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At least 217 records · Page 12

To have value, comparisons of high-throughput phenotyping methods need statistical tests of bias and variance

The gap between genomics and phenomics is narrowing. The rate at which it is narrowing, however, is being slowed by improper statistical comparison of methods. Quantification using Pearson’s correlation coefficient ( r ) is commonly used to assess method quality, but it is an often misleading statistic for this purpose as it is unable to provide information about the relative quality of two methods. Using r can both erroneously discount methods that are inherently more precise and validate methods that are less accurate. These errors occur because of logical flaws inherent in the use of r when comparing methods, not as a problem of limited sample size or the unavoidable possibility of a type I error. A popular alternative to using r is to measure the limits of agreement (LOA). However both r and LOA fail to identify which instrument is more or less variable than the other and can lead to incorrect conclusions about method quality. An alternative approach, comparing variances of methods, requires repeated measurements of the same subject, but avoids incorrect conclusions. Variance comparison is arguably the most important component of method validation and, thus, when repeated measurements are possible, variance comparison provides considerable value to these studies. Statistical tests to compare variances presented here are well established, easy to interpret and ubiquitously available. The widespread use of r has potentially led to numerous incorrect conclusions about method quality, hampering development, and the approach described here would be useful to advance high throughput phenotyping methods but can also extend into any branch of science. The adoption of the statistical techniques outlined in this paper will help speed the adoption of new high throughput phenotyping techniques by indicating when one should reject a new method, outright replace an old method or conditionally use a new method.

59 BASIC BIOLOGICAL SCIENCES↗

Physics-Informed Machine Learning of Dynamical Systems for Efficient Bayesian Inference

Although the no-u-turn sampler (NUTS) is a widely adopted method for performing Bayesian inference, it requires numerous posterior gradients which can be expensive to compute in practice. Recently, there has been a significant interest in physics-based machine learning of dynamical (or Hamiltonian) systems and Hamiltonian neural networks (HNNs) is a noteworthy architecture. But these types of architectures have not been applied to solve Bayesian inference problems efficiently. We propose the use of HNNs for performing Bayesian inference efficiently without requiring numerous posterior gradients. We introduce latent variable outputs to HNNs (L-HNNs) for improved expressivity and reduced integration errors. We integrate L-HNNs in NUTS and further propose an online error monitoring scheme to prevent sampling degeneracy in regions where L-HNNs may have little training data. We demonstrate L-HNNs in NUTS with online error monitoring consider several complex high-dimensional posterior densities and compare its performance to NUTS.

97 MATHEMATICS AND COMPUTING↗

A Markov framework for generalized post-event systems recovery modeling: From single to multihazards

State-dependent models can be used to represent the system recovery process as a series of stochastic transitions from lower to higher functional states. However, the applications of these models have been limited in scope and there is a lack of a generalized recovery modeling framework. A generalized framework would permit a robust forecasting of systems and system-of-systems recovery under multiple hazards, and more broadly, would contribute to community disaster preparedness. This paper develops a generalized post hazard-event recovery modeling framework based on state-dependent Markov-type processes. We then apply the proposed framework to solve a spectrum of problems that range from hind-casting single-system recovery following a single hazard event to forecasting post-event trajectories under multiple hazards and modeling the recovery of a system-of-systems. First, Markov chains are used to hind-cast the observed recovery for a portfolio of buildings affected by the 2014 South Napa, California, earthquake. Next, Markov processes are used to formulate a parametric post hazard-event recovery model, which can be updated using Bayesian statistics when relevant datasets become available. Semi-Markov processes are then used to develop a more general model of single hazard recovery, which accounts for the intensity of the loading and level of damage caused by the event. Semi-Markov processes with non-renewal features are then used to account for multihazard interactions in a post-event recovery model, and applied to a case study that involves a community in Charleston, South Carolina. Lastly, Markov-type processes are combined with Bayesian networks to model the recovery of residential, commercial, educational, and industrial buildings (system-of-systems) following a hazard event. Overall, these applications demonstrate the versatility of the Markov framework towards handling recovery problems with varying levels of complexity.

