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At least 631 records · Page 35

Basic Research Needs Workshop on Synthesis Science for Energy Relevant Technology

The technology that lies at our fingertips becomes more powerful each day. Smartphones connect us instantly to family, friends, and co-workers around the globe; give us access to a limitless stream of information; control the heating in our homes; and serve as our cameras, calculators, flashlights, music players, boarding passes and, on occasion, our phones. Cars are ever more fuel-efficient, safer, semi-autonomous, and have more computing power than the systems that guided humankind to the moon. LED lighting and solar panels are becoming commonplace, replacing less efficient technologies and expanding the energy options available worldwide. Novel polymers and nanoparticles are playing a crucial role in enhanced oil recovery. None of these advances would have been possible without the discovery and development of, and ability to create, new materials and chemical processes. Now imagine what our world would be like if we could accelerate those discoveries a thousandfold. What if the only limit to synthesizing new forms of matter were the imagination? We could build complex assemblies of atoms and molecules with architectures and capabilities far exceeding those of materials found in nature—for example, develop catalysts that turn garbage into fuels, design solar cells to power our homes directly from sunlight, make batteries with the energy density of gasoline, and create one- and two-dimensional solids that transport charge hundreds of times faster than silicon or allow us to build quantum bits based on the spins of electrons or photons to realize the promise of “beyond Moore’s law” computing. Advances in synthesis science are required to bring about this future—we not only must know how to design new molecules and materials with desired functions and properties through theory and computational techniques; we also must be able to make the materials we envision. New approaches to discovering as yet unimagined matter require a sea change in the way we think about the science of synthesis. Chemical and materials sciences have traditionally focused on understanding structure–function relationships with the goal of predicting where the atoms should be placed to achieve a targeted property or process. Much less effort has been directed toward a predictive science of synthesis—understanding how to get the atoms where they need to go to achieve the desired structure. This report, which is the result of the Basic Energy Sciences Workshop on Basic Research Needs for Synthesis Science for Energy Technologies, lays out the scientific challenges and opportunities in synthesis science. The workshop was attended by more than 100 leading national and international scientific experts. Its five topical and two crosscutting panels identified four priority research directions (PRDs) for realizing the vision of predictive, science-directed synthesis.

99 GENERAL AND MISCELLANEOUS↗

Randomized Algorithms for Scientific Computing (RASC)

Randomized algorithms have propelled advances in artificial intelligence (AI) and represent a foundational research area in advancing AI for Science. Future advancements in DOE Office of Science priority areas such as climate science, astrophysics, fusion, advanced materials, combustion, and quantum computing all require randomized algorithms for surmounting challenges of complexity, robustness, and scalability. Advances in data collection and numerical simulation have changed the dynamics of scientific research and motivate the need for randomized algorithms. For instance, advances in imaging technologies such as X-ray ptychography, electron microscopy, electron energy loss spectroscopy, or adaptive optics lattice light-sheet microscopy collect hyperspectral imaging and scattering data in terabytes, at breakneck speed enabled by state-of-the-art detectors. The data collection is exceptionally fast compared with its analysis. Likewise, advances in high-performance architectures have made exascale computing a reality and changed the economies of scientific computing in the process. Floating-point operations that create data are essentially free in comparison with data movement. Thus far, most approaches have focused on creating faster hardware. Ironically, this faster hardware has exacerbated the problem by making data still easier to create. Under such an onslaught, scientists often resort to heuristic deterministic sampling schemes (e.g., low-precision arithmetic, sampling every nth element) and sacrifice potentially valuable accuracy. Dramatically better results can be achieved via randomized algorithms, reducing the data size as much as or more than naive deterministic subsampling can achieve, while retaining the high accuracy of computing on the full data set. By randomized algorithms we mean those algorithms that employ some form of randomness in internal algorithmic decisions to accelerate time to solution, increase scalability, or improve reliability. Examples include matrix sketching for solving large-scale least-squares problems (see Figure 1) and stochastic gradient descent for training machine learning models. We are not recommending heuristic methods but rather randomized algorithms that have certificates of correctness and probabilistic guarantees of optimality and near-optimality. Such approaches can be useful beyond acceleration, for example, in understanding how to avoid measure zero worst-case scenarios that plague methods such as QR matrix factorization.

