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DOE OSTI2025

Explaining word embeddings with perfect fidelity: a case study in predicting research impact

The best-performing approaches for scholarly document quality prediction are based on embedding models. In addition to their performance when used in classifiers, embedding models can also provide predictions even for words that were not contained in the labelled training data for the classification model, which is important in the context of the ever-evolving research terminology. Although model-agnostic explanation methods, such as Local interpretable model-agnostic explanations, can be applied to explain machine learning classifiers trained on embedding models, these produce results with questionable correspondence to the model. We introduce a new feature importance method, Self-Model Entities Rated (SMER), for logistic regression-based classification models trained on word embeddings. We show that SMER has theoretically perfect fidelity with the explained model, as the average of logits of SMER scores for individual words (SMER explanation) exactly corresponds to the logit of the prediction of the explained model. Quantitative and qualitative evaluation is performed through five diverse experiments conducted on 50,000 research articles (papers) from the CORD-19 corpus. In conclusion, through an AOPC curve analysis, we experimentally demonstrate that SMER produces better explanations than LIME, SHAP and global tree surrogates.

Coarse-grained models↗

NASA NTRS2020

Mark Twain National Forest Ecological Forecasting - Utilizing NASA Earth Observations to Classify Ground Cover Types in the Mark Twain National Forest

The Mark Twain National Forest (MTNF) encompasses 1.5 million acres of public land in the Ozarks region of southeastern Missouri. The industrial boom between the 1880s and 1920s had devastating effects on the shortleaf pine (Pinus echinata),Missouri’s only native pine species. The combination of fire suppression on this fire-dependent species and timber harvest of mature pine stands inhibited the development of pine seedlings and promoted the establishment of hardwood stands. Partners at the US Forest Service’s MTNF are currently involved in restoration efforts in two ranger districts, which includes removing invasive eastern red cedar (Juniperus virginiana) and prescribed burning. To expand spatial coverage for the MTNF beyond in situ observation sites, the NASA DEVELOP team analyzed land cover change from 1986 through 2019 and forecasted changes based on a ‘business-as-usual' scenario out to 2040. The team incorporated remotely sensed data from Landsat 5 Thematic Mapper (TM) and Landsat 8 Operational Land Imager (OLI) into the random trees supervised classification tool in ArcGIS Pro. This tool spectrally separated pixels into five distinct land cover classes and produced classifications for 1986 and 2019, with kappa statistics of 0.87 and 0.81, respectively. Overall, there was a net decrease in conifer and meadow land cover between 1986 and 2019 along with a net increase in water, developed, and deciduous land cover. The team used TerrSet’s Land Change Modeler to forecast land cover through 2040. Results showed an increase in coniferous land cover and a decrease in deciduous cover, indicating a high probability that current restoration efforts will produce the intended effect.

Kaitlyn Bretz↗

NASA NTRS2020

Mark Twain National Forest Ecological Forecasting: Utilizing NASA Earth Observations to Classify Ground Cover Types in the Mark Twain National Forest

DEVELOP Tech Paper↗

NASA NTRS1993

Polarimetric radar data decomposition and interpretation

Significant efforts have been made to decompose polarimetric radar data into several simple scattering components. The components which are selected because of their physical significance can be used to classify SAR (Synthetic Aperture Radar) image data. If particular components can be related to forest parameters, inversion procedures may be developed to estimate these parameters from the scattering components. Several methods have been used to decompose an averaged Stoke's matrix or covariance matrix into three components representing odd (surface), even (double-bounce) and diffuse (volume) scatterings. With these decomposition techniques, phenomena, such as canopy-ground interactions, randomness of orientation, and size of scatters can be examined from SAR data. In this study we applied the method recently reported by van Zyl (1992) to decompose averaged backscattering covariance matrices extracted from JPL SAR images over forest stands in Maine, USA. These stands are mostly mixed stands of coniferous and deciduous trees. Biomass data have been derived from field measurements of DBH and tree density using allometric equations. The interpretation of the decompositions and relationships with measured stand biomass are presented in this paper.

Sun, Guoqing↗

NASA NTRS2003

Enhancing and Archiving the APS Catalog of the POSS I

We have worked on two different projects: 1) Archiving the APS Catalog of the POSS I for distribution to NASA's NED at IPAC, SIMBAD in France, and individual astronomers and 2) The automated morphological classification of galaxies. We have completed archiving the Catalog into easily readable binary files. The database together with the software to read it has been distributed on DVD's to the national and international data centers and to individual astronomers. The archived Catalog contains more than 89 million objects in 632 fields in the first epoch Palomar Observatory Sky Survey. Additional image parameters not available in the original on-line version are also included in the archived version. The archived Catalog is also available and can be queried at the APS web site (URL: http://aps.umn.edu) which has been improved with a much faster and more efficient querying system. The Catalog can be downloaded as binary datafiles with the source code for reading it. It is also being integrated into the SkyQuery system which includes the Sloan Digital Sky Survey, 2MASS, and the FIRST radio sky survey. We experimented with different classification algorithms to automate the morphological classification of galaxies. This is an especially difficult problem because there are not only a large number of attributes or parameters and measurement uncertainties, but also the added complication of human disagreement about the adopted types. To solve this problem we used 837 galaxy images from nine POSS I fields at the North Galactic Pole classified by two independent astronomers for which they agree on the morphological types. The initial goal was to separate the galaxies into the three broad classes relevant to issues of large scale structure and galaxy formation and evolution: early (ellipticals and lenticulars), spirals, and late (irregulars) with an accuracy or success rate that rivals the best astronomer classifiers. We also needed to identify a set of parameters derived from the digitized images that separate the galaxies by type. The human eye can easily recognize complicated patterns in images such as spiral arms which can be spotty, blotchy affairs that are difficult for automated techniques. A galaxy image can potentially be described by hundreds of parameters, all of which may have some relation to the morphological type. In the set of initial experiments we used 624 such parameters, in two colors, blue and red. These parameters include the surface brightness and color measured at different radii, ratios of these parameters at different radii, concentration indices, Fourier transforms and wavelet decomposition coefficients. We experimented with three different classes of classification algorithms; decision trees, k-nearest neighbors, and support vector machines (SVM). A range of experiments were conducted and we eventually narrowed the parameters to 23 selected parameters. SVM consistently outperformed the other algorithms with both sets of features. By combining the results from the different algorithms in a weighted scheme we achieved an overall classification success of 86%.

Humphreys, Roberta M.↗

NASA NTRS2005

Inductive Learning Approaches for Improving Pilot Awareness of Aircraft Faults

Neural network flight controllers are able to accommodate a variety of aircraft control surface faults without detectable degradation of aircraft handling qualities. Under some faults, however, the effective flight envelope is reduced; this can lead to unexpected behavior if a pilot performs an action that exceeds the remaining control authority of the damaged aircraft. The goal of our work is to increase the pilot s situational awareness by informing him of the type of damage and resulting reduction in flight envelope. Our methodology integrates two inductive learning systems with novel visualization techniques. One learning system, the Inductive Monitoring System (IMS), learns to detect when a simulation includes faulty controls, while two others, Inductive Classification System (INCLASS) and multiple binary decision tree system (utilizing C4.5), determine the type of fault. In off-line training using only non-failure data, IMS constructs a characterization of nominal flight control performance based on control signals issued by the neural net flight controller. This characterization can be used to determine the degree of control augmentation required in the pitch, roll, and yaw command channels to counteract control surface failures. This derived information is typically sufficient to distinguish between the various control surface failures and is used to train both INCLASS and C4.5. Using data from failed control surface flight simulations, INCLASS and C4.5 independently discover and amplify features in IMS results that can be used to differentiate each distinct control surface failure situation. In real-time flight simulations, distinguishing features learned during training are used to classify control surface failures. Knowledge about the type of failure can be used by an additional automated system to alter its approach for planning tactical and strategic maneuvers. The knowledge can also be used directly to increase the pilot s situational awareness and inform manual maneuver decisions. Our multi-modal display of this information provides speech output to issue control surface failure warnings to a lesser-used communication channel and provides graphical displays with pilot-selectable !eve!s of details to issues additional information about the failure. We also describe a potential presentation for flight envelope reduction that can be viewed separately or integrated with an existing attitude indicator instrument. Preliminary results suggest that the inductive approach is capable of detecting that a control surface has failed and determining the type of fault. Furthermore, preliminary evaluations suggest that the interface discloses a concise summary of this information to the pilot.