42 ENGINEERING↗

Identification of Material Type and Thickness Using Combined X-ray and Fast Neutron Radiography

Material identification (ID) using radiography is a problem that has implicitly existed since the discovery of the X-ray. Since 9-11, this problem has received renewed attention for homeland security applications of the generic, “what is in the box?” type1. Examples of items potentially in the box include: roadside bombs, nuclear weapons, contraband shipments and the like. In these cases, the “what” can include: explosives, projectiles, fissile material, or drugs. Here we investigate the ability of 60Co gamma-rays, 14MeV neutrons, and their combination to tease apart information about density, thickness and atomic number of items in the box. That information subset can be combined with other types of independent information (e.g. neutron and gammaspectroscopy, intelligence, photographs etc.) to assert a more complete picture of what, exactly, is in the box? That more complete information set can form the basis for actions including: remote detonation, evacuations, disablement, detention, search, arrest etc.

36 MATERIALS SCIENCE↗

thornado-hydro: A Discontinuous Galerkin Method for Supernova Hydrodynamics with Nuclear Equations of State

This paper describes algorithms for non-relativistic hydrodynamics in the toolkit for high-order neutrino radiation hydrodynamics (thornado), which is being developed for multiphysics simulations of core-collapse supernovae (CCSNe) and related problems with Runge–Kutta discontinuous Galerkin (RKDG) methods. More specifically, thornado employs a spectral type nodal collocation approximation, and we have extended limiters — a slope limiter to prevent non-physical oscillations and a bound-enforcing limiter to prevent non-physical states — from the standard RKDG framework to be able to accommodate a tabulated nuclear equation of state (EoS). To demonstrate the efficacy of the algorithms with a nuclear EoS, we first present numerical results from basic test problems in idealized settings in one and two spatial dimensions, employing Cartesian, spherical-polar, and cylindrical coordinates. Then, we apply the RKDG method to the problem of adiabatic collapse, shock formation, and shock propagation in spherical symmetry, initiated with a 15 M ⊙ progenitor. Herein, we find that the extended limiters improve the fidelity and robustness of the RKDG method in idealized settings. The bound-enforcing limiter improves robustness of the RKDG method in the adiabatic collapse application, while we find that slope limiting in characteristic fields is vulnerable to structures in the EoS — more specifically, in the phase transition from nuclei and nucleons to bulk nuclear matter. The success of these applications marks an important step toward applying RKDG methods to more realistic CCSN simulations with thornado in the future.

Nuclear astrophysics (1129)↗

The Effect of the Flux Separability Approximation on Multigroup Neutron Transport

The angular dependence of flux-weighted multigroup cross sections is commonly neglected when generating multigroup libraries. The error of this flux separability approximation is typically not isolated from other error sources due to a lack of availability of library generation and corresponding solvers that cannot relax this approximation. These errors can now be isolated and quantified with the availability of a multigroup Monte Carlo transport and multigroup library-generation capability in the OpenMC Monte Carlo transport code. This work will discuss relevant details of the OpenMC implementation, provide an example case useful for detailing the type of errors one can expect from making the flux separability approximation, and end with more realistic problems which show the impact of the approximation and highlight how it can strongly arise from an energy-dependent resonance absorption effect. Since the angle-dependence is intrinsically linked to the energy group structure, these examples also show that relaxing the flux separability approximation with angle-dependent cross sections could be used to reduce either the fine-tuning required to set a multigroup energy structure for a specific reactor type or the number of energy groups required to obtain a desired level of accuracy for a given problem. This trade-off could increase the costs of generating multigroup cross sections, and has the potential to require more memory for storing the multigroup library during the transport calculations, but it can significantly reduce the computational time required since the runtime of a discrete ordinates or method of characteristics neutron transport solver scales roughly linearly with the number of groups.

