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At least 325 records · Page 18

Automated detection of pulmonary nodules in PET/CT images: Ensemble false-positive reduction using a convolutional neural network technique

Purpose: Automated detection of solitary pulmonary nodules using positron emission tomography (PET) and computed tomography (CT) images shows good sensitivity; however, it is difficult to detect nodules in contact with normal organs, and additional efforts are needed so that the number of false positives (FPs) can be further reduced. In this paper, the authors propose an improved FP-reduction method for the detection of pulmonary nodules in PET/CT images by means of convolutional neural networks (CNNs). Methods: The overall scheme detects pulmonary nodules using both CT and PET images. In the CT images, a massive region is first detected using an active contour filter, which is a type of contrast enhancement filter that has a deformable kernel shape. Subsequently, high-uptake regions detected by the PET images are merged with the regions detected by the CT images. FP candidates are eliminated using an ensemble method; it consists of two feature extractions, one by shape/metabolic feature analysis and the other by a CNN, followed by a two-step classifier, one step being rule based and the other being based on support vector machines. Results: The authors evaluated the detection performance using 104 PET/CT images collected by a cancer-screening program. The sensitivity in detecting candidates at an initial stage was 97.2%, with 72.8 FPs/case. After performing the proposed FP-reduction method, the sensitivity of detection was 90.1%, with 4.9 FPs/case; the proposed method eliminated approximately half the FPs existing in the previous study. Conclusions: An improved FP-reduction scheme using CNN technique has been developed for the detection of pulmonary nodules in PET/CT images. The authors’ ensemble FP-reduction method eliminated 93% of the FPs; their proposed method using CNN technique eliminates approximately half the FPs existing in the previous study. These results indicate that their method may be useful in the computer-aided detection of pulmonary nodules using PET/CT images.

60 APPLIED LIFE SCIENCES↗

A method for bounding high-order finite element functions: Applications to mesh validity and bounds-preserving limiters

We introduce a novel method for bounding high-order multi-dimensional polynomials in finite element approximations. The method involves precomputing optimal piecewise-linear bounding boxes for polynomial basis functions, which can then be used to locally bound any combination of these basis functions. This approach can be applied to any element/basis type at any approximation order, can provide local (i.e., subcell) extremum bounds to a desired level of accuracy, and can be evaluated efficiently on-the-fly in simulations. Furthermore, we show that this approach generally yields more accurate bounds in comparison to traditional methods based on convex hull properties (e.g., Bernstein polynomials). Furthermore, the efficacy of this technique is shown in applications such as mesh validity checks and optimization for high-order curved meshes, where positivity of the element Jacobian determinant can be ensured throughout the entire element, and continuously bounds-preserving limiters for hyperbolic systems, which can enforce maximum principle bounds across the entire solution polynomial.

Bounding box↗

A new efficient approach for 3D hydrodynamics simulation

LANL’s CHICOMA code solves the compressible hydrodynamic equations on moving tetrahedral grids. Hydrodynamic equations can be solved in Lagrangian, Eulerian, and Arbitrary Lagrangian-Eulerian reference frames. The equations are solved using a finite element method coupled to approximate Riemann solvers. The methods have been extensively verified against relevant analytical solutions. CHICOMA is 10 3 -10 4 times faster than current production codes for the same level of accuracy!

42 ENGINEERING↗

Asymptotic solution for heat convection-radiation equation

In this paper, we employ a new approximate analytical method called the optimal homotopy asymptotic method (OHAM) to solve steady state heat transfer problem in slabs. The heat transfer problem is modeled using nonlinear two-point boundary value problem. Using OHAM, we obtained the approximate analytical solution for dimensionless temperature with different values of a parameter ε. Further, the OHAM results for dimensionless temperature have been presented graphically and in tabular form. Comparison has been provided with existing results from the use of homotopy perturbation method, perturbation method and numerical method. For numerical results, we used Runge-Kutta Fehlberg fourth-fifth order method. It was found that OHAM produces better approximate analytical solutions than those which are obtained by homotopy perturbation and perturbation methods, in the sense of closer agreement with results obtained from the use of Runge-Kutta Fehlberg fourth-fifth order method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Well-Balanced Second-Order Convex Limiting Technique for Solving the Serre–Green–Naghdi Equations