97 MATHEMATICS AND COMPUTING↗

DUNE Software and Computing Challenges

The DUNE experiment will begin running in the late 2020's. The goals of the experiment include 1) studying neutrino oscillations using a beam of neutrinos from Fermilab in Illinois to the Sanford Underground Research Facility, 2) studying astrophysical neutrino sources and rare processes and 3) understanding the physics of neutrino interactions in matter. The DUNE Far Detector, consisting of four 17 kt LArTPC modules, will produce "events" rang-ing in size from 6 GBs to more than 100 TBs, posing unique challenges for DUNE software and computing. The data processing algorithms, particularly for raw data, drive the requirements for the future DUNE software framework documented here.

97 MATHEMATICS AND COMPUTING↗

Ising-Traffic: Using Ising Machine Learning to Predict Traffic Congestion under Uncertainty

This paper addresses the challenges in accurate and realtime traffic congestion prediction with uncertainty by proposing Ising-Traffic, a novel quantum-inspired dual-model Ising based traffic prediction framework which delivers higher accuracy and lower latency than SOTA solutions. While traditional and deep learning methods face the trade-off between algorithm complexity and computational efficiency, our Ising-based method leverages Ising’s inherent and unique capability of finding the state of a system with the lowest energy and applying it to traffic prediction. In this work, traffic prediction under uncertainty is formulated into two separate Ising models: Reconstruct-Ising and Predict-Ising. Reconstruct-Ising is mapped onto modern Ising machine and handles uncertainty in traffic accurately with negligible latency and energy consumption, while Predict-Ising is mapped onto traditional processors and predicts future congestion precisely with only at most 1.8% computational demands of existing solutions. Our evaluation shows Ising-Traffic delivers on average 98× speedups and 5% accuracy improvement over SOTA.

traffic flow control, Ising↗

Transformational Regional-Scale Earthquake Simulations with the DOE EarthQuake SIMulation Exascale Framework

Earthquakes present worldwide risk to economic and human safety. The 2023 earthquakes in Turkiye provided a reminder of the potential for catastrophic consequences with 50,700 deaths and 15.7 million people affected. The ability to predict ground motions and infrastructure damage for earthquakes continues to be a challenging problem for scientists and engineers. Until now, estimates of ground motions have been performed empirically by looking at sparse data from past earthquakes. This approach can provide statistical information on intensity amplitudes but cannot inform site-specific ground motions essential to developing the most effective resilience. Interest has grown in large-scale computational models to simulate earthquakes at regional scale. The U.S. Department of Energy EarthQuake SIMulation (EQSIM) framework was developed for regional-scale earthquake simulations at unprecedented fidelity, taking advantage of emerging GPU-accelerated systems. This article describes the EQSIM workflow and demonstrates regional-scale simulations with the new computational capability available to scientists in their quest to mitigate future disasters.

58 GEOSCIENCES↗

A Conceptual World Information Library (WIL) and Land Use Information System (LUIS) - 16181

