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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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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Classification of bacterial plasmid and chromosome derived sequences using machine learning

Plasmids are important genetic elements that facilitate horizonal gene transfer between bacteria and contribute to the spread of virulence and antimicrobial resistance. Most bacterial genome sequences in the public archives exist in draft form with many contigs, making it difficult to determine if a contig is of chromosomal or plasmid origin. Using a training set of contigs comprising 10,584 chromosomes and 10,654 plasmids from the PATRIC database, we evaluated several machine learning models including random forest, logistic regression, XGBoost, and a neural network for their ability to classify chromosomal and plasmid sequences using nucleotide k-mers as features. Based on the methods tested, a neural network model that used nucleotide 6-mers as features that was trained on randomly selected chromosomal and plasmid subsequences 5kb in length achieved the best performance, outperforming existing out-of-the-box methods, with an average accuracy of 89.38% ± 2.16% over a 10-fold cross validation. The model accuracy can be improved to 92.08% by using a voting strategy when classifying holdout sequences. In both plasmids and chromosomes, subsequences encoding functions involved in horizontal gene transfer—including hypothetical proteins, transporters, phage, mobile elements, and CRISPR elements—were most likely to be misclassified by the model. This study provides a straightforward approach for identifying plasmid-encoding sequences in short read assemblies without the need for sequence alignment-based tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Gray-Box Modeling for Distribution Systems With Inverter-Based Resources: Integrating Physics-Based and Data-Driven Approaches

Here, in this paper, we develop a novel gray-box modeling approach for distribution systems with inverter-based resources (IBRs). The proposed gray-box modeling method aims to improve estimation accuracy by taking advantages of both physics-based (white-box) and data-driven (black-box) modeling approaches. To this end, we utilize partial physical knowledge of the system, including the inverters’ structures and control diagrams, as well as the equivalent network model simplified through Kron reduction. The white-box model containing unknown parameters is then constructed with mathematical equations and an optimization-based method is subsequently employed to identify these unknown parameters within the white-box model. Next, the graybox modeling framework is then constructed by embedding the output variables of the white-box model into the input vector of a black-box model (represented using a neural network). Finally, the black-box section is trained using the collected input-output datasets and the gray-box model is then obtained. Furthermore, case studies demonstrate that our gray-box modeling approach effectively improves estimation accuracy compared to purely physics-based or data-driven methods.

42 ENGINEERING↗
DOE OSTI2021

Surrogate Model of Flexible Research Platform EnergyPlus Models to Enable Sensitivity Analysis

This letter report describes the surrogate models developed from the EnergyPlus model of Oak Ridge National Laboratory’s Flexible Research Platform. Two data-driven black-box models were developed, and the outputs of the surrogate models were compared with the EnergyPlus model. The two models developed are a multilayer perceptron deep learning model, and a long short-term memory (LSTM) neural network model. The three factors for selecting the black-box models are scalability, computation time, and accuracy. A total of 107 input variables were the dominant variables in determining the outputs of building energy consumptions and thermal comfort. A total of 54 output variables were identified as the prediction targets, including the system- and zone-level outputs. The large set of the simulation cases were generated by integrating sensor errors into an emulator based on EnergyPlus and Python EMS, which includes advanced control sequences from ASHRAE Guideline 36-2018: High-Performance Sequences of Operation. The surrogate models were developed based on a set of large-scale simulation runs (i.e., 4,000 runs) on a cloud platform. The comparison analysis shows that the two black-box models had good accuracy for predicting new outputs for sensitivity analysis using the root mean square error metric. As a next step, the developed surrogate models will be used to perform sensitivity analysis for different sensor impacts (e.g., sensor types, sensor locations).

