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DOE OSTI2022

Encouraging voluntary government action via a solar-friendly designation program to promote solar energy in the United States

Sustainable development requires an accelerated transition toward renewable energy. In particular, substantially scaling up solar photovoltaics (PV) adoption is a crucial component of reducing the impacts of climate change and promoting sustainable development. However, it is challenging to convince local governments to take action. This study uses a combination of propensity score matching (PSM) and difference-in-differences (DID) models to assess the effectiveness of a voluntary environmental program (VEP) called SolSmart that targets local governments to engage in solar-friendly practices to promote the local solar PV market in the United States. Via specific designation requirements and technical assistance, SolSmart simplifies the process of acting on interest in being solar friendly, has a wide coverage of basic solar-friendly actions with flexible implementation, and motivates completion with multiple levels of designation. We find that a local government’s participation in SolSmart is associated with an increased installed capacity of 18 to 19%/mo or with less statistical significance, an increased number of installations of 17%/mo in its jurisdiction. However, SolSmart has not shown a statistically significant impact on soft cost reductions to date. In evaluating the impact of the SolSmart program, this study improves our understanding of the causation between a VEP that encourages solar-friendly local government practices and multiple solar market outcomes. VEPs may be able to promote shifts toward sustainable development at the local level. Our findings have several implications for the design of VEPs that promote local sustainability.

14 SOLAR ENERGY↗

DOE OSTI2023

Multiverse: Bayesian model selection for neural networks

Multiverse is a code repository for a set of tools for Bayesian model selection for neural networks. The goal of the tools is to provide capabilities for selecting among prior and model specifications for Bayesian neural networks. Multiverse will include tools for creating Bayesian neural networks, evaluating the Bayesian model evidence, and performing inference in Bayesian neural networks. These components are written in Python, a high-level programming language that takes advantage of the Python ecosystem of high-quality open-source packages for machine learning and signal processing.

Klein, Natalie↗

DOE OSTI2021

SISGR: Chemomechanics of Far-From-Equilibrium Interfaces (COFFEI)

Portable, reliable, and deployable devices for energy storage and conversion require fundamental changes in design of solid-state composites comprising ceramics and metals. These materials comprise the electrodes and electrolytes of next-generation solid-oxide fuel cells and all solid-state batteries, forming solid-state functional composites. The advent of solid-state batteries – which replace liquid electrolytes with solid electrolytes capable of lithium ion transport for reliable energy storage in portable batteries – and the increased demand space for all solid-state fuel cells capable of oxygen reduction at intermediate temperatures remain important challenges for improved material stability and decreased system cost. However, little is understood about three fundamental facets of materials that enable such solid-state energy applications. First, how do such materials deform, fracture, or delaminate under operando conditions? Second, how does such mechanical deformation limit or facilitate electronic and ionic transport within and across such material interfaces? Third, how we can predictably design interface-rich composites to engineer both structural and electrochemical stability? This COFFEI Group comprised expertise from Materials Science & Engineering and Nuclear Science & Engineering to integrate unique in situ experiments, simulations, and fabricated interfaces that address these fundamental questions in solid-state interfaces of nanoscale composites that will guide solid-state electrochemistry, transport kinetics, and mechanical deformation for nonstoichiometric materials that enable such applications. In particular, we built on COFFEI’s understanding of chemomechanical coupling among defect concentrations, ionic transport, electron transport, and stored elastic energy that is particularly acute in the far-from-equilibrium conditions typical of energy device applications. By tailoring our focus to solid-state interfaces, we addressed these important issues by (a) developing and applying advanced in situ and ex situ characterization tools to characterize model materials and interfaces synthesized with molecular-level control, under both laboratory-controlled and extreme environments representative of energy device operation; and (b) employing computational modeling and simulation frameworks to predict transport mechanisms, reactivity and stability of these model materials and interfaces under significant chemical strains typical of energy device operation. Recent progress provided insights to additional materials systems and electrochemomechanical fatigue and fracture that were not fully envisioned when the program was initiated. Specifically, in the final three years of COFFEI we pursued two integrated thrusts, with complementary focus. Thrust I focused on failure-resistant electrochemomechanical composites, while Thrust II focused on strain-modulated conductivity and reactivity across interfaces. In contrast to our initial COFFEI focus, these thrusts concentrated wholly on solid-state material interfacial interactions and included greater integration of multiscale visualization including in situ electron microscopy of strained structures/interactions and mesoscale simulations. Successful development of functionally superior and long-lived battery and fuel cell systems and stress adaptable oxides requires a deeper, fundamental understanding of the coupling among the historically important subfields of solid-state electrochemistry, transport kinetics, and mechanical deformation for nonstoichiometric metal oxide electrodes. In this program, the understanding and the application of chemomechanical coupling of defect concentrations, ionic transport, electro-catalytic activity and stored elastic energy, particularly acute in the far-from-equilibrium conditions typical of energy device applications, are being refined and implications for device operation clarified, including for miniaturized solid-state batteries and fuel cells.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Data Driven Analysis for Modernization Program Management

