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At least 109 records · Page 6

Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models

The co-expression extrapolation (COXEN) method has been successfully used in multiple studies to select genes for predicting the response of tumor cells to a specific drug treatment. Here, we enhance the COXEN method to select genes that are predictive of the efficacies of multiple drugs for building general drug response prediction models that are not specific to a particular drug. The enhanced COXEN method first ranks the genes according to their prediction power for each individual drug and then takes a union of top predictive genes of all the drugs, among which the algorithm further selects genes whose co-expression patterns are well preserved between cancer cases for building prediction models. We apply the proposed method on benchmark in vitro drug screening datasets and compare the performance of prediction models built based on the genes selected by the enhanced COXEN method to that of models built on genes selected by the original COXEN method and randomly picked genes. Models built with the enhanced COXEN method always present a statistically significantly improved prediction performance (adjusted p-value ≤ 0.05). Our results demonstrate the enhanced COXEN method can dramatically increase the power of gene expression data for predicting drug response.

60 APPLIED LIFE SCIENCES↗

Random and systematic measurement errors in acoustic impedance as determined by the transmission line method

The effect of random and systematic errors associated with the measurement of normal incidence acoustic impedance in a zero-mean-flow environment was investigated by the transmission line method. The influence of random measurement errors in the reflection coefficients and pressure minima positions was investigated by computing fractional standard deviations of the normalized impedance. Both the standard techniques of random process theory and a simplified technique were used. Over a wavelength range of 68 to 10 cm random measurement errors in the reflection coefficients and pressure minima positions could be described adequately by normal probability distributions with standard deviations of 0.001 and 0.0098 cm, respectively. An error propagation technique based on the observed concentration of the probability density functions was found to give essentially the same results but with a computation time of about 1 percent of that required for the standard technique. The results suggest that careful experimental design reduces the effect of random measurement errors to insignificant levels for moderate ranges of test specimen impedance component magnitudes. Most of the observed random scatter can be attributed to lack of control by the mounting arrangement over mechanical boundary conditions of the test sample.

Parrott, T. L.↗

A Method for the Calculation of the Lateral Response of Airplanes to Random Turbulence

In this method, the gust velocities are represented as rolling gusts, yawing gusts, and side gusts. Random distributions of gust velocities across the span are taken into account in defining the rolling and yawing gusts. Complex stability derivatives are used to account for the random distribution of side gusts along the fuselage and vertical tail and the lag effects in gust penetration. A sample calculation procedure is presented for obtaining the response of the airplane in each degree of freedom.

LOADS, GUST - WINGS↗

Comparisons of one- and two- interface methods for tunnel wall interference calculation

Tunnel wall interference in two-dimensional subsonic flow can be analytically calculated on the basis of the one- or two-interface method. The application of numerical integration by means of matrix multiplication to both methods has been found to significantly reduce CPU time in on-line operation. An investigation of the sensitivity of these methods to random velocity-measurement disturbances shows the one-interface method to be less sensitive to measurement errors, and therefore to be preferable for practical applications.

Lo, C. F.↗

Concepts for a theoretical and experimental study of lifting rotor random loads and vibrations. Phase 5B: Analysis of gust alleviation methods and rotor dynamic stability

The effects of various gust alleviation methods on the random blade response in flapping were studied analytically, assuming a rigid rotor support. The analytical model assumes rigid flapping blades with elastic root restraints. Linearized equations which are approximately valid at low lift conditions were used. Because of the interblade coupling from the feedback devices, the method of multiblade generalized coordinates was most convenient and was extended to include coning, differential coning, and warping of the rotor. The numerical examples cover the dynamic stability characteristics as affected by feedback gains of three- to six-bladed rotors. The number of blades had large effects on stability limits and modal time functions at these limits. The random flapping response of the blades to atmospheric turbulence was determined at 1.6 rotor advance ratio using feedback gains below the stability limit. The most effective reduction of the flapping response per unit gain was achieved with a rotor coning angle feedback.