42 ENGINEERING↗
DOE OSTI2022

1D Modeling for the Development of a Digital Twin for Hydropower Systems with Applications for a Testing Rig

Modeling and simulation constitute two important parts in constructing a sensible digital twin to mimic the dynamics of hydropower systems. Because of the physical nature of a hydropower system, the basic modeling should cover the water flow systems from the reservoir to the penstock (inlet water pipes), penstock to hydro turbine, and hydro turbine to generator and from the linkage of the hydropower systems to the grid. This report describes initial attempts to model these dynamic components, including the formulation of the linearized state space model for hydro turbine systems using the well-known six-coefficients linearization method and the formulation of the voltage and power dynamical models of a synchronous generator. To validate the accuracy of the proposed model, data collected from Norwegian University of Science and Technology were used to obtain relevant parameters for the model, and the desired simulation results were obtained. Additionally, neural network modeling and learning were also developed and applied to model the generation torque and water flow rate subsystems to demonstrate a potential learning scheme, which can be used in the development of a digital twin.

13 HYDRO ENERGY↗
DOE OSTI2020

Estimating vehicle fuel economy from overhead camera imagery and application for traffic control

In this work, we explore the ability to estimate vehicle fuel consumption using imagery from overhead fisheye lens cameras deployed as traffic sensors. We utilize this information to simulate vision-based control of a traffic intersection, with a goal of improving fuel economy with minimal impact to mobility. We introduce the ORNL Overhead Vehicle Dataset (OOVD), consisting of a data set of paired, labeled vehicle images from a ground-based camera and an overhead fisheye lens traffic camera. The data set includes segmentation masks based on Gaussian mixture models for vehicle detection. We show the dataset utility through three applications: the estimate of fuel consumption based on segmentation bounding boxes, vehicle discrimination for those vehicles with largest bounding boxes, and a fine-grained classification on a limited number of vehicle makes and models using a pre-trained set of convolutional neural network models. We compare these results with estimates based on a large open-source data set based on web-scraped imagery. Finally, we show the utility of the approach using reinforcement learning in a traffic simulator using the open source Simulation of Urban Mobility (SUMO) package. Our results show the feasibility of the approach for controlling traffic lights for better fuel efficiency based solely on visual vehicle estimates from commercial, fisheye lens cameras.

Karnowski, Thomas↗
DOE OSTI2021

CyBERT: Cybersecurity Claim Classification by Fine-Tuning the BERT Language Model

We introduce CyBERT, a cybersecurity feature claims classifier based on bidirectional encoder representations from transformers and a key component in our semi-automated cybersecurity vetting for industrial control systems (ICS). To train CyBERT, we created a corpus of labeled sequences from ICS device documentation collected across a wide range of vendors and devices. This corpus provides the foundation for fine-tuning BERT’s language model, including a prediction-guided relabeling process. We propose an approach to obtain optimal hyperparameters, including the learning rate, the number of dense layers, and their configuration, to increase the accuracy of our classifier. Fine-tuning all hyperparameters of the resulting model led to an increase in classification accuracy from 76% obtained with BertForSequenceClassification’s original architecture to 94.4% obtained with CyBERT. Furthermore, we evaluated CyBERT for the impact of randomness in the initialization, training, and data-sampling phases. CyBERT demonstrated a standard deviation of ±0.6% during validation across 100 random seed values. Finally, we also compared the performance of CyBERT to other well-established language models including GPT2, ULMFiT, and ELMo, as well as neural network models such as CNN, LSTM, and BiLSTM. The results showed that CyBERT outperforms these models on the validation accuracy and the F1 score, validating CyBERT’s robustness and accuracy as a cybersecurity feature claims classifier.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1999

Thermal Analysis of the X-38 Aft Fin During Re-Entry

This document contains the details of the thermal analysis of the X-38 aft fin during re-entry. This analysis was performed in order to calculate temperature response of the aft fin components. This would be provided as input to a structural analysis and would also define the operating environment for the electromechanical actuator (EMA). The calculated structural temperature response would verify the performance of the thermal protection system (TPS). The geometric representation of the aft fin was derived from an I-DEAS finite element model that was used for structural analysis. The thermal mass network model was derived from the geometric representation.