42 ENGINEERING↗

Variational encoder geostatistical analysis (VEGAS) with an application to large scale riverine bathymetry

Estimation of riverbed profiles, also known as bathymetry, plays a vital role in many applications, such as safe and efficient inland navigation, prediction of bank erosion, land subsidence, and flood risk management. The high cost and complex logistics of direct bathymetry surveys, i.e, depth imaging, have encouraged the use of indirect measurements such as surface flow velocities. However, estimating high-resolution bathymetry from indirect measurements is an inverse problem that can be computationally challenging. Here, we propose a reduced-order model (ROM) based approach that utilizes a variational autoencoder (VAE), a type of deep neural network with a narrow layer in the middle, to compress bathymetry and flow velocity information and accelerate bathymetry inverse problems from flow velocity measurements. In our application, the shallow-water equations (SWE) with appropriate boundary conditions (BCs), e.g., the discharge and/or the free surface elevation, constitute the forward problem, to predict flow velocity. Then, ROMs of the SWEs are constructed on a nonlinear manifold of low dimensionality through a variational encoder and the bathymetry inversion problem is derived on the low-dimensional latent space in a Hierarchical Bayesian setting. Further, the reformulation allows variational inference with a small number (e.g., $\mathscr{O}$ (100) of ROM runs and efficient uncertainty quantification. We have tested our inversion approach on a one-mile reach of the Savannah River, GA, USA. Once the neural network is trained (offline stage), the proposed technique can perform the inversion operation orders of magnitude faster than traditional inversion methods that are commonly based on linear projections, such as principal component analysis (PCA), or the principal component geostatistical approach (PCGA). Furthermore, tests show that the algorithm can estimate the bathymetry with good accuracy even with sparse flow velocity measurements.

54 ENVIRONMENTAL SCIENCES↗

A taxonomy of constraints in black-box simulation-based optimization

The types of constraints encountered in black-box simulation-based optimization problems differ significantly from those addressed in nonlinear programming. Here, we introduce a characterization of constraints to address this situation. We provide formal definitions for several constraint classes and present illustrative examples in the context of the resulting taxonomy. This taxonomy, denoted KARQ, is useful for modeling and problem formulation, as well as optimization software development and deployment. It can also be used as the basis for a dialog with practitioners in moving problems to increasingly solvable branches of optimization.

42 ENGINEERING↗

Hydro-mechanical coupled modeling of hydraulic fracturing using the mesh fragmentation technique

The inclusion of special interface elements between standard finite elements is becoming a common technique to model discontinuities in porous media using the finite element method (FEM). Recently, it was proved that high aspect ratio (HAR) elements can reproduce very satisfactorily the main features of behavior observed in a single hydraulically-induced fracture. In this paper, the mesh fragmentation technique (MFT) is proposed to extend the application of HAR elements to simulate more general problems involving the formation of hydraulic fractures in rocks by introducing this type of element in-between the standard FE of a typical mesh. The proposed framework makes use of standard FE techniques. Therefore, it is relatively easy to upgrade an existing FE program for continuous porous media to deal with evolving discontinuities. The proposed approach is verified and validated against available analytical and numerical solutions. The crack patterns predicted by the MFT are also compared with the ones observed in the laboratory. The formation of multiple fractures is also analyzed. In all cases, the proposed technique was able to properly capture the main features of rock behavior subjected to hydraulic fracturing.

58 GEOSCIENCES↗

Side chain engineering control of mixed conduction in oligoethylene glycol-substituted polythiophenes

A major limitation for polymeric mixed ionic/electronic conductors (MIECs) is the trade-off between ionic and electronic conductivity; changes made that improve one typically hinder the other. In order to address this fundamental problem, this work provides insight into ways that we could improve one type of conduction without hindering the other. Here, we investigated a common oligoethylene glycol side chain polymer by adjusting the oxygen atom content and position, providing structural insights for materials that better balanced the two conduction pathways. The investigated polymer series showed the prototypical conflict between ionic and electronic conduction for oxygen atom content, with increasing oxygen atom content increasing ionic conductivity, but decreasing electronic conductivity; however, by increasing the oxygen atom distance from the polymer backbone, both ionic and electronic conductivity could be improved. Following these rules, we show that poly(3-(methoxyethoxybutyl)thiophene), when blended with lithium bistrifluoromethanesulfonimide (LiTFSI), matches the ionic conductivity of a comparable MIEC [poly(3-(methoxyethoxyethoxymethyl)thiophene)], while simultaneously showing higher electronic conductivity, highlighting the potential of this design strategy. We also provide strategies for tuning the MIEC performance to fit a desired application, depending on if electronic, ionic, or balanced conduction is most important. These results have implications beyond just polythiophene-based MIECs, as these strategies for balancing backbone crystallization and coordinating group interconnectivity apply for all semicrystalline conjugated polymers.

