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All sourcesNASA NTRSDOE OSTI
NASA NTRS2022

T-Rex: The NASA Technology Taxonomy Recommender System

NASA tracks over 16,000 technology projects across the Agency, from propulsion systems to software. These projects are classified according to NASA’s Technology Taxonomy to facilitate data search, extraction, and application. In 2020, the Taxonomy was revised to better align strategic goals with project technical disciplines. Manual re-classification of cur-rent and historical projects was estimated to take thousands of technologist labor hours. Instead of manual classification, our team developed T-Rex, a recommender engine, trained on just a small set of manually classified projects. T-Rex was used to classify the projects and then integrate the data into TechPort to recommend classes to users when updating projects. The system and methodology are used in other NASA projects, and T-Rex has achieved 95% accepted accuracy overall.

Space Technology↗
DOE OSTI2024

Predictive Indicators of the Performance of Large Language Models

In several mission contexts, it is desirable to estimate the performance of large language models (LLMs) on tasks that we cannot run directly. In light of published “scaling laws” our hypothesis is that some tasks should be consistently more challenging than others based on characteristics of the task. The goal of this project was to begin quantifying how much information about LLM performance can be gained from the features of a model and a task. Two of our statistical models struggled to converge. Pass/fail test results may provide limited information for inference beyond model quality and task difficulty, but we see no evidence at this time for significant feature interaction effect sizes, arguing for simple models. Future work extending the models to capitalize on perplexity of ground truth answers is suggested. This project also introduces “Depth of Knowledge Variant Testing” as a strategy for more finely assessing language models on open domain question and answer tasks. We developed sets of questions that ask a language model to produce similar information while demonstrating increasing depth of knowledge, and also relabeled existing Q&A test questions with their depth of knowledge. Our results suggest further consideration of Bloom’s taxonomy and further refinement of prompts to properly elicit information at varying depths. In the course of this work, we set up a basic infrastructure for standardizing tasks and testing many language models on these tasks. In addition to testing the predictive quality of model features and performance across test suites, with this project we have introduced two new task features to contextualize each test question: the Dewey Classification main category of information covered, and the Bloom’s taxonomy level that corresponds to the depth of knowledge probed by the question. Splits across these and other features produced over five hundred task subtypes with distinct feature vectors, which we tested on half a dozen models.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, for this work, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Four principles to establish a universal virus taxonomy

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., “arboviruses”), infecting a certain type of host (e.g., “mycoviruses,” “bacteriophages”) or displaying specific pathogenicity (e.g., “human immunodeficiency viruses”), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1985

A new taxonomy for distributed computer systems based upon operating system structure

Characteristics of the resource structure found in the operating system are considered as a mechanism for classifying distributed computer systems. Since the operating system resources, themselves, are too diversified to provide a consistent classification, the structure upon which resources are built and shared are examined. The location and control character of this indivisibility provides the taxonomy for separating uniprocessors, computer networks, network computers (fully distributed processing systems or decentralized computers) and algorithm and/or data control multiprocessors. The taxonomy is important because it divides machines into a classification that is relevant or important to the client and not the hardware architect. It also defines the character of the kernel O/S structure needed for future computer systems. What constitutes an operating system for a fully distributed processor is discussed in detail.

Foudriat, E. C.↗
DOE OSTI2022

Phylogenomics and the first higher taxonomy of Placozoa, an ancient and enigmatic animal phylum

