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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Scalable Combinatorial Tools for Health Disparities Research

Despite staggering investments made in unraveling the human genome, current estimates suggest that as much as 90% of the variance in cancer and chronic diseases can be attributed to factors outside an individual’s genetic endowment, particularly to environmental exposures experienced across his or her life course. New analytical approaches are clearly required as investigators turn to complicated systems theory and ecological, place-based and life-history perspectives in order to understand more clearly the relationships between social determinants, environmental exposures and health disparities. While traditional data analysis techniques remain foundational to health disparities research, they are easily overwhelmed by the ever-increasing size and heterogeneity of available data needed to illuminate latent gene x environment interactions. This has prompted the adaptation and application of scalable combinatorial methods, many from genome science research, to the study of population health. Most of these powerful tools are algorithmically sophisticated, highly automated and mathematically abstract. Their utility motivates the main theme of this paper, which is to describe real applications of innovative transdisciplinary models and analyses in an effort to help move the research community closer toward identifying the causal mechanisms and associated environmental contexts underlying health disparities. The public health exposome is used as a contemporary focus for addressing the complex nature of this subject.

Environmental Sciences & Ecology↗
DOE OSTI2015

Consistent Feature Extraction From Vector Fields: Combinatorial Representations and Analysis Under Local Reference Frames

This dissertation presents research on addressing some of the contemporary challenges in the analysis of vector fields—an important type of scientific data useful for representing a multitude of physical phenomena, such as wind flow and ocean currents. In particular, new theories and computational frameworks to enable consistent feature extraction from vector fields are presented. One of the most fundamental challenges in the analysis of vector fields is that their features are defined with respect to reference frames. Unfortunately, there is no single “correct” reference frame for analysis, and an unsuitable frame may cause features of interest to remain undetected, thus creating serious physical consequences. This work develops new reference frames that enable extraction of localized features that other techniques and frames fail to detect. As a result, these reference frames objectify the notion of “correctness” of features for certain goals by revealing the phenomena of importance from the underlying data. An important consequence of using these local frames is that the analysis of unsteady (time-varying) vector fields can be reduced to the analysis of sequences of steady (timeindependent) vector fields, which can be performed using simpler and scalable techniques that allow better data management by accessing the data on a per-time-step basis. Nevertheless, the state-of-the-art analysis of steady vector fields is not robust, as most techniques are numerical in nature. The residing numerical errors can violate consistency with the underlying theory by breaching important fundamental laws, which may lead to serious physical consequences. This dissertation considers consistency as the most fundamental characteristic of computational analysis that must always be preserved, and presents a new discrete theory that uses combinatorial representations and algorithms to provide consistency guarantees during vector field analysis along with the uncertainty visualization of unavoidable discretization errors. Together, the two main contributions of this dissertation address two important concerns regarding feature extraction from scientific data: correctness and precision. The work presented here also opens new avenues for further research by exploring more-general reference frames and more-sophisticated domain discretizations.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2005

Development of the Architectural Simulation Model for Future Launch Systems and its Application to an Existing Launch Fleet

A significant portion of lifecycle costs for launch vehicles are generated during the operations phase. Research indicates that operations costs can account for a large percentage of the total life-cycle costs of reusable space transportation systems. These costs are largely determined by decisions made early during conceptual design. Therefore, operational considerations are an important part of vehicle design and concept analysis process that needs to be modeled and studied early in the design phase. However, this is a difficult and challenging task due to uncertainties of operations definitions, the dynamic and combinatorial nature of the processes, and lack of analytical models and the scarcity of historical data during the conceptual design phase. Ultimately, NASA would like to know the best mix of launch vehicle concepts that would meet the missions launch dates at the minimum cost. To answer this question, we first need to develop a model to estimate the total cost, including the operational cost, to accomplish this set of missions. In this project, we have developed and implemented a discrete-event simulation model using ARENA (a simulation modeling environment) to determine this cost assessment. Discrete-event simulation is widely used in modeling complex systems, including transportation systems, due to its flexibility, and ability to capture the dynamics of the system. The simulation model accepts manifest inputs including the set of missions that need to be accomplished over a period of time, the clients (e.g., NASA or DoD) who wish to transport the payload to space, the payload weights, and their destinations (e.g., International Space Station, LEO, or GEO). A user of the simulation model can define an architecture of reusable or expendable launch vehicles to achieve these missions. Launch vehicles may belong to different families where each family may have it own set of resources, processing times, and cost factors. The goal is to capture the required resource levels of the major launch elements and their required facilities. The model s output can show whether or not a certain architecture of vehicles can meet the launch dates, and if not, how much the delay cost would be. It will also produce aggregate figures of missions cost based on element procurement cost, processing cost, cargo integration cost, delay cost, and mission support cost. One of the most useful features of this model is that it is stochastic where it accepts statistical distributions to represent the processing times mimicking the stochastic nature of real systems.