In this article, we introduce a numerical method for approximating the dispersive Serre–Green–Naghdi equations with topography using continuous finite elements. The method is an extension of the hyperbolic relaxation technique introduced in Guermond et al. (J Comput Phys 450:110809, 2022). It is explicit, second-order accurate in space, third-order accurate in time, and is invariant-domain preserving. It is also well balanced and parameter free. Special attention is given to the convex limiting technique when physical source terms are added in the equations. The method is verified with academic benchmarks and validated by comparison with laboratory experimental data.

97 MATHEMATICS AND COMPUTING↗

Deep Koopman operators for causal discovery

Causal discovery aims to identify cause-effect mechanisms for better scientific understanding, explainable decision-making, and more accurate modeling. Standard statistical frameworks, such as Granger causality, lack the ability to quantify causal relationships in nonlinear dynamics due to the presence of complex feedback mechanisms, timescale mixing, and nonstationarity. Thus, applying these methods to study causal dynamics in real-world systems, such as the Earth, is a major challenge. Addressing this shortcoming, we leverage deep learning and a Koopman operator-theoretic formalism to present a class of causal discovery algorithms. Kausal uses deep Koopman operator methods to approximate nonlinear dynamics in a linearized vector space in which traditional causal inference methods such as Granger causality can be more easily applied. Our idealized experiments demonstrate Kausal’s superior ability in discovering and characterizing causal signals compared to existing deep learning and non-deep learning state-of-the-art approaches. Finally, the successful identification of major El Niño and La Niña events in observations showcases Kausal’s skill to handle real-world applications.

54 ENVIRONMENTAL SCIENCES↗

Supervised Learning for Distribution Secondary Systems Modeling: Improving Solar Interconnection Processes

The current interconnection process and hosting capacity analysis for distributed energy resources (DERs), such as photovoltaics (PV) and battery energy storage systems, are based on analyzing grid network constraints (voltage and thermal) using only medium-voltage distribution network models. This is because most utilities do not have secondary low-voltage system models that connect service transformers and residential customers. This is important because in many cases the main impact of interconnecting DERs could occur on the low-voltage distribution systems. This paper proposes a supervised learning method to approximate local secondary models to improve the interconnection process. The proposed supervised learning method includes a decision tree model that predicts the secondary topology and a logistic regression model that predicts conductor types. The case studies demonstrate the benefits of including secondary low-voltage circuits in the interconnection process. We report the proposed modeling methodology is readily scalable and thus can reduce the cost and effort of PV interconnection for the industry and stakeholders.

14 SOLAR ENERGY↗

Computed Tomography by Combining Transmission and Scatter Radiography Methods

In 2015, approximately 13 billion tons of freight was transported in the US, roughly 40 tons per person. 40% of all freight on a ton-mile basis will be transported by railroads. Class I railroads have approximately 140,000 miles (224,000 km) of railroad track across the country. Approximately 3,200 crossties per mile secure the rails at the proper gauge, transmit loads to the ballast, and prevent lateral and longitudinal shifting. Wood crossties can fail in many ways including rotting, breaking, cracking, and splitting. Developing new technologies to inspect these crossties are necessary to help maintain and ensure safe railroad operations. The Georgetown Railroad Equipment Company partnered with the University of Florida to develop the Aurora Xi X-ray backscatter inspection system. This system generates 2D backscatter images at 25 mph to detect weakness in wood crossties long before the internal degradation is visible on the tie surface. The railroad industry has a need for a high-speed high resolution 3D inspection method to inspect approximately 20 million newly fabricated railroad crossties per year. Currently new ties are not radiographically inspected to reject internal flaws and verify that rot prevention treatments have adequately penetrated into the crosstie. Current spiral scan computed tomography (CT) systems are not designed for the 100 cm/s to 400 cm/s speed of a wood crosstie production line. Building on the technology developed for the 2D Aurora Xi system, a new 3D fan-beam inspection system and CT method is being developed. A previous scatter CT method by Arsenault and Hussein required moving the Xray source to many positions, averaging the X-ray spectra, and ignoring the Compton scatter change of energy. The proposed design and method combines transmission and scatter radiography in all directions without moving or rotating the X-ray sources or detectors. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Expectation propagation for nonlinear inverse problems – with an application to electrical impedance tomography

