Search NASA⌕ Search

SEARCH · Search NASA

Results for “Learning algorithms”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Multi‐Scale Model‐Informed Deep Learning for Plasma‐Nanoparticle Interaction

The Overarching Goal of this proposed research is to understand and quantitively determine the interactions between non-thermal plasma (hot electrons, reactive radicals, vibrationally excited species) and surface reactions on influencing the activity and selectivity of the desired reactions via developing multi-scale model informed deep learning algorithm. Investigating non-thermal plasma-surface interaction is feasible due to the low bulk temperature in the discharge region. To investigate the role of plasma-nanoparticle interaction on enhancing the reaction kinetics, we will focus on ammonia cracking to generate clean hydrogen over earth-abundant, non-critical metallic nanoparticles, which is of great significance for decarbonization. We hypothesize that (1) reactive radicals interacting with surface reaction species via Eley–Rideal mechanism will significantly lower the energetics of the potential rate-limiting step of nitrogen formation; (2) the surface will be charged heterogeneously under non-thermal plasma conditions and the charged site will lower the energetics of ammonia cracking through Langmuir– Hinshelwood mechanism; (3) vibrationally excited ammonia will further promote the initial N-H bond cleavage. To access the hypothesis, we will (1) reveal the surface charge effects on tunning the reaction energetics via interpretable, physics-informed deep learning accelerated density functional theory (DFT) calculations; (2) determine the reactive radicals interacting with surface reaction species on tuning the reaction energetics via DFT; (3) reveal the surface charge effects on tunning the reaction energetics via DFT and deep learning models, (4) quantify how vibrationally excited species, reactive radicals, and surface charging effects on enhancing the catalysis via developing DFT-based microkinetic modeling (MKM) and active learning. Deep and active learning of plasma-nanoparticle interactions effects on enhancing ammonia cracking to generate hydrogen represents a new paradigm for designing high performance plasma materials. The fundamental science of how plasma-nanoparticle interactions will change the plasma kinetics and will improve the energy efficiency for decarbonization and sustainability. The interpretable and physics-informed machine learning model will accelerate low temperature plasma chemistry and material discovery with physics rules and model interpretation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
NASA NTRS2021

Predicting Arrival and Departure Runway Assignments with Machine Learning

Runway assignments at major airports are made by air traffic controllers subject to various constraints, and to achieve various objectives. In this research, we describe our efforts training machine learning (ML) models to predict both departure and arrival runway assignments using an entirely data-driven approach. This approach is compared to existing rule-based approaches developed in previous research using input from Subject Matter Experts. The models have features derived from various FAA data feeds, and leverage multiple machine learning algorithms. Results for models trained for nine major U.S. airports are described and compared to one another across various important dimensions. Particular attention was paid to developing a repeatable framework for training these models so the approach could be scaled to other airports, and to developing models that are useful in a real-time environment. In addition, the models were designed to be functional in a real-time environment to support NASA’s ATD-2 project, as part of an ML-powered shadow system to compare against the performance of the fielded system.

machine learning↗
DOE OSTI2024

Constituent Data Replacement Tool

The purpose of this tool is to estimate key parameters that may be missing in public wastewater composition datasets. The tool can be applied to develop complete treatment and critical mineral extraction profiles for leachate, produced water and other aqueous waste streams. The tool applies machine learning algorithms to replace missing data in a user’s water data set that are adjusted based on user preferences for options including algorithm type, number of features, and classification variables. The tool can use the user’s data alone or combine user data with the NEWTS USGS Produced Water Database for more robust training. This research was funded by the U.S. Department of Energy’s Office Fossil Energy and Carbon Management (FECM) through National Energy Technology Laboratory’s ongoing research under the Water Management for Power System Field Work Proposal, DE-FECM 1022428 and Critical Minerals Field Work Proposal, DE-FECM 1022420.