Rabadi, Ghaith↗
DOE OSTI2014

Conforming Morse-Smale Complexes

Morse-Smale (MS) complexes have been gaining popularity as a tool for feature-driven data analysis and visualization. However, the quality of their geometric embedding and the sole dependence on the input scalar field data can limit their applicability when expressing application-dependent features. In this paper we introduce a new combinatorial technique to compute an MS complex that conforms to both an input scalar field and an additional, prior segmentation of the domain. The segmentation constrains the MS complex computation guaranteeing that boundaries in the segmentation are captured as separatrices of the MS complex. We demonstrate the utility and versatility of our approach with two applications. First, we use streamline integration to determine numerically computed basins/mountains and use the resulting segmentation as an input to our algorithm. This strategy enables the incorporation of prior flow path knowledge, effectively resulting in an MS complex that is as geometrically accurate as the employed numerical integration. Our second use case is motivated by the observation that often the data itself does not explicitly contain features known to be present by a domain expert. We introduce edit operations for MS complexes so that a user can directly modify their features while maintaining all the advantages of a robust topology-based representation.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1991

Estimating slash pine biomass using radar backscatter

L-band HV multiple-incidence-angle aircraft synthetic aperture radar (SAR) data were analyzed in relation to average stand biomass, basal area, and tree height for 55 slash pine plantations located in northern Florida. This information was used to develop a system of equations to predict average stand biomass as a function of L-band (24.5-cm) radar backscatter. The system of equations developed in this study using three-stage least-squares and combinatorial screening accounted for 97 percent of the variability observed in average stand biomass per hectare. When applied to an independent data set, the biomass equations had an average bias of less than 1 percent with a standard error of approximately 3 percent. These results indicate that future Shuttle Imaging Radar Systems (e.g., SIR-C, which will have cross-polarized radar sensors) should be able to obtain better estimates of forest biomass than were obtained with previous satellite radar missions, which utilized only HH-polarized SAR data.

Hussin, Yousif Ali↗
DOE OSTI2015

A Parallel Computing Framework for Finding the Supported Solutions to a Biobjective Network Optimization Problem

Abstract Solving multi‐objective combinatorial optimization problems can quickly become computationally challenging when applied to large networks generated from big data. Present‐day first‐rate Mixed Integer Programming (MIP) solvers have parallelism built‐in to take advantage of multicore architectures; but specialized network optimization algorithms that can often solve graph problems more efficiently than a general MIP solver are typically programmed serially. Thus, these network algorithm implementations do not take full advantage of modern multicore computer capabilities. Many parallel computing languages include a fork/join framework into their concurrency packages that allow for simple conversion of recursive serial algorithms to operate in parallel without having to use complicated low‐level message‐passing interfaces. Fork/join is particularly well suited to divide and conquer algorithms such as Non‐Inferior Set Estimation (NISE) method for computing the supported Pareto front of a multi‐objective optimization problem. This work develops a simple general parallel NISE (pNISE) implementation using the Java 7 concurrency tools, and then offers results from a specific implementation of solving a bi‐objective shortest path problem. The results indicate that this method is capable of sizeable speed‐ups on both small‐scale personal computers as well as large‐scale shared memory supercomputers. Finally, other network problems suitable to this method are discussed, including multi‐objective variants of the minimum spanning tree problem, transportation problem, assignment problem, maximum flow problem, and the minimum‐cost flow problem. Copyright © 2015 John Wiley & Sons, Ltd.

Medrano, Fernando Antonio↗
DOE OSTI2022

Decoding the Mechanisms of Phase Transitions from In Situ Microscopy Observations

Abstract Analysis of the temperature‐ and stimulus‐dependent imaging data toward elucidation of the physical transformations is an ubiquitous problem in multiple fields. Here, temperature‐induced phase transition in BaTiO 3 is explored using the machine learning analysis of domain morphologies visualized via variable‐temperature scanning transmission electron microscopy (STEM) imaging data. This approach is based on the multivariate statistical analysis of the time or temperature dependence of the statistical descriptors of the system, derived in turn from the categorical classification of observed domain structures or projection on the continuous parameter space of the feature extraction‐dimensionality reduction transform. The proposed workflow offers a powerful tool for the exploration of the dynamic data based on the statistics of image representation as a function of the external control variable to visualize the transformation pathways during phase transitions and chemical reactions. This can include the mesoscopic STEM data as demonstrated here, but also optical, chemical imaging, etc., data. It can further be extended to the higher dimensional spaces, for example, analysis of the combinatorial libraries of materials compositions.