NNSA is responsible for managing national nuclear security missions: ensuring a safe, secure, and reliable nuclear deterrent; supplying nuclear fuel to the Navy; and supporting the nation’s nuclear nonproliferation efforts. However, over half of NNSA’s facilities are more than 40 years old, and roughly one-third date back to the Manhattan Project. To execute its critical nuclear security missions, NNSA is making large investments to modernize its nuclear production capabilities. This ramp up represents NNSA’s largest modernization effort since the Cold War. Given the scale of these efforts, NNSA’s Office of Secondary Stage Production Modernization has implemented data driven techniques to prioritize investments and inform strategic decision making. NNSA, with support from its site managing contractors, has developed and implemented an integrated schedule and risk management system to address the issues and limitations with the traditional approach. The multi-year integrated schedules are key to identifying program linkages and managing large portfolios comprised of many different projects and efforts. In conjunction with the integrated schedule, a new program risk management system has also been developed and implemented, which manages program risks and opportunities, along with specific mitigation strategies to reduce or eliminate the risks per timelines that are tracked in the integrated schedule. This paper is supplemented with a follow-on presentation on effective management of program material and throughput modeling.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

ChatHPC: Building the Foundations for a Productive and Trustworthy AI-Assisted HPC Ecosystem

ChatHPC democratizes large language models for the high-performance computing (HPC) community by providing the infrastructure, ecosystem, and knowledge needed to apply modern generative AI technologies to rapidly create specific capabilities for critical HPC components while using relatively modest computational resources. Our divide-and-conquer approach focuses on creating a collection of reliable, highly specialized, and optimized AI assistants for HPC based on the cost-effective and fast Code Llama fine-tuning processes and expert supervision. We target major components of the HPC software stack, including programming models, runtimes, I/O, tooling, and math libraries. Thanks to AI, ChatHPC provides a more productive HPC ecosystem by boosting important tasks related to portability, parallelization, optimization, scalability, and instrumentation, among others. With relatively small datasets (on the order of KB), the AI assistants, which are created in a few minutes by using one node with two NVIDIA H100 GPUs and the ChatHPC library, can create new capabilities with Meta’s 7-billion parameter Code Llama base model to produce high-quality software with a level of trustworthiness of up to 90% higher than the 1.8-trillion parameter OpenAI ChatGPT-4o model for critical programming tasks in the HPC software stack.

