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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families

Comparative network analysis provides effective computational means for gaining novel insights into the structural and functional compositions of biological networks. In recent years, various methods have been developed for biological network alignment, whose main goal is to identify important similarities and critical differences between networks in terms of their topology and composition. A major impediment to advancing network alignment techniques has been the lack of gold-standard benchmarks that can be used for accurate and comprehensive performance assessment of such algorithms. The original NAPAbench (network alignment performance assessment benchmark) was developed to address this problem, and it has been widely utilized by many researchers for the development, evaluation, and comparison of novel network alignment techniques. In this work, we introduce NAPAbench 2—a major update of the original NAPAbench that was introduced in 2012. NAPAbench 2 includes a completely redesigned network synthesis algorithm that can generate protein-protein interaction (PPI) network families whose characteristics closely match those of the latest real PPI networks. Furthermore, the network synthesis algorithm comes with an intuitive GUI that allows users to easily generate PPI network families with an arbitrary number of networks of any size, according to a flexible user-defined phylogeny. In addition, NAPAbench 2 provides updated benchmark datasets—created using the redesigned network synthesis algorithm—which can be used for comprehensive performance assessment of network alignment algorithms and their scalability.

42 ENGINEERING↗
DOE OSTI2022

An Exact Algorithm for the Linear Tape Scheduling Problem

Magnetic tapes are often considered as an outdated storage technology, yet they are still used to store huge amounts of data. Their main interests are a large capacity and a low price per gigabyte, which come at the cost of a much larger file access time than on disks. With tapes, finding the right ordering of multiple file accesses is thus key to performance. Moving the reading head back and forth along a kilometer long tape has a non-negligible cost and unnecessary movements thus have to be avoided. However, the optimization of tape request ordering has rarely been studied in the scheduling literature, much less than I/O scheduling on disks. For instance, minimizing the average service time for several read requests on a linear tape remains an open question. Therefore, in this paper, we aim at improving the quality of service experienced by users of tape storage systems, and not only the peak performance of such systems. To this end, we propose a reasonable polynomial-time exact algorithm while this problem and simpler variants have been conjectured NP-hard. We also refine the proposed model by considering U-turn penalty costs accounting for inherent mechanical accelerations. Then, we propose a low-cost variant of our optimal algorithm by restricting the solution space, yet still yielding an accurate suboptimal solution. Finally, we compare our algorithms to existing solutions from the literature on logs of the mass storage management system of a major datacenter. This allows us to assess the quality of previous solutions and the improvement achieved by our low-cost algorithm. Aiming for reproducibility, we make available the complete implementation of the algorithms used in our evaluation, alongside the dataset of tape requests that is, to the best of our knowledge, the first of its kind to be publicly released.

Honoré, Valentin↗
DOE OSTI2021

Error Analysis on Numerical Integration Algorithms in a Hypoelasticity Framework

This report determines local truncation errors for common stress integration algorithms used in explicit finite element codes with hypoelastic material models. The hypoelastic integration algorithms in question utilize an operator splitting procedure in a rotation neutralized configuration, where the stress response is determined from de- coupling the total deformation into rotational and strain dependent components. This document analyzes the error in evolving the stress given a one-step time increment Δt and compares the errors associated with both the rotational and strain components of the operator splitting method. A slight modification to a traditional algorithm is proposed and studied, where the rate of deformation is appropriately rotated from the midstep configuration at t n+1/2 to the end step configuration at t n+1 before the constitutive evaluation. The proposed modification either completely eliminates the error associated with the rotation rate or is of the same order of magnitude as the original algorithm for the three test cases considered in this report. These cases consist of an unaxial stretch with a constant true strain rate with a rigid body rotation, an uniaxial stretch with a constant engineering strain rate with a rigid body rotation, and a simple shear deformation. All three cases are compared to a closed form solution, and in almost every test case the alternative algorithm yields the most accurate one-step local truncation error.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Anomaly Detection in Gamma Spectra Using Hopfield Neural Network with B-SAT and Grover’s Algorithm on a Quantum Computing Simulator