Aqueous Chemistry↗
NASA NTRS2021

Predicting Arrival and Departure Runway Assignments with Machine Learning

Runway assignments at major airports are made by air traffic controllers subject to various constraints, and to achieve various objectives. In this research, we describe our efforts training machine learning (ML) models to predict both departure and arrival runway assignments using an entirely data-driven approach. This approach is compared to existing rule-based approaches developed in previous research using input from Subject Matter Experts. The models have features derived from various FAA data feeds, and leverage multiple machine learning algorithms. Results for models trained for nine major U.S. airports are described and compared to one another across various important dimensions. Particular attention was paid to developing a repeatable framework for training these models so the approach could be scaled to other airports, and to developing models that are useful in a real-time environment. In addition, the models were designed to be functional in a real-time environment to support NASA’s ATD-2 project, as part of an ML-powered shadow system to compare against the performance of the fielded system.

machine learning↗
NASA NTRSDate not supplied

Using Coordinated, Multi-Agent Platforms for Dynamic Ocean Worlds Science

Planetary science missions have the opportunity to enhance science return through deployment of autonomous capabilities designed to dynamically respond to new information. Future outer solar system missions to ocean worlds in particular would benefit from this technology - intelligent science payloads (ISP) - because it would allow for a coordinated, near real-time response to ephemeral ‘events’ such as plumes, tectonism, surface implantation, volatile releases, thermal and magnetic anomalies, or radiation, as well as increasing the cadence and coverage of data collection. Prioritization and decision-making frameworks from ISP could be deployed at various scales - from analysis onboard a spacecraft with multiple instruments – to coordinated analyses among separate spacecraft in an e.g., distributed systems mission (DSM) composed of multiple SmallSats. Goddard’s Intelligent Science Payload team is developing an agile autonomous architecture for an icy ocean worlds DSM concept. Our goals are to coordinate data collection and onboard data analysis, and to make autonomous decisions for new data collection and analysis based on science priorities between multiple spacecraft with variable instrumentation and orbits. We use a range of data analysis tools to coordinate the DSM response, spanning from observations of data over a specified threshold to more computationally intensive machine learning algorithms (ML). ML algorithms here currently focus on determining the composition of an ocean world using mass spectrometry, and specifically methods for understanding ‘novelties’ and potential biosignatures. These algorithms could be used to quickly process and analyze onboard data that would be significantly delayed in downlink due to long communication delays for outer solar system missions in order to make dynamic science observations. Our ocean worlds case study ISP architecture is intended as an ‘agile’ and modular framework that could be used as a whole or as particular modules based on mission needs.

Distributed Systems↗
NASA NTRSDate not supplied

Adaptive Stress Testing of Collision Avoidance Systems for Small UASs with Deep Reinforcement Learning

The next-generation Airborne Collision Avoidance System for smaller UASs (ACAS sXu) is currently being developed and tested by the Federal Aviation Administration (FAA) to provide detect-and-avoid capability for small unmanned aircraft operating beyond line-of-sight. Due to the complexity and safety-critical nature of the system, safety validation is important not only for the certification of the final system, but also for informing changes during the iterative development process. In this paper, we analyze a prototype of ACAS sXu in simulated aircraft encounters to discover scenarios of small near mid-air collisions (sNMACs), an important safety event in which two aircraft come closer than 50 feet horizontally and 15 feet vertically. Due to the size and complexity of the system as well as rarity of sNMAC events, traditional methods such as Monte Carlo testing often require informed setup and targeting to elicit failures. However, such a dependence on domain knowledge can be incompatible with the independent verification and validation (IV&V) process, the aim of which is to discover unforeseen issues. To address these challenges, we apply an accelerated validation method called adaptive stress testing (AST) to find the most likely sNMAC scenarios without reliance on system introspection. AST uses reinforcement learning to adapt the search towards the most promising areas of the search space as it progresses. We use a state-of-the-art deep reinforcement learning algorithm, proximate policy optimization, to more efficiently search the large and continuous state space. We find that this approach significantly improves the performance of AST compared to a prior approach based on Monte Carlo tree search. We perform experiments using AST to find sNMAC events under various encounter configurations, varying parameters pertaining to dynamics and coordination. Our experiments show AST to be very effective at finding sNMAC scenarios. We summarize our findings, presenting high-level categories of discovered sNMACs and specific examples of encounters in each category.

aircraft collision avoidance↗
DOE OSTI2024

Anomaly Detection and Mitigation for Dynamic Frequency Regulation in Hydropower-Battery Systems