Placozoa is an ancient phylum of extraordinarily unusual animals: miniscule, ameboid creatures that lack most fundamental animal features. Despite high genetic diversity, only recently have the second and third species been named. While prior genomic studies suffer from incomplete placozoan taxon sampling, we more than double the count with protein sequences from seven key genomes and produce the first nuclear phylogenomic reconstruction of all major placozoan lineages. This leads us to the first complete Linnaean taxonomic classification of Placozoa, over a century after its discovery: This may be the only time in the 21st century when an entire higher taxonomy for a whole animal phylum is formalized. Our classification establishes 2 new classes, 4 new orders, 3 new families, 1 new genus, and 1 new species, namely classes Polyplacotomia and Uniplacotomia; orders Polyplacotomea, Trichoplacea, Cladhexea, and Hoilungea; families Polyplacotomidae, Cladtertiidae, and Hoilungidae; and genus Cladtertia with species Cladtertia collaboinventa, nov. Our likelihood and gene content tree topologies refine the relationships determined in previous studies. Adding morphological data into our phylogenomic matrices suggests sponges (Porifera) as the sister to other animals, indicating that modest data addition shifts this node away from comb jellies (Ctenophora). Furthermore, by adding the first genomic protein data of the exceptionally distinct and branching Polyplacotoma mediterranea , we solidify its position as sister to all other placozoans; a divergence we estimate to be over 400 million years old. Yet even this deep split sits on a long branch to other animals, suggesting a bottleneck event followed by diversification. Ancestral state reconstructions indicate large shifts in gene content within Placozoa, with Hoilungia hongkongensis and its closest relatives having the most unique genetics.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1982

Characteristic variations in reflectance of surface soils

Surface soil samples from a wide range of naturally occurring soils were obtained for the purpose of studying the characteristic variations in soil reflectance as these variations relate to other soil properties and soil classification. A total 485 soil samples from the U.S. and Brazil representing 30 suborders of the 10 orders of 'Soil Taxonomy' was examined. The spectral bidirectional reflectance factor was measured on uniformly moist soils over the 0.52 to 2.32 micron wavelength range with a spectroradiometer adapted for indoor use. Five distinct soil spectral reflectance curve forms were identified according to curve shape, the presence or absence of absorption bands, and the predominance of soil organic matter and iron oxide composition. These curve forms were further characterized according to generically homogeneous soil properties in a manner similar to the subdivisions at the suborder level of 'Soil Taxonomy'. Results indicate that spectroradiometric measurements of soil spectral bidirectional reflectance factor can be used to characterize soil reflectance in terms that are meaningful to soil classification, genesis, and survey.

Stoner, E. R.↗
DOE OSTI2026

Feedback and Oscillations: Constructing Feedback Systems for Root Cause Analysis of Oscillations in Power Grids

Dynamic phenomena linked to inverter-based resources (IBRs) have gained global attention. Several IBR-induced dynamics have caused bulk power system-connected wind or solar power plants to trip, and some have even led to widespread outages. In addition, many oscillations have been observed involving IBR power plants. In 2023, the IEEE Power & Energy Society (PES) IBR Subsynchronous Oscillations (SSO) task force published a journal article, “Real-World Subsynchronous Oscillation Events in Power Grids With High Penetrations of Inverter-Based Resources,” in which 19 IBR oscillation events were examined for their causation. Earlier in 2020, another PES task force article, “Definition and Classification of Power System Stability-Revisited & Extended,” authored by prominent academics, introduced converter-driven stability as a new category of stability. The international power grid industry community also took action by publishing the CIGRE Green Book, Power System Dynamic Modelling and Analysis in Evolving Networks (led by Babak Badrzadeh and Zia Emin) in 2024. In August 2024, the Energy Systems Integration Group (ESIG) released a practical guide led by Nick Miller, “Diagnosis and Mitigation of Observed Oscillations in IBR-Dominant Power System: A Practical Guide.” The goal of the guide is to assist practicing engineers in making initial judgments and conducting detailed analyses about oscillations. Finally, when addressing the classification of stability and oscillations, the guide emphasizes a causality-based taxonomy for grouping, such as voltage control-induced oscillations, synchronization-induced oscillations, and frequency or active power control-induced oscillations.