Young, Aaron [ORNL] (ORCID:0000000254484667)↗

DOE OSTI2023

Fuel Injection Dynamics and Composition Effects on RDE Performance

Rotating detonation engines (RDEs) provide a promising route to substantially increasing cycle efficiency in stationary gas turbines. Much of this increase relies on the ability to achieve consistent pressure gain within the combustor. In particular, the design of injectors that feed fuel and air into the detonation channel plays a crucial role. Such injectors have to ensure proper mixing of fuel and oxidizer, while minimizing backflow of detonation products into the feed plenums, and reduce susceptibility to the complex wave structures that exist within the combustor. From a practical perspective, such RDEs also need to operate with variable fuel composition. When fuel mixtures with components that possess vastly different oxidation pathways and time-scales are used, there could be additional losses through deflagrative burning instead of detonation-driven heat release. Such sensitivity to the complete flow path is akin to the physics of thermoacoustic instabilities in conventional gas turbines. In this sense, RDEs pose a unique research challenge: the performance of the device relies on the small-scale heat release process, which is highly dependent on the flow interactions within the full-scale system. As a result, canonical flow configurations, instrumented with detailed diagnostics or modeled using high-fidelity tools, but only focus on the small-scale processes will not contain the key system-level interactions. At the same time, macroscopic measurements and models that only capture system-level performance will not provide insight into the key sources of pressure losses. These couplings and sensitivities provide a formidable challenge to both experimental and simulation studies of the effects Thus, a joint experimental/computational program designed specifically to address these challenges was undertaken in this program. The focus of this program was on two key topics: a) the interaction between injector flow and the overall wave dynamics within the combustor, and b) the deflagration/detonation structure in multi-component fuels that are of practical interest. Both topics involve interaction of small-scale heat release processes with the geometry-dependent wave structure. Studies focused on the study of full-scale RDE systems, based on a 6-inch conventional annular geometry. Experimentally RDEs were studied using a combination of diagnostics. A combination of optical diagnostics and aero-thermo-acoustic analysis based on a combination of spectral and mode decomposition analysis was used to identify the dynamics of the detonation wave and other secondary waves that exist in the system. These studies have helped the identification and investigation of injector and detonation dynamics arising from coupling, and how they affect RDE mixing, detonation structure, operability and performance. Performance of RDEs was investigated through thrust stand measurements, which was used to evaluate the effective pressure gain generated by the system through the concept of equivalent available pressure. Optical diagnostics were developed and implemented to investigate the distribution of heat release, across the detonation wave. Novel optical diagnostics of NIR imaging was also developed and applied to investigate the high temperature / high pressure distribution across the detonation wave. In order to complement the experiments, the computational tools were geared to simulate the full experimental setup. GPU-based acceleration of the models and computations were developed to enable rapid simulation of the full system. In addition, the use of adaptive mesh refinement, and unstructured grid formulation, enabled the investigation of realistic geometries studied in the laboratory. The simulations produced a wealth of detail on the structure of the detonation wave under different operating conditions. Emphasis was placed on quantifying mixture pre-burning and the impact on wave propagation and structure.

03 NATURAL GAS↗

DOE OSTI2023

The Early Career Research Program Annual Progress Report: Using ARM Data and Multiscale Models to Advance the Understanding of Liquid-Phase Cloud Response to Aerosol Perturbation over Ocean and Land

This project aims to study the response of liquid-phase clouds to aerosol perturbation and reduce the related uncertainty in the DOE Earth system model. Specific objectives include: Objective 1: Quantify the aerosol indirect effect on liquid-phase clouds using ARM observations and satellite retrievals while constraining the confounding large-scale conditions; Objective 2: Harness LES case studies, untangle the confounding meteorological impacts on the observed aerosol indirect effect, and identify key cloud processes controlling the net radiative forcing of aerosol-cloud interactions at different spatiotemporal scales; Objective 3: Evaluate the aerosol indirect effect on liquid-phase clouds with process-level understanding in E3SM multiscale model configurations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

A stochastic biomass blending problem in decentralized supply chains

Blending biomass materials of different physical or chemical properties provides an opportunity to adjust the quality of the feedstock to meet the specifications of the conversion platform. We propose a model which identifies the right mix of biomass to optimize the performance of the thermochemical conversion process at the mini-mum cost. This is a chance-constraint programming (CCP) model which takes into account the stochastic nature of biomass quality. The proposed CCP model ensures that process requirements, which are impacted by physical and chemical properties of biomass, are met most of the time. We consider two problem settings, a centralized and a decentralized supply chain. We propose a mixed-integer linear program to model the blending problem in the centralized setting and a bilevel program to model the blending problem in the decentralized setting. We use the sample average approximation method to approximate the chance constraints, and propose solution algorithms to solve this approximation. We develop a case study for South Carolina using data provided by the Billion Ton Study. Based on our results, the blends identified consist mainly of pine and softwood residues. The blends identified and the suppliers selected by both models are different. The cost of the centralized supply chain is 2%–6% lower. The implications of these results are twofold. First, these results could lead to improved collaborations in the supply chain. Second, these results provide an estimate of the approximation error from assuming centralized decision making in the supply chain.