Hong, Andrew E.↗
DOE OSTI2018

Reinforced dynamics for enhanced sampling in large atomic and molecular systems

A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this new approach. Like metadynamics, it allows for an efficient exploration of the configuration space by adding an adaptively computed biasing potential to the original dynamics. Like deep reinforcement learning, this biasing potential is trained on the fly using deep neural networks, with data collected judiciously from the exploration and an uncertainty indicator from the neural network model playing the role of the reward function. Parameterization using neural networks makes it feasible to handle cases with a large set of collective variables. This has the potential advantage that selecting precisely the right set of collective variables has now become less critical for capturing the structural transformations of the system. Finally, the method is illustrated by studying the full-atom explicit solvent models of alanine dipeptide and tripeptide, as well as the system of a polyalanine-10 molecule with 20 collective variables.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning

Accurately predicting small molecule partitioning and hydrophobicity is critical in the drug discovery process. There are many heterogeneous chemical environments within a cell and entire human body. For example, drugs must be able to cross the hydrophobic cellular membrane to reach their intracellular targets, and hydrophobicity is an important driving force for drug–protein binding. Atomistic molecular dynamics (MD) simulations are routinely used to calculate free energies of small molecules binding to proteins, crossing lipid membranes, and solvation but are computationally expensive. Machine learning (ML) and empirical methods are also used throughout drug discovery but rely on experimental data, limiting the domain of applicability. We present atomistic MD simulations calculating 15,000 small molecule free energies of transfer from water to cyclohexane. This large data set is used to train ML models that predict the free energies of transfer. We show that a spatial graph neural network model achieves the highest accuracy, followed closely by a 3D-convolutional neural network, and shallow learning based on the chemical fingerprint is significantly less accurate. A mean absolute error of ~4 kJ/mol compared to the MD calculations was achieved for our best ML model. We also show that including data from the MD simulation improves the predictions, tests the transferability of each model to a diverse set of molecules, and show multitask learning improves the predictions. This work provides insight into the hydrophobicity of small molecules and ML cheminformatics modeling, and our data set will be useful for designing and testing future ML cheminformatics methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A Parallel Alternative for Energy-Efficient Neural Network Training and Inferencing

Energy efficiency of training and inferencing with large neural network models is a critical challenge facing the future of sustainable large-scale machine learning workloads. This paper introduces an alternative strategy, called phantom parallelism, to minimize the net energy consumption of traditional tensor (model) parallelism, the most energy-inefficient component of large neural network training. The approach is presented in the context of feed-forward network architectures as a preliminary, but comprehensive, proof-of-principle study of the proposed methodology. We derive new forward and backward propagation operators for phantom parallelism, implement them as custom autograd operations within an end-to-end phantom parallel training pipeline and compare its parallel performance and energy-efficiency against those of conventional tensor parallel training pipelines. Formal analyses that predict lower bandwidth and FLOP counts are presented with supporting empirical results on up to 256 GPUs that corroborate these gains. Experiments are shown to deliver ∼50% reduction in the energy consumed to train FFNs using the proposed phantom parallel approach when compared with conventional tensor parallel methods. Additionally, the proposed approach is shown to train smaller phantom models to the same model loss on smaller GPU counts as larger tensor parallel models on larger GPU counts offering the possibility for even greater energy savings.

Seal, Sudip [ORNL] (ORCID:0000000332330656)↗
DOE OSTI2020

Stress effects on flow and transport in three-dimensional fracture networks

We investigate the effects of various external stress regimes on fracture apertures, fluid flow, and solute transport in three-dimensional fracture networks. We use well-established geomechanics equations coupled with discrete fracture network modeling to characterize changes in primary flow paths within a complex network as a function of stress magnitude and orientation. These changes manifest in the alterations of the fluid flow field and are measured in terms of Eulerian and Lagrangian flow observables including solute transport, which is a key problem in many hydrologic applications. Changes in primary flow paths affect the solute transport in the network by promoting anomalously early arrival or long tailing behavior. However, early time arrival is not ubiquitous in anisotropically stressed networks and in most cases there is a delayed arrival of solute, which is attributed to (i) the presence of low-velocity zones normal to the flow direction, (ii) the angle between flow direction and major compressive principal stress directions, and (iii) changes in the primary flow paths (i.e., increases in tortuosity and active network structure). Overall, flows become more channelized in anisotropically stressed fracture networks than in unstressed and isotropically stressed networks.

