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DOE OSTI2022

TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks

Background: With cancer as one of the leading causes of death worldwide, accurate primary tumor type prediction is critical in identifying genetic factors that can inhibit or slow tumor progression. There have been efforts to categorize primary tumor types with gene expression data using machine learning, and more recently with deep learning, in the last several years. Methods In this paper, we developed four 1-dimensional (1D) Convolutional Neural Network (CNN) models to classify RNA-seq count data as one of 17 highly represented primary tumor types or 32 primary tumor types regardless of imbalanced representation. Additionally, we adapted the models to take as input either all Ensembl genes (60,483) or protein coding genes only (19,758). Unlike previous work, we avoided selection bias by not filtering genes based on expression values. RNA-seq count data expressed as FPKM-UQ of 9,025 and 10,940 samples from The Cancer Genome Atlas (TCGA) were downloaded from the Genomic Data Commons (GDC) corresponding to 17 and 32 primary tumor types respectively for training and validating the models. Results: All 4 1D-CNN models had an overall accuracy of 94.7% to 97.6% on the test dataset. Further evaluation indicates that the models with protein coding genes only as features performed with better accuracy compared to the models with all Ensembl genes for both 17 and 32 primary tumor types. For all models, the accuracy by primary tumor type was above 80% for most primary tumor types. Conclusions: We packaged all 4 models as a Python-based deep learning classification tool called TULIP (TUmor CLassIfication Predictor) for performing quality control on primary tumor samples and characterizing cancer samples of unknown tumor type. Further optimization of the models is needed to improve the accuracy of certain primary tumor types.

Jones, Sara↗

DOE OSTI2025

AI in Astrophysics: Tackling Domain Shift, Model Robustness and Uncertainty

Artificial Intelligence (AI) is revolutionizing physics research from probing the large-scale structure of the Universe to modeling subatomic interactions and fundamental forces. Yet, a major challenge persists: AI models trained on simulations or old experiment / astronomical survey often perform poorly when applied to new data exposing issues of dataset (domain) shift, model robustness, and uncertainty in predictions. This talk will introduce common challenges in applying AI across domains and present solutions based on domain adaptation a set of techniques designed to improve model generalization under domain shift. We will cover foundational ideas, practical strategies, and current research frontiers in this area. Through examples in astrophysics, we'll explore how domain adaptation can help bridge the gap between synthetic and real-world data, improve trust in model outputs, and advance scientific discovery.

Ciprijanvoic, Aleksandra [Fermilab] (ORCID:0000000↗

DOE OSTI2022

Development of an open-source regional data assimilation system in PEcAn v. 1.7.2: application to carbon cycle reanalysis across the contiguous US using SIPNET

Abstract. The ability to monitor, understand, and predict the dynamics of the terrestrial carbon cycle requires the capacity to robustly and coherently synthesize multiple streams of information that each provide partial information about different pools and fluxes. In this study, we introduce a new terrestrial carbon cycle data assimilation system, built on the PEcAn model–data eco-informatics system, and its application for the development of a proof-of-concept carbon “reanalysis” product that harmonizes carbon pools (leaf, wood, soil) and fluxes (GPP, Ra, Rh, NEE) across the contiguous United States from 1986–2019. We first calibrated this system against plant trait and flux tower net ecosystem exchange (NEE) using a novel emulated hierarchical Bayesian approach. Next, we extended the Tobit–Wishart ensemble filter (TWEnF) state data assimilation (SDA) framework, a generalization of the common ensemble Kalman filter which accounts for censored data and provides a fully Bayesian estimate of model process error, to a regional-scale system with a calibrated localization. Combined with additional workflows for propagating parameter, initial condition, and driver uncertainty, this represents the most complete and robust uncertainty accounting available for terrestrial carbon models. Our initial reanalysis was run on an irregular grid of ∼ 500 points selected using a stratified sampling method to efficiently capture environmental heterogeneity. Remotely sensed observations of aboveground biomass (Landsat LandTrendr) and leaf area index (LAI) (MODIS MOD15) were sequentially assimilated into the SIPNET model. Reanalysis soil carbon, which was indirectly constrained based on modeled covariances, showed general agreement with SoilGrids, an independent soil carbon data product. Reanalysis NEE, which was constrained based on posterior ensemble weights, also showed good agreement with eddy flux tower NEE and reduced root mean square error (RMSE) compared to the calibrated forecast. Ultimately, PEcAn's new open-source regional data assimilation framework provides a scalable workflow for harmonizing multiple data constraints and providing a uniform synthetic platform for carbon monitoring, reporting, and verification (MRV) as well as accelerating terrestrial carbon cycle research.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Nonlinear Photovoltaic Degradation Rates: Modeling and Comparison Against Conventional Methods