In this paper, we study a fast approximate inference method based on expectation propagation for exploring the posterior probability distribution arising from the Bayesian formulation of nonlinear inverse problems. It is capable of efficiently delivering reliable estimates of the posterior mean and covariance, thereby providing an inverse solution together with quantified uncertainties. Some theoretical properties of the iterative algorithm are discussed, and the efficient implementation for an important class of problems of projection type is described. The method is illustrated with one typical nonlinear inverse problem, electrical impedance tomography with complete electrode model, under sparsity constraints. Numerical results for real experimental data are presented, and compared with that by Markov chain Monte Carlo. The results indicate that the method is accurate and computationally very efficient.

97 MATHEMATICS AND COMPUTING↗

Variational principles with Padé approximants for tearing mode analysis

Tearing modes occur in several distinct physical regimes, and it is often important to compute the inner layer response for these modes with various effects. There is a need for an approximate and efficient method of solving the inner layer equations in all these regimes. In this paper, we introduce a method of solving the inner layer equations based on using a variational principle with Padé approximants. For all the regimes considered, the main layer equations to be solved are inhomogeneous, and Padé approximants give a convenient and efficient method of satisfying the correct asymptotic behavior at the edge of the layer. Results using this variational principle—Padé approximant method in three of these regimes is presented. These regimes are the constant-ψ resistive-inertial (RI) regime, the constant-ψ viscoresistive regime, and the non-constant-ψ inviscid tearing regime. The last regime includes the constant-ψ RI regime and the inertial regime. The results show that reasonable accuracy can be obtained very efficiently with Padé approximants having a small number of parameters.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Hybrid Finite Element--Spectral Method for the Fractional Laplacian: Approximation Theory and Efficient Solver

Here, a numerical scheme is presented for approximating fractional order Poisson problems in two and three dimensions. The scheme is based on reformulating the original problem posed over $\Omega$ on the extruded domain $\mathcal{C}=\Omega\times[0,\infty)$ following. The resulting degenerate elliptic integer order PDE is then approximated using a hybrid FEM-spectral scheme. Finite elements are used in the direction parallel to the problem domain $\Omega$, and an appropriate spectral method is used in the extruded direction. The spectral part of the scheme requires that we approximate the true eigenvalues of the integer order Laplacian over $\Omega$. We derive an a priori error estimate which takes account of the error arising from using an approximation in place of the true eigenvalues. We further present a strategy for choosing approximations of the eigenvalues based on Weyl's law and finite element discretizations of the eigenvalue problem. The system of linear algebraic equations arising from the hybrid FEM-spectral scheme is decomposed into blocks which can be solved effectively using standard iterative solvers such as multigrid and conjugate gradient. Numerical examples in two and three dimensions suggest that the approach is quasi-optimal in terms of complexity.

97 MATHEMATICS AND COMPUTING↗

Computing partition functions in the one-clean-qubit model

We present a method to approximate partition functions of quantum systems using mixed-state quantum computation. For positive-semidefinite Hamiltonians, our method has an expected running-time that is almost linear in [M/( ε rel Z )] 2 , where M is the dimension of the quantum system, Z is the partition function, and ε rel is the relative precision. It is based on approximations of the exponential operator as linear combinations of certain operators related to block-encoding of Hamiltonians or Hamiltonian evolutions. The trace of each operator is estimated using a standard algorithm in the one-clean-qubit model. For large values of Z , our method may run faster than exact classical methods, whose complexities are polynomial in M . We also prove that a version of the partition function estimation problem within additive error is complete for the so-called DQC1 complexity class, suggesting that our method provides a superpolynomial speedup for certain parameter values. Overall, to attain a desired relative precision, we develop a classical procedure based on a sequence of approximations within predetermined additive errors that may be of independent interest.

97 MATHEMATICS AND COMPUTING↗

Density scaling approximation for Monte-Carlo simulations of radioactive plumes

The release of radioactive gas into the atmