured by the conventional c-parameter model. These findings provide confidence in CR-39 track diameter based spectroscopy of all three species and provide invaluable insight for designing filtering for all CR-39 based diagnostics.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

An Electrical Resistance Diagnostic for Conductivity Monitoring in Laser Powder Bed Fusion

With the growing interest in metal additive manufacturing using laser powder bed fusion (LPBF), there is a need for advanced in-situ nondestructive evaluation (NDE) methods that can dynamically monitor manufacturing process-related variations, that can be used as a feedback mechanism to further improve the manufacturing process, leading to parts with improved microstructural properties and mechanical properties. Current NDE techniques either lack sensitivity beyond build layer, are costly or time-consuming, or are not compatible for in-situ integration. In this research, we develop an electrical resistance diagnostic for in-situ monitoring of powder fused regions during laser powder bed fusion printing. The technique relies on injecting current into the build plate and detecting voltage differences from conductive variations during printing using a simple, cheap four-point electrode array directly connected to the build plate. A computational model will be utilized to determine sensitivities of the approach, and preliminary experiments will be performed during the printing process to test the overall approach.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Online and Offline Data Quality Monitoring for the Mu2e Calorimeter

This thesis presents the design, implementation, and validation of a calorimeter Data Quality Monitoring (DQM) toolchain for the Mu2e experiment at Fermilab. Mu2e searches for charged lepton flavor violation via coherent muon-to-electron conversion in the field of an aluminum nucleus, $\mu^- Al \rightarrow e^-Al$, a process whose observation would constitute clear evidence of physics beyond the Standard Model. Achieving target sensitivity requires stringent control of detector performance and data integrity during acquisition, as subtle issues in readout configuration, data formatting, or electronics behavior can compromise reconstruction and bias downstream analyzes. To address these challenges, this work develops a multi-layer DQM approach spanning both raw data validation and reconstructed digi-level diagnostics. At the low level, a fragment analysis component performs word- and bit-field decoding of calorimeter readout blocks, enabling sanity checks of the expected structure and producing detailed error and integrity statistics useful for commissioning and troubleshooting. At the digi level, the CaloDigiDQM analyzer is implemented within the art framework and transforms each CaloDigiCollection into a structured hierarchy of ROOT histograms designed for fast drill-down diagnostics. The module generates coherent monitoring views at global, disk, board, and channel granularity, including occupancy, waveform-derived features (baseline, RMS, peak amplitude and position), and left-right sensor consistency metrics. Detector-aware channel-to-electronics mapping is performed through the conditions system (CaloDAQMap), ensuring that diagnostics remain aligned with hardware identifiers used in operations. For end-to-end testing without reliance on live DAQ data, a synthetic CaloDigi producer is developed to generate realistic waveforms with controlled noise and pulse shapes. The resulting system supports both offline ROOT-file production and online operation, including optional histogram streaming through otsdaq via ots::HistoSender. This toolchain provides a practical and scalable foundation for calorimeter commissioning and stable data collection, enabling early detection of anomalies and reducing operational risk for Mu2e.

Vakulenko, Mark [Drew U.] (ORCID:0009000276197818)↗
DOE OSTI2021

COVID-19 Testing R&D (Final Report)

Eleven Labs within the US Department of Energy (DOE), National Virtual Biotechnology Laboratory (NVBL), came together as a team to address significant R&D gaps in COVID-19 testing. Beginning in March 2020, the NVBL COVID Testing Team developed an R&D agenda, worked with DOE and other agencies to set priorities, and collaborated to deliver timely results. Priority was given to quick implementation as well as development of novel capabilities for immediate and evolving pandemic needs without placing additional burden on operational performers. Priority elements capitalized on DOE National Laboratory strengths and expertise. The Team delivered: testing and evaluation that enabled decisions on testing options, forwardleaning approaches to prepare for future scale-up needs, and models and experiments that supported prioritization of diagnostic and therapeutic candidates.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Building Initial Dynamic System Models for Digital Twins of the Cryogenic Moderator System at the ORNL Spallation Neutron Source