Fan, Lingling [Univ. of South Florida, Tampa, FL (↗
NASA NTRS2019

An Evolutionary System of Mineralogy: Proposal for A Classification of Planetary Materials Based on Natural Kind Clustering

Minerals reveal the nature of the co-evolving geosphere and biosphere through billions of years of Earth history. Mineral classification systems have the potential to elucidate this rich evolutionary story; however, the present mineral taxonomy, based as it is on idealized major element chemistry and crystal structure, lacks a temporal aspect, and thus cannot reflect planetary evolution. A complementary evolutionary system of mineralogy based on the quantitative recognition of “natural kind clustering” for a wide range of condensed planetary materials with different paragenetic origins has the potential to amplify, though not supersede, the present classification system.

Philosophy of mineralogy↗
DOE OSTI2025

Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification

Accurate metagenomic classification relies on comprehensive, up-to-date, and validated reference databases. While the NCBI BLAST Nucleotide (nt) database, encompassing a vast collection of sequences from all domains of life, represents an invaluable resource, its massive size—currently exceeding 10 12 nucleotides—and exponential growth pose significant challenges for researchers seeking to maintain current nt-based indices for metagenomic classification. Recognizing that no current nt-based indices exist for the widely used Centrifuge classifier, and the last public version currently available was released in 2018, we addressed this critical gap by leveraging advanced high-performance computing resources. We present new Centrifuge-compatible nt databases, meticulously constructed using a novel pipeline incorporating different quality control measures, including reference decontamination and filtering. These measures demonstrably reduce spurious classifications, as shown through our reanalysis of published metagenomic data where Plasmodium annotations were dramatically reduced using our decontaminated database, highlighting how database quality can significantly impact research conclusions. Through temporal comparisons, we also reveal how our approach minimizes inconsistencies in taxonomic assignments stemming from asynchronous updates between public sequence and taxonomy databases. These discrepancies are particularly evident in taxa such as Listeria monocytogenes and Naegleria fowleri, where classification accuracy varied significantly across database versions. These new databases, made available as pre-built Centrifuge indexes, respond to the need for an open, robust, nt-based pipeline for taxonomic classification in metagenomics. Applications such as environmental metagenomics, forensics, and clinical metagenomics, which require comprehensive taxonomic coverage, will benefit from this resource. Our work highlights the importance of treating reference databases as dynamic entities, subject to ongoing quality control and validation akin to software development best practices. This approach is crucial for ensuring accuracy and reliability of metagenomic analysis, especially as databases continue to expand in size and complexity.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1974

Craters on Earth, Moon, and Mars - Multivariate classification and mode of origin

Testing extraterrestrial craters and candidate terrestrial analogs for morphologic similitude is treated as a problem in numerical taxonomy. According to a principal-components solution and a cluster analysis, 402 representative craters on the Earth, the Moon, and Mars divide into two major classes of contrasting shapes and modes of origin. Craters of net accumulation of material (cratered lunar domes, Martian calderas, and all terrestrial volcanoes except maars and tuff rings) group apart from craters of excavation (terrestrial meteorite impact and experimental explosion craters, typical Martian craters, and all other lunar craters). Maars and tuff rings belong to neither group but are transitional. The classification criteria are four independent attributes of topographic geometry derived from seven descriptive variables by the principal-components transformation. Morphometric differences between crater bowl and raised rim constitute the strongest of the four components.

Pike, R. J.↗
NASA NTRS1989

A three-parameter asteroid taxonomy

Broadband U, V, and x photometry together with IRAS asteroid albedos have been used to construct an asteroid classification system. The system is based on three parameters (U-V and v-x color indices and visual geometric albedo), and it is able to place 96 percent of the present sample of 357 asteroids into 11 taxonomic classes. It is noted that all but one of these classes are analogous to those previously found using other classification schemes. The algorithm is shown to account for the observational uncertainties in each of the classification parameters.

