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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Using machine learning to improve efficiency and accuracy of burnup measurements at PBR reactors [Slides]

The outline of the slides include: Motivations of the work; Modeling and simulation; Machine learning model; Results and comparison study with linear regression; and Conclusions. This work was done to help PBR designers and operators understand the burnup measurement better. We look forward to discussing the results in detail with industrial collaborators.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Developing predictive models for µ opioid receptor binding using machine learning and deep learning techniques

Opioids exert their analgesic effect by binding to the µ opioid receptor (MOR), which initiates a downstream signaling pathway, eventually inhibiting pain transmission in the spinal cord. However, current opioids are addictive, often leading to overdose contributing to the opioid crisis in the United States. Therefore, understanding the structure-activity relationship between MOR and its ligands is essential for predicting MOR binding of chemicals, which could assist in the development of non-addictive or less-addictive opioid analgesics. This study aimed to develop machine learning and deep learning models for predicting MOR binding activity of chemicals. Chemicals with MOR binding activity data were first curated from public databases and the literature. Molecular descriptors of the curated chemicals were calculated using software Mold2. The chemicals were then split into training and external validation datasets. Random forest, k-nearest neighbors, support vector machine, multi-layer perceptron, and long short-term memory models were developed and evaluated using 5-fold cross-validations and external validations, resulting in Matthews correlation coefficients of 0.528–0.654 and 0.408, respectively. Furthermore, prediction confidence and applicability domain analyses highlighted their importance to the models’ applicability. Our results suggest that the developed models could be useful for identifying MOR binders, potentially aiding in the development of non-addictive or less-addictive drugs targeting MOR.

Research & Experimental Medicine↗
NASA NTRSDate not supplied

Machine Learning Approach for Aircraft Performance Model Parameter Estimation for Trajectory Prediction Applications

Inaccurate prediction of aircraft trajectory by ground-based decision support tools (DST) is a major concern in air traffic management (ATM). Aircraft trajectory prediction tools rely on a simplified point-mass aircraft performance model (APM) to make their predictions. Even though the performance coefficients and weight of an aircraft are a vital part of the APM’s predictions and accuracy, these coefficients are proprietary in nature and therefore, unavailable to DSTs. Current ATM research focuses on improving the estimate of some APM parameters by freezing all other coefficients. This simplified approach introduces unwanted sources of bias and negatively impacts the accuracy of the performance model. In this paper, we apply machine learning (ML) techniques for the simultaneous prediction of three key APM parameters (two drag coefficients and the initial aircraft weight). To accomplish this, we employ an ordinary differential equation (ODE) fitting approach to generate optimized APM parameter labels customized to each individual flight record. Subsequently, we train ML models to capture the relationship between the historical data and the optimized APM parameters. Two different ML model solutions are applied and APM coefficients are predicted for unseen flights. The results indicate that the ML models are able to capture the relationship between APM parameters and flight-related features with good accuracy.

trajectory prediction, machine learning, aircraft ↗
DOE OSTI2020

Spectroscopic Probe Molecule Selection Using Quantum Theory, First-Principles Calculations, and Machine Learning

Probe molecule vibrational spectra have a long history of being used to characterize materials including metals, oxides, metal-organic frameworks, and even human proteins. Furthermore, recent advances in machine learning have enabled computationally generated spectra to aid in detailed characterization of complex surfaces with probe molecules. Despite widespread use of probe molecules, the science of probe molecule selection is underdeveloped. Here, we develop physical concepts, including orbital interaction energy and the energy overlap integral, to explain and predict the ability of probe molecules to discriminate structural descriptors. We resolve the crystal orbital overlap population (COOP) to specific molecular orbitals and quantify their bonding character, which directly influences vibrational frequencies. Using only a single adsorbate calculation from density function theory (DFT), we compute the interaction energy of individual adsorbate molecular orbitals with adsorption site atomic orbitals across many different sites. Combining the molecular orbital resolved COOP and changes in orbital interaction energy enables probe molecule selection for improved discrimination of various sites. We demonstrate these concepts by comparing the predicted effectiveness of carbon monoxide (CO), nitric oxide (NO), and ethylene (C 2 H 4 ) to probe Pt adsorption sites. Finally, using a previously developed machine learning framework, we show that models trained on hundreds of thousand C 2 H 4 spectra, computed from DFT, which regress surface binding-type and generalized coordination number (GCN), outperform those trained using CO and NO spectra. Lastly, a python package, pDOS_overlap, for implementing the electron density based analysis on any combination of adsorbates and materials, is also made available.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Machine learning surrogates for surface complexation model of uranium sorption to oxides