The Organization for Economic Co-operation and Development Nuclear Energy Agency initiative on the Preservation of Records, Knowledge and Memory is addressing the topic of communicating with future generations on the location, specific contents, and potential risks associated with deep geologic nuclear waste repositories. At the Waste Isolation Pilot Plant (WIPP) in the United States, the U.S. Department of Energy (DOE) has committed, prior to the facility closure, to develop a Passive Institutional Controls (PICs) program designed to last as long as practicable. A portion of this PICs program includes development of records packages, selection of data storage materials and methods, and a determination of records retention/storage locations. The approved plan for record retention at WIPP includes the storage of information including hard copies of data, figures and maps in multiple libraries and archive record centers. With this in mind, it is easy to envision reams of various paper documents in a robust physical archive record center similar to one of the museums in Washington D.C., or DOE's Legacy Management facility in Morgantown, West Virginia. While some portion of records for nuclear waste burial sites should be maintained in this fashion for near-term retrieval purposes, it is widely accepted that this is not an efficient way to communicate with future generations even 1,000 years from now. Transmitting large detailed volumes of information to the future should be captured in an electronic format; maintained on computers, translated by computers, and perhaps updated by artificial intelligence as machine and human languages change over the centuries. In addition to a physical records development and storage process for transmittal to future generations, a web-based electronic database system should be developed. A World Electronic Library (WEL) database could be funded from various nations and perhaps sanctioned by the United Nations and/or the IAEA. This WEL could contain information regarding several different subjects with the intent of being a one-stop-information-shop for future generations. This database would require updates and maintenance for as long as there is a recipient. One subset of the WEL would be a spatial database containing all the information available to any set of GPS coordinates, anywhere within the world. This Land Use Information System (LUIS) database would contain information on past and present land use, natural resources, known geology, hydrology and atmospheric conditions, potential warnings, and other pertinent information. The LUIS database is where specific electronic information, a subset of all the records data gathered for a nuclear waste repository, could reside. For not only would LUIS provide the information on a nuclear waste repository when specific GPS coordinates were entered; but a search from the LUIS on 'Nuclear Waste Repositories' could bring up information, including data on location of repositories, radionuclides, operations, D and D, maps, and regulations, plus many other details for locations throughout the world. This tool could be used by future generations for a number of land use or resource exploration decisions. So what can we do now? We can agree to the types of information that should be captured into an electronic database for nuclear waste repositories. We can agree to the levels of detail, the file names and the formats, for ease of combining information sets in the future. Perhaps we can agree to a central electronic data storage site, or sites, where this information will reside for import into a centralized electronic record system, if one is ever developed. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Integration of PanDA workload management system with Titan supercomputer at OLCF

The PanDA (Production and Distributed Analysis) workload management system (WMS) was developed to meet the scale and complexity of LHC distributed computing for the ATLAS experiment. While PanDA currently distributes jobs to more than 100,000 cores at well over 100 Grid sites, the future LHC data taking runs will require more resources than Grid computing can possibly provide. To alleviate these challenges, ATLAS is engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. We will describe a project aimed at integration of PanDA WMS with Titan supercomputer at Oak Ridge Leadership Computing Facility (OLCF). The current approach utilizes a modified PanDA pilot framework for job submission to Titan’s batch queues and local data management, with light-weight MPI wrappers to run single threaded workloads in parallel on Titan’s multi-core worker nodes. It also gives PanDA new capability to collect, in real time, information about unused worker nodes on Titan, which allows precise definition of the size and duration of jobs submitted to Titan according to available free resources. This capability significantly reduces PanDA job wait time while improving Titan’s utilization efficiency. This implementation was tested with a variety of Monte-Carlo workloads on Titan and is being tested on several other supercomputing platforms.

97 MATHEMATICS AND COMPUTING↗

Technical Characterization and Benefit Evaluation of 5G-Enabled Grid Data Transport and Applications

This report summarizes the Year 1 work of Pacific Northwest National Laboratory’s (PNNL’s) 5G Fabricated Resource and Asset Management Encompassment for energy infrastructure (Energy FRAME) project funded by the Department of Energy Office of Science’s Advanced Scientific Computing Research Program. 5G is a breakthrough technology that enables a fully mobile and connected society, and a 5G-enabled digital continuum will be one of the critical foundations for a clean energy economy and grid modernization. In collaboration with PNNL’s Advanced Wireless Communication team and Center for Advanced Technology Evaluation team, the project team has been evaluating the system performance of 5G testbeds in the PNNL 5G Innovation Studio, and has formulated a co-simulation test case of power system transmission, distribution, and communication (T&D&C) networks considering 5G technology and high penetration of distributed energy resources. The methodology developed in the 5G Energy FRAME project can be customized to fit different future grid scenarios to evaluate multiple (dynamic) configurations (computing, sensing, communication, environment) for different stakeholders. In summary, our main technical highlights in project Year 1 are as follows: 1) Technical characterization of 5G standalone architectures, 2) Formulation of co-simulation test case of T&D&C networks embedded with 5G, 3) Initial benefit evaluation of 5G communication platform for grid use cases, and 4) Additional extended discussions on edge computing, artificial intelligence and machine learning, and high-performance computing and cloud computing adoptions. In addition, a collection of system performance data is shared through the publicly available weblink, https://www.pnnl.gov/projects/5g-energy-frame/publications