Valleti, Sai Mani Prudhvi↗
DOE OSTI2025

Geometric GNNs for charged particle tracking at GlueX

Nuclear physics experiments are aimed at uncovering the fundamental building blocks of matter. The experiments involve high-energy collisions that produce complex events with many particle trajectories. Tracking charged particles resulting from collisions in the presence of a strong magnetic field is critical to enable the reconstruction of particle trajectories and precise determination of interactions. It is traditionally achieved through combinatorial approaches that scale worse than linearly as the number of hits grows. Since particle hit data naturally form a point cloud and can be structured as graphs, graph neural networks (GNNs) emerge as an intuitive and effective choice for this task. In this study, we evaluate the GNN model for track finding on the data from the GlueX experiment at Jefferson Lab. We use simulation data to train the model and test on both simulation and real GlueX measurements. We demonstrate that GNN-based track finding outperforms the currently used traditional method at GlueX in terms of segment-based efficiency at a fixed purity while providing faster inferences. We show that the GNN model can achieve significant speedup by processing multiple events in batches, which exploits the parallel computation capability of graphical processing units (GPUs). Finally, we compare the GNN implementation on GPU and field-programmable gate array and describe the trade-off.

batched GNN pipeline↗
DOE OSTI2017

Spectral partitioning with blends of eigenvectors

We report many common methods for data analysis rely on linear algebra. We provide new results connecting data analysis error to numerical accuracy in the context of spectral graph partitioning. We provide pointwise convergence guarantees so that spectral blends (linear combinations of eigenvectors) can be employed to solve data analysis problems with confidence in their accuracy. We apply this theory to an accessible model problem, the ring of cliques, by deriving the relevant eigenpairs and finding necessary and sufficient solver tolerances. Analysis of the ring of cliques provides an upper bound on eigensolver tolerances for graph partitioning problems. These results bridge the gap between linear algebra based data analysis methods and the convergence theory of iterative approximation methods. These results explain how the combinatorial structure of a problem can be recovered much faster than numerically accurate solutions to the associated linear algebra problem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

A systematic comparison of genome-scale clustering algorithms

Background: A wealth of clustering algorithms has been applied to gene co-expression experiments. These algorithms cover a broad range of approaches, from conventional techniques such as k-means and hierarchical clustering, to graphical approaches such as k-clique communities, weighted gene co-expression networks (WGCNA) and paraclique. Comparison of these methods to evaluate their relative effectiveness provides guidance to algorithm selection, development and implementation. Most prior work on comparative clustering evaluation has focused on parametric methods. Graph theoretical methods are recent additions to the tool set for the global analysis and decomposition of microarray co-expression matrices that have not generally been included in earlier methodological comparisons. In the present study, a variety of parametric and graph theoretical clustering algorithms are compared using well-characterized transcriptomic data at a genome scale from Saccharomyces cerevisiae. Methods: For each clustering method under study, a variety of parameters were tested. Jaccard similarity was used to measure each cluster’s agreement with every GO and KEGG annotation set, and the highest Jaccard score was assigned to the cluster. Clusters were grouped into small, medium, and large bins, and the Jaccard score of the top five scoring clusters in each bin were averaged and reported as the best average top 5 (BAT5) score for the particular method. Results: Clusters produced by each method were evaluated based upon the positive match to known pathways. This produces a readily interpretable ranking of the relative effectiveness of clustering on the genes. Methods were also tested to determine whether they were able to identify clusters consistent with those identified by other clustering methods. Conclusions: Validation of clusters against known gene classifications demonstrate that for this data, graph-based techniques outperform conventional clustering approaches, suggesting that further development and application of combinatorial strategies is warranted.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Accelerated Discovery of Solar Thermochemical Hydrogen Production Materials via High-Throughput Computational and Experimental Methods