Environmental screening of gamma radiation consists of detecting weak nuisance and anomaly signal in the presence of strong and highly varying background. In a typical scenario, a mobile detector-spectrometer continuously measures gamma radiation spectra in short, e.g., one-second, signal acquisition intervals. In principle, gamma radiation sources can be detected and identified by their unique spectral lines. However, detecting sources from data measured in a search scenario is difficult due to the highly varying background because of naturally occurring radioactive material (NORM), and low signal-to-noise ratio (S/N) of spectral signal measured during one-second acquisition intervals. In recent prior work, we have developed a Hopfield Neural Network (HNN) in conjunction with an image processing algorithm to detect a weak signal anomaly hidden among the highly fluctuating background spectra. The objective of this work is to explore quantum computing methods to increase the speed of HNN. The approach is based on the Grover’s search algorithm in conjunction with a 3-SAT problem formalism. The Grover’s algorithm is implemented on a quantum computing simulator using Qiskit software. Performance of HNN algorithm is benchmarked using search data from an environmental screening campaign, where the anomaly is a subset of measurements containing a 137 Cs source. Results indicate that using Grover’s algorithm on a quantum simulator reduces runtime of HNN by two orders of magnitude.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2023

Benchmarking the PCMCI Causal Discovery Algorithm for Spatiotemporal Systems

Causal discovery algorithms construct hypothesized causal graphs that depict causal dependencies among variables in observational data. While powerful, the accuracy of these algorithms is highly sensitive to the underlying dynamics of the system in ways that have not been fully characterized in the literature. In this report, we benchmark the PCMCI causal discovery algorithm in its application to gridded spatiotemporal systems. Effectively computing grid-level causal graphs on large grids will enable analysis of the causal impacts of transient and mobile spatial phenomena in large systems, such as the Earth’s climate. We evaluate the performance of PCMCI with a set of structural causal models, using simulated spatial vector autoregressive processes in one- and two-dimensions. We develop computational and analytical tools for characterizing these processes and their associated causal graphs. Our findings suggest that direct application of PCMCI is not suitable for the analysis of dynamical spatiotemporal gridded systems, such as climatological data, without significant preprocessing and downscaling of the data. PCMCI requires unrealistic sample sizes to achieve acceptable performance on even modestly sized problems and suffers from a notable curse of dimensionality. This work suggests that, even under generous structural assumptions, significant additional algorithmic improvements are needed before causal discovery algorithms can be reliably applied to grid-level outputs of earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Metrics and Methods for Radiation Detection Algorithm Characterization for Nuclear/Radiological Source Search

This report presents a series of recommendations for data to train and evaluate radiation detection algorithms and performance metrics to evaluate these algorithms. These recommendations were formed through a community consensus approach through the Detection Radiation Algorithms Group (DRAG), a multi-institution collaboration spanning eight Department of Energy laboratories and John Hopkins Applied Physics Laboratory. This report includes recommendations on background data variability, and metrics to quantify variability, sources and shielding configurations to include in data collection campaigns and detector response variability. In addition, this report describes several anomaly detection and identification algorithms and recommends metrics to report their performance. Finally, this report ends with a discussion on machine learning algorithms.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Automatic Generation of Algorithms for High-Speed Reliable Lossy Data Compression (Final Report)