Hohenemser, K. H.↗

Plasma Thermionic Diodes

Randomization of electron energies in one- dimensional thermionic converter by computer methods

ELECTRON ENERGY↗

A randomized sketching trust-region secant method for low-memory dynamic optimization

The numerical solution of dynamic optimization problems is often limited by the memory required to store the state trajectory, which is used to evaluate the objective function and its derivatives. Recently, [R. Muthukumar et al., SIAM Journal on Optimization 31(2), pp. 1242–1275 (2021)] introduced a trust-region method for dynamic optimization that employs randomized sketching to compress the state trajectory, resulting in inexact derivative computations. By adaptively learning the sketch rank, the trust-region algorithm achieves rigorous convergence guarantees. Here, we extend this approach to use secant Hessian approximations. Due to the randomness introduced by the sketch, the traditional secant update formulae can produce poor Hessian approximations. In particular, the difference of two gradients, computed from two different sketches, may be inconsistent. To overcome this, we employ a sketched approximation of the Hessian application, in lieu of computing the gradient difference. We numerically demonstrate the improved stability of this approach on an example from PDE-constrained optimization.

dynamic optimization↗

Adaptive Data-Driven Deep-Learning Surrogate Model for Frontal Polymerization in Dicyclopentadiene

Frontal polymerization (FP) is a self-sustaining curing process that enables rapid and energy-efficient manufacturing of thermoset polymers and composites. Computational methods conventionally used to simulate the FP process are time-consuming, and repeating simulations are required for sensitivity analysis, uncertainty quantification, or optimization of the manufacturing process. Here, in this work, we develop an adaptive surrogate deep-learning model for FP of dicyclopentadiene (DCPD), which predicts the evolution of temperature and degree of cure orders of magnitude faster than the finite-element method (FEM). The adaptive algorithm provides a strategy to select training samples efficiently and save computational costs by reducing the redundancy of FEM-based training samples. The adaptive algorithm calculates the residual error of the FP governing equations using automatic differentiation of the deep neural network. A probability density function expressed in terms of the residual error is used to select training samples from the Sobol sequence space. The temperature and degree of cure evolution of each training sample are obtained by a 2D FEM simulation. The adaptive method is more efficient and has a better prediction accuracy than the random sampling method. With the well-trained surrogate neural network, the FP characteristics (front speed, shape, and temperature) can be extracted quickly from the predicted temperature and degree-of-cure fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spline approximation of quantile functions

The study reported here explored the development and utility of a spline representation of the sample quantile function of a continuous probability distribution in providing a functional description of a random sample and a method of generating random variables. With a spline representation, the random samples are generated by transforming a sample of uniform random variables to the interval of interest. This is useful, for example, in simulation studies in which a random sample represents the only known information about the distribution. The spline formulation considered here consists of a linear combination of cubic basis splines (B-splines) fit in a least squares sense to the sample quantile function using equally spaced knots. The following discussion is presented in five parts. The first section highlights major results realized from the study. The second section further details the results obtained. The methodology used is described in the third section, followed by a brief discussion of previous research on quantile functions. Finally, the results of the study are evaluated.

Schiess, J. R.↗

A Stochastic Quasi-Newton Method in the Absence of Common Random Numbers

We present Q-SASS, a quasi-Newton method for unconstrained stochastic optimization that does not rely on common random numbers. Most existing quasi-Newton approaches leverage common random numbers to construct second-order updates. However, motivated by challenges in variational quantum algorithms—where such coordination is not possible—we consider the setting in which function values and gradients are accessible only through noisy probabilistic zeroth- and first-order oracles, and no common random numbers can be exploited. We derive high-probability tail bounds on the iteration complexity of our algorithm for nonconvex, convex, and strongly convex (more generally, those satisfying the PL condition) objective functions. Finally, we demonstrate the empirical benefits of our quasi-Newton updating scheme on both synthetic and quantum chemistry problems.