This work describes the initial development of dynamic system models of the cryogenic moderator system (CMS) of the Spallation Neutron Source (SNS) at ORNL as a part of the ORNL LDRD funded project Building TRANSFORM to Accelerate Digital Twin Applications for Nuclear Systems, LOIS 10563. The goal of the work is to start the dynamic system modeling effort with the end goal of using them for real-time applications as digital twins. The CMS is a cryogenic liquid hydrogen flow loop that provides moderation of the neutrons that are generated by the SNS. For optimal neutron production, the CMS needs to maintain a steady and controlled density of cryogenic hydrogen in the moderator section thus requiring precise temperature and pressure control. Due to the varied time scales and system characteristics, control of the system is complex, and diagnostics are also difficult. Difficulty in accessing the flow loop during operations, limited instrumentation and unknown design details of the equipment combine to make the case for having sophisticated digital twin models of the system. Operationally the CMS also provides a strong use case for digital twins due to the constant need of optimization and for troubleshooting/diagnostics. The large amount of data collected which are freely available for using in building the model and verifying and validating the model also makes it a great candidate for a proof-of-concept for digital twins. The project extends ORNL's capacity of development and implementation of the open-source dynamic system modeling tool TRANSFORM for engineering design and digital twin/real-time applications. Specific system configuration data for the CMS have been gathered and an initial dynamic model was created in the TRANSFORM library using Dymola as the solution platform. Models of increasing complexity are created to demonstrate the need for a multi-layered approach in digital twin modeling depending on the scale and phenomena being focused on. The dynamic modeling is shown to bring the dynamic operational aspects to the design process for systems as well as serve as a digital twin to the hardware and allow for models to be tuned and compared against real time operational data. These aims should help to push forward strategic goals of application of digital twins and increase the impact of ORNL systems modeling capabilities with TRANSFORM/Modelica for various advanced energy systems.

42 ENGINEERING↗
DOE OSTI2026

Building Operation Model (Morpheus) for Dallas Fort Worth Airport (CRADA CRD-19-16301 Final Report)

The primary objective of this project was to leverage digital twin technology to enhance the design and operation of DFW Airport terminals and their associated energy systems. To achieve this, Morpheus, a building digital twin, was developed to guide improvements in airport operations, specifically targeting reductions in peak power demand and overall energy consumption.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Tensile Property and Lifetime Prediction for Low-Temperature Aged Uranium-Niobium Alloys

Thermal aging models and lifetime predictions for uranium-niobium (U-Nb) alloys were created using an approach similar to those previously employed. Lifetime estimates for generic U-6Nb components were thus updated; the reported value being 800 years. This update represents a small change in lifetime vs. that of the 2012 assessment (540 years). This lifetime estimate emerged from consideration of several model fits specific to the aging datasets and properties chosen. Aging was quantified using quasi-static tensile properties measured on specimens artificially aged for up to 10 years. The major change relative to the most recent 2012 LANL assessment was that a more comprehensive body of U-Nb literature data was mined, in addition to being augmented by the latest LANL and UK AWE data. The tensile data compilation was published separately (LANL report LA-14493, December 2016). Recognizing the chemical banding of industrially produced U-6Nb, models were developed for the mid-range (6 wt.%) and extrema (4 and 8 wt.%) compositions. Lifetime estimates were calculated for all three alloy classes (4, 6, 8 wt.% nominal) and two measures of total tensile elongation (TE) to failure, namely TE-ext. — extensometer method, and TE-NCD — normalized crosshead displacement method. The conservative assumption was made that whichever composition (4, 6, or 8 wt.% Nb) and property (TE-ext or TE-NCD) was the first to cross the ductility failure threshold would limit the lifetime of the entire component. Tensile strength properties did not figure into the lifetime predictions, but could be useful as age-sensitive diagnostics and were also modeled. Of these, only first yield strength is expected to show a change at 40°C aging vs. time = 0 over the ~100-year timespan of engineering interest. Second yield strength evolves more slowly, and ultimate tensile strength slower still. Among all the models, the apparent activation energies for aging were mostly in the narrow 29– 37 kcal/mol range, which is close to that for diffusion of Nb in gamma-uranium. This agreement may be coincidental. The data from recent long-term aging studies substantially improved the model fit quality and robustness of the lifetimes. Appendices document sensitivity studies of the model fits and lifetimes with respect to using more limited datasets. These results highlight the limitations of relying solely on data from scattered literature studies and smaller datasets more generally.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A scoping review of non-destructive testing (NDT) techniques in building performance diagnostic inspections

Understanding building envelope thermodynamics is an essential foundation of building sciences, mainly due to the envelope’s role as a boundary layer for exterior environments, as well as a container and regulator of internal microclimates. This paper presents a scoping literature review of select Non-destructive Testing (NDT) techniques for building envelope scanning and surveying for thermodynamic diagnostics. The investigation focuses specifically on reviewing six NDT techniques: Ground Penetrating Radar (GPR), Light Detection and Ranging (LiDAR)/Laser Scanning, Thermography, Ultrasound, Close-Range Photogrammetry and Through Wall Imaging Radar (TWIR). The aim is to identify knowledge gaps in terms of their use in accurately characterizing envelope compositions for further integration in Building Energy Modeling (BEM). Each technique was evaluated according to set categories imbibed from the American Society of Heating, Refrigerating, and Air Conditioning Engineering (ASHRAE) Standard 211P that showcase the technique’s ability to extract various relevant information. A framework is then developed to inform users on how to use hybrid NDT-based workflows applied in building envelope energy audits. The study concludes by discussing possibilities of utilizing NDT in large-scale audit automation, BEM integration, and developing built environment policies focusing on increasing existing building performance through retrofitting design.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Bridging Nano- and Microscale X-Ray Tomography for Battery Research by Leveraging Artificial Intelligence