Abstract The safety assessments of the geological storage of spent nuclear fuel require understanding the underground radionuclide mobility in case of a leakage from multi-barrier canisters. Uranium, the most common radionuclide in non-reprocessed spent nuclear fuels, is immobile in reduced form (U(IV) and highly mobile in an oxidized state (U(VI)). The latter form is considered one of the most dangerous environmental threats in the safety assessments of spent nuclear fuel repositories. The sorption of uranium to mineral surfaces surrounding the repository limits their mobility. We quantify uranium sorption using surface complexation models (SCMs). Unfortunately, numerical SCM solvers often encounter convergence problems due to the complex nature of convoluted equations and correlations between model parameters. This study explored two machine learning surrogates for the 2-pK Triple Layer Model of uranium retention by oxide surfaces if released as U(IV) in the oxidizing conditions: random forest regressor and deep neural networks. Our surrogate models, particularly DNN, accurately reproduce SCM model predictions at a fraction of the computational cost without any convergence issues. The safety assessment of spent fuel repositories, specifically the migration of leaked radioactive waste, will benefit from having ultrafast AI/ML surrogates for the computationally expensive sorption models that can be easily incorporated into larger-scale contaminant migration models. One such model is presented here.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2018

Fast Learning for Immersive Engagement in Energy Simulations

The fast computation which is critical for immersive engagement with and learning from energy simulations would be furthered by developing a general method for creating rapidly computed simplified versions of NREL's computation-intensive energy simulations. Created using machine learning techniques, these 'reduced form' simulations can provide statistically sound estimates of the results of the full simulations at a fraction of the computational cost with response times - typically less than one minute of wall-clock time - suitable for real-time human-in-the-loop design and analysis. Additionally, uncertainty quantification techniques can document the accuracy of the approximate models and their domain of validity. Approximation methods are applicable to a wide range of computational models, including supply-chain models, electric power grid simulations, and building models. These reduced-form representations cannot replace or re-implement existing simulations, but instead supplement them by enabling rapid scenario design and quality assurance for large sets of simulations. We present an overview of the framework and methods we have implemented for developing these reduced-form representations.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Machine Learning-Based Regression Models for Ironmaking Blast Furnace Automation

Computational fluid dynamics (CFD)-based simulation has been the traditional way to model complex industrial systems and processes. One very large and complex industrial system that has benefited from CFD-based simulations is the steel blast furnace system. The problem with the CFD-based simulation approach is that it tends to be very slow for generating data. The CFD-only approach may not be fast enough for use in real-time decisionmaking. To address this issue, in this work, the authors propose the use of machine learning techniques to train and test models based on data generated via CFD simulation. Regression models based on neural networks are compared with tree-boosting models. In particular, several areas (tuyere, raceway, and shaft) of the blast furnace are modeled using these approaches. The results of the model training and testing are presented and discussed. The obtained R 2 metrics are, in general, very high. The results appear promising and may help to improve the efficiency of operator and process engineer decisionmaking when running a blast furnace.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Machine-Learning Assisted Identification of Accurate Battery Lifetime Models with Uncertainty

Reduced-order battery lifetime models, which consist of algebraic expressions for various aging modes, are widely utilized for extrapolating degradation trends from accelerated aging tests to real-world aging scenarios. Identifying models with high accuracy and low uncertainty is crucial for ensuring that model extrapolations are believable, however, it is difficult to compose expressions that accurately predict multivariate data trends; a review of cycling degradation models from literature reveals a wide variety of functional relationships. Here, a machine-learning assisted model identification method is utilized to fit degradation in a stand-out LFP-Gr aging data set, with uncertainty quantified by bootstrap resampling. The model identified in this work results in approximately half the mean absolute error of a human expert model. Models are validated by converting to a state-equation form and comparing predictions against cells aging under varying loads. Parameter uncertainty is carried forward into an energy storage system simulation to estimate the impact of aging model uncertainty on system lifetime. The new model identification method used here reduces life-prediction uncertainty by more than a factor of three (86% ± 5% relative capacity at 10 years for human-expert model, 88.5% ± 1.5% for machine-learning assisted model), empowering more confident estimates of energy storage system lifetime.