Complexity bound↗

A Randomization-Based, Zero-Trust Cyberattack Detection Method for Hierarchical Systems

This paper demonstrates a novel randomization-based approach for verifying power system control signals with application to detecting cyberattacks. We consider fully connected hierarchical systems containing multiple local agents and a global "trust" agent. The global agent uses a time-varying randomized assignment scheme to identify corrupt network links based on principles of zero trust and majority rule. To evaluate the performance of this detection approach, we implement our algorithm in MATLAB and run it against nearly 43 million unique attack scenarios spanning a range of system sizes. For each scenario, the algorithm determines whether the identified corruptions satisfy a set of validity constraints reflecting network topology and uses that result to say whether the recovered state value for one or more local agents is malicious. We compare the algorithm's determination to the true state of the system to assess performance and find that classification accuracy converges to 100% as system size increases, suggesting that the validity constraints become more difficult to satisfy for larger systems. We further explore the scenarios that evade detection to understand practical implications for employing this detection approach.

cybersecurity↗

Convergence acceleration of Monte Carlo many-body perturbation methods by direct sampling

In the Monte Carlo many-body perturbation (MC-MP) method, the conventional correlation-correction formula, which is a long sum of products of low-dimensional integrals, is first recast into a short sum of high-dimensional integrals over electron-pair and imaginary-time coordinates. These high-dimensional integrals are then evaluated by the Monte Carlo method with random coordinates generated by the Metropolis–Hasting algorithm according to a suitable distribution. The latter algorithm, while advantageous in its ability to sample nearly any distribution, introduces autocorrelation in sampled coordinates, which in turn increases the statistical uncertainty of the integrals and thus the computational cost. It also involves wasteful rejected moves and an initial “burn-in” step as well as displays hysteresis. Here, an algorithm is proposed that directly produces a random sequence of electron-pair coordinates for the same distribution used in the MC-MP method, which is free from autocorrelation, rejected moves, a burn-in step, or hysteresis. Furthermore, this direct-sampling algorithm is shown to accelerate second- (MC-MP2) and third-order Monte Carlo many-body perturbation (MC-MP3) calculations by up to 222% and 38%, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Methods for semi-automated indexing for high precision information retrieval

OBJECTIVE: To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to generate textbook indexes that are more detailed and more useful to readers. DESIGN: Pilot evaluation: simple, nonrandomized trial comparing ISAID with manual indexing methods. Methods evaluation: randomized, cross-over trial comparing three versions of ISAID and usability survey. PARTICIPANTS: Pilot evaluation: two physicians. Methods evaluation: twelve physicians, each of whom used three different versions of the system for a total of 36 indexing sessions. MEASUREMENTS: Total index term tuples generated per document per minute (TPM), with and without adjustment for concordance with other subjects; inter-indexer consistency; ratings of the usability of the ISAID indexing system. RESULTS: Compared with manual methods, ISAID decreased indexing times greatly. Using three versions of ISAID, inter-indexer consistency ranged from 15% to 65% with a mean of 41%, 31%, and 40% for each of three documents. Subjects using the full version of ISAID were faster (average TPM: 5.6) and had higher rates of concordant index generation. There were substantial learning effects, despite our use of a training/run-in phase. Subjects using the full version of ISAID were much faster by the third indexing session (average TPM: 9.1). There was a statistically significant increase in three-subject concordant indexing rate using the full version of ISAID during the second indexing session (p < 0.05). SUMMARY: Users of the ISAID indexing system create complex, precise, and accurate indexing for full-text documents much faster than users of manual methods. Furthermore, the natural language processing methods that ISAID uses to suggest indexes contributes substantially to increased indexing speed and accuracy.