X-ray computed tomography (CT) is a non-destructive imaging technique in which contrast originates from the materials' absorption coefficient. The recent development of laboratory nanoscale CT (nano-CT) systems has pushed the spatial resolution for battery material imaging to voxel sizes of 50 nm, a limit previously achievable only with synchrotron facilities. Given the non-destructive nature of CT, in situ and operando studies have emerged as powerful methods to quantify morphological parameters, such as tortuosity factor, porosity, surface area and volume expansion, during battery operation or cycling. Combined with artificial intelligence and machine learning analysis techniques, nano-CT has enabled the development of predictive models to analyse the impact of the electrode microstructure on cell performances or the influence of material heterogeneities on electrochemical responses. In this Review, we discuss the role of X-ray CT and nano-CT experimentation in the battery field, discuss the incorporation of artificial intelligence and machine learning analyses and provide a perspective on how the combination of multiscale CT imaging techniques can expand the development of predictive multiscale battery behavioural models.

diagnostics↗
DOE OSTI2026

Tori, Klein bottles, and modulo 8 parity/time-reversal anomalies of 2+1d staggered fermions

We study the symmetries of lattice staggered fermions in 2+1d. Using the symmetries, we can place the system on any sheared torus or Klein bottle. These different backgrounds provide diagnostics of various ’t Hooft anomalies associated with the crystalline symmetries. We then compare the lattice model to its continuum limit. The symmetries of the lattice system are mapped in a nontrivial way to the symmetries of the continuum theories. Using this map, we match the ’t Hooft anomalies on the lattice and the continuum. Along the way, we develop a general formalism to study Hamiltonian lattice models on nontrivial, compact, flat spaces.

Algorithms and Theoretical Developments↗
DOE OSTI2025

VERITAS : A density-functional theory-based multiband kinetic model for understanding x-ray spectroscopy of dense plasmas

X-ray spectroscopy has long been a powerful diagnostic tool for hot, dilute plasmas, providing insights into plasma conditions by measuring line shifts and broadenings of atomic transitions. The technique critically depends on the accuracy of atomic physics models used to interpret spectroscopic measurements for inferring plasma properties such as free-electron density and temperature. Over the past decades, the atomic and plasma physics communities have developed robust atomic physics models to account for various processes in hot, dilute classical plasmas. While these models have been successful in that regime, their applicability becomes uncertain when interpreting x-ray spectroscopy experiments of above-solid-density plasmas. Given that finite-temperature density-functional theory (DFT) offers a more accurate description of dense plasma environments, we present the development of a DFT-based multi-band kinetic model, VERITAS, designed to improve the interpretation of x-ray spectroscopic measurements in high-density plasmas produced by laser-driven spherical implosions. This work details the VERITAS model and its application to both time-integrated and time-resolved x-ray spectra from implosion experiments on OMEGA. The advantages and limitations of the VERITAS model will also be discussed, along with potential directions for advancing x-ray spectroscopy of dense and superdense plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

The multi-faceted inverted harmonic oscillator: Chaos and complexity

The harmonic oscillator is the paragon of physical models; conceptually and computationally simple, yet rich enough to teach us about physics on scales that span classical mechanics to quantum field theory. This multifaceted nature extends also to its inverted counterpart, in which the oscillator frequency is analytically continued to pure imaginary values. In this article we probe the inverted harmonic oscillator (IHO) with recently developed quantum chaos diagnostics such as the out-of-time-order correlator (OTOC) and the circuit complexity. In particular, we study the OTOC for the displacement operator of the IHO with and without a non-Gaussian cubic perturbation to explore genuine and quasi scrambling respectively. In addition, we compute the full quantum Lyapunov spectrum for the inverted oscillator, finding a paired structure among the Lyapunov exponents. We also use the Heisenberg group to compute the complexity for the time evolved displacement operator, which displays chaotic behaviour. Finally, we extended our analysis to N-inverted harmonic oscillators to study the behaviour of complexity at the different timescales encoded in dissipation, scrambling and asymptotic regimes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

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↗
DOE OSTI2023

Non-Equilibrium Plasma Interactions with Biomaterials, Biological Solutions and Tissues