36 MATERIALS SCIENCE↗

Boosting the performance of Brillouin amplification at sub-quarter-critical densities via reduction of parasitic Raman scattering

Brillouin amplification of laser pulses in plasma has been shown to be a promising approach to produce picosecond pulses of petawatt power. A key challenge is preservation of the quality of the amplified pulse, which requires control of parasitic instabilities that accompany the amplification process. At high plasma densities (> cr /4), ponderomotive filamentation has been identified as the biggest threat to the integrity of the amplifying pulse. It has therefore been proposed to perform Brillouin scattering at densities below n cr /4 to reduce the influence of filamentation. However, parasitic Raman scattering can become a problem at such densities, contrary to densities above n cr /4 where it is forbidden. In this paper, we investigate the influence of parasitic Raman scattering on Brillouin amplification at densities below n cr /4. We expose the specific problems posed by both Raman backward and forward scattering, and how both types of scattering can be mitigated, leading to an increased performance of the Brillouin amplification process.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Topology, criticality, and dynamically generated qubits in a stochastic measurement-only Kitaev model

Here we consider a paradigmatic solvable model of topological order in two dimensions, Kitaev's honeycomb Hamiltonian, and turn it into a measurement-only dynamics consisting of stochastic measurements of two-qubit bond operators. We find an entanglement phase diagram that resembles that of the Hamiltonian problem in some ways, while being qualitatively different in others. When one type of bond is dominantly measured, we find area-law entangled phases that protect two topological qubits (on a torus) for a time exponential in system size. This generalizes the recently proposed idea of Floquet codes, where logical qubits are dynamically generated by a time-periodic measurement schedule, to a stochastic setting. When all types of bonds are measured with comparable frequency, we find a critical phase with a logarithmic violation of the area law, which sharply distinguishes it from its Hamiltonian counterpart. The critical phase has the same set of topological qubits, as diagnosed by the tripartite mutual information, but protects them only for a time polynomial in system size. Furthermore, we observe an unusual behavior for the dynamical purification of mixed states, characterized at late times by the dynamical exponent z = $\frac{1}{2}$ a superballistic dynamics made possible by measurements.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Fast emulation of quantum three-body scattering

Here, we develop a class of emulators for solving quantum three-body scattering problems. They are based on combining the variational method for scattering observables and the recently proposed eigenvector continuation concept. The emulators are first trained by the exact scattering solutions of the governing Hamiltonian at a small number of points in its parameter space, and then employed to make interpolations and extrapolations in that space. Through a schematic nuclear-physics model with finite-range two and three-body interactions, we demonstrate the emulators to be extremely accurate and efficient. The computing time for emulation is on the scale of milliseconds (on a laptop), with relative errors ranging from 10 –13 to 10 –4 depending on the case. The emulators also require little memory. We argue that these emulators can be generalized to even more challenging scattering problems. Furthermore, this general strategy may be applicable for building the same type of emulators in other fields, wherever variational methods can be developed for evaluating physical models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Mapping and probing Froggatt-Nielsen solutions to the quark flavor puzzle

The Froggatt-Nielsen (FN) mechanism is an elegant solution to the flavor problem. In its minimal application to the quark sector, the different quark types and generations have different charges under a 𝑈⁢(1)𝑋 flavor symmetry. The SM Yukawa couplings are generated below the flavor breaking scale with hierarchies dictated by the quark charge assignments. Only a handful of charge assignments are generally considered in the literature. We analyze the complete space of possible charge assignments with |𝑋 𝑞𝑖 | ≤ 4 and perform both a set of Bayesian-inspired numerical scans and an analytical spurion analysis to identify those charge assignments that reliably generate SM-like quark mass and mixing hierarchies. The resulting set of top-20 flavor charge assignments significantly enlarges the viable space of FN models but is still compact enough to enable focused phenomenological study. We then apply our numerical methodology to demonstrate that these distinct charge assignments result in the generation of correlated flavor-violating four-quark operators characterized by significantly varied strengths, potentially differing substantially from the possibilities previously explored in the literature. Future precision measurement of Δ⁢𝐹 = 2 observables, along with increasingly accurate SM predictions, may therefore enable us to distinguish among otherwise equally plausible FN charges, thus shedding light on the UV structure of the flavor sector.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Descriptor Aided Bayesian Optimization for Many-Level Qualitative Variables With Materials Design Applications

