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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.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A Massively Parallel Implementation of the CCSD(T) Method Using the Resolution-of-the-Identity Approximation and a Hybrid Distributed/Shared Memory Parallelization Model

In this work, a parallel algorithm is described for the coupled-cluster singles and doubles method augmented with a perturbative correction for triple excitations [CCSD(T)] using the resolution-of-the-identity (RI) approximation for two-electron repulsion integrals (ERIs). The algorithm bypasses the storage of four-center ERIs by adopting an integral-direct strategy. The CCSD amplitude equations are given in a compact quasi-linear form by factorizing them in terms of amplitude-dressed three-center intermediates. A hybrid MPI/OpenMP parallelization scheme is employed, which uses the OpenMP-based shared memory model for intranode parallelization and the MPI-based distributed memory model for internode parallelization. Parallel efficiency has been optimized for all terms in the CCSD amplitude equations. Two different algorithms have been implemented for the rate-limiting terms in the CCSD amplitude equations that entail and -scaling computational costs, where N O and N V denote the number of correlated occupied and virtual orbitals, respectively. One of the algorithms assembles the four-center ERIs requiring N V 4 and N O 2 N V 2 -scaling memory costs in a distributed manner on a number of MPI ranks, while the other algorithm completely bypasses the assembling of quartic memory-scaling ERIs and thus largely reduces the memory demand. It is demonstrated that the former memory-expensive algorithm is faster on a few hundred cores, while the latter memory-economic algorithm shows a better strong scaling in the limit of a few thousand cores. The program is shown to exhibit a near-linear scaling, in particular for the compute-intensive triples correction step, on up to 8000 cores. The performance of the program is demonstrated via calculations involving molecules with 24–51 atoms and up to 1624 atomic basis functions. As the first application, the complete basis set (CBS) limit for the interaction energy of the π-stacked uracil dimer from the S66 data set has been investigated. This work reports the first calculation of the interaction energy at the CCSD(T)/aug-cc-pVQZ level without local orbital approximation. The CBS limit for the CCSD correlation contribution to the interaction energy was found to be -8.01 kcal/mol, which agrees very well with the value -7.99 kcal/mol reported by Schmitz, Hättig, and Tew [ Phys. Chem. Chem. Phys. 2014 , 16 , 22167-22178]. The CBS limit for the total interaction energy was estimated to be -9.64 kcal/mol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Impact of survey spatial variability on galaxy redshift distributions and the cosmological 3 × 2-point statistics for the Rubin Legacy Survey of Space and Time (LSST)

We investigate the impact of spatial survey non-uniformity on the galaxy redshift distributions for forthcoming data releases of the Rubin Observatory Legacy Survey of Space and Time (LSST). Specifically, we construct a mock photometry data set degraded by the Rubin OpSim observing conditions, and estimate photometric redshifts of the sample using a template-fitting photo-z estimator, BPZ, and a machine learning method, FlexZBoost. We select the Gold sample, defined as $i\lt 25.3$ for 10 yr LSST data, with an adjusted magnitude cut for each year and divide it into five tomographic redshift bins for the weak lensing lens and source samples. We quantify the change in the number of objects, mean redshift, and width of each tomographic bin as a function of the coadd i-band depth for 1-yr (Y1), 3-yr (Y3), and 5-yr (Y5) data. In particular, Y3 and Y5 have large non-uniformity due to the rolling cadence of LSST, hence provide a worst-case scenario of the impact from non-uniformity. We find that these quantities typically increase with depth, and the variation can be $10\!-\!40~{{\rm per\ cent}}$ at extreme depth values. Using Y3 as an example, we propagate the variable depth effect to the weak lensing $3\times 2$ pt analysis, and assess the impact on cosmological parameters via a Fisher forecast. We find that galaxy clustering is most susceptible to variable depth, and non-uniformity needs to be mitigated below 3 per cent to recover unbiased cosmological constraints. There is little impact on galaxy–shear and shear–shear power spectra, given the expected LSST Y3 noise.

cosmology↗
DOE OSTI2025

Graph-Based Prediction of Spatio-Temporal Vaccine Hesitancy From Insurance Claims Data