Although common practice for estimating photovoltaic (PV) degradation rate (RD) assumes a linear behavior, field data have shown that degradation rates are frequently nonlinear. This article presents a new methodology to detect and calculate nonlinear RD based on PV performance time-series from nine different systems over an eight-year period. Prior to performing the analysis and in order to adjust model parameters to reflect actual PV operation, synthetic datasets were utilized for calibration purposes. A change-point analysis is then applied to detect changes in the slopes of PV trends, which are extracted from constructed performance ratio (PR) time-series. Once the number and location of change points is found, the ordinary least squares method is applied to the different segments to compute the corresponding rates. The obtained results verified that the extracted trends from the PR time-series may not always be linear and therefore, “nonconventional” models need to be applied. All thin-film technologies demonstrated nonlinear behavior whereas nonlinearity detected in the crystalline silicon systems is thought to be due to a maintenance event. A comparative analysis between the new methodology and other conventional methods demonstrated levelized cost of energy differences of up to 6.14%, highlighting the importance of considering nonlinear degradation behavior

14 SOLAR ENERGY↗

DOE OSTI2022

Evaluating the Impact of Proprietary Oil & Gas Data on Machine Learning Model Performance Using a Quasi-Experimental Analytical Approach

This study implements a data-intensive supervised ML approach through a quasi-experimental framework with the objective of quantifying the impact of oil and gas operator-specific proprietary data on ML-based predictive model performance relative to using oil and gas datasets that may be more commonly publicly available. The models are designed to jointly predict daily oil, gas, and water production for horizontal wells as a function of bottom-hole pressure drawdown, spatial placement across the study domain, and well completion attributes. Model performance is quantified on holdout test data to evaluate how each dataset affects resulting model variant performance.

02 PETROLEUM↗

NASA NTRS1994

Dust extinction of the stellar continua in starburst galaxies: The ultraviolet and optical extinction law

We analyze the International Ultraviolet Explorer (IUE) UV and the optical spectra of 39 starburst and blue compact galaxies in order to study the average properties of dust extinction in extended regions of galaxies. The optical spectra have been obtained using an aperture which matches that of IUE, so comparable regions within each galaxy are sampled. The data from the 39 galaxies are compared with five models for the geometrical distribution of dust, adopting as extinction laws both the Milky Way and the Large Magellanic Cloud laws. The commonly used uniform dust screen is included among the models. We find that none of the five models is in satisfactory agreement with the data. In order to understand the discrepancy between the data and the models, we have derived an extinction law directly from the data in the UV and optical wavelength range. The resulting curve is characterized by an overall slope which is more gray than the Milky Way extinction law's slope, and by the absence of the 2175 A dust feature. Remarkably, the difference in optical depth between the Balmer emission lines H(sub alpha) and H(sub beta) is about a factor of 2 larger than the difference in the optical depth between the continuum underlying the two Balmer lines. We interpret this discrepancy as a consequence of the fact that the hot ionizing stars are associated with dustier regions than the cold stellar population is. The absence of the 2175 A dust feature can be due either to the effects of the scattering and clumpiness of the dust or to a chemical composition different from that of the Milky Way dust grains. Disentangling the two interpretations is not easy because of the complexity of the spatial distribution of the emitting regions. The extinction law of the UV and optical spectral continua of extended regions can be applied to the spectra of medium- and high-redshift galaxies, where extended regions of a galaxy are, by necessity, sampled.