Evaluation Studies↗

Tortuosity Computations of Porous Materials using the Direct Simulation Monte Carlo

Low-density carbon fiber preforms, used as thermal protection systems (TPS) materials for planetary entry systems, have permeable, highly porous microstructures consisting of interlaced fibers. Internal gas transport in TPS is important in modeling the penetration of hot boundary-layer gases and the in-depth transport of pyrolysis and ablation products. The gas effective diffusion coefficient of a porous material must be known before the gas transport can be modeled in material response solvers; however, there are very little available data for rigid fibrous insulators used in heritage TPS.The tortuosity factor, which reflects the efficiency of the percolation paths, can be computed from the effective diffusion coefficient of a gas inside a porous material and is based on the micro-structure of the material. It is well known, that the tortuosity factor is a strong function of the Knudsen number. Due to the small characteristic scales of porous media used in TPS applications (typical pore size of the order of 50 micron), the transport of gases can occur in the rarefied and transitional regimes, at Knudsen numbers above 1. A proper way to model the gas dynamics at these conditions consists in solving the Boltzmann equation using particle-based methods that account for movement and collisions of atoms and molecules.In this work we adopt, for the first time, the Direct Simulation Monte Carlo (DSMC) method to compute the tortuosity factor of fibrous media in the rarefied regime. To enable realistic simulations of the actual transport of gases in the porous medium, digitized computational grids are obtained from X-ray micro-tomography imaging of real TPS materials. The SPARTA DSMC solver is used for simulations. Effective diffusion coefficients and tortuosity factors are obtained by computing the mean-square displacement of diffusing particles.We first apply the method to compute the tortuosity factors as a function of the Knudsen number for computationally designed materials such as random cylindrical fibers and packed bed of spheres with prescribed porosity. Results are compared to literature values obtained using random walk methods in the rarefied and transitional regime and a finite-volume method for the continuum regime. We then compute tortuosity factors for a real carbon fiber material with a transverse isotropic structure (FiberForm), quantifying differences between through-thickness and in-plain tortuosities at various Knudsen regimes.

Tortuosity↗

Fast yaw optimization for wind plant wake steering using Boolean yaw angles

Abstract. In wind plants, turbines can be yawed into the wind to steer their wakes away from downstream turbines and achieve an overall increase in plant power. Mathematical optimization is typically used to determine the best yaw angles at which to operate the turbines in a plant. In this paper, we present a new heuristic to rapidly determine the yaw angles in a wind plant. In this method, we define the turbine yaw angles as Boolean – either yawed at a predefined angle or nonyawed – as opposed to the typical methods of defining yaw angles as continuous or with fine discretizations. We then optimize which turbines should be yawed with an algorithm that sweeps through the turbines from the most upstream to the most downstream. We demonstrate that our new Boolean optimization method can find turbine yaw angles that perform well compared to a traditionally used gradient-based optimizer for which the yaw angles are defined as continuous. There is less than 0.6 % difference in the optimized power between the two optimization methods for randomly placed turbine layouts and less than a 0.6 % difference in the optimal annual energy production between the two optimization methods for a real wind farm. Additionally, we show that our new method is much more computationally efficient than the traditional method. For plants with nonzero optimal yaw angles, our new method is generally able to solve for the turbine yaw angles 50–150 times faster, and in some extreme cases up to 500 times faster, than the traditional method.

17 WIND ENERGY↗

Probabilistic structural mechanics research for parallel processing computers

Aerospace structures and spacecraft are a complex assemblage of structural components that are subjected to a variety of complex, cyclic, and transient loading conditions. Significant modeling uncertainties are present in these structures, in addition to the inherent randomness of material properties and loads. To properly account for these uncertainties in evaluating and assessing the reliability of these components and structures, probabilistic structural mechanics (PSM) procedures must be used. Much research has focused on basic theory development and the development of approximate analytic solution methods in random vibrations and structural reliability. Practical application of PSM methods was hampered by their computationally intense nature. Solution of PSM problems requires repeated analyses of structures that are often large, and exhibit nonlinear and/or dynamic response behavior. These methods are all inherently parallel and ideally suited to implementation on parallel processing computers. New hardware architectures and innovative control software and solution methodologies are needed to make solution of large scale PSM problems practical.

Sues, Robert H.↗