Fast reliable data compression is urgently needed for many leading-edge scientific instruments and for exascale high-performance computing applications because they produce vast amounts of data at extremely high rates. The goal of this project has been to develop a framework named LC that is able to automatically generate high-speed lossless and reliable lossy compression and decompression algorithms that can be customized for different kinds of data. The resulting LC framework is freely available on GitHub. To achieve high-speed operation, LC outputs optimized and parallelized CPU and GPU implementations of the generated algorithms. To ensure the quality of lossily compressed data, LC guarantees the user-provided error bound. To be able to customize the compression algorithm to various use cases, LC can synthesize millions of different algorithms and automatically search for the one that works best for the given data. We have already employed LC to create state-of-the-art lossless and lossy compressors for scientific data as well as leading lossless compressors for images. We hope that LC and the customized, fast, reliable, and CPU/GPU-compatible compression algorithms that it can generate will greatly benefit the many scientific applications that need not only high trustworthiness but also high performance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Prediction and compression of lattice QCD data using machine learning algorithms on quantum annealer

We present regression and compression algorithms for lattice QCD data utilizing the efficient binary optimization ability of quantum annealers. In the regression algorithm, we encode the correlation between the input and output variables into a sparse coding machine learning algorithm. The trained correlation pattern is used to predict lattice QCD observables of unseen lattice configurations from other observables measured on the lattice. In the compression algorithm, we define a mapping from lattice QCD data of floating-point numbers to the binary coefficients that closely reconstruct the input data from a set of basis vectors. Since the reconstruction is not exact, the mapping defines a lossy compression, but, a reasonably small number of binary coefficients are able to reconstruct the input vector of lattice QCD data with the reconstruction error much smaller than the statistical fluctuation. In both applications, we use D-Wave quantum annealers to solve the NP-hard binary optimization problems of the machine learning algorithms.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

A general quantum algorithm for open quantum dynamics demonstrated with the Fenna-Matthews-Olson complex

Using quantum algorithms to simulate complex physical processes and correlations in quantum matter has been a major direction of quantum computing research, towards the promise of a quantum advantage over classical approaches. In this work we develop a generalized quantum algorithm to simulate any dynamical process represented by either the operator sum representation or the Lindblad master equation. We then demonstrate the quantum algorithm by simulating the dynamics of the Fenna-Matthews-Olson (FMO) complex on the IBM QASM quantum simulator. This work represents a first demonstration of a quantum algorithm for open quantum dynamics with a moderately sophisticated dynamical process involving a realistic biological structure. We discuss the complexity of the quantum algorithm relative to the classical method for the same purpose, presenting a decisive query complexity advantage of the quantum approach based on the unique property of quantum measurement.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Comparing Calibration Algorithms for the Rapid Characterization of Pretreated Corn Stover Using Near-Infrared Spectroscopy

Rapid characterization of biomass composition is a key enabling technology for biorefineries—the ability to measure the chemical composition of biomass materials entering the biorefinery as well as the composition of key process intermediate streams would allow real-time process control and the development of robust models to predict process performance. The utility of near-infrared (NIR) spectroscopy for rapid characterization requires multivariate algorithms for building calibration models. The most prevalent algorithm used for building calibration models using NIR spectra is the linear modeling algorithm Partial Least Squares Regression (PLS). Nonlinear regression algorithms (which are typically more computationally intensive than linear modeling approaches) have gained popularity in recent years due to their ability to solve a wide variety of classification and regression problems and the dramatic increase in available computational resources. In this work, we demonstrate that a calibration model can predict the composition of corn stover process intermediate samples pretreated with three different treatments—hot water (HW), dilute acid (DA), and deacetylation followed by dilute acid (DDA). We quantitatively compare three different algorithms for building prediction models based on near-infrared spectroscopy—partial least squares (PLS), support vector machines (SVM), and random forests (RF). We demonstrate the utility of improving model performance by accounting for instrument performance variability using repeated measurements of standard materials (e.g., the “repeatability file” strategy) and investigate its performance with nonlinear regression techniques, and we discuss methods for quantifying the uncertainties of specific predictions among the three methods.