Spikovska, Lilly↗

DOE OSTI2025

Leveraging intermediate resonances to probe CP violation at colliders

We explore the phenomenological impact of interference in tree-level contributions to three-body final states in $2\rightarrow 3$ scattering processes. This work introduces a novel search strategy leveraging asymmetries to enable sensitivity to CP-violating effects in less well-explored regions of phase space. Analytically, we demonstrate the effectiveness of this observable in probing interference between Standard Model charged-current decays and effective left-handed vector interactions, illustrated in a toy model featuring a scalar leptoquark, $S_1 \sim (3, 1, -\,1/3)$. Numerically, we apply this framework to studying the process $pp\rightarrow b \tau \nu $; unlike traditional high-$p_T$ searches or “bump hunts”, this approach utilizes an intermediate energy regime – where new physics is neither light enough to be produced on shell or heavy enough to justify an effective field theory treatment. A proof-of-principle analysis at parton level demonstrates a percent-level asymmetry, with sensitivity also to BSM weak-CP phase. While the specific phase sensitivity is diminished at particle level due to showering and detector effects, a machine learning classifier can recover sensitively to the presence of SM-BSM interference, significantly outperforming standard analysis methods. Notably discrimination between BSM signal and SM background could be achieved at the 2$\sigma $ level for the current LHC dataset and 8$\sigma $ at the High-Luminosity LHC. Moreover, this asymmetry observable as defined can also be more broadly applied to other searches for CP-violation in $2\rightarrow 3$ processes in present and future collider environments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses

Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Removal of Antibiotics from Swine Wastewater Using an Environmentally Friendly Biochar: Performance and Mechanisms

Antibiotics used in the swine industry to treat diseases and improve animal growth are poorly absorbed by swine and have been classified as micropollutants due to their occurrence in surface water, wastewater, and soil. This study investigated the capacity of biochar produced from eastern red cedar to remove target antibiotics that have been extensively used in the swine industry. Biochar was produced by pyrolysis from eastern red cedar at 450 °C. The sorption tests were performed by mixing biochar and a solution (1:10 ratio) containing each antibiotic in 100, 300, 600, and 900 μg L –1 concentrations. The results indicate that red cedar biochar was able to effectively remove up to 99.93% tetracycline, 96.23% oxytetracycline, 98.28% chlortetracycline, 76.4% sulfadiazine, and 78.6% sulfamethazine at the lowest concentrations. The removal efficiencies at higher concentrations declined up to 83.52, 47.23, 64.16, 69.8, and 58.4% for tetracycline, oxytetracycline, chlortetracycline, sulfadiazine, and sulfamethazine, respectively. The biochar exhibited stronger adsorption capacity for chlortetracycline and sulfamethazine compared to the other antibiotics. The likely adsorption mechanisms driving the removal of tetracyclines and sulfonamides are hydrogen-bonding and π–π electron-donor–acceptor, supported by FTIR analyses of the biochar itself. Overall, the results highlighted the potential utilization of eastern red cedar biochar for practical applications, mitigating antibiotic residues from swine wastewater in a cost-effective and environmentally friendly manner due to its relatively low pyrolysis temperature (450 °C) and sustainable repurposing of an invasive tree species.

09 BIOMASS FUELS↗

NASA NTRS2001

Ectomycorrhizal fungal associates of Pinus contorta in soils associated with a hot spring in Norris Geyser Basin, Yellowstone National Park, Wyoming

Molecular methods and comparisons of fruiting patterns (i.e., presence or absence of fungal fruiting bodies in different soil types) were used to determine ectomycorrhizal (EM) associates of Pinus contorta in soils associated with a thermal soil classified as ultra-acidic to extremely acidic (pH 2 to 4). EM were sampled by obtaining 36 soil cores from six paired plots (three cores each) of both thermal soils and forest soils directly adjacent to the thermal area. Fruiting bodies (mushrooms) were collected for molecular identification and to compare fruiting body (above-ground) diversity to below-ground diversity. Our results indicate (i) that there were significant decreases in both the level of EM infection (130 +/- 22 EM root tips/core in forest soil; 68 +/- 22 EM root tips/core in thermal soil) and EM fungal species richness (4.0 +/- 0.5 species/core in forest soil; 1.2 +/- 0.2 species/core in thermal soil) in soils associated with the thermal feature; (ii) that the EM mycota of thermal soils was comprised of a small set of dominant species and included very few rare species, while the EM mycota of forest soils contained a few dominant species and several rare EM fungal species; (iii) that Dermocybe phoenecius and a species of Inocybe, which was rare in forest soils, were the dominant EM fungal species in thermal soils; (iv) that other than the single Inocybe species, there was no overlap in the EM fungal communities of the forest and thermal soils; and (v) that the fungal species forming the majority of the above-ground fruiting structures in thermal soils (Pisolithus tinctorius, which is commonly used in remediation of acid soils) was not detected on a single EM root tip in either type of soil. Thus, P. tinctorius may have a different role in these thermal soils. Our results suggest that this species may not perform well in remediation of all acid soils and that factors such as pH, soil temperature, and soil chemistry may interact to influence EM fungal community structure. In addition, we identified at least one new species with potential for use in remediation of hot acidic soil.

Pinus/microbiology↗