24 POWER TRANSMISSION AND DISTRIBUTION↗

Electric Field Control of Magnetic Skyrmion Helicity in a Centrosymmetric 2D van der Waals Magnet

Two-dimensional van der Waals magnets hosting topological magnetic textures, such as skyrmions, show promise for spintronics and quantum computing. Electrical control of these topological spin textures is crucial for enhancing operational performance and functionality. Here, using electron microscopy combined with in situ electric and magnetic biasing, we show that the skyrmion helicity in insulating Cr 2 Ge 2 Te 6 can be controlled by the direction of the external electric field applied during the field cooling process. The electric field-tuned helicity remains stable at low temperature, even amid variations in magnetic and electric fields. Our theoretical investigation reveals that nonzero Dzyaloshinskii-Moriya interactions between nearest neighbors, induced by the electric field, change their sign upon reversing the electric field direction, thereby facilitating helicity selection. The electrical control of magnetic helicity demonstrated in this study can be extended to other centrosymmetric skyrmion-hosting magnets, paving the way for future device designs in topological spintronics and quantum computing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Response of hypoxia to future climate change is sensitive to methodological assumptions

Climate-induced changes in hypoxia are among the most serious threats facing estuaries, which are among the most productive ecosystems on Earth. Future projections of estuarine hypoxia typically involve long-term multi-decadal continuous simulations or more computationally efficient time slice and delta methods that are restricted to short historical and future periods. We make a first comparison of these three methods by applying a linked terrestrial–estuarine model to the Chesapeake Bay, a large coastal-plain estuary in the eastern United States. Results show that the time slice approach accurately captures the behavior of the continuous approach, indicating a minimal impact of model memory. However, increases in mean annual hypoxic volume by the mid-twenty-first century simulated by the delta approach (+ 19%) are approximately twice as large as the time slice and continuous experiments (+ 9% and + 11%, respectively), indicating an important impact of changes in climate variability. Our findings suggest that system memory and projected changes in climate variability, as well as simulation length and natural variability of system hypoxia, should be considered when deciding to apply the more computationally efficient delta and time slice methods.

54 ENVIRONMENTAL SCIENCES↗

Improving Projections of Antarctic Ice Sheet Contribution to Sea‐Level Change Through 2300 by Capturing Gravitational, Rotational, and Deformational Effects

Ice-mass change induces regionally varying patterns of sea-level change due to gravitational, rotational, and deformational (GRD) effects, which in turn influence marine-based ice stability in Antarctica. For improved projection of the Antarctic Ice Sheet (AIS), there is a need for including GRD effects in modeling and improving understanding of basin-by-basin sensitivity of ice evolution to GRD effects under a range of climate scenarios. We couple a high-resolution, higher-order ice-sheet model with a 1D global sea-level model that fully captures GRD effects, and simulate ice evolution in Antarctica under the Ice Sheet Model Intercomparison Project for CMIP6 experiments. We perform two sets of coupled simulations incorporating 1D Maxwell solid Earth structure suitable for West and East Antarctica and show that the Amundsen Sea Embayment (ASE) in West Antarctica has the highest sensitivity to GRD effects—in high-emission scenarios, grounding-line retreat accelerates by hundreds of kilometers by 2300 without GRD effects, but GRD effects delay this retreat on a timescale of decades. However, we find that delay times do not show a clear relationship to the strength of climate forcing alone. Furthermore, GRD effects can influence ice-sheet dynamics more than the choice of climate model for a given emissions scenario. In contrast, East Antarctica exhibits minimal sensitivity to GRD effects throughout the study period. These findings underscore the critical role of GRD effects in shaping future West AIS evolution, highlighting the importance of constraining the regional 3D Earth structure and bed topography in West Antarctica, particularly the ASE.