09 BIOMASS FUELS↗

DOE OSTI2024

Stress intensity factor models using mechanics-guided decomposition and symbolic regression

The finite element method can be used to compute accurate stress intensity factors (SIFs) for cracks with complex geometries and boundary conditions. In contrast, handbook solutions act as surrogate SIF models that provide significantly faster evaluation times. However, the development of conventional surrogate SIF models relies on manual development based on low-order parameterizations. This limits surrogate model accuracy and generalizability. Here, in this paper, we develop a framework for the automated development of mechanics-guided handbook SIF solutions by using interpretable machine learning via genetic programming for symbolic regression (GPSR). Formalizing the mechanics-based approach of Raju and Newman, SIF training data is decomposed into multiple subsets. This decomposition enables parallel GPSR model development of subfunctions, each of which accounts for specific geometrical corrections with respect to a known analytical model. Using this mechanics-based approach with GPSR allows for equations to be learned with improved accuracy and reduced complexity relative to the Raju Newman equations while maintaining the inherent interpretability of mathematical expressions. In this paper, we present equations that match the complexity of the Raju Newman equations while having reduced error, as well as equations with similar errors and reduced complexity.

42 ENGINEERING↗

DOE OSTI2023

Transient Efficiency, Flexibility, and Reliability Optimization of Coal-Fired Power Plants - Final Report

This program developed an advanced model-based monitoring and model-predictive control algorithms for a coal fired power plant (CFPP), and deployed these algorithms in a real-time platform to demonstrate performance benefits for transient flexibility and plant operation efficiency. More specifically, the objectives were successfully achieved through a combination of (i) developing a high-fidelity transient plant model in Apros, which was used as a high-fidelity plant simulation between $100-50\% TMCR$ where TMCR denotes the turbine maximum continuous rating, i.e., baseload, (ii) developing a very fast physics-based reduced-order model (ROM) of the plant, which ran more than $100\times$ faster than real-time, enabling its use as real-time embedded model for model-based estimation (MBE) and model predictive control (MPC) (iii) implementing a real-time MBE based on ROM using a robust unscented Kalman filter (UKF) to continuously tune the ROM to match the measurements from high-fidelity Apros plant model despite significant plant-model mismatch, and thus, obtain a Digital Twin of the plant (iv) designing and implementing a real-time MPC with dual objectives of transient plant load tracking with high ramp rates and minimizing coal consumption, i.e., improving plant efficiency in the baseload-partload operation range of $100-50\% TMCR$. Each key element above was developed and tested individually, and has been reported in corresponding Topical Reports. Finally, all the individual elements were integrated in an overall closed-loop system, that was successfully tested in desktop Simulink test harness simulations with ROM or high-fidelity model as the plant. Thereafter, the Simulink implementation was used to auto-generate C-code and deploy as real-time Docker microservice containers in Linux, and validate that they can run in real-time in the hardware-in-the loop (HIL) setup and produce the same results as in Simulink. The results of the integrated simulation tests in Simulink as well as the real-time HIL deployment are documented in this final report, showing good load tracking for load ramps at $3-4\%/min$ ramp rates, and achieving up to $5.5\%$ reduction in coal relative to baseline operation at $50\% TMCR$ load. The desktop and HIL simulations show successful performance of the overall model based estimation and control solution and achieve the key objectives of the program for flexible, efficient and reliable operation of subcritical coal fired power plants.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2023

Transient Efficiency, Flexibility, and Reliability Optimization of Coal-Fired Power Plants - Final Program Review

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2021

Development of phenomena identification and ranking table for Westinghouse lead fast reactor’s safety