Growing vaccine hesitancy is contributing to the decline in immunization rates for highly contagious, vaccine-preventable childhood diseases. Therefore, there has been a significant interest in understanding how hesitancy is spreading at higher spatio-temporal resolutions, enabling more targeted interventions. Motivated by this, we study the problem of prediction of vaccine hesitancy at the ZIP Code level, referred to as the VaxHesitancy problem. A significant challenge for this problem is the lack of high-resolution data that indicates hesitancy. Here, we develop a hybrid VaxHesSTL framework that combines a Graph Neural Network (GNN) and a Recurrent Neural Network (RNN) to address the VaxHesitancy problem. The GNN uses a ZIP Code-level network to capture spatial signals from neighboring areas, while the RNN models the temporal dynamics present in the data. We train and evaluate VaxHesSTL using a large dataset, namely the All-Payer Claims Databases (APCD), for Virginia, consisting of insurance claims from over five million individuals for six years. We find that an aggregated contact network or graph, developed from a detailed activity-based population network, plays an important role in the performance of VaxHesSTL, compared to graph models based solely on spatial proximity. Experiments demonstrate that VaxHesSTL outperforms a range of state-of-the-art baselines, which rely solely on historical time series data without accounting for spatial relationships. Since hesitancy data at higher spatial resolution is often unavailable or hard to get, we incorporate an active learning approach with our VaxHesSTL framework to optimize the training set without compromising the prediction performance. We find that hesitancy data for only 18% of ZIP Codes selected by active learning allows us to forecast hesitancy for all the ZIP Codes in the Virginia.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Physics‐Informed Machine Learning Method for Large‐Scale Data Assimilation Problems

Abstract We develop a physics‐informed machine learning approach for large‐scale data assimilation and parameter estimation and apply it for estimating transmissivity and hydraulic head in the two‐dimensional steady‐state subsurface flow model of the Hanford Site given synthetic measurements of said variables. In our approach, we extend the physics‐informed conditional Karhunen‐Loéve expansion (PICKLE) method to modeling subsurface flow with unknown flux (Neumann) and varying head (time‐dependent Dirichlet) boundary conditions. We demonstrate that the PICKLE method is comparable in accuracy with the standard maximum a posteriori (MAP) method, but is significantly faster than MAP for large‐scale problems. Both methods use a mesh to discretize the computational domain. In MAP, the parameters and states are discretized on the mesh; therefore, the size of the MAP parameter estimation problem directly depends on the mesh size. In PICKLE, the mesh is used to evaluate the residuals of the governing equation, while the parameters and states are approximated by the truncated conditional Karhunen‐Loéve expansions with the number of parameters controlled by the smoothness of the parameter and state fields, and not by the mesh size. For a considered example, we demonstrate that the computational cost of PICKLE increases near linearly (as N 1.15 ) with the number of grid nodes N , while that of MAP increases much faster (as N 3.28 ). We also show that once trained for one set of Dirichlet boundary conditions (i.e., one river stage), the PICKLE method provides accurate estimates of the hydraulic head for any value of the Dirichlet boundary conditions (i.e., for any river stage).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A robust synthetic data generation framework for machine learning in high-resolution transmission electron microscopy (HRTEM)

Machine learning techniques are attractive options for developing highly-accurate analysis tools for nanomaterials characterization, including high-resolution transmission electron microscopy (HRTEM). However, successfully implementing such machine learning tools can be difficult due to the challenges in procuring sufficiently large, high-quality training datasets from experiments. In this work, we introduce Construction Zone, a Python package for rapid generation of complex nanoscale atomic structures which enables fast, systematic sampling of realistic nanomaterial structures and can be used as a random structure generator for large, diverse synthetic datasets. Using Construction Zone, we develop an end-to-end machine learning workflow for training neural network models to analyze experimental atomic resolution HRTEM images on the task of nanoparticle image segmentation purely with simulated databases. Further, we study the data curation process to understand how various aspects of the curated simulated data—including simulation fidelity, the distribution of atomic structures, and the distribution of imaging conditions—affect model performance across three benchmark experimental HRTEM image datasets. Using our workflow, we are able to achieve state-of-the-art segmentation performance on these experimental benchmarks and, further, we discuss robust strategies for consistently achieving high performance with machine learning in experimental settings using purely synthetic data. Construction Zone and its documentation are available at https://github.com/lerandc/construction_zone.