Abstract Engineering design often involves qualitative and quantitative design variables, which requires systematic methods for the exploration of these mixed-variable design spaces. Expensive simulation techniques, such as those required to evaluate optimization objectives in materials design applications, constitute the main portion of the cost of the design process and underline the need for efficient search strategies—Bayesian optimization (BO) being one of the most widely adopted. Although recent developments in mixed-variable Bayesian optimization have shown promise, the effects of dimensionality of qualitative variables have not been well studied. High-dimensional qualitative variables, i.e., with many levels, impose a large design cost as they typically require a larger dataset to quantify the effect of each level on the optimization objective. We address this challenge by leveraging domain knowledge about underlying physical descriptors, which embody the physics of the underlying physical phenomena, to infer the effect of unobserved levels that have not been sampled yet. We show that physical descriptors can be intuitively embedded into the latent variable Gaussian process approach—a mixed-variable GP modeling technique—and used to selectively explore levels of qualitative variables in the Bayesian optimization framework. This physics-informed approach is particularly useful when one or more qualitative variables are high dimensional (many-level) and the modeling dataset is small, containing observations for only a subset of levels. Through a combination of mathematical test functions and materials design applications, our method is shown to be robust to certain types of incomplete domain knowledge and significantly reduces the design cost for problems with high-dimensional qualitative variables.

Engineering↗

SAS4A/SASSYS-1 Verification Testing for Sodium Fast Reactor Applications: Acceptance Testing Report

SAS4A/SASSYS-1 (SAS) is a simulation tool used to perform deterministic analyses of anticipated events as well as design basis and beyond design basis accidents for advanced liquid-metal-cooled nuclear reactors. With its origin as SAS1A in the late 1960s, the SAS series of codes has been under continuous use and development for over forty-five years and represents a critical investment in safety analysis capabilities for the U.S. Department of Energy. To support demonstration of software pedigree and confirm key functional requirements, this report has been generated to provide detailed verification of the software. Although SAS was developed to support the analysis of any liquid-metal-cooled nuclear reactor, the acceptance testing described in this document focuses on the verification of SAS capabilities as they relate to pool-type Sodium Fast Reactors (SFRs). This report includes documentation of the test problem definition, analytical solution(s), computational solution(s), acceptance criteria, comparisons of analytical/computational solutions, and determination of acceptance of the computational solution(s). Deviations from acceptance criteria are noted.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

SAS4A/SASSYS-1 Verification Testing for Sodium Fast Reactor Applications (Acceptance Testing Report)

SAS4A/SASSYS-1 (SAS) is a simulation tool used to perform deterministic analyses of anticipated events as well as design basis and beyond design basis accidents for advanced liquid-metal- cooled nuclear reactors. With its origin as SAS1A in the late 1960s, the SAS series of codes has been under continuous use and development for over fifty years and represents a critical investment in safety analysis capabilities for the U.S. Department of Energy. To support demonstration of software pedigree and confirm key functional requirements, this report has been generated to provide detailed verification of the software. Although SAS was developed to support the analysis of any liquid-metal-cooled nuclear reactor, the acceptance testing described in this document focuses on the verification of SAS capabilities as they relate to pool-type Sodium Fast Reactors (SFRs). This report includes documentation of the test problem definition, analytical solution(s), computational solution(s), acceptance criteria, comparisons of analytical/computational solutions, and determination of acceptance of the computational solution(s). Deviations from acceptance criteria are noted.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Grid Expansion Optimal Planning Tools (GridEO): Manual for Users and Developers

This report describes Grid Expansion Optimal Planning Tools (GridEO). GridEO is a Python package for electric power grid capacity expansion modeling. With GridEO, the user can build and solve instances of the Capacity Expansion Planning (CEP) problem to determine an optimal plan of investment in capacity of various types of power grid equipment.

24 POWER TRANSMISSION AND DISTRIBUTION↗