In this project, combinatorial synthesis and testing methods were combined with high-throughput materials theory calculations to greatly accelerate the discovery of thermodynamically suitable candidates for green hydrogen production via a two-stage solar thermochemical water splitting (STCH) process. Over the course of the project, more than 8000 quinary and higher oxide compositions were computationally screened for STCH viability, and detailed stability calculations were performed for more than 30 of the most promising identified compositional archetypes. As a result, three new STCH capable compositional families were discovered and experimentally verified. The first, Ce x Sr 2-x MnO 4 (CSM), represents the first known Ruddlesden-Popper compound to show STCH activity, and thus demonstrates that perovskite-related structures may hold promise for this application. The second family, Sr 1-x Ce x MnO 3 (SCM), is the simple perovskite sister-analog to CSM. Sr 0.7 Ce 0.3 MnO 3 (SCM30), a member of this compositional family, was found to produce the highest hydrogen yields of any compound tested in this project, exceeding the end of project milestone target of > 150 μmol H 2 /gram oxide at a reduction temperature of 1350 °C, although only at steam-to-hydrogen ratios greater than 1000:1. Finally, we proved that a third novel Sr-and Mn-containing family, Sr 1-x Ca x Ti 1-y Mn y O 3 (SCTM), which was identified by Materials Project tools, also splits water. The behavior of the SCTM system was found to be similar to the previously discovered Sr 1-x La x Al 1-y Mn y O 3 (SLMA) family, albeit with lower H 2 yields. Across the three thrusts of the project (computational, combinatorial, and bulk testing), five journal articles were published. As part of Program End Analysis and Data Dissemination, relevant data used for the publications was uploaded to the HydroGEN Data Hub for public access, and in certain cases, results were added to public materials databases.

08 HYDROGEN↗
DOE OSTI2018

Status of the framework for research in nuclear science and engineering - 25460

The Framework for Research in Nuclear Science and Engineering (FRENSIE) is a collection of packages written in C++ that are designed primarily to aid in methods development. New features are continually being added to the various packages and as a result, the Forward Adjoint Continuous Energy Monte Carlo (FACEMC) tool provided by FRENSIE continues to undergo verification and validation. While FRENSIE is not currently open source, the ultimate goal is for it to be released as such. A few of the more recent developments in FRENSIE include the addition of combinatorial geometry capabilities using ROOT, tet and hex meshing, support for thermal neutron S (α; β) data, photon Doppler broadening, electron interactions using basic analog electron physics models as well as an elastic moment-preserving model, and atomic relaxation. Preliminary verification results for much of the newly added physics models show good agreement between FACEMC and MCNP6. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

A differentiable approach to the maximum independent set problem using dataless neural networks

The success of machine learning solutions for reasoning about discrete structures has brought attention to its adoption within combinatorial optimization algorithms. Such approaches generally rely on supervised learning by leveraging datasets of the combinatorial structures of interest drawn from some distribution of problem instances. Reinforcement learning has also been employed to find such structures. Here, in this paper, we propose a different approach in that no data is required for training the neural networks that produce the solution. In this sense, what we present is not a machine learning solution, but rather one that is dependent on neural networks and where backpropagation is applied to a loss function defined by the structure of the neural network architecture as opposed to a training dataset. In particular, we reduce the popular combinatorial optimization problem of finding a maximum independent set to a neural network and employ a dataless training scheme to refine the parameters of the network such that those parameters yield the structure of interest. Additionally, we propose a universal graph reduction procedure to handle large-scale graphs. The reduction exploits community detection for graph partitioning and is applicable to any graph type and/or density. Experimental results on both real and synthetic graphs demonstrate that our proposed method performs on par or outperforms state-of-the-art learning-based methods in terms of the size of the found set without requiring any training data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Deducing subnanometer cluster size and shape distributions of heterogeneous supported catalysts

Abstract Infrared (IR) spectra of adsorbate vibrational modes are sensitive to adsorbate/metal interactions, accurate, and easily obtainable in-situ or operando. While they are the gold standards for characterizing single-crystals and large nanoparticles, analogous spectra for highly dispersed heterogeneous catalysts consisting of single-atoms and ultra-small clusters are lacking. Here, we combine data-based approaches with physics-driven surrogate models to generate synthetic IR spectra from first-principles. We bypass the vast combinatorial space of clusters by determining viable, low-energy structures using machine-learned Hamiltonians, genetic algorithm optimization, and grand canonical Monte Carlo calculations. We obtain first-principles vibrations on this tractable ensemble and generate single-cluster primary spectra analogous to pure component gas-phase IR spectra. With such spectra as standards, we predict cluster size distributions from computational and experimental data, demonstrated in the case of CO adsorption on Pd/CeO 2 (111) catalysts, and quantify uncertainty using Bayesian Inference. We discuss extensions for characterizing complex materials towards closing the materials gap.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2009

Parametric Analysis of a Hover Test Vehicle using Advanced Test Generation and Data Analysis

