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At least 865 records · Page 48

Modeling I/O Performance Variability Using Conditional Variational Auto Encoders

Storage system performance modeling is crucial for efficient use of heterogeneous shared resources on leadership class computers. Variability in application performance, particularly variability arising from concurrent applications sharing I/O resources, is a major hurdle in the development of accurate performance models. We adopt a deep learning approach based on conditional variational auto encoders (CVAE) for I/O performance modeling, and use it to quantify performance variability. We illustrate our approach using the data collected on Edison, a production supercomputing system at the National Energy Research Scientific Computing Center (NERSC). The CVAE approach is investigated by comparing it to a previously proposed sensitivity-based Gaussian process (GP) model. We find that the CVAE model performs slightly better than the GP model in cases where training and testing data come from different applications, since CVAE can inherently leverage the whole data from multiple applications whereas GP partitions the data and builds separate models for each partition. Hence, the CVAE offers an alternative modeling approach that does not need preprocessing; it has enough flexibility to handle data from a wide variety of applications without changing the inference approach.

I/O perfornance variability↗

Optimization of Simultaneous Measurement for Variational Quantum Eigensolver Applications

Variational quantum eigensolver (VQE) is a promising algorithm suitable for near-term quantum computers. VQE aims to approximate solutions to exponentially-sized optimization problems by executing a polynomial number of quantum sub-problems. However, the number of subproblems scales as N-4 for typical problems of interest-a daunting growth rate that poses a serious limitation for emerging applications such as quantum computational chemistry. We mitigate this issue by exploiting the simultaneous measurability of subproblems corresponding to commuting terms. Our technique transpiles VQE instances into a format optimized for simultaneous measurement, ultimately yielding 8-30x lower cost. Our work also encompasses a synthesis tool for compiling simultaneous measurement circuits with minimal overhead. We demonstrate experimental validation of our techniques by estimating the ground state energy of deuteron with a quantum computer. We also investigate the underlying statistics of simultaneous measurement and devise an adaptive strategy for mitigating harmful covariance terms.

quantum computing↗

Dynamic Frequency Regulation Improvement in Hydropower-Hybrid System using Variational Mode Decomposition

Providing frequency response, especially fast frequency response such as Red D in the Pennsylvania-New Jersey-Maryland Interconnection (PJM) market, is challenging for many generation plants to deliver on their own. If they have adequate flexibility, hydropower plants are typically able to provide slower regulation support (e.g., Reg A in PJM), but do not respond fast enough to provide Reg D. The ability to provide Reg D would improve their revenue because this service is typically more valuable. This work presents a control approach to use hydropower, battery, and ultracapacitor systems to provide fast regulation in a way that uses the response contribution of each asset. In particular, the proposed control architecture applies a variational mode decomposition (VMD) technique on the incoming Reg D signal to extract multiple dynamic-regulation components with non-overlapping frequencies. With the response-speed dependent alignment, these regulation components are fed to the hydrogenator and hybrid energy storage system (HESS). The paper evaluates the proposed approach on a direct-current (DC)-coupled active system by computing several performance measures and analyzing sensitivity based on HESS component proportional capacities. The results reveal that the proposed VMD-based signal conditioning performs well and that optimizing the sizing of the battery and ultracapacitor components further enhances performance.

13 HYDRO ENERGY↗

Variational Dirichlet Blur Kernel Estimation

Blind image deconvolution involves two key objectives: 1) latent image and 2) blur estimation. For latent image estimation, we propose a fast deconvolution algorithm, which uses an image prior of nondimensional Gaussianity measure to enforce sparsity and an undetermined boundary condition methodology to reduce boundary artifacts. For blur estimation, a linear inverse problem with normalization and nonnegative constraints must be solved. However, the normalization constraint is ignored in many blind image deblurring methods, mainly because it makes the problem less tractable. In this paper, we show that the normalization constraint can be very naturally incorporated into the estimation process by using a Dirichlet distribution to approximate the posterior distribution of the blur. Making use of variational Dirichlet approximation, we provide a blur posterior approximation that considers the uncertainty of the estimate and removes noise in the estimated kernel. Furthermore, experiments with synthetic and real data demonstrate that the proposed method is very competitive to the state-of-the-art blind image restoration methods.

97 MATHEMATICS AND COMPUTING↗

Bayesian K-SVD Using Fast Variational Inference

Recent work in signal processing in general and image processing in particular deals with sparse representation related problems. Two such problems are of paramount importance: an overriding need for designing a well-suited overcomplete dictionary containing a redundant set of atoms— i.e., basis signals—and how to find a sparse representation of a given signal with respect to the chosen dictionary. Dictionary learning techniques, among which we find the popular K-singular value decomposition algorithm, tackle these problems by adapting a dictionary to a set of training data. A common drawback of such techniques is the need for parameter-tuning. In order to overcome this limitation, we propose a fullyautomated Bayesian method that considers the uncertainty of the estimates and produces a sparse representation of the data without prior information on the number of non-zeros in each representation vector. We follow a Bayesian approach that uses a three-tiered hierarchical prior to enforce sparsity on the representations and develop an efficient variational inference framework that reduces computational complexity. Furthermore, we describe a greedy approach that speeds up the whole process. Lastly, we present experimental results that show superior performance on two different applications with real images: denoising and inpainting.

97 MATHEMATICS AND COMPUTING↗

SU-F-T-161: The Effect of Pencil Beam Scanning Gantry Angle Dependent Spot Size Variations On Plan Quality

Purpose: To investigate the effect of spot size variation as function of gantry angle on the quality of treatment plans for pencil beam scanning proton plans. Method: Three homogeneous 26×26×7cm dose volumes with different ranges and SOBPs were delivered on the matrixxPT 2D array at gantry angles of 0 and 270 degrees. The spot size sigma varies by 1.8, 7.8, and 1.4%, for nominal energies of 215, 183, and 103 MeV (Range 29, 22, and 8cm, respectively). The resulting dose planes are compared and evaluated with the gamma index for 2%/2mm and 1%/1mm criteria. Results: Patient specific QA is performed at a gantry angle of 0 degrees. However, beam sigmas vary as function of gantry angle because of the beam optics for each gantry. This will cause differences between the delivered and planned treatment plans. Delivered plans were compared and a gamma pass rate of 96.5% for criteria of 2%/2mm and 91.4% for 1%/1mm were seen for plans with a nominal energy of 183 MeV. For plans with a nominal energy of 103 MeV, gamma pass rates of 97.3% for 2%/2mm and 91.5% for 1%/1mm were seen. For plans with a nominal energy of 215 MeV the pass rate was 99.8% for 1%/1mm between the two gantry angles. Conclusion: Differences in beam sigma of up to 7.8% do not cause significant differences in the dose distribution of different spot size gammas.

60 APPLIED LIFE SCIENCES↗

SU-G-201-13: Investigation of Dose Variation Induced by HDR Ir-192 Source Global Shift Within the Varian Ring Applicator Using Monte Carlo Methods

Purpose: The Varian tandem and ring applicators are used to deliver HDR Ir-192 brachytherapy for cervical cancer. The source path within the ring is hard to predict due to the larger interior ring lumen. Some studies showed the source could be several millimeters different from planned positions, while other studies demonstrated minimal dosimetric impact. A global shift can be applied to limit the effect of positioning offsets. The purpose of this study was to assess the necessities of implementing a global source shift using Monte Carlo (MC) simulations. Methods: The MCNP5 radiation transport code was used for all MC simulations. To accommodate TG-186 guidelines and eliminate inter-source attenuation, a BrachyVision plan with 10 dwell positions (0.5cm step sizes) was simulated as the summation of 10 individual sources with equal dwell times for simplification. To simplify the study, the tandem was also excluded from the MC model. Global shifts of ±0.1, ±0.3, ±0.5 cm were then simulated as distal and proximal from the reference positions. Dose was scored in water for all MC simulations and was normalized to 100% at the normalization point 0.5 cm from the cap in the ring plane. For dose comparison, Point A was 2 cm caudal from the buildup cap and 2 cm lateral on either side of the ring axis. With seventy simulations, 108 photon histories gave a statistical uncertainties (k=1) <2% for (0.1 cm)3 voxels. Results: Compared to no global shift, average Point A doses were 0.0%, 0.4%, and 2.2% higher for distal global shifts, and 0.4%, 2.8%, and 5.1% higher for proximal global shifts, respectively. The MC Point A doses differed by < 1% when compared to BrachyVision. Conclusion: Dose variations were not substantial for ±0.3 cm global shifts, which is common in clinical practice.

60 APPLIED LIFE SCIENCES↗

SU-G-JeP3-12: Use of Cone Beam CT and Deformable Image Registration for Assessing Geometrical and Dosimetric Variations During Lung Radiotherapy

Purpose: To assess the value of cone beam CT (CBCT) combined with deformable image registration in estimating the accuracy of the delivered treatment and the suitability of the applied target margins. Methods: Two patients with lung tumor were selected. Using their CT images intensity modulated radiation therapy (IMRT) treatment plans were developed to deliver 66Gy to the 95% of the PTV in 2Gy fractions. Using the Velocity AI software, the planning CT of each patient was registered with the fractional CBCT images that were obtained through the course of the treatment. After a CT to CBCT deformable image registration (DIR), the same fractional deformation matrix was used for the deformation of the planned dose distributions, as well as of all the contoured volumes, to each CBCT dataset. The dosimetric differences between the planning target volume (PTV) and various organs at risk (OARs) were recorded and compared. Results: CBCT data such as CTV volume change and PTV coverage was analyzed. There was a moderate relationship between volume changes and contouring method (automatic contouring using the DIR transformation vs. manual contouring on each CBCT) for patient #1 (r = 0.49), and a strong relationship for patient #2 (r = 0.83). The average PTV volume coverage from all the CBCT datasets was 91.2% for patient #1 and 95.6% for patient #2. Conclusion: Daily setup variations, tumor volume motion and lung deformation due to breathing yield differences in the actual delivered dose distributions versus the planned ones. The results presented indicate that these differences are apparent even with the use of daily IGRT. In certain fractions, the margins used seem to be insufficient to ensure acceptable lung tumor coverage. The observed differences notably depend on the tumor volume size and location. A larger cohort of patient is under investigation to verify those findings.

60 APPLIED LIFE SCIENCES↗

TU-H-CAMPUS-IeP3-01: Simultaneous PET Restoration and PET/CT Co-Segmentation Using a Variational Method

Purpose: PET images are usually blurred due to the finite spatial resolution, while CT images suffer from low contrast. Segment a tumor from either a single PET or CT image is thus challenging. To make full use of the complementary information between PET and CT, we propose a novel variational method for simultaneous PET image restoration and PET/CT images co-segmentation. Methods: The proposed model was constructed based on the Γ-convergence approximation of Mumford-Shah (MS) segmentation model for PET/CT co-segmentation. Moreover, a PET de-blur process was integrated into the MS model to improve the segmentation accuracy. An interaction edge constraint term over the two modalities were specially designed to share the complementary information. The energy functional was iteratively optimized using an alternate minimization (AM) algorithm. The performance of the proposed method was validated on ten lung cancer cases and five esophageal cancer cases. The ground truth were manually delineated by an experienced radiation oncologist using the complementary visual features of PET and CT. The segmentation accuracy was evaluated by Dice similarity index (DSI) and volume error (VE). Results: The proposed method achieved an expected restoration result for PET image and satisfactory segmentation results for both PET and CT images. For lung cancer dataset, the average DSI (0.72) increased by 0.17 and 0.40 than single PET and CT segmentation. For esophageal cancer dataset, the average DSI (0.85) increased by 0.07 and 0.43 than single PET and CT segmentation. Conclusion: The proposed method took full advantage of the complementary information from PET and CT images. This work was supported in part by the National Cancer Institute Grants R01CA172638. Shan Tan and Laquan Li were supported in part by the National Natural Science Foundation of China, under Grant Nos. 60971112 and 61375018.

60 APPLIED LIFE SCIENCES↗

Exploring variations in the gauge sector of a six-dimensional flavour model

In the context of extra-dimensional models that describe three families of fermions (including their masses and mixing in terms of a single 6-dimensional family), we explore possible variations (including of the extra dimensions) and argue that the apparent plethora of variants does not lead to drastic changes in the expected phenomenology.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Gaussian variational ansatz in the problem of anomalous sea waves: Comparison with direct numerical simulation

The nonlinear dynamics of an obliquely oriented wave packet on a sea surface is analyzed analytically and numerically for various initial parameters of the packet in relation to the problem of the so-called rogue waves. Within the Gaussian variational ansatz applied to the corresponding (1+2)-dimensional hyperbolic nonlinear Schrödinger equation (NLSE), a simplified Lagrangian system of differential equations is derived that describes the evolution of the coefficients of the real and imaginary quadratic forms appearing in the Gaussian. This model provides a semi-quantitative description of the process of nonlinear spatiotemporal focusing, which is one of the most probable mechanisms of rogue wave formation in random wave fields. The system of equations is integrated in quadratures, which allows one to better understand the qualitative differences between linear and nonlinear focusing regimes of a wave packet. Predictions of the Gaussian model are compared with the results of direct numerical simulation of fully nonlinear long-crested waves.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Variational Monte Carlo calculations of lithium atom in strong magnetic field

The variational Monte Carlo method is applied to investigate the ground state and some excited states of the lithium atom and its ions up to Z = 10 in the presence of an external magnetic field regime with γ = 0–100 arb. units. The effect of increasing field strength on the ground state energy is studied and precise values for the crossover field strengths were obtained. Our calculations are based on using accurate forms of trial wave functions, which were put forward in calculating energies in the absence of magnetic field. Furthermore, the value of Y at which ground-state energy of the lithium atom approaches to zero was calculated. The obtained results are in good agreement with the most recent values and also with the exact values.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Excited States of the dtμ, pdμ, and tpμ Mesomolecules in the Variational Method

The energy spectra of excited bound states are calculated for the muonic molecules ptμ, pdμ, and dtμ on the basis of the stochastic variational method. The basis wave functions are taken as the Gaussian in shape. The matrix elements of the Hamiltonian are calculated analytically. To perform numerical calculations, computer code is written in MATLAB. Numerical values are obtained for energies of excited P states in the muonic molecules ptμ, pdμ, and dtμ.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Kinetics of the Variation in the Magnetic Impurity Ion Concentration in Pb{sub 1–x–y}Sn{sub x}V{sub y}Te Alloys upon Doping

The field and temperature dependences of the magnetization (magnetic fields B ≤ 7.5 T, temperatures T = 2.0–75 K) of samples from a Pb{sub 1–x–y}Sn{sub x}V{sub y}Te (x = 0.08, y = 0.01) single-crystal ingot synthesized by the Bridgman–Stockbarger method. It is established that the sample magnetization contains two main contributions, notably, the paramagnetism of vanadium ions and diamagnetism of the crystal lattice. The field and temperature dependences of the magnetization are approximated by the sum of modified Brillouin functions corresponding to the paramagnetic contributions of vanadium in two different charge states and the diamagnetic contribution linear in terms of field. The concentrations of vanadium ions in two different magnetic states and the character of their variation along the ingot are determined within the scope of the alloy’s electronic-structure rearrangement because of doping. The results are compared with the data of X-ray fluorescence microanalysis and the results of studying the galvanomagnetic properties of the samples.

36 MATERIALS SCIENCE↗

Improved Guarantees for Optimal Nash Equilibrium Seeking and Bilevel Variational Inequalities

We consider a class of hierarchical variational inequality (VI) problems that subsumes VI-constrained optimization and several other problem classes, including the optimal solution selection problem and the optimal Nash equilibrium (NE) seeking problem. Our main contribution is threefold. (i) We consider bilevel VIs with monotone and Lipschitz continuous mappings and devise a single-timescale iteratively regularized extragradient method, named IR-EG 𝚖,𝚖 . We improve the existing iteration complexity results for addressing both bilevel VI and VI-constrained convex optimization problems. (ii) Under the strong monotonicity of the outer-level mapping, we develop a method named IR-EG 𝚜,𝚖 and derive faster guarantees than those in (i). We also study the iteration complexity of this method under a constant regularization parameter. These results appear to be new for both bilevel VIs and VI-constrained optimization. (iii) To our knowledge, complexity guarantees for computing the optimal NE in nonconvex settings do not exist. Motivated by this lacuna, we consider VI-constrained nonconvex optimization problems and devise an inexactly projected gradient method, named IPR-EG, where the projection onto the unknown set of equilibria is performed using IR-EG 𝚜,𝚖 with a prescribed termination criterion and an adaptive regularization parameter. We obtain new complexity guarantees in terms of a residual map and an infeasibility metric for computing a stationary point. Here, we validate the theoretical findings using preliminary numerical experiments for computing the best and the worst NEs.