25 ENERGY STORAGE↗
DOE OSTI2015

Metabolome of human gut microbiome is predictive of host dysbiosis

Background: Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. However, the community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome’s interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent on its community metabolome; an emergent property of the microbiome. Results: Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles. Conclusions: Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome–host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.

human microbiome↗
NASA NTRSDate not supplied

Designing Molten Salt Eutectics

Designing stable electrolytes with target properties is an important challenge in realizing next generation energy storage devices. Molten salt eutectics-based electrolytes are known for their stability with minimal parasitic reactions when compared to traditional organic electrolytes and are an attractive option for different battery chemistries. The operating temperature of the molten salt batteries depends on the melting temperature of the eutectic and hence there is a necessity to discover novel low melting temperature molten salt eutectic mixtures for energy storage applications. In this work we develop a high throughput computational screening approach for molten salt mixtures using thermodynamic modeling and machine learning (ML). COSMO-SAC model and ML approaches were independently developed based on the existing experimental data and these models were further used to predict the eutectic melting temperature and composition of several new binary, ternary, and quaternary mixtures. We show that combining ML and thermodynamic modeling strategies is effective in exploring the vast design space of molten salt mixtures.

Ashwin Ravichandran↗
DOE OSTI2019

A machine learning approach to thermal conductivity modeling: A case study on irradiated uranium-molybdenum nuclear fuels

A deep neural network was developed for the purpose of predicting thermal conductivity with a case study performed on irradiated nuclear fuel. Traditional thermal conductivity modeling approaches rely on existing theoretical frameworks that describe known, relevant phenomena that govern the microstructural evolution processes during neutron irradiation (such as recrystallization, and pore size, distribution and morphology). Current empirical modeling approaches, however, do not represent all irradiation test data well. We develop a machine learning approach to thermal conductivity modeling that does not require a priori knowledge of a specific material microstructure and system of interest. Our approach allows re-searchers to probe dependency of thermal conductivity on a variety of reactor operating and material conditions. The purpose of building such a model is to allow for improved predictive capabilities linking structure-property-processing-performance relationships in the system of interest (here, irradiated nuclear fuel), which could lead to improved experimental test planning and characterization. The uranium-molybdenum system is the fuel system studied in this work, and historic irradiation test data is leveraged for model development. Our model achieved a mean absolute percent error of approximately 10%. Results indicate our model generalizes well to never before seen data, and thus use of deep learning methods for material property predictions from limited, historic irradiation data is a viable approach. This work challenges the current paradigm in materials science, where material property models are based on limited experimental data fitted to low-dimensionality phenomenological models, or by simulations in which fundamental equations are explicitly solved. The work presented here aims to demonstrate the potential and limitations of machine learning in the field of materials science and material property modeling.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
NASA NTRS2018

Application of Machine-Learning Algorithms for On-Board Asteroid Shape Model Determination

The Application of Machine-learning Algorithms for On-board Asteroid Shape Model Determination project will develop an innovative system for spacecraft navigation to expand the capability of small spacecraft to meet the critical challenges associated with small-body exploration. Such challenges include accurate navigation in a microgravity environment and precision targeting of particular locations on an asteroid surface for sample collection. This on-board system will cut the computational "umbilical" back to Earth-currently necessary for the generation of a global shape model that requires thousands of images with sufficient resolution and adequate variation of incidence and emission angles, processed manually by a team of experts on Earth for several months. Small satellites have limited bandwidth and are unable to downlink the data volume required for this processing, restricting their ability to perform deep-space asteroid exploration.

Machine learning algorithms↗
DOE OSTI2024

Building an ab initio solvated DNA model using Euclidean neural networks

Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine-learned electron density model based on a Euclidean neural network framework that includes a built-in understanding of equivariance to model explicitly solvated double-stranded DNA. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Physics-Reinforced Machine Learning Algorithms for Multiscale Closure Model Discovery

The central objective of this project was to address the challenge of modeling and simulating complex multiscale turbulence phenomena by leveraging physics-guided machine learning (PGML) and hybrid modeling approaches. By integrating physics-based methods with data-driven models, the research focused on achieving robust and scalable solutions for geophysical turbulence, enhancing numerical weather prediction and climate research tools. The project resulted in significant advancements in computational modeling paradigms, predictive tools for reduced-order modeling, and innovative algorithms for fluid dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Machine learning prediction of incidence of Alzheimer’s disease using large-scale administrative health data

Nationwide population-based cohort provides a new opportunity to build an automated risk prediction model based on individuals’ history of health and healthcare beyond existing risk prediction models. We tested the possibility of machine learning models to predict future incidence of Alzheimer’s disease (AD) using large-scale administrative health data. From the Korean National Health Insurance Service database between 2002 and 2010, we obtained de-identified health data in elders above 65 years (N = 40,736) containing 4,894 unique clinical features including ICD-10 codes, medication codes, laboratory values, history of personal and family illness and socio-demographics. To define incident AD we considered two operational definitions: “definite AD” with diagnostic codes and dementia medication (n = 614) and “probable AD” with only diagnosis (n = 2026). We trained and validated random forest, support vector machine and logistic regression to predict incident AD in 1, 2, 3, and 4 subsequent years. For predicting future incidence of AD in balanced samples (bootstrapping), the machine learning models showed reasonable performance in 1-year prediction with AUC of 0.775 and 0.759, based on “definite AD” and “probable AD” outcomes, respectively; in 2-year, 0.730 and 0.693; in 3-year, 0.677 and 0.644; in 4-year, 0.725 and 0.683. The results were similar when the entire (unbalanced) samples were used. Important clinical features selected in logistic regression included hemoglobin level, age and urine protein level. This study may shed a light on the utility of the data-driven machine learning model based on large-scale administrative health data in AD risk prediction, which may enable better selection of individuals at risk for AD in clinical trials or early detection in clinical settings.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Findings on Subtask 3.1 - Bakken Rich Gas Enhanced Oil Recovery Project