Cold atmospheric pressure plasma discharges offer an abundant source of reactive oxygen and nitrogen species (RONS) at room temperature enabling unique interactions with biomaterials, biological solutions and tissues. These interactions particularly with living matter are presently an important intellectual frontier in plasma science with promising potential applications ranging from human health care to advanced biomaterial processing. Exciting case studies have been reported that illustrate the huge potential of cold atmospheric plasma technology in wound healing and cancer treatment. The interaction of plasma with conducting and dielectric biomaterials such as tissue strongly influences the plasma properties. In turn this changes the impact of the plasma on the biomaterial. Particularly in the case of living matter, liquid based solutions are ubiquitous which complicates interfacial processes. The lack of insight into the underlying mechanisms of the interaction of plasma with wounds and tumors is currently a bottleneck for the further development of the technology and gives rise to many interesting scientific questions. This project was focused on plasma properties and kinetics during plasma-biomaterial interactions. Both DC pulsed and RF driven atmospheric pressure plasma jets, extensively used by the plasma community were studied. The bio-interfaces included hydrogel as a tissue model, (saline) solutions, bacteria and virus. Plasma diagnostics used include Thomson scattering, Rayleigh scattering, Raman scattering, (two-photon absorption) laser induced fluorescence, optical emission spectroscopy, absorption spectroscopy, molecular beam mass spectrometry and fast imaging allowing to determine electron densities and temperatures, ionic species, reactive species including radicals, gas temperatures, gas composition, electric fields and solution components transferred to the gas phase.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Preparing for the next pandemic via transfer learning from existing diseases with hierarchical multi-modal BERT: a study on COVID-19 outcome prediction

Abstract Developing prediction models for emerging infectious diseases from relatively small numbers of cases is a critical need for improving pandemic preparedness. Using COVID-19 as an exemplar, we propose a transfer learning methodology for developing predictive models from multi-modal electronic healthcare records by leveraging information from more prevalent diseases with shared clinical characteristics. Our novel hierarchical, multi-modal model ( $${\textsc {TransMED}}$$ T R A N S MED ) integrates baseline risk factors from the natural language processing of clinical notes at admission, time-series measurements of biomarkers obtained from laboratory tests, and discrete diagnostic, procedure and drug codes. We demonstrate the alignment of $${\textsc {TransMED}}$$ T R A N S MED ’s predictions with well-established clinical knowledge about COVID-19 through univariate and multivariate risk factor driven sub-cohort analysis. $${\textsc {TransMED}}$$ T R A N S MED ’s superior performance over state-of-the-art methods shows that leveraging patient data across modalities and transferring prior knowledge from similar disorders is critical for accurate prediction of patient outcomes, and this approach may serve as an important tool in the early response to future pandemics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

FutureTense

Protective vaccines and reliable diagnostics are essential tools for controlling viral diseases. However, the efficacy of these tools can be diminished by mutations in viral genomes. The delay between the emergence of new viral strains and the redesign of vaccines and diagnostics allows for continued viral transmission. Is it possible to address this challenge by computationally predicting viral genome sequence evolution? Can we “future-proof” vaccines and diagnostics by targeting both current and anticipated future sequence variants? While predicting viral evolution is still an unsolved, “grand challenge” problem in biology, the large, and rapidly growing, number of SARS-CoV-2 genome sequences provide an opportunity to quantify the ability of machine learning to predict viral genome sequence evolution. Towards this end, we have developed a simple computational model for predicting viral evolution at the level of individual nucleotides. The key metric for quantifying the per-base, prediction accuracy for viral evolution is the Mann-Whitney U statistic (or, equivalently, the area under the receiver operator curve). Since the Mann-Whitney U statistic is not a differentiable function, existing deep leaning packages (like Pytorch and Keras/TensorFlow) are not useful, as they require that the accuracy metric/objective function be analytically differentiable with respect to the model parameters. To overcome this challenge, we have implemented custom software, “FutureTense”, that can train a machine learning model by maximizing the non-differentiable Mann-Whitney U statistic. This software trains a machine learning model by exploring along the direction of the discrete gradient of the Mann-Whitney U statistic in the model parameter space. Parallel computing and genome sequence-specific optimizations are used to accelerate model training. The resulting machine learning model learns the observed high C->U mutation rates in the SARS-CoV-2 genome (which are potentially induced by host defenses) and provides prediction accuracies that are significantly better than one would expect from random chance. While predicting viral evolution is still quite far from a solved problem, the surprising performance of this simple model gives hope that the accuracy of predicting viral genome evolution can be further increased by more sophisticated approaches.

Gans, Jason↗