The Westinghouse Lead-cooled Fast Reactor (LFR) is a medium-size, passively safe, economic, Gen-IV nuclear reactor. An important effort within the Westinghouse LFR program is the development of the safety analysis methodology, which comprises computer code development, model development, and experimental testing. A key initial task associated with the development of the safety analysis methodology is the identification of processes and phenomena that affect the plant's capability to meet selected safety performance indicators. This is accomplished through the development of a Phenomena Identification and Ranking Table (PIRT) for selected accident scenarios which, for this specific PIRT effort, included selected postulated design basis accidents and hypothetical beyond design basis accidents in LFRs. This paper describes the role of PIRT in the development of the Westinghouse LFR safety analysis methodology and the process used in the PIRT development. Specifically, the Westinghouse LFR PIRT assessed importance of pertinent phenomena and identified gaps in their knowledge-base by evaluating current modeling capabilities and data available for validation. The ultimate goal was to provide guidance on computer code development and validation efforts and to prioritize testing to support LFR design and licensing. The key phenomena and processes that are deemed highly important for the safety performance indicators, but for which the state of knowledge is low, are presented. The testing program and analyses development are planned to address significant phenomena in the PIRT.

Lead fast reactor↗

DOE OSTI2023

Small Reactors in Microgrids: Technology Modeling and Selection (Net-Zero Microgrid Program Project Report)

This report demonstrates the capabilities of the net-zero microgrid (NZM) Xendee platform for modeling an SR module with electricity, heat extraction and thermal storage in microgrids configurations. The model effectively captures the most important technical and economic considerations for SR technology specific analysis: cost and operational characteristics of SR technology and financial costs and incentives. The model can analyze multiple scenarios to establish metrics for cost-competitive and zero-carbon microgrids connected to the grid or completely isolated. The model is fully integrated within the Xendee platform for modeling and analysis of clean energy microgrids with storage and generation from renewable energy sources. The model captures the capabilities, constraints, and nuances of SR by incorporating parameters related to plant economics, design efficiency and performance, plant operation and component and fuel lifespan. The cost and operational parameters modeled in the SR module are specific to the technology selected for integration in the microgrid. Cost parameters recognize advanced nuclear technology for modular production and installation based on economies of scale from factory manufacture and related commissioning, and cost reduction through technology maturation—first-of-a-kind (FOAK) and nth-of-a-Kind (NOAK). The cost parameters include installation, operations and maintenance (O&M), fuel refueling cycle, and reactor life. Installation cost reflects economies of scale due to unit sizing at scale and colocation. O&M economies of scale for both fixed- and variable-cost fuel life-cycle costs are incurred at every refueling interval, with separate front- and back-end fuel costs, as well as waste-handling and disposition costs. This report investigates key characteristics of different SR technologies suitable for microgrid applications, including design principles, sizing, coolant properties, temperature ratings, fuel structures, and life-cycle considerations. This also includes fuel technologies applicable to these SR systems, alongside strategies for nuclear-waste and spent-fuel management and approaches to address safety, security, and proliferation challenges. Four primary groups of SR technologies are examined: water-cooled, liquid-metal-cooled, high-temperature gas-cooled, and molten-salt-cooled systems. In this report, an initial guideline for technology selection is established, aligning the characteristics of the technologies with the requirements of microgrids. The selection of technology in a microgrid is influenced by various factors, including financial capacity, location and accessibility, demand type and characteristics, reliability and resilience requirements, area constraints, and the lifespan of the microgrid. The types of electrical and non-electrical applications within the microgrid also play a significant role in technology selection. The characteristics of SRs, such as their smaller size, modularity, transportability, long refueling interval, improved safety features, ability to operate in autonomous or semi-autonomous mode, and provision of high-grade heat, are particularly appealing for microgrids. Furthermore, a list of considerations for implementing SRs in microgrids is outlined. The SR model is created to be continuously improved with the acquisition of actual data on investment and operational costs, experience with supply chains, production at scale, and field deployments. In the near term, performance data on applications in microgrids will become available from lessons learned from laboratory tests, such as those planned for the Microreactor Applications Research Validation and Evaluation Project (MARVEL), led by Idaho National Laboratory (INL). The SR model incorporates scenario data and known SR design specifications, enabling technoeconomic analysis for SR deployment in microgrids. It specifically considers the distinctive attributes of SRs as generators in technoeconomic studies. SRs can be modeled and analyzed with generation from renewable-energy sources, energy storage, and flexible loads over a range of functionality and applications. This offers a comprehensive tool for feasibility studies, scenario development, and sensitivity analysis for “what-if” consideration of any range of assumptions about SRs in microgrids and other aggregations of distributed-energy resources, including virtual power plants.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2023