Large complex aerospace systems are generally validated in regions local to anticipated operating points rather than through characterization of the entire feasible operational envelope of the system. This is due to the large parameter space, and complex, highly coupled nonlinear nature of the different systems that contribute to the performance of the aerospace system. We have addressed the factors deterring such an analysis by applying a combination of technologies to the area of flight envelop assessment. We utilize n-factor (2,3) combinatorial parameter variations to limit the number of cases, but still explore important interactions in the parameter space in a systematic fashion. The data generated is automatically analyzed through a combination of unsupervised learning using a Bayesian multivariate clustering technique (AutoBayes) and supervised learning of critical parameter ranges using the machine-learning tool TAR3, a treatment learner. Covariance analysis with scatter plots and likelihood contours are used to visualize correlations between simulation parameters and simulation results, a task that requires tool support, especially for large and complex models. We present results of simulation experiments for a cold-gas-powered hover test vehicle.

Gundy-Burlet, Karen↗
DOE OSTI2016

On microscopic theory of radiative nuclear reaction characteristics

A survey of some results in the modern microscopic theory of properties of nuclear reactions with gamma rays is given. First of all, we discuss the impact of Phonon Coupling (PC) on the Photon Strength Function (PSF) because it represents the most natural physical source of additional strength found for Sn isotopes in recent experiments that could not be explained within the standard HFB + QRPA approach. The self-consistent version of the Extended Theory of Finite Fermi Systems in the Quasiparticle Time Blocking Approximation is applied. It uses the HFB mean field and includes both the QRPA and PC effects on the basis of the SLy4 Skyrme force. With our microscopic E1 PSFs, the following properties have been calculated for many stable and unstable even–even semi-magic Sn and Ni isotopes as well as for double-magic {sup 132}Sn and {sup 208}Pb using the reaction codes EMPIRE and TALYS with several Nuclear Level Density (NLD) models: (1) the neutron capture cross sections; (2) the corresponding neutron capture gamma spectra; (3) the average radiative widths of neutron resonances. In all the properties considered, the PC contribution turned out to be significant, as compared with the standard QRPA one, and necessary to explain the available experimental data. The results with the phenomenological so-called generalized superfluid NLD model turned out to be worse, on the whole, than those obtained with the microscopic HFB + combinatorial NLD model. The very topical question about the M1 resonance contribution to PSFs is also discussed.Finally, we also discuss the modern microscopic NLD models based on the self-consistent HFB method and show their relevance to explain the experimental data as compared with the phenomenological models. The use of these self-consistent microscopic approaches is of particular relevance for nuclear astrophysics, but also for the study of double-magic nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Multi-Agent Graph-Attention Deep Reinforcement Learning for Post-Contingency Grid Emergency Voltage Control

Grid emergency voltage control (GEVC) is paramount in electric power systems to improve voltage stability and prevent cascading outages and blackouts in case of contingencies. While most deep reinforcement learning (DRL)-based paradigms perform single agents in a static environment, real-world agents for GEVC are expected to cooperate in a dynamically shifting grid. Moreover, due to high uncertainties from combinatory natures of various contingencies and load consumption, along with the complexity of dynamic grid operation, the data efficiency and control performance of the existing DRL-based methods are challenged. To address these limitations, we propose a multi-agent graph-attention (GATT)-based DRL algorithm for GEVC in multi-area power systems. Here, we develop graph convolutional network (GCN)-based agents for feature representation of the graph-structured voltages to improve the decision accuracy in a data-efficient manner. Furthermore, a cutting-edge attention mechanism concentrates on effective information sharing among multiple agents, synergizing different-sized subnetworks in the grid for cooperative learning. We address several key challenges in the existing DRL-based GEVC approaches, including low scalability and poor stability against high uncertainties. Test results in the IEEE benchmark system verify the advantages of the proposed method over several recent multi-agent DRL-based algorithms.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

On the Solution of ℓ 0 -Constrained Sparse Inverse Covariance Estimation Problems

The sparse inverse covariance matrix is used to model conditional dependencies between variables in a graphical model to fit a multivariate Gaussian distribution. Estimating the matrix from data are well known to be computationally expensive for large-scale problems. Sparsity is employed to handle noise in the data and to promote interpretability of a learning model. Although the use of a convex ℓ 1 regularizer to encourage sparsity is common practice, the combinatorial ℓ 0 penalty often has more favorable statistical properties. In this paper, we directly constrain sparsity by specifying a maximally allowable number of nonzeros, in other words, by imposing an ℓ 0 constraint. Here, we introduce an efficient approximate Newton algorithm using warm starts for solving the nonconvex ℓ 0 -constrained inverse covariance learning problem. Numerical experiments on standard data sets show that the performance of the proposed algorithm is competitive with state-of-the-art methods.

$\ell_0$-Constrained↗