36 MATERIALS SCIENCE↗
DOE OSTI2024

First Constraints on the Epoch of Reionization Using the Non-Gaussianity of the Kinematic Sunyaev-Zel’dovich Effect from the South Pole Telescope and Herschel-SPIRE Observations

We report results from an analysis aimed at detecting the trispectrum of the kinematic Sunyaev-Zel’dovich (kSZ) effect by combining data from the South Pole Telescope (SPT) and Herschel-SPIRE experiments over a 100 deg 2 field. The SPT observations combine data from the previous and current surveys, namely SPTpol and SPT-3G, to achieve depths of 4.5, 3, and 16 μ K - arcmin in bands centered at 95, 150, and 220 GHz. For SPIRE, we include data from the 600 and 857 GHz bands. We reconstruct the velocity-induced large-scale correlation of the small-scale kSZ signal with a quadratic estimator that uses two cosmic microwave background (CMB) temperature maps, constructed by optimally combining data from all the frequency bands. We reject the null hypothesis of a zero trispectrum at 10.3 σ level. However, the measured trispectrum contains contributions from both the kSZ and other undesired components, such as CMB lensing and astrophysical foregrounds, with kSZ being sub-dominant. We use the agora simulations to estimate the expected signal from CMB lensing and astrophysical foregrounds. After accounting for the contributions from CMB lensing and foreground signals, we do not detect an excess kSZ-only trispectrum and use this nondetection to set constraints on reionization. By applying a prior based on observations of the Gunn-Peterson trough, we obtain an upper limit on the duration of reionization of Δ z re , 50 < 4.5 (95% confidence level). We find these constraints are fairly robust to foregrounds assumptions. This trispectrum measurement is independent of, but consistent with, Planck’s optical depth measurement. This result is the first constraint on the epoch of reionization using the non-Gaussian nature of the kSZ signal.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Model-Based Framework to Optimize Charger Station Deployment for Battery Electric Vehicles

The development of battery electric vehicles (BEVs) is accelerating due to their environmental advantages over gasoline and diesel-powered vehicles, including a decrease in air pollution and an increase in energy efficiency. The deployment of charging infrastructure will need to increase to keep pace with demand, especially for large commercial vehicles for which few public chargers currently exist. In this paper, a new flexible framework is proposed for optimizing the placement of charging stations for BEVs, within which different physical models and optimization techniques may be used. Furthermore, a set of metrics is suggested to help enforce complex constraints and facilitate direct comparison between different optimization techniques. Unlike many existing charger placement techniques, the proposed method directly considers the historical driving patterns on a vehicle-by-vehicle basis, using transparent models to assess impacts of candidate charger placements, thus improving the explainability of the results. In the developed framework, modeled BEVs are first generated along the road network to mimic historical traffic data and are simulated traveling along a given route according to a simplified vehicle model. During the simulation, the charger placement problem is initially relaxed to allow vehicles to charge at any node along the road network, and vehicle states are tracked to assess areas of high charging demand. Charging stations are then placed based on the results of the relaxed simulation, and suggested placements are evaluated via road network simulation with fixed charger locations. This proposed framework is applied to a sample problem of placing charging stations along five major highway corridors for Class 8 over-the-road electric trucks. A novel mixed integer programming (MIP) formulation is proposed to optimize charger placements based upon the expected charging demand. Constraints were imposed on the final placement results to limit expected wait times at each station and ensure a minimum threshold of trucking routes are viable for BEVs. The results demonstrate the flexibility and potential effectiveness of the developed model-based framework for scalable charger station deployment.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

Improving the Capabilities and Computational Efficiency of the RTE+RRTMGP Radiation Code (Final Report)

This report details progress on the RTE+RRTMGP radiation codes made during the period of performance. RTE+RRTMGP is a set of codes for computing radiative fluxes in planetary atmospheres. RRTMGP uses a k-distribution to provide an optical description (absorption and possibly Rayleigh optical depth) of the gaseous atmosphere, along with the relevant source functions, on a pre-determined spectral grid given temperatures, pressures, and gas concentration. RTE computes fluxes given spectrally-resolved optical descriptions and source functions. Spectrally-resolved fluxes are summarized (“reduced”) via a user extensible class. The initial release of the code and the design choices are described in Pincus et al. 2019; the codes are available on Github. Although RRTMGP was based on current (at the time) empirical spectroscopic data, RTE and RRTMGP were developed in large part to modernize software practices. The design focused on flexibility broadly interpreted: by separating code from data and allowing data to drive computation; in coupling to the host model (e.g. the coupling of clouds to radiative fluxes is user-controlled); with respect to programming languages (computational tasks are accessed via widely-compatible C interfaces); and with respect to hardware (the codes run on a range of CPU and GPU architectures). The code also puts an emphasis on modularity and clarity. RTE+RRTMGP v1.0 was released in September 20219. This award supported the evolution of the RTE+RRTMGP code base to support greater flexibility, accuracy, and efficiency.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Streaming Large-Scale Microscopy Data to a Supercomputing Facility

Data management is a critical component of modern experimental workflows. As data generation rates increase, transferring data from acquisition servers to processing servers via conventional file-based methods is becoming increasingly impractical. The 4D Camera at the National Center for Electron Microscopy generates data at a nominal rate of 480 Gbit s -1 (87,000 frames s -1 ⁠), producing a 700 GB dataset in 15 s. To address the challenges associated with storing and processing such quantities of data, we developed a streaming workflow that utilizes a high-speed network to connect the 4D Camera’s data acquisition system to supercomputing nodes at the National Energy Research Scientific Computing Center, bypassing intermediate file storage entirely. In this work, we demonstrate the effectiveness of our streaming pipeline in a production setting through an hour-long experiment that generated over 10 TB of raw data, yielding high-quality datasets suitable for advanced analyses. Additionally, we compare the efficacy of this streaming workflow against the conventional file-transfer workflow by conducting a postmortem analysis on historical data from experiments performed by real users. Our findings show that the streaming workflow significantly improves data turnaround time, enables real-time decision-making, and minimizes the potential for human error by eliminating manual user interactions.

4D-STEM↗
DOE OSTI2021

Evaluating causal‐based feature selection for fuel property prediction models

Abstract In‐silico screening of novel biofuel molecules based on chemical and fuel properties is a critical first step in the biofuel evaluation process due to the significant volumes of samples required for experimental testing, the destructive nature of engine tests, and the costs associated with bench‐scale synthesis of novel fuels. Predictive models are limited by training sets of few existing measurements, often containing similar classes of molecules that represent just a subset of the potential molecular fuel space. Software tools can be used to generate every possible molecular descriptor for use as input features, but most of these features are largely irrelevant and training models on datasets with higher dimensionality than size tends to yield poor predictive performance. Feature selection has been shown to improve machine learning models, but correlation‐based feature selection fails to provide scientific insight into the underlying mechanisms that determine structure–property relationships. The implementation of causal discovery in feature selection could potentially inform the biofuel design process while also improving model prediction accuracy and robustness to new data. In this study, we investigate the benefits causal‐based feature selection might have on both model performance and identification of key molecular substructures. We found that causal‐based feature selection performed on par with alternative filtration methods, and that a structural causal model provides valuable scientific insights into the relationships between molecular substructures and fuel properties.

Nguyen, Bernard↗
DOE OSTI2021

Macroecological distributions of gene variants highlight the functional organization of soil microbial systems

Abstract The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Data-centric framework for crystal structure identification in atomistic simulations using machine learning

Atomic-level modeling performed at large scales enables the investigation of mesoscale materials properties with atom-by-atom resolution. The spatial complexity of such cross-scale simulations renders them unsuitable for simple human visual inspection. Instead, specialized structure characterization techniques are required to aid interpretation. These have historically been challenging to construct, requiring significant intuition and effort. Here we propose an alternative framework for a fundamental structural characterization task: classifying atoms according to the crystal structure to which they belong. Our approach is data-centric and favors the employment of Machine Learning over heuristic rules of classification. A group of data-science tools and simple local descriptors of atomic structure are employed together with an efficient synthetic training set. We also introduce the first standard and publicly available benchmark data set for evaluation of algorithms for crystal-structure classification. Further, it is demonstrated that our data-centric framework outperforms all of the most popular heuristic methods—especially at high temperatures when lattices are the most distorted—while introducing a systematic route for generalization to new crystal structures. Moreover, through the use of outlier detection algorithms our approach is capable of discerning between amorphous atomic motifs (i.e., noncrystalline phases) and unknown crystal structures, making it uniquely suited for exploratory materials synthesis simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2023

WiP Abstract: Edge-Based Privacy of Naturalistic Driving Data Collection

Collecting large driving datasets is important for data-driven transportation research and studied in naturalistic driving [3]. Due to the standard implementation of a Controller Area Network (CAN) bus for a vehicle’s inter-module communication, many off-the-shelf devices can easily transform a vehicle into a rich data collection utility [2]. Vehicles with Adaptive Cruise Control (ACC) are an example of a feature resulting in emergent traffic behavior when scaled [4]. While these utilities were designed with particular data use cases, data may be publicly shared to benefit other researchers through online tools like CyVerse [1]. However, such data should only be shared when any private information is removed. This private information may exist as a set of GPS coordinates, since the start and end points of a trip may designate a driver’s place of residence or work. When considering larger continuously-collected data sets with a focus on naturalistic driving, many drivers are needed to make data collection feasible. Removal of private information becomes much more of a challenge since every driver may uniquely define their geographic privacy. This project aims to build upon the foundation of libpanda [2] by adding features of edge-based data privacy enforcement. In it’s current form, libpanda uses a GPS in conjunction with a CAN interface to record data. Libpanda feature s a set of startup and shutdown scripts to perform automatic data collection and upload. With additional support hardware on a Raspberry Pi, the Pi can maintain power on vehicle shutdown to automatically upload data before shutdown.

Bunting, Matt↗
DOE OSTI2021

Deep active learning for classifying cancer pathology reports

Abstract Background Automated text classification has many important applications in the clinical setting; however, obtaining labelled data for training machine learning and deep learning models is often difficult and expensive. Active learning techniques may mitigate this challenge by reducing the amount of labelled data required to effectively train a model. In this study, we analyze the effectiveness of 11 active learning algorithms on classifying subsite and histology from cancer pathology reports using a Convolutional Neural Network as the text classification model. Results We compare the performance of each active learning strategy using two differently sized datasets and two different classification tasks. Our results show that on all tasks and dataset sizes, all active learning strategies except diversity-sampling strategies outperformed random sampling, i.e., no active learning. On our large dataset (15K initial labelled samples, adding 15K additional labelled samples each iteration of active learning), there was no clear winner between the different active learning strategies. On our small dataset (1K initial labelled samples, adding 1K additional labelled samples each iteration of active learning), marginal and ratio uncertainty sampling performed better than all other active learning techniques. We found that compared to random sampling, active learning strongly helps performance on rare classes by focusing on underrepresented classes. Conclusions Active learning can save annotation cost by helping human annotators efficiently and intelligently select which samples to label. Our results show that a dataset constructed using effective active learning techniques requires less than half the amount of labelled data to achieve the same performance as a dataset constructed using random sampling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evaluation of Nuclear Spent Fuel Disposal in Clay-Bearing Rock - Process Model Development and Experimental Studies

This report represents the milestone deliverable M2SF-23SN010301072 “Evaluation of Nuclear Spent Fuel Disposal in Clay-Bearing Rock - Process Model Development and Experimental Studies” The report provides a status update of FY23 activities for the work package Argillite Disposal work packages for the DOE-NE Spent Fuel Waste Form Science and Technology (SFWST) Program. Clay-rich geological media (often referred as shale or argillite) are among the most abundant type of sedimentary rock near the Earth’s surface. Argillaceous rock formations have the following advantageous attributes for deep geological nuclear waste disposal: widespread geologic occurrence, found in stable geologic settings, low permeability, self-sealing properties, low effective diffusion coefficient, high sorption capacity, and have the appropriate depth and thickness to host nuclear waste repository concepts. The DOE R&D program under the Spent Fuel Waste Science Technology (SFWST) campaign has made key progress (through experiment, modeling, and testing) in the study of chemical and physical phenomena that could impact the long-term safety assessment of heat-generating nuclear waste disposition in clay/shale/argillaceous rock. International collaboration activities comprising field-scale heater tests, field data monitoring, and laboratory-scale experiments provide key information on changes to the engineered barrier system (EBS) material exposed high thermal loads. Moreover, consideration of direct disposal of large capacity dual-purpose canisters (DPCs) as part of the back-end SNF waste disposition strategy has generated interest in improving our understanding of the effects of elevated temperatures on the engineered barrier system (EBS) design concepts. Chemical and structural analyses of sampled bentonite material from laboratory tests at elevated temperatures are key to the characterization of thermal effects affecting bentonite clay barrier performance. The knowledge provided by these experiments is crucial to constrain the extent of sacrificial zones in the EBS design during the thermal period. Thermal, hydrologic, mechanical, and chemical (THMC) data collected from heater tests and laboratory experiments have been used in the development, validation, and calibration of THMC simulators to model near-field coupled processes. This information leads to the development of simulation approaches to assess issues on coupled processes involving porous media flow, transport, geomechanical phenomena, chemical interactions with barrier/geologic materials, and the development of EBS concepts. These lines of knowledge are central to the design of deep geological backfilled repository concepts where temperature plays a key role in the EBS behavior, potential interactions with host rock, and long-term performance in the safety assessment.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Enhanced Resistance Pines for Improved Renewable Biofuel and Chemical Production (Technical Report)

We completed phenotyping constitutive and inducible oleoresin flow across two seasons, constitutive resin canal number and density and wood terpene content in our ADEPT2 and CCLONES populations. We completed genetic association between 19 oleoresin phenotypes and a total of 523,192 SNP markers from ADEPT2 and 13,883 SNP markers in CCLONES using four mixed linear models. A total of 293 significant SNPs (FDR = 0.20) were identified. We used the MENTOR tool to mine mechanistic connections from a multiplex network constructed from poplar multi-omic data to construct a conceptual model for a subset of these significant SNPs. Our model contains 6 transcriptional regulators in addition to 3 monoterpene synthases. To generate more lines of evidence for these significant SNPs, we completed a time course RNAseq experiment after inducing vascular zone cells to differentiate into new resin canals with a methyl jasmonate treatment, a single nuclei RNAseq that identified differentiating resin canal epithelial cells and are completing analysis for a QTL study in a hybrid pine population. The time course identified 4634 significantly down and 1890 significantly up regulated transcripts after treatment with methyl jasmonate, an inducer of new resin canal formation in the vascular cambial meristem. To analyze this large set of differentially regulated genes, we created a predictive expression network and analyzed it with random walk restart using 6 seed genes coding for transcription factors regulating xylem differentiation in poplar. Of the top ranked 200 transcripts, 119 transcripts were significant differentially expressed supporting these transcripts as potential candidates regulating resin canal formation. Analysis of single nuclei sequencing of shoot tips that contain differentiating resin canals, identified 10 clusters. One cluster was highly enriched in transcripts coding for 9 of the enzymes in the MEP pathway 3 prenyl synthetases, and 3 monoterpene synthases strongly suggesting that this cluster represents resin canal epithelial cells. We are mining the additional transcripts to create a trajectory analysis. In summary, we have identified > 10 novel genes that are strongly supported candidates for further analysis in breeding lines and for genetic engineering over- and under- expressing lines to increase wood terpene content to improve resistance to insect and fungal pathogens while simultaneously increasing terpene supplies for renewable chemicals and biofuels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Review of Grey Box/Black Box Data Contamination Metrics on Open and Commercial Models

Dataset contamination is a problem where benchmarks and tasks used to evaluate the capabilities of Large Language Models (LLMs) have been incorporated into the training dataset of the models. This gives a false sense of performance that can overestimate how these models will function on truly unseen data. This problem becomes worse with commercial LLMs with larger and non-accessible training data, so techniques have been developed to try to measure the degree to which a model is contaminated with a benchmark’s data. To understand the effectiveness of these techniques, particularly when evaluating contamination on coding tasks, we review trends and categorize techniques by the degree of access to the model that is required. The research literature on this topic has reported mixed effectiveness of these techniques, so we select a set of black box (text access only) and grey box (access to model loss/probabilities required) techniques and apply them to both commercial and non-commercial models. We implement these metrics as part of a framework to test the contamination of Python code in LLMs to see to what extent we can replicate the effectiveness (or ineffectiveness) of these contamination detection techniques. Though we find mixed results in the capabilities of these metrics to identify contamination, we do observe evidence that they can identify contamination (broadly) in fine-tuned models when both a baseline and fine-tuned model is present. Additionally, similarity metrics were able to identify between contaminated and uncontaminated data even in situations where the data is distributionally similar (e.g., drawn from the same set of code projects).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Probabilistic Data Association for Orbital-Element Estimation Using Multistage Expectation–Maximization

Tracking space objects is important for managing space traffic and predicting collisions, but is difficult in part due to data association and orbit model uncertainty. Expectation–maximization (EM) is a commonly used tracking method that has not been widely considered for tracking space objects. The technique consists of iteratively computing data association probabilities with a set of current element estimates, and updating estimates of the elements by solving a nonlinear weighted least-squares regression problem where the weights are the data association probabilities. In this paper, we demonstrate the use of EM for probabilistic data association and orbital-element estimation by applying the technique to simulated data from two angles-only tracking scenarios. In both scenarios, EM provides correct data associations and accurate maximum likelihood estimates of orbital elements. One scenario considers tracking a single object in clutter and quantifies the improvement of the orbital-element estimates and data associations as the detection probability increases. However, standard application of EM requires knowing the number of objects or may fail when a large number of objects are present. To address these issues, this paper employs a multistage version of EM that is applicable when there are a large and possibly unknown number of objects.

97 MATHEMATICS AND COMPUTING↗