Hydropower operators and energy storage providers are increasingly interested in participating in frequency regulation services, driven by the incentives offered by independent system operators, such as the PJM Interconnection. This transition, however, unfolds against the backdrop of a modernizing and rapidly digitizing power grid, exposing the integrated legacy infrastructure to a multitude of cybersecurity threats. This work presents an approach for developing an anomaly detection and mitigation system to address cybersecurity challenges during the participation of a hydropower-integrated battery energy storage system (BESS) in a frequency regulation market. The applied anomaly detector utilizes machine learning algorithms to provide detailed classification of cyber-physical events. Later, the applied mitigation system triggers predefined corrective actions to minimize the impact of data integrity attacks on the regulation market and system stability. We evaluated the proposed approach on a hydropower-integrated BESS topology, specifically analyzing the slow regulation signal (Reg A) coming from the PJM market. Our simulation results demonstrate that the proposed approach performs well in detecting data integrity attacks within the allocated time frame and also minimizes the system's transient instability during the participation of hydropower and BESS in the regulation market.

battery energy storage system↗
NASA NTRS2021

Machine Learning the COSMO Model for Predicting Thermodynamics of Electrolyte Mixtures

Bottom-up design of electrolyte mixtures for battery systems requires predicting macro thermodynamic properties from molecular constituents. For instance, molten salt electrolyte batteries require conditions far above room temperature to operate. Therefore, discovering mixtures with increasingly lower eutectic melting points is desirable. A model that can approximate chemical activity is a valuable tool to search through the vast compositional design space. Machine learning can predict properties of materials such as vibrational free energies, electronic energy gaps, and thermal conductivities. Moreover, they can learn physical models such as interatomic potentials. The COSMO-SAC model uses theory and empirical parameterization to predict liquid-vapor and liquid-solid properties using first-principles calculations. However, obtaining activity coefficients required for parameterizing the COSMO-SAC model is costly and limited to a select chemical space. In this work, we explored if machine learning methods could improve the COSMO-SAC model and bridge density functional theory calculations to liquid phase thermodynamic properties. Our data-driven approach uses existing databases for sigma-profiles of organic solvents and reconciles their methodological differences via ensemble averaging. First, an optimal machine learning model is constructed for each dataset. Our machine learning algorithms use the sigma-profile as an input feature to predict binary mixtures' activity coefficients using multi-output regression. Each dataset uses different choices of functionals, methods, and basis sets. Therefore, our ensemble model attempts to predict corrected activity coefficients given the combination of all the model outputs. The activity coefficients used for training are generated using the COSMO-SAC model. This approach enables the extraction of meaningful information from the existing datasets to improve the COSMO-SAC model for obtaining thermodynamic properties of electrolyte mixtures. With the liquid phase activities, we can identify electrolyte mixtures that meet desired phase equilibria conditions.

Thermodynamics↗
DOE OSTI2024

Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS

Type 1 polyketides are a major class of natural products used as antiviral, antibiotic, antifungal, antiparasitic, immunosuppressive, and antitumor drugs. Analysis of public microbial genomes leads to the discovery of over sixty thousand type 1 polyketide gene clusters. However, the molecular products of only about a hundred of these clusters are characterized, leaving most metabolites unknown. Characterizing polyketides relies on bioactivity-guided purification, which is expensive and time-consuming. To address this, we present Seq2PKS, a machine learning algorithm that predicts chemical structures derived from Type 1 polyketide synthases. Seq2PKS predicts numerous putative structures for each gene cluster to enhance accuracy. The correct structure is identified using a variable mass spectral database search. Benchmarks show that Seq2PKS outperforms existing methods. Applying Seq2PKS to Actinobacteria datasets, we discover biosynthetic gene clusters for monazomycin, oasomycin A, and 2-aminobenzamide-actiphenol.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Baseflow Identification via Explainable AI With Kolmogorov‐Arnold Networks