58 GEOSCIENCES↗

Benchmarking the Performance of Neuromorphic and Spiking Neural Network Simulators

Software simulators play a critical role in the development of new algorithms and system architectures in any field of engineering. Neuromorphic computing, which has shown potential in building brain-inspired energy-efficient hardware, suffers a slow-down in the development cycle due to a lack of flexible and easy-to-use simulators of either neuromorphic hardware itself or of spiking neural networks (SNNs), the type of neural network computation executed on most neuromorphic systems. While there are several openly available neuromorphic or SNN simulation packages developed by a variety of research groups, they have mostly targeted computational neuroscience simulations, and only a few have targeted small-scale machine learning tasks with SNNs. Evaluations or comparisons of these simulators have often targeted computational neuroscience-style workloads. In this work, we seek to evaluate the performance of several publicly available SNN simulators with respect to non-computational neuroscience workloads, in terms of speed, flexibility, and scalability. We evaluate the performance of the NEST, Brian2, Brian2GeNN, BindsNET and Nengo packages under a common front-end neuromorphic framework. Our evaluation tasks include a variety of different network architectures and workload types to mimic the computation common in different algorithms, including feed-forward network inference, genetic algorithms, and reservoir computing. We also study the scalability of each of these simulators when running on different computing hardware, from single core CPU workstations to multi-node supercomputers. Our results show that the BindsNET simulator has the best speed and scalability for most of the SNN workloads (sparse, dense, and layered SNN architectures) on a single core CPU. However, when comparing the simulators leveraging the GPU capabilities, Brian2GeNN outperforms the others for these workloads in terms of scalability. NEST performs the best for small sparse networks and is also the most flexible simulator in terms of reconfiguration capability NEST shows a speedup of at least 2x compared to the other packages when running evolutionary algorithms for SNNs. The multi-node and multi-thread capabilities of NEST show at least 2x speedup compared to the rest of the simulators (single core CPU or GPU based simulators) for large and sparse networks. We conclude our work by providing a set of recommendations on the suitability of employing these simulators for different tasks and scales of operations. We also present the characteristics for a future generic ideal SNN simulator for different neuromorphic computing workloads.

97 MATHEMATICS AND COMPUTING↗

Quantum computing and quantum information storage

Quantum storage, transmission, and processing is the future of information technology. Here, the promise of quantum hardware stems from the inherent complexity of an entangled quantum system—the size of the wave-function scales exponentially with the number of particles, whether represented in real space or in a parameter space. In contrast, a classical N-body system can be completely represented by only 6N variables (positions and momenta of all particles). This complexity of quantum systems creates a yet-unsolved challenge of modeling quantum systems by means of classical computing—the curse of dimensionality. Indeed, although we can easily write the Schrödinger equation for any system of interacting nuclei and electrons, we can only solve it exactly on classical computers for very small systems.

97 MATHEMATICS AND COMPUTING↗

Reduction of the molecular hamiltonian matrix using quantum community detection

Abstract Quantum chemistry is interested in calculating ground and excited states of molecular systems by solving the electronic Schrödinger equation. The exact numerical solution of this equation, frequently represented as an eigenvalue problem, remains unfeasible for most molecules and requires approximate methods. In this paper we introduce the use of Quantum Community Detection performed using the D-Wave quantum annealer to reduce the molecular Hamiltonian matrix in Slater determinant basis without chemical knowledge. Given a molecule represented by a matrix of Slater determinants, the connectivity between Slater determinants (as off-diagonal elements) is viewed as a graph adjacency matrix for determining multiple communities based on modularity maximization. A gauge metric based on perturbation theory is used to determine the lowest energy cluster. This cluster or sub-matrix of Slater determinants is used to calculate approximate ground state and excited state energies within chemical accuracy. The details of this method are described along with demonstrating its performance across multiple molecules of interest and bond dissociation cases. These examples provide proof-of-principle results for approximate solution of the electronic structure problem using quantum computing. This approach is general and shows potential to reduce the computational complexity of post-Hartree–Fock methods as future advances in quantum hardware become available.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Application of artificial intelligence methods in the international roughness index prediction of rigid and composite pavements: a systematic review