58 GEOSCIENCES↗
DOE OSTI2023

Gene loss during a transition to multicellularity

Multicellular evolution is a major transition associated with momentous diversification of multiple lineages and increased developmental complexity. The volvocine algae comprise a valuable system for the study of this transition, as they span from unicellular to undifferentiated and differentiated multicellular morphologies despite their genomes being similar, suggesting multicellular evolution requires few genetic changes to undergo dramatic shifts in developmental complexity. Here, the evolutionary dynamics of six volvocine genomes were examined, where a gradual loss of genes was observed in parallel to the co-option of a few key genes. Protein complexes in the six species exhibited novel interactions, suggesting that gene loss could play a role in evolutionary novelty. This finding was supported by gene network modeling, where gene loss outpaces gene gain in generating novel stable network states. These results suggest gene loss, in addition to gene gain and co-option, may be important for the evolution developmental complexity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Entanglement phase transitions in random stabilizer tensor networks

Here we explore a class of random tensor network models with “stabilizer” local tensors which we name random stabilizer tensor networks (RSTNs). For RSTNs defined on a two-dimensional square lattice, we perform extensive numerical studies of entanglement phase transitions between volume-law and area-law entangled phases of the one-dimensional boundary states. These transitions occur when either (a) the bond dimension D of the constituent tensors is varied or (b) the tensor network is subject to random breaking of bulk bonds, implemented by forced measurements. In the absence of broken bonds, we find that the RSTN supports a volume-law entangled boundary state with bond dimension D ≥ 3 where D is a prime number, and an area-law entangled boundary state for D = 2. Upon breaking bonds at random in the bulk with probability p, there exists a critical measurement rate p c for each D ≥ 3 above which the boundary state becomes area-law entangled. To explore the conformal invariance at these entanglement transitions for different prime D, we consider tensor networks on a finite rectangular geometry with a variety of boundary conditions, and extract universal operator scaling dimensions via extensive numerical calculations of the entanglement entropy, mutual information, and mutual negativity at their respective critical points. Our results at large D approach known universal data of percolation conformal field theory, while showing clear discrepancies at smaller D, suggesting a distinct entanglement transition universality class for each prime D. We further study universal entanglement properties in the volume-law phase and demonstrate quantitative agreement with the recently proposed description in terms of a directed polymer in a random environment.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Gene network analysis of poplar root transcriptome in response to drought stress identifies a PtaJAZ3PtaRAP2.6-centered hierarchical network

Using time-series transcriptomic data from poplar roots undergoing polyethylene glycol (PEG)-induced drought stress, we built a genetic network model of the involved putative molecular responses. We found that the network resembled a hierarchical structure. The highest hierarchical level in this structure is occupied by 9 genes, which we called superhubs because they were primarily connected to 18 hub genes, which are then connected to 2,934 terminal genes. We were only able to regenerate transgenic plants overexpressing two of the superhubs, suggesting that the majority of the superhubs might interfere with the regeneration process and did not allow recovery of transgenic plants. The two superhubs encode proteins with closest homology to JAZ3 and RAP2.6 genes of Arabidopsis and were consequently named PtaJAZ3 and PtaRAP2.6. PtaJAZ3 and PtaRAP2.6 overexpressing transgenic lines showed a significant increase in both root elongation and lateral root proliferation and these responses were specific for the drought stress conditions and were highly correlated with the levels of overexpression of the transgenes. Several lines of evidence suggest of regulatory interactions between the two superhubs. Both superhubs were significantly induced by methyl jasmonate (MeJA). Because jasmonate signaling involves ubiquitin-mediated proteasome degradation, treatment with proteasome inhibitor abolished the MeJA induction for both genes. PtaRAP2.6 was upregulated in PtaJAZ3 transgenics but PtaJAZ3 expression was not affected in the PtaRAP2.6 overexpressors. The discovery of the two genes and further future insights into the associated mechanisms can lead to improved understanding and novel approaches to regulate root architecture in relation to drought stress.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1990