bilevel optimization↗

Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast

Imidazolium ionic liquids (IILs) have a range of biotechnological applications, including as pretreatment solvents that extract cellulose from plant biomass for microbial fermentation into sustainable bioenergy. However, residual levels of IILs, such as 1-ethyl-3-methylimidazolium chloride ([C 2 C 1 im]Cl), are toxic to biofuel-producing microbes, including the yeast Saccharomyces cerevisiae. S. cerevisiae strains isolated from diverse ecological niches differ in genomic sequence and in phenotypes potentially beneficial for industrial applications, including tolerance to inhibitory compounds present in hydrolyzed plant feedstocks. We evaluated >100 genome-sequenced S. cerevisiae strains for tolerance to [C 2 C 1 im]Cl and identified one strain with exceptional tolerance. By screening a library of genomic DNA fragments from the [C 2 C 1 im]Cl-tolerant strain for improved IIL tolerance, we identified SGE1, which encodes a plasma membrane multidrug efflux pump, and a previously uncharacterized gene that we named ionic liquid tolerance 1 (ILT1), which encodes a predicted membrane protein. Analyses of SGE1 sequences from our panel of S. cerevisiae strains together with growth phenotypes implicated two single nucleotide polymorphisms (SNPs) that associated with IIL tolerance and sensitivity. We confirmed these phenotypic effects by transferring the SGE1 SNPs into a [C 2 C 1 im]Cl-sensitive yeast strain using CRISPR/Cas9 genome editing. Further studies indicated that these SNPs affect Sge1 protein stability and cell surface localization, influencing the amount of toxic IILs that cells can pump out of the cytoplasm. Our results highlight the general potential for discovering useful biotechnological functions from untapped natural sequence variation and provide functional insight into emergent SGE1 alleles with reduced capacities to protect against IIL toxicity.

09 BIOMASS FUELS↗

Intra-canopy leaf trait variation facilitates high LAI and compensatory growth in a clonal woody encroaching shrub in the tallgrass prairie

This data package contains the data for Tooley et al. (2022) Intra-canopy leaf trait variation facilitates high leaf area index and compensatory growth in a clonal woody encroaching shrub. The purpose of this project was to evaluate the leaf ecophysiological traits of Cornus drummondii C.A. Mey to better understand how C. drummondii maximizes photosynthetic rates across large gradients of light availability in its short, dense canopies. We also evaluate how C. drummondii modifies its allocation of leaf traits in response to grassland disturbance. High LAI canopies and a compensatory growth response to disturbance are two key factors contributing to the success of C. drummondii and other woody species responsible for the encroachment of grasslands.The data package contains ecophysiological measurements, including leaf morphological, physiological, and chemical traits; photosynthetic measurements, leaf carbon and nitrogen stable isotopes, leaf area index, and photosynthetically active radiation. All measurements were taken vertically across canopies of the clonal woody-encroaching shrub Cornus drummondii under browsed, grazed, and control (unbrowsed and ungrazed) conditions.Files:SeasonalMeasurements_Archive.csv - Data for all seasonal measurements used in the study.LeafPhotoSeasonalRaw_Archive.zip - zip file containing raw data from an li-6400 for each sampling period in the study.LAI_Archive.xlsx - Data for LAI Measurements.ACiandLightCurveResults_Archive.xlsx - Contains parameters extracted from A-ci and Light Response curves along with the morphological and chemical traits for each leaf.ACiRaw Archive.xlsx - Raw data from Li-6400 for A-ci response curvesLightCurves_Raw.zip - zip file containing raw data for Li-6400 light response curves. Excel file format: "IslandID"-"Depth"-lc.xlsx (or .csv)DataCollectionMethods.docx - file containing the methods of data collection, processing, and QA/QC for all data files. File also contains a list of excel file headers, abbreviations, and their units.

54 ENVIRONMENTAL SCIENCES↗

Inverse Analysis with Variational Autoencoders: A Comparison of Shallow and Deep Networks

Inverse problems are applied to determine unknown properties by matching observational data with a physical model that often takes many parameters as input. To overcome the underconstrained nature of inverse problems and achieve good performance, an approach is presented involving regularization with a technique known as a variational autoencoder (VAE), which is trained to map a high-dimensional parameter space with a complex structure to a low-dimensional latent space with a simple structure. We apply this approach to unconditioned realizations of the parameters (heterogeneous hydraulic fields) for a hydrogeological inverse problem. Two types of hydraulic conductivity fields are used to evaluate the characterization for the different levels of heterogeneity complexity of the physical inputs. This approach keeps the computational cost of generating the training data low. The reason is unconditioned realizations neither rely on the observational data used to perform the inverse analysis nor require any groundwater flow model forward runs. In addition, this approach applies regularization on a low-dimensional latent space from the VAE and increases optimization efficiency through automatic differentiation. Furthermore, two different neural network (NN) structures are tested for their utility in using the VAE for inverse analysis. The performance of a deep, convolutional neural network strongly depends on the dimensionality of the latent space, which requires tuning. In contrast, a shallow, dense neural network provides consistently accurate characterization without tuning. Furthermore, our approach evaluates the advantages of the shallow, dense neural network over the deep, convolutional one and enables future application to a wide range of inverse problems.

97 MATHEMATICS AND COMPUTING↗