The International Roughness Index (IRI) is a widely adopted metric for quantifying pavement roughness, directly influencing vehicle safety, ride comfort, and overall roadway performance. In recent years, the use of Machine Learning (ML) models for IRI prediction has gained momentum, with the goal of improving the allocation of maintenance and rehabilitation resources by enabling accurate assessments of pavement conditions. Most prior reviews, however, have concentrated on flexible pavements, leaving a notable gap regarding rigid and composite pavements. To address this gap, the present study conducts a systematic review of Artificial Intelligence (AI) methods applied to IRI prediction for rigid and composite pavements. Literature published between 2004 and 2025 is synthesized to highlight prevailing trends, methodological contributions, and directions for future research. Particular attention is given to the types of models employed, the datasets used for training and validation, and the role of input variables and data-processing strategies. Across the included studies, ensemble learning methods (especially gradient boosting variants such as XGBoost), artificial neural networks, and hybrid architectures frequently achieved high predictive skill, with several models reporting test-set coefficients of determination approaching 0.9–0.96, indicating strong potential for capturing the influence of traffic, pavement structure, and climatic factors. Since these results are obtained from heterogeneous datasets and evaluation protocols, they are interpreted qualitatively rather than as strict cross-study rankings. Analysis of input variables revealed that pavement age and initial IRI were included in 91% (21 of 23) and 78% (18 of 23) of studies, respectively. Climatic variables such as the freezing index appeared in 57% (13 of 23), while traffic-related factors were considered in 65% (15 of 23). The findings underscore the importance of standardized, high-quality datasets, such as those from the Long-Term Pavement Performance (LTPP) program, along with data consistency, model interpretability, computational efficiency, and replicability in enhancing IRI prediction. Future research should focus on incorporating input variable selection techniques to identify the most influential predictors, thereby improving accuracy and robustness. Integrating these approaches with advanced non-linear data-driven models, coupled with robust hyperparameter optimization, holds considerable promise for strengthening the reliability of IRI prediction and supporting resilient pavement management strategies.

42 ENGINEERING↗

SST-GPU: A Scalable SST GPU Component for Performance Modeling and Profiling

Programmable accelerators have become commonplace in modern computing systems. Advances in programming models and the availability of unprecedented amounts of data have created a space for massively parallel accelerators capable of maintaining context for thousands of concurrent threads resident on-chip. These threads are grouped and interleaved on a cycle-by-cycle basis among several massively parallel computing cores. One path for the design of future supercomputers relies on an ability to model the performance of these massively parallel cores at scale. The SST framework has been proven to scale up to run simulations containing tens of thousands of nodes. A previous report described the initial integration of the open-source, execution-driven GPU simulator, GPGPU-Sim, into the SST framework. This report discusses the results of the integration and how to use the new GPU component in SST. It also provides examples of what it can be used to analyze and a correlation study showing how closely the execution matches that of a Nvidia V100 GPU when running kernels and mini-apps.

97 MATHEMATICS AND COMPUTING↗

Balar: A SST GPU Component for Performance Modeling and Profiling

Programmable accelerators have become commonplace in modern computing systems. Advances in programming models and the availability of massive amounts of data have created a space for massively parallel accelerators capable of maintaining context for thousands of concurrent threads resident on-chip. These threads are grouped and interleaved on a cycle-by-cycle basis among several massively parallel computing cores. One path for the design of future supercomputers relies on an ability to model the performance of these massively parallel cores at scale. The SST framework has been proven to scale up to run simulations containing tens of thousands of nodes. A previous report described the initial integration of the open-source, execution-driven GPU simulator, GPGPU-Sim, into the SST framework. This report discusses the results of the integration and how to use the new GPU component in SST. It also provides examples of what it can be used to analyze and a correlation study showing how closely the execution matches that of a Nvidia V100 GPU when running kernels and mini-apps.

97 MATHEMATICS AND COMPUTING↗

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↗