Tedesco, Edward F.↗
DOE OSTI2023

Radio galaxy zoo EMU: towards a semantic radio galaxy morphology taxonomy

We present a novel natural language processing (NLP) approach to deriving plain English descriptors for science cases otherwise restricted by obfuscating technical terminology. We address the limitations of common radio galaxy morphology classifications by applying this approach. We experimentally derive a set of semantic tags for the Radio Galaxy Zoo EMU (Evolutionary Map of the Universe) project and the wider astronomical community. We collect 8486 plain English annotations of radio galaxy morphology, from which we derive a taxonomy of tags. The tags are plain English. The result is an extensible framework, which is more flexible, more easily communicated, and more sensitive to rare feature combinations, which are indescribable using the current framework of radio astronomy classifications.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

On Developing a Taxonomy for Multidisciplinary Design Optimization: A Decision-Based Perspective

In this paper, we approach MDO from a Decision-Based Design (DBD) perspective and explore classification schemes for designing complex systems and processes. Specifically, we focus on decisions, which are only a small portion of the Decision Support Problem (DSP) Technique, our implementation of DBD. We map coupled nonhierarchical and hierarchical representations from the DSP Technique into the Balling-Sobieski (B-S) framework (Balling and Sobieszczanski-Sobieski, 1994), and integrate domain-independent linguistic terms to complete our taxonomy. Application of DSPs to the design of complex, multidisciplinary systems include passenger aircraft, ships, damage tolerant structural and mechanical systems, and thermal energy systems. In this paper we show that Balling-Sobieski framework is consistent with that of the Decision Support Problem Technique through the use of linguistic entities to describe the same type of formulations. We show that the underlying linguistics of the solution approaches are the same and can be coalesced into a homogeneous framework with which to base the research, application, and technology MDO upon. We introduce, in the Balling-Sobieski framework, examples of multidisciplinary design, namely, aircraft, damage tolerant structural and mechanical systems, and thermal energy systems.

Lewis, Kemper↗
NASA NTRS2015

Phase-Angle Dependence of Determinations of Diameter, Albedo, and Taxonomy: A Case Study of NEO 3691 Bede

Parameters important for NEO risk assessment and mitigation include Near-Earth Object diameter and taxonomic classification, which translates to surface composition. Diameters of NEOs are derived from the thermal fluxes measured by WISE, NEOWISE, Spitzer Warm Mission and ground-based telescopes including the IRTF and UKIRT. Diameter and its coupled parameters Albedo and IR beaming parameter (a proxy for thermal inertia and/or surface roughness) are dependent upon the phase angle, which is the Sun-target-observer angle. Orbit geometries of NEOs, however, typically provide for observations at phase angles greater than 20 degrees. At higher phase angles, the observed thermal emission is sampling both the day and night sides of the NEO. We compare thermal models for NEOs that exclude (NEATM) and include (NESTM) night-side emission. We present a case study of NEO 3691 Bede, which is a higher albedo object, X (Ec) or Cgh taxonomy, to highlight the range of H magnitudes for this object (depending on the albedo and phase function slope parameter G), and to examine at different phase angles the taxonomy and thermal model fits for this NEO. Observations of 3691 Bede include our observations with IRTF+SpeX and with the 10 micrometer UKIRT+Michelle instrument, as well as WISE and Spitzer Warm mission data. By examining 3691 Bede as a case study, we highlight the interplay between the derivation of basic physical parameters and observing geometry, and we discuss the uncertainties in H magnitude, taxonomy assignment amongst the X-class (P, M, E), and diameter determinations. Systematic dependencies in the derivation of basic characterization parameters of H-magnitude, diameter, albedo and taxonomy with observing geometry are important to understand. These basic characterization parameters affect the statistical assessments of the NEO population, which in turn, affects the assignment of statistically-assessed basic parameters to discovered but yet-to-be-fully-characterized NEOs.

Albedo and taxonomy↗
NASA NTRS2003

A Framework for Categorizing Important Project Variables

While substantial research has led to theories concerning the variables that affect project success, no universal set of such variables has been acknowledged as the standard. The identification of a specific set of controllable variables is needed to minimize project failure. Much has been hypothesized about the need to match project controls and management processes to individual projects in order to increase the chance for success. However, an accepted taxonomy for facilitating this matching process does not exist. This paper surveyed existing literature on classification of project variables. After an analysis of those proposals, a simplified categorization is offered to encourage further research.

Parsons, Vickie S.↗