Abstract Hydrological models often involve constitutive laws that may not be optimal in every application. We propose to replace such laws with the Kolmogorov‐Arnold networks (KANs), a class of neural networks designed to identify symbolic expressions. We demonstrate KAN's potential on the problem of baseflow identification, a notoriously challenging task plagued by significant uncertainty. KAN‐derived functional dependencies of the baseflow components on the aridity index outperform their original counterparts; they demonstrate that water availability, rather than potential evapotranspiration, drives baseflow by constraining actual evapotranspiration under arid conditions. On a test set, they increase the Nash‐Sutcliffe efficiency (NSE) by 65%, decrease the root mean squared error by 29%, and increase the Kling‐Gupta efficiency by 34%. This superior performance is achieved while reducing the number of fitting parameters from three to two. Next, we use data from 378 catchments across the continental United States to refine the water‐balance equation at the mean‐annual scale. The KAN‐derived equations based on the refined water balance outperform both the current aridity index model, with up to a 105% increase in NSE, and the KAN‐derived equations based on the original water balance. While the performance of our model and tree‐based machine learning methods is similar, KANs offer the advantage of simplicity and transparency and require no specific software or computational tools. This case study focuses on the aridity index formulation, but the approach is flexible and transferable to other hydrological processes. Plain Language Summary Equations used in hydrologic model are often suboptimal, resulting in reduced prediction accuracy and efficiency. We implemented Kolmogorov‐Arnold networks (KAN), a machine learning algorithm for deriving symbolic formulations, to estimate groundwater recharge and showed that it outperforms an existing state‐of‐the‐art semi‐empirical formulation. In hydrology, Nash‐Sutcliffe efficiency (NSE), root mean squared error (RMSE), and Kling‐Gupta efficiency (KGE) are commonly used to evaluate model performance. Higher NSE and KGE values indicate better performance, while lower RMSE values are preferable. Our results show that NSE increased by 71%, RMSE decreased by 32%, and KGE improved by 25%. In addition, KAN identifies an optimal functional form and can be used to derive new analytical formulas using the prior knowledge. The KAN‐inspired equation outperformed the original formulation and reduced the fitting parameters. Furthermore, we refined the water‐balance equation at the mean‐annual scale and showed that, based on the new water‐balance equation, KAN can derive new formulations that are superior to the original aridity index formulations (up to 105% increase in NSE) and KAN‐derived equations based on the original water balance. These findings highlight the significant potential of KAN to advance the scientific understanding of a wide range of hydrologic processes. Key Points Kolmogorov‐Arnold networks (KANs) enhance interpretability of machine‐learned hydrological models KAN‐derived symbolic formulations outperform state‐of‐the‐art semi‐empirical aridity indices KAN‐identified functional form yields an analytical index with fewer fitting parameters and improved performance

baseflow↗
DOE OSTI2024

Characterization of Fuel Cladding Chemical Interaction on a High Burnup U-10Zr Metallic Fuel via Electron Energy Loss Spectroscopy Enhanced by Machine Learning

Fuel cladding chemical interaction (FCCI) is one of the main performance limiting factors for metallic nuclear fuels. The interaction destabilizes the martensitic microstructure and deteriorates mechanical properties of HT-9 cladding. The detection of low atomic number elements (Z<10) and overlapping of elemental peaks can be problematic in interpreting energy dispersive X-ray spectroscopy (EDS) data. Electron energy loss spectroscopy (EELS) provides precise elemental edge energy values and can detect elements with a low atomic number. This work utilizes EELS to study the distribution of lanthanides and light elements at the interaction region. The sample was prepared from the FCCI region of a U-10Zr (wt.%) solid fuel with HT-9 cladding, irradiated to a burnup of 13.2 at.%. Processing the EELS data included three major steps: 1) enhance the signal to noise ratio by denoising the spectrum with principal component analysis (PCA) method, removing background and performing deconvolution; 2) identify chemical elements with core energy loss edges; 3) confirm different phases using a popular machine learning method, K-means. This work presents qualitative assessment of lanthanides and light elements like carbon (C) and oxygen (O) enhanced by the application of machine learning algorithms. By comparing with EDS elemental maps, EELS provides higher resolution chemical maps, reveals the distribution of carbon at the interaction region supporting the formation of zirconium carbide, a rind-like microstructure feature that was proposed to mitigate the chemical interaction. Furthermore, the plasmon peak map was also found to indicate an energy shift associated with the formation of phases/compounds. K-means clustering method was used on the processed electron energy loss (EEL) spectrum to automatically reveal different phases. The resulting clustered maps from K-means clustering align well with elemental maps confirming certain phases, especially Fe-Ce and Zr-C, in the FCCI region.