Potential Constraints to Neutrino-Nucleus Interactions Based on Electron Scattering Data

A thorough understanding of neutrino-nucleus interactions physics is crucial to achieving precision goals in broader neutrino physics programs. The complexity of nuclei comprising the detectors and limited understanding of their weak response constitutes one of the biggest systematic uncertainties in neutrino experiments - both at intermediate energies affecting the short- and long-baseline neutrino programs as well as at lower energies affecting coherent scattering neutrino programs. While electron and neutrino interactions are different at the primary vertex, many underlying relevant physical processes in the nucleus are the same in both cases, and electron scattering data collected with precisely controlled kinematics, large statistics and high precision allows one to constrain nuclear properties and specific interaction processes. To this end, electron-nucleus scattering experiments provide vital complementary information to test, assess and validate different nuclear models and event generators intended to be used in neutrino experiments. In fact, for many decades, the study of electron scattering off a nucleus has been used as a tool to probe the properties of that nucleus and its electromagnetic response. While previously existing electron scattering data provide important information, new and proposed measurements are tied closely to what is required for the neutrino program in terms of expanding kinematic reach, the addition of relevant nuclei and information on the final states hadronic system.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Disentangling the confounding spectroscopy of C 1 molecules: Without symmetry as a guide, everything is allowed

The spectra of C 1 molecules are confounding in that each of the fundamental vibrational modes transform as the same irreducible representation (A) and hence each band consists of a seemingly random distribution of a-, b-, and c-type transitions. This is in contrast to higher symmetry molecules for which band types are readily deduced by simple symmetry rules. Herein, we present a method to simulate the convoluted rotational contours in the gas-phase spectra of C 1 molecules by combining existing ab initio calculations with Colin Western’s PGOPHER rotational contour program. Specifically, ab initio calculations in the NWC HEM suite of programs were employed to predict the components of the dipole moment derivatives along the principal axes of the moments of inertia. This information was then input into PGOPHER to model the fundamental band contours as a sum of a-, b-, and c-type transitions. This method was applied to simulate the rotational contour spectra of a series of representative C 1 molecules which were then compared against both ab initio stick spectra and experimentally measured broadband IR spectra from the Pacific Northwest National Laboratory infrared gas-phase database. In addition to providing further insight beyond what is revealed in a typical stick spectrum, the simulated contours showed good agreement with the measured spectra.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Wattile: Probabilistic Deep Learning-based Forecasting of Building Energy Consumption [SWR-20-94]

Accurate energy forecasting is becoming critical due to many reasons: i ) optimal distributed energy resources operations and dispatch, ii) fault detection and diagnostics, and iii) meeting operational energy efficiency targets. Wattile uses deep learning (DL) for the building's short-term load forecasting application. Two specific types of neural networks called, Long Short Term Memory (LSTM) and Sequence-to-Sequence (S2S) models are used to make predictions. Forecasting models are trained using online historical weather and occupancy indicator data streams from the Intelligent Campus Program's data acquisition systems at the National Renewable Energy Laboratory (NREL) for main meters and sub-meters of multiple building types. These models use probabilistic methods to provide quantile-based forecasts in addition to nominal conditional median predictions of electricity consumption.

Frank, Stephen↗

DOE OSTI2021

A survey of software implementations used by application codes in the Exascale Computing Project

The US Department of Energy Office of Science and the National Nuclear Security Administration initiated the Exascale Computing Project (ECP) in 2016 to prepare mission-relevant applications and scientific software for the delivery of the exascale computers starting in 2023. The ECP currently supports 24 efforts directed at specific applications and six supporting co-design projects. These 24 application projects contain 62 application codes that are implemented in three high-level languages—C, C++, and Fortran—and use 22 combinations of graphical processing unit programming models. The most common implementation language is C++, which is used in 53 different application codes. The most common programming models across ECP applications are CUDA and Kokkos, which are employed in 15 and 14 applications, respectively. This article provides a survey of the programming languages and models used in the ECP applications codebase that will be used to achieve performance on the future exascale hardware platforms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

DL-TODA: A Deep Learning Tool for Omics Data Analysis

Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.

59 BASIC BIOLOGICAL SCIENCES↗