09 BIOMASS FUELS↗
DOE OSTI2021

Ocean Surface Flux Algorithm Effects on Earth System Model Energy and Water Cycles

Earth system models parameterize ocean surface fluxes of heat, moisture, and momentum with empirical bulk flux algorithms, which introduce biases and uncertainties into simulations. We investigate the atmosphere and ocean model sensitivity to algorithm choice in the Energy Exascale Earth System Model (E3SM). Flux differences between algorithms are larger in atmosphere simulations (where wind speeds can vary) than ocean simulations (where wind speeds are fixed by forcing data). Surface flux changes lead to global scale changes in the energy and water cycles, notably including ocean heat uptake and global mean precipitation rates. Compared to the control algorithm, both COARE and University of Arizona (UA) algorithms reduce global mean precipitation and top of atmosphere radiative biases. Further, UA may slightly reduce biases in ocean meridional heat transport. We speculate that changes seen here, especially in the ocean, could be even larger in coupled simulations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Capturing the interactions between ice sheets, sea level and the solid Earth on a range of timescales: a new “time window” algorithm

Retreat and advance of ice sheets perturb the gravitational field, solid surface and rotation of the Earth, leading to spatially variable sea-level changes over a range of timescales $\textit{O}$ (10 0–6 years), which in turn feed back onto ice-sheet dynamics. Coupled ice-sheet–sea-level models have been developed to capture the interactive processes between ice sheets, sea level and the solid Earth, but it is computationally challenging to capture short-term interactions $\textit{O}$ (10 0–2 years) precisely within longer $\textit{O}$ (10 3–6 years) simulations. The standard forward sea-level modelling algorithm assigns a uniform temporal resolution in the sea-level model, causing a quadratic increase in total CPU time with the total number of input ice history steps, which increases with either the length or temporal resolution of the simulation. In this study, we introduce a new “time window” algorithm for 1D pseudo-spectral sea-level models based on the normal mode method that enables users to define the temporal resolution at which the ice loading history is captured during different time intervals before the current simulation time. Utilizing the time window, we assign a fine temporal resolution $\textit{O}$ (10 0–2 years) for the period of ongoing and recent history of surface ice and ocean loading changes and a coarser temporal resolution $\textit{O}$ (10 3–6 years) for earlier periods in the simulation. This reduces the total CPU time and memory required per model time step while maintaining the precision of the model results. We explore the sensitivity of sea-level model results to the model temporal resolution and show how this sensitivity feeds back onto ice-sheet dynamics in coupled modelling. We apply the new algorithm to simulate sea-level changes in response to global ice-sheet evolution over two glacial cycles and the rapid collapse of marine sectors of the West Antarctic Ice Sheet in the coming centuries and provide appropriate time window profiles for each application. The time window algorithm reduces the total CPU time by ~ 50 % in each of these examples and changes the trend of the total CPU time increase from quadratic to linear. This improvement would increase with longer simulations than those considered here. Our algorithm also allows for coupling time intervals of annual temporal scale for coupled ice-sheet–sea-level modelling of regions such as West Antarctica that are characterized by rapid solid Earth response to ice changes due to the thin lithosphere and low mantle viscosities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Algebraic Algorithms for Betweenness and Percolation Centrality

Abstract In this paper, we explored different ways to write the algebraic version of betweenness centrality algorithm. Particularly, we focused on Brandes' algorithm. We aimed for algebraic betweenness centrality that can be parallelized easily. We proposed 3-tuple geodetic semiring as an extension to the usual geodetic semiring with 2-tuples. Using the 3-tuple geodetic semiring, Dijkstra's and Brandes' algorithm, we wrote more concise and general algebraic betweenness centrality (ABC) algorithm which is valid for weighted and directed graphs. We also proposed an alternative version of ABC using the usual geodetic semiring with 2-tuple where we used a simple way to construct shortest path tree after computing shortest path distances in the usual geodetic semiring. This allows us to avoid computational complexity of ABC implementation using 3-tuple geodetic semiring. We used numba to optimize and parallelize ABC. We evaluated the performance of ABC using 2-tuple geodetic semiring as compared to NetworkX, a common python package for graph algorithms. We did scalability experiments on parallel ABC and showed its total speedup. We also showed that with small modification, ABC can be adapted to algebraicly compute other centrality measures such as percolation centrality.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1972

Design of automata theory of cubical complexes with applications to diagnosis and algorithmic description

The following problems are considered: (1) methods for development of logic design together with algorithms, so that it is possible to compute a test for any failure in the logic design, if such a test exists, and developing algorithms and heuristics for the purpose of minimizing the computation for tests; and (2) a method of design of logic for ultra LSI (large scale integration). It was discovered that the so-called quantum calculus can be extended to render it possible: (1) to describe the functional behavior of a mechanism component by component, and (2) to compute tests for failures, in the mechanism, using the diagnosis algorithm. The development of an algorithm for the multioutput two-level minimization problem is presented and the program MIN 360 was written for this algorithm. The program has options of mode (exact minimum or various approximations), cost function, cost bound, etc., providing flexibility.

Roth, J. P.↗
NASA NTRS1975

Four-dimensional guidance algorithms for aircraft in an air traffic control environment

Theoretical development and computer implementation of three guidance algorithms are presented. From a small set of input parameters the algorithms generate the ground track, altitude profile, and speed profile required to implement an experimental 4-D guidance system. Given a sequence of waypoints that define a nominal flight path, the first algorithm generates a realistic, flyable ground track consisting of a sequence of straight line segments and circular arcs. Each circular turn is constrained by the minimum turning radius of the aircraft. The ground track and the specified waypoint altitudes are used as inputs to the second algorithm which generates the altitude profile. The altitude profile consists of piecewise constant flight path angle segments, each segment lying within specified upper and lower bounds. The third algorithm generates a feasible speed profile subject to constraints on the rate of change in speed, permissible speed ranges, and effects of wind. Flight path parameters are then combined into a chronological sequence to form the 4-D guidance vectors. These vectors can be used to drive the autopilot/autothrottle of the aircraft so that a 4-D flight path could be tracked completely automatically; or these vectors may be used to drive the flight director and other cockpit displays, thereby enabling the pilot to track a 4-D flight path manually.

Pecsvaradi, T.↗
NASA NTRS1976

An algorithm for propagating the square-root covariance matrix in triangular form

A method for propagating the square root of the state error covariance matrix in lower triangular form is described. The algorithm can be combined with any triangular square-root measurement update algorithm to obtain a triangular square-root sequential estimation algorithm. The triangular square-root algorithm compares favorably with the conventional sequential estimation algorithm with regard to computation time.

Tapley, B. D.↗
NASA NTRS1978

A multilevel system of algorithms for detecting and isolating signals in a background of noise

Signal information is processed with the help of algorithms, and then on the basis of such processing, a part of the information is subjected to further processing with the help of more precise algorithms. Such a system of algorithms is studied, a comparative evaluation of a series of lower level algorithms is given, and the corresponding algorithms of higher level are characterized.

Gurin, L. S.↗
NASA NTRS1978

A fast D.F.T. algorithm using complex integer transforms

Winograd (1976) has developed a new class of algorithms which depend heavily on the computation of a cyclic convolution for computing the conventional DFT (discrete Fourier transform); this new algorithm, for a few hundred transform points, requires substantially fewer multiplications than the conventional FFT algorithm. Reed and Truong have defined a special class of finite Fourier-like transforms over GF(q squared), where q = 2 to the p power minus 1 is a Mersenne prime for p = 2, 3, 5, 7, 13, 17, 19, 31, 61. In the present paper it is shown that Winograd's algorithm can be combined with the aforementioned Fourier-like transform to yield a new algorithm for computing the DFT. A fast method for accurately computing the DFT of a sequence of complex numbers of very long transform-lengths is thus obtained.

Reed, I. S.↗