Calzetti, Daniela↗

DOE OSTI2023

Exact Gaussian processes for massive datasets via non-stationary sparsity-discovering kernels

Abstract A Gaussian Process (GP) is a prominent mathematical framework for stochastic function approximation in science and engineering applications. Its success is largely attributed to the GP’s analytical tractability, robustness, and natural inclusion of uncertainty quantification. Unfortunately, the use of exact GPs is prohibitively expensive for large datasets due to their unfavorable numerical complexity of $$O(N^3)$$ O ( N 3 ) in computation and $$O(N^2)$$ O ( N 2 ) in storage. All existing methods addressing this issue utilize some form of approximation—usually considering subsets of the full dataset or finding representative pseudo-points that render the covariance matrix well-structured and sparse. These approximate methods can lead to inaccuracies in function approximations and often limit the user’s flexibility in designing expressive kernels. Instead of inducing sparsity via data-point geometry and structure, we propose to take advantage of naturally-occurring sparsity by allowing the kernel to discover—instead of induce—sparse structure. The premise of this paper is that the data sets and physical processes modeled by GPs often exhibit natural or implicit sparsities, but commonly-used kernels do not allow us to exploit such sparsity. The core concept of exact, and at the same time sparse GPs relies on kernel definitions that provide enough flexibility to learn and encode not only non-zero but also zero covariances. This principle of ultra-flexible, compactly-supported, and non-stationary kernels, combined with HPC and constrained optimization, lets us scale exact GPs well beyond 5 million data points.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2004

Pulsed Lidar Performance/Technical Maturity Assessment

This report describes the results of investigations performed by the Georgia Tech Research Institute (GTRI) and the National Center for Atmospheric Research (NCAR) under a task entitled 'Pulsed Lidar Performance/Technical Maturity Assessment' funded by the Crew Systems Branch of the Airborne Systems Competency at the NASA Langley Research Center. The investigations included two tasks, 1.1(a) and 1.1(b). The Tasks discussed in this report are in support of the NASA Virtual Airspace Modeling and Simulation (VAMS) program and are designed to evaluate a pulsed lidar that will be required for active wake vortex avoidance solutions. The Coherent Technologies, Inc. (CTI) WindTracer LIDAR is an eye-safe, 2-micron, coherent, pulsed Doppler lidar with wake tracking capability. The actual performance of the WindTracer system was to be quantified. In addition, the sensor performance has been assessed and modeled, and the models have been included in simulation efforts. The WindTracer LIDAR was purchased by the Federal Aviation Administration (FAA) for use in near-term field data collection efforts as part of a joint NASA/FAA wake vortex research program. In the joint research program, a minimum common wake and weather data collection platform will be defined. NASA Langley will use the field data to support wake model development and operational concept investigation in support of the VAMS project, where the ultimate goal is to improve airport capacity and safety. Task 1.1(a), performed by NCAR in Boulder, Colorado to analyze the lidar system to determine its performance and capabilities based on results from simulated lidar data with analytic wake vortex models provided by NASA, which were then compared to the vendor's claims for the operational specifications of the lidar. Task 1.1(a) is described in Section 3, including the vortex model, lidar parameters and simulations, and results for both detection and tracking of wake vortices generated by Boeing 737s and 747s. Task 1.1(b) was performed by GTRI in Atlanta, Georgia and is described in Section 4. Task 1.1(b) includes a description of the St. Louis Airport (STL) field test being conducted by the Volpe National Transportation Systems Center, and it also addresses the development of a test plan to validate simulation studies conducted as part of Task 1.1(a). Section 4.2 provides a description of the Volpe STL field tests, and Section 4.3 describes 3 possible ways to validate the WindTracer lidar simulations performed in Task 1.1(a).

Gimmestad, Gary G.↗

NASA NTRS2017

Biogeochemical Protocols and Diagnostics for the CMIP6 Ocean Model Intercomparison Project (OMIP)

The Ocean Model Intercomparison Project (OMIP) focuses on the physics and biogeochemistry of the ocean component of Earth system models participating in the sixth phase of the Coupled Model Intercomparison Project (CMIP6). OMIP aims to provide standard protocols and diagnostics for ocean models, while offering a forum to promote their common assessment and improvement. It also offers to compare solutions of the same ocean models when forced with reanalysis data (OMIP simulations) vs. when integrated within fully coupled Earth system models (CMIP6). Here we detail simulation protocols and diagnostics for OMIP's biogeochemical and inert chemical tracers. These passive-tracer simulations will be coupled to ocean circulation models, initialized with observational data or output from a model spin-up, and forced by repeating the 1948-2009 surface fluxes of heat, fresh water, and momentum. These so-called OMIP-BGC simulations include three inert chemical tracers (CFC-11, CFC-12, SF [subscript] 6) and biogeochemical tracers (e.g., dissolved inorganic carbon, carbon isotopes, alkalinity, nutrients, and oxygen). Modelers will use their preferred prognostic BGC model but should follow common guidelines for gas exchange and carbonate chemistry. Simulations include both natural and total carbon tracers. The required forced simulation (omip1) will be initialized with gridded observational climatologies. An optional forced simulation (omip1-spunup) will be initialized instead with BGC fields from a long model spin-up, preferably for 2000 years or more, and forced by repeating the same 62-year meteorological forcing. That optional run will also include abiotic tracers of total dissolved inorganic carbon and radiocarbon, CTabio and 14CTabio, to assess deep-ocean ventilation and distinguish the role of physics vs. biology. These simulations will be forced by observed atmospheric histories of the three inert gases and CO2 as well as carbon isotope ratios of CO2. OMIP-BGC simulation protocols are founded on those from previous phases of the Ocean Carbon-Cycle Model Intercomparison Project. They have been merged and updated to reflect improvements concerning gas exchange, carbonate chemistry, and new data for initial conditions and atmospheric gas histories. Code is provided to facilitate their implementation.

Carbon↗

NASA NTRS2016

The Model Intercomparison Project on the Climatic Response to Volcanic Forcing (VolMIP): Experimental Design and Forcing Input Data for CMIP6

The enhancement of the stratospheric aerosol layer by volcanic eruptions induces a complex set of responses causing global and regional climate effects on a broad range of timescales. Uncertainties exist regarding the climatic response to strong volcanic forcing identified in coupled climate simulations that contributed to the fifth phase of the Coupled Model Intercomparison Project (CMIP5). In order to better understand the sources of these model diversities, the Model Intercomparison Project on the climatic response to Volcanic forcing (VolMIP) has defined a coordinated set of idealized volcanic perturbation experiments to be carried out in alignment with the CMIP6 protocol. VolMIP provides a common stratospheric aerosol data set for each experiment to minimize differences in the applied volcanic forcing. It defines a set of initial conditions to assess how internal climate variability contributes to determining the response. VolMIP will assess to what extent volcanically forced responses of the coupled ocean-atmosphere system are robustly simulated by state-of-the-art coupled climate models and identify the causes that limit robust simulated behavior, especially differences in the treatment of physical processes. This paper illustrates the design of the idealized volcanic perturbation experiments in the VolMIP protocol and describes the common aerosol forcing input data sets to be used.

Volcanoes↗

DOE OSTI2024

Collective excitations and low-energy ionization signatures of relativistic particles in silicon detectors

Abstract Solid-state detectors with a low energy threshold have several applications, including searches of non-relativistic halo dark-matter particles with sub-GeV masses. When searching for relativistic, beyond-the-Standard-Model particles with enhanced cross sections for small energy transfers, a small detector with a low energy threshold may have better sensitivity than a larger detector with a higher energy threshold. In this paper, we calculate the low-energy ionization spectrum from high-velocity particles scattering in a dielectric material. We consider the full material response including the excitation of bulk plasmons. We generalize the energy-loss function to relativistic kinematics, and benchmark existing tools used for halo dark-matter scattering against electron energy-loss spectroscopy data. Compared to calculations commonly used in the literature, such as the Photo-Absorption-Ionization model or the free-electron model, including collective effects shifts the recoil ionization spectrum towards higher energies, typically peaking around 4–6 electron-hole pairs. We apply our results to the three benchmark examples: millicharged particles produced in a beam, neutrinos with a magnetic dipole moment produced in a reactor, and upscattered dark-matter particles. Our results show that the proper inclusion of collective effects typically enhances a detector’s sensitivity to these particles, since detector backgrounds, such as dark counts, peak at lower energies.

Physics↗

DOE OSTI2024

Resource Assessment for Distributed Wind Energy: An Evaluation of Best-Practice Methods in the Continental US

Current wind resources within the United States (US) indicate a potential to profitably install nearly 1,400 gigawatts of distributed wind (DW) capacity. This amount is equivalent to over half of the United States’ current energy demand from electricity, making it enough to power millions of homes and businesses and replace countless fossil fuel-based generating plants. Despite the potential growth of DW in the US, deployments are presently hindered by a lack of confidence in resource estimation methods. One potential challenge is that smaller-scale turbines, with hub heights of 40 meters or less, are disproportionately impacted by obstacles such as buildings and vegetation. These obstacles may produce complex wake effects, best modeled with high-fidelity complex fluid dynamics (CFD) models that are too computationally expensive to use for routine siting and resource assessment. Thus, installers today make use of heuristics and simple equations to approximate the impact of obstacles while also leveraging long-term resource data from commercial or publicly available atmospheric models. This study evaluates these historical and commonly used methods alongside new lower-order obstacle models produced from CFD simulations and measurement-based bias correction. The preliminary results from this study show the importance of taking care in the choice and application of mesoscale atmospheric models and the significant value of bias correction using measurements from nearby meteorological towers. Detailed obstacle modeling provides only modest additional gains in performance and, in some cases, can add error, especially at sites where turbines have already been located to avoid obvious impact from upwind obstacles. These findings reinforce the importance of collecting in situ measurements and suggest that obstacle models may be better applied in practice to automated or computer-aided siting, rather than in economic wind resource assessments.

17 WIND ENERGY↗

DOE OSTI2025

Measurement of event shapes in minimum-bias events from proton-proton collisions at $\sqrt{s}$ = 13

A measurement of event-shape variables is presented, using a data sample produced in a special run with approximately one inelastic proton-proton collision per bunch crossing. The data were collected with the CMS detector at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 64 μ⁢b −1 . A number of observables related to the overall distribution of charged particles in the collisions are corrected for detector effects and compared with simulations. Inclusive event-shape distributions, as well as differential distributions of event shapes as functions of charged-particle multiplicity, are studied. None of the models investigated are able to satisfactorily describe the data. Moreover, there are significant features common amongst all generator setups studied, particularly showing data being more isotropic than any of the simulations. Multidimensional unfolded distributions are provided, along with their correlations.

Chekhovsky, V. [Yerevan Physics Institute]↗

DOE OSTI2020

Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics

Limited therapy options due to antibiotic resistance underscore the need for optimization of current diagnostics. In some bacterial species, antimicrobial resistance can be unambiguously predicted based on their genome sequence. In this study, we sequenced the genomes and transcriptomes of 414 drug-resistant clinical Pseudomonas aeruginosa isolates. By training machine learning classifiers on information about the presence or absence of genes, their sequence variation, and expression profiles, we generated predictive models and identified biomarkers of resistance to four commonly administered antimicrobial drugs. Using these data types alone or in combination resulted in high (0.8–0.9) or very high (> 0.9) sensitivity and predictive values. For all drugs except for ciprofloxacin, gene expression information improved diagnostic performance. Our results pave the way for the development of a molecular resistance profiling tool that reliably predicts antimicrobial susceptibility based on genomic and transcriptomic markers. Finally, the implementation of a molecular susceptibility test system in routine microbiology diagnostics holds promise to provide earlier and more detailed information on antibiotic resistance profiles of bacterial pathogens and thus could change how physicians treat bacterial infections.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Measuring Intelligence with the Sandia Matrices: Psychometric Review and Recommendations for Free Raven-Like Item Sets

The Sandia Matrices are a free alternative to the Raven’s Progressive Matrices (RPMs). This study offers a psychometric review of Sandia Matrices items focused on two of the most commonly investigated issues regarding the RPMs: (a) dimensionality and (b) sex differences. Model-data fit of three alternative factor structures are compared using confirmatory multidimensional item response theory (IRT) analyses, and measurement equivalence analyses are conducted to evaluate potential sex bias. Although results are somewhat inconclusive regarding factor structure, results do not show evidence of bias or mean differences by sex. Finally, although the Sandia Matrices software can generate infinite items, editing and validating items may be infeasible for many researchers. Further, to aide implementation of the Sandia Matrices, we provide scoring materials for two brief static tests and a computer adaptive test. Implications and suggestions for future research using the Sandia Matrices are discussed.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1972

A dynamic response and eye scanning data base useful in the development of theories and methods for the description of control/display relationships

A set of specially prepared digital tapes is reported which contain synchronized measurements of pilot scanning behavior, control response, and vehicle response obtained during instrument landing system approaches made in a fixed-base DC-8 transport simulator. The objective of the master tape is to provide a common data base which can be used by the research community to test theories, models, and methods for describing and analyzing control/display relations and interactions. The experimental conditions and tasks used to obtain the data and the detailed format of the tapes are described. Conventional instrument panel and controls were used, with simulated vertical gust and glide slope beam bend forcing functions. Continuous pilot eye fixations and scan traffic on the panel were measured. Both flight director and standard localizer/glide slope types of approaches were made, with both fixed and variable instrument range sensitivities.

Klein, R.↗

NASA NTRS2013

Psychoacoustic Analysis of Synthesized Jet Noise

An aircraft noise synthesis capability is being developed so the annoyance caused by proposed aircraft can be assessed during the design stage. To make synthesized signals as realistic as possible, high fidelity simulation is required for source (e.g., engine noise, airframe noise), propagation and receiver effects. This psychoacoustic study tests whether the jet noise component of synthesized aircraft engine noise can be made more realistic using a low frequency oscillator (LFO) technique to simulate fluctuations in level observed in recordings. Jet noise predictions are commonly made in the frequency domain based on models of time-averaged empirical data. The synthesis process involves conversion of the frequency domain prediction into an audible pressure time history. However, because the predictions are time-invariant, the synthesized sound lacks fluctuations observed in recordings. Such fluctuations are hypothesized to be perceptually important. To introduce time-varying characteristics into jet noise synthesis, a method has been developed that modulates measured or predicted 1/3-octave band levels with a (<20Hz) LFO. The LFO characteristics are determined through analysis of laboratory jet noise recordings. For the aft emission angle, results indicate that signals synthesized using a generic LFO are perceived as more similar to recordings than those using no LFO, and signals synthesized with an angle-specific LFO are more similar to recordings than those synthesized with a generic LFO.

Okcu, Selen↗

DOE OSTI2021

Artificial Intelligence for Data Center Operations (AI Ops)

HPC data centers such as the one at NREL's ESIF will increasingly need to rely on automation to keep pace with exascale growth in compute capability and to manage and optimize the data center environment and facility resources. Artificial intelligence (AI) and machine learning (ML) approaches provide the means to improve HPC data center efficiency (energy, operational, and managerial efficiency) and resiliency by learning historical trends and training models to operate on real-time data collected from both IT and facilities sources. The goal of coupled improvement of data center resiliency and energy efficiency through automated data collection and AI has led to a multi-year, multi-staged collaboration between NREL and Hewlett-Packard Enterprise's Advanced Technology Group, referred to as Artificial Intelligence for Data Center Operations (AIOps). The extended efforts within the AIOps project include a common goal of building capabilities for an advanced smart facility and demonstration of data collection and AI modeling techniques in the ESIF data center.

97 MATHEMATICS AND COMPUTING↗