Total in-place oil for the Bakken petroleum system (BPS) (which includes the Bakken and Three Forks Formations) has been estimated to be 600 billion barrels (bbl). However, BPS wells have decline rates as high as 85% over the first 3 years of their lives, and primary recovery factors typically range from 3% to 10% of original oil in place. Given the low initial recovery rates, even small incremental productivity improvements could dramatically increase technically recoverable oil in the BPS. One potential solution is enhanced oil recovery (EOR) using gas injection, such as carbon dioxide (CO2) or hydrocarbon (HC) gases. While commonly used in conventional reservoirs, CO2 EOR in unconventional tight oil reservoirs has been limited to pilot tests. EOR using rich gas (mixture of methane, ethane, and propane) has also been employed in numerous pilots in several unconventional plays and has recently been successfully applied in the Eagle Ford play. If successful, large-scale gas-based EOR in the BPS could dramatically increase oil productivity and recovery factors and extend the life of the play for decades. While CO2 may be a technically suitable working fluid for EOR in the BPS, supplies are limited and costs for using CO2 in EOR pilots are prohibitively high. Meanwhile, produced gas flaring has presented challenges for BPS operators in North Dakota. Analysis conducted by the North Dakota Pipeline Authority indicates that the current gas-gathering infrastructure in North Dakota is insufficient to accommodate all of the associated gas that is produced from the BPS. The geographically isolated location of North Dakota relative to large natural gas markets, combined with suppressed natural gas prices, has made it economically challenging for industry to invest capital in expanding gas-gathering infrastructure in the state. These circumstances led to a research program conducted by the Energy & Environmental Research Center (EERC) in partnership with Liberty Resources Management Company LLC (LR) to examine the potential to use rich gas injection for EOR and mitigate flaring. A rich gas EOR pilot test was designed and executed by LR at its Stomping Horse development area in Williams County, North Dakota. From July 2018 through May 2019, a total of 160 million standard cubic feet (MMscf) of rich produced gas was injected into the BPS using five different wells in a sequential injection strategy. LR’s Leon–Gohrick drill spacing unit (DSU) was used as the test site. Regulatory oversight was provided by the North Dakota Industrial Commission (NDIC). Technical support was provided by the EERC through a series of laboratory, modeling, and field-based activities, and additional post-pilot research activities incorporated learnings from the test, developed new laboratory data, improved fracture modeling methods, and developed machine learning and big data analytics. The results from the Stomping Horse rich gas EOR pilot activities indicate that developing an effective, economical EOR approach for the BPS will require more field tests. Another key lesson learned from the Stomping Horse tests is that detailed pre- and posttest data on reservoir conditions and fluids production are essential. Robust reservoir characterization provides information that is crucial to creating realistic geomodels and conducting valid dynamic simulations of potential EOR scenarios. A detailed understanding of the completions and production history of offset wells is also necessary for valid test result interpretations. This knowledge is essential to designing the operational parameters of injectivity tests and interpreting the results. A conformance control strategy is also essential to success. Laboratory-based examinations of rich gas interactions with reservoir fluids and rocks were conducted, with an emphasis on determining the ability to mobilize oil in the tight reservoir rocks and shales of the BPS. Injection fluid composition was shown to have a positive impact on reducing reservoir oil minimum miscibility pressure (MMP), reducing interfacial tension (IFT), and altering wettability. IFT and contact angle measurements demonstrated that wettability can be altered in the presence of rich gas, suggesting the potential to improve oil recovery. Iterative modeling of surface infrastructure and reservoir performance using data generated by the various project activities was conducted. A geologic model of the Stomping Horse area was built; history-matched oil, gas, and water production was used in simulations of various EOR scenarios. Early programmatic modeling results were used to support LR’s design and operation of the EOR pilot and to provide insight regarding optimization of future commercial-scale BPS EOR design and operations. Post-pilot modeling focused on alternative methods of understanding complex fracture networks and accelerating simulation time. These led to improved simulation run times and provide excellent history-matching results. Several of these iterative models were used as the bases for developing algorithms into machine learning and big data analytics. History matching in reservoir simulation is time-consuming and computer processing-intensive. Machine learning algorithms were created, and an automated history-matching tool was developed. A large set of synthetic reservoir simulations were created to generate well responses (oil, gas, and water production, well bottomhole pressure [BHP], and tracer or propane breakthrough) for a set of EOR operating parameters that included offset well status (open or closed), injectate (rich gas or propane), injection rate, and injection well BHP. A user interface was developed to provide real-time visualization. Machine learning-based models were developed to provide rapid forecasting of well performance given a set of user-defined EOR operating parameters. These predictive models allow the user to modify the offset well status, injection rate, and injection well BHP and rapidly forecast future production performance. The combination of real-time visualization tools with real-time forecasting tools provides a framework for real-time control—operational changes that the EOR site operator can enact (e.g., changing gas injection rates) to affect the observed performance and potentially improve the EOR outcome. There is great reason to be optimistic about the future of EOR in the Bakken. The results of the laboratory studies suggest significant potential for high rates of oil mobilization using produced field gas injection under the right conditions. The results of the lab studies, combined with rigorous statistical analysis of well production data and associated modeling efforts, confirm the notion that fluid mobility within the reservoir is controlled by fractures. As more knowledge is gained about the nature and distribution of fracture networks in the Bakken, the industry will be in a better position to predict and, ultimately, influence fluid mobility. New field tests are necessary to develop a more complete understanding of those conditions. Thoughtful and creatively engineered field tests within a well-characterized geologic setting will yield the fundamental knowledge needed to take Bakken oil production to the next level. This subtask was cofunded through the EERC–U.S. Department of Energy Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE-FE0024233. Nonfederal funding was provided by the North Dakota Industrial Commission’s Oil and Gas Research Program and Computer Modelling Group.

04 OIL SHALES AND TAR SANDS↗
NASA NTRS2018

Machine Learning Application to Atmospheric Chemistry Modeling

Atmospheric chemistry is a high-dimensionality, large-data problem and thus may be suited to machine-learning algorithms. We show here the potential of a random forest regression algorithm to replace the gas-phase chemistry solver in the GEOS-Chem chemistry model. In this proof-of-concept study, we used one month of model output to train random forest regression models to predict the concentrations of each long-lived chemical species after integration based upon the physical and chemical conditions before the chemical integration. The choice of prediction type has a strong impact on the skill of the regression model. We find best results from predicting the change in concentration for very long-lived species and the absolute concentration for shorter lived species. The skill of the machine learning algorithm is further improved by using a family approach for NO and NO2 rather than treating them independently.By replacing the numerical integrator with the random forest algorithm and running this model for one month, we find that the model is able to reproduce many of the features of the reference chemistry simulation. Replacing the integration methodology with a machine learning algorithm has the potential to be substantially faster. There are a wide range of applications for such an approach, e.g. to generate boundary conditions, for use in air quality forecasts or chemical data assimilation systems, etc.

Keller, Christoph A.↗
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↗