EELS↗
DOE OSTI2025

Fine-tuning machine-learned particle-flow reconstruction for new detector geometries in future colliders

We demonstrate transfer learning capabilities in a machine-learned algorithm trained for particle-flow reconstruction in high energy particle colliders. This paper presents a cross-detector fine-tuning study, where we initially pretrain the model on a large full simulation dataset from one detector design, and subsequently fine-tune the model on a sample with a different collider and detector design. Specifically, we use the Compact Linear Collider detector (CLICdet) model for the initial training set and demonstrate successful knowledge transfer to the CLIC-like detector (CLD) proposed for the Future Circular Collider in electron-positron mode. We show that with an order of magnitude less samples from the second dataset, we can achieve the same performance as a costly training from scratch, across particle-level and event-level performance metrics, including jet and missing transverse momentum resolution. Furthermore, we find that the fine-tuned model achieves comparable performance to the traditional rule-based particle-flow approach on event-level metrics after training on 100,000 CLD events, whereas a model trained from scratch requires at least 1 million CLD events to achieve similar reconstruction performance. To our knowledge, this represents the first full-simulation cross-detector transfer learning study for particle-flow reconstruction. These findings offer valuable insights towards building large foundation models that can be fine-tuned across different detector designs and geometries, helping to accelerate the development cycle for new detectors and opening the door to rapid detector design and optimization using machine learning.

43 PARTICLE ACCELERATORS↗
NASA NTRSDate not supplied

Machine Learning Application in Aircraft Engine Conceptual Design

In the current competitive environment, the successful creation and application of machine learning (ML) technologies have become crucial across multiple industries. This study outlines the process of creating and implementing ML models for conceptualizing and evaluating aircraft engines. These models use supervised deep-learning algorithms to analyze patterns within an open-source repository containing data on both production and research conventional turbofan engines. Key focus areas include crucial engine parameters such as thrust-specific fuel consumption (TSFC), engine weight, engine diameter, and turbomachinery stage counts. While developing ML models is fundamental, ensuring their seamless deployment is equally important. To address this, a conversational AI chatbot is constructed using natural language processing (NLP) techniques to facilitate the deployment of these ML models. The comprehensive workflow includes several key stages: gathering and enhancing engine data, training and cross validating the ML models, testing and evaluating their performance, and finally, deploying, monitoring, and updating the ML models. By following this systematic approach, the aim is to streamline the development and deployment process of ML models tailored for aircraft engine conceptual design.

Aircraft Engine↗
NASA NTRSDate not supplied

The Development and Deployment of Machine Learning Models for Aircraft Engine Concept Assessment

In today's competitive landscape, the effective development and utilization of machine-learning (ML) applications have become imperative across various sectors. This study presents an outline of the procedure involved in creating and implementing ML models for conceptualizing and evaluating aircraft engines. These models leverage supervised deep-learning algorithms to analyze patterns within an open-source repository containing data on both production and research conventional turbofan engines. The main areas of focus encompass crucial engine parameters like thrust-specific fuel consumption (TSFC), engine weight, engine diameter, and turbomachinery stage counts. While the creation of ML models is fundamental for their utilization, ensuring their seamless deployment holds equal significance. To address this aspect, a conversational AI chatbot is constructed, utilizing natural language processing (NLP) techniques, to facilitate the deployment of these ML models. The comprehensive workflow encompasses several key stages: gathering and enhancing engine data, training and cross validating the ML models, testing and evaluating their performance, and finally, deploying, monitoring, and updating the ML models. By following this systematic approach, the aim is to streamline the development and deployment process of ML models tailored for aircraft engine assessment.

Development↗
NASA NTRSDate not supplied

The Development and Deployment of Machine Learning Models for Aircraft Engine Concept Assessment

In today's competitive landscape, the effective development and utilization of machine-learning (ML) applications have become imperative across various sectors. This study presents an outline of the procedure involved in creating and implementing ML models for conceptualizing and evaluating aircraft engines. These models leverage supervised deep-learning algorithms to analyze patterns within an open-source repository containing data on both production and research conventional turbofan engines. The main areas of focus encompass crucial engine parameters like thrust-specific fuel consumption (TSFC), engine weight, engine diameter, and turbomachinery stage counts. While the creation of ML models is fundamental for their utilization, ensuring their seamless deployment holds equal significance. To address this aspect, a conversational AI chatbot is constructed, utilizing natural language processing (NLP) techniques, to facilitate the deployment of these ML models. The comprehensive workflow encompasses several key stages: gathering and enhancing engine data, training and cross validating the ML models, testing and evaluating their performance, and finally, deploying, monitoring, and updating the ML models. By following this systematic approach, the aim is to streamline the development and deployment process of ML models tailored for aircraft engine assessment.

Development↗
DOE OSTI2026

Automation of Laser Plasma Focused Ion Beam Microscopy for Next-Gen Energy Materials

Automation can revolutionize the use of ultrafast laser ablation and plasma-focused ion beam (PFIB) techniques for high-throughput, reproducible cross-sectioning and various sample preparation in materials characterization. As these methods become essential for analyzing complex energy materials and next-generation devices, efficient, standardized workflows are needed to minimize variability and enhance precision. This work highlights our advancements in developing automated processes for sample preparation that integrates machine learning, workflow optimization, and large-scale data acquisition to improve efficiency and scalability in applications such as electrolyzers, photovoltaic cells, and microelectronics. To streamline cross-sectioning and lamella fabrication, we have implemented fully automated workflows that standardize laser ablation and PFIB milling sequences. These workflows incorporate pre-programmed protocols for material removal, alignment, and thinning, reducing user intervention and ensuring consistency across different sample types. Machine learning algorithms further enhance automation by predicting optimal milling strategies and adapting parameters based on material properties and sectioning requirements. This approach significantly improves throughput while maintaining the structural integrity of prepared samples for high-resolution imaging and analysis, including transmission electron microscopy. Beyond sample preparation, our automation platform enables the acquisition of large, high-resolution datasets through serial sectioning, image alignment, and 3D reconstruction. These automated routines facilitate multi-scale characterization, capturing structural and compositional details from the nanoscale to the device level. By reducing variability and increasing efficiency, our automated approach enhances defect analysis, failure diagnostics, and process optimization, accelerating advancements in materials research and device engineering.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Surrogate models for development of unconventional shale reservoirs by an integrated numerical approach of hydraulic fracturing, flow and geomechanics, and machine learning

We develop well-completion surrogate models by taking an integrated workflow of hydraulic fracturing, flow, geomechanics, and machine learning simulation. There are three steps in the proposed workflow. First, history-matching processes are conducted with the field data including pumping and production data for characterization. Second, full-physics simulation is performed with various parameters of the field development (e.g., cluster spacing, clusters per stage, pumping rates and times, amount of proppant, and well spacing) to generate multiple simulation results by changing the parameters of the completion design with well-known hydraulic fracturing, reservoir, geomechanics simulators to calculate fracture geometry, reservoir depressurization, induced stress changes. The workflow is demonstrated over a field in the Southern Midland Basin. Here, we take two completion scenarios: a single well case followed by a multi-well case. Finally, a Long Short-Term Memory (LSTM) machine learning algorithm is employed to create surrogate models that can replicate the full-physics simulation results. Furthermore, results show that the trained models applied in the single well and multi-well cases for a particular geological system can provide good accuracy close to those provided by full-physics simulations. Specifically, the site-specific surrogate models can predict fracture parameters (length, height, and surface area) and cumulative production accurately with computational efficiency, suggesting our proposed workflow can be used as a pragmatic tool for expediting the well completion optimization process.

Geomechanics↗
DOE OSTI2024

Genomic factors shaping codon usage across the Saccharomycotina subphylum

Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. It has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. We characterized codon usage across 1,154 strains from 1,051 species from the fungal subphylum Saccharomycotina to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns. We found a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is distinct between the 12 orders to such a degree that yeasts can be classified with an accuracy >90% using a machine learning algorithm. We also characterized the degree to which codon usage bias is impacted by translational selection. We found it was influenced by a combination of features, including the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that avoidance of the CGN codons is associated with a decline in arginine tRNA function. Consistent with previous findings, codon usage bias within the Saccharomycotina is shaped by genomic features and GC bias. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.

59 BASIC BIOLOGICAL SCIENCES↗