Satellite image analysis using neural networks

The tremendous backlog of unanalyzed satellite data necessitates the development of improved methods for data cataloging and analysis. Ford Aerospace has developed an image analysis system, SIANN (Satellite Image Analysis using Neural Networks) that integrates the technologies necessary to satisfy NASA's science data analysis requirements for the next generation of satellites. SIANN will enable scientists to train a neural network to recognize image data containing scenes of interest and then rapidly search data archives for all such images. The approach combines conventional image processing technology with recent advances in neural networks to provide improved classification capabilities. SIANN allows users to proceed through a four step process of image classification: filtering and enhancement, creation of neural network training data via application of feature extraction algorithms, configuring and training a neural network model, and classification of images by application of the trained neural network. A prototype experimentation testbed was completed and applied to climatological data.

Sheldon, Roger A.↗
DOE OSTI2017

Beyond Fine Tuning: Adding capacity to leverage few labels

In this paper we present a technique to train neural network models on small amounts of data. Current methods for training neural networks on small amounts of rich data typically rely on strategies such as fine-tuning a pre-trained neural networks or the use of domain-specific hand-engineered features. Here we take the approach of treating network layers, or entire networks, as modules and combine pre-trained modules with untrained modules, to learn the shift in distributions between data sets. The central impact of using a modular approach comes from adding new representations to a network, as opposed to replacing representations via fine-tuning. Using this technique, we are able surpass results using standard fine-tuning transfer learning approaches, and we are also able to significantly increase performance over such approaches when using smaller amounts of data.

data science↗
DOE OSTI2018

Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints

Abstract Background Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cycles (TICs) causing unbounded metabolic flux ranges are often encountered. TICs satisfy the mass balance and directionality constraints but violate the second law of thermodynamics. Current practices involve implementing additional constraints to ensure not only optimal but also loopless flux distributions. However, the mixed integer linear programming problems required to solve become computationally intractable for genome-scale metabolic models. Results We aimed to identify the fewest needed constraints sufficient for optimality under the loopless requirement. We found that loopless constraints are required only for the reactions that share elementary flux modes representing TICs with reactions that are part of the objective function. We put forth the concept of localized loopless constraints (LLCs) to enforce this minimal required set of loopless constraints. By combining with a novel procedure for minimal null-space calculation, the computational time for loopless flux variability analysis (ll-FVA) is reduced by a factor of 10–150 compared to the original loopless constraints and by 4–20 times compared to the current fastest method Fast-SNP with the percent improvement increasing with model size. Importantly, LLCs offer a scalable strategy for loopless flux calculations for multi-compartment/multi-organism models of large sizes, for example, shortening the CPU time for ll-FVA from 35 h to less than 2 h for a model with more than104 reactions. Availability and implementation Matlab functions are available in the Supplementary Material or at https://github.com/maranasgroup/lll-FVA Supplementary information Supplementary data are available at Bioinformatics online.

Chan, Siu H. J. (ORCID:000000027707656X)↗
NASA NTRS1988

Performance modeling and measurement of real-time multiprocessors with time-shared buses

A closed queueing network model is constructed to address workload effects on computer performance for a highly reliable unibus multiprocessor used in real-time control. The queueing model consists of multiserver nodes and a nonpreemptive priority queue. Use of this model requires partitioning the workload into task classes. The time average steady-state solution of the queueing model directly produces useful results that are necessary in performance evaluation. The model is experimentally justified with the Fault-Tolerant Multiprocessor (FTMP) located at the NASA AIRLAB. Extensive experiments are performed on FTMP with a synthetic workload generator (SWG) to directly measure performance parameters, such as processor idle time, system bus contention, and task processing times. These measurements determine values for parameters in the queueing model. Experimental and analytic results are then compared.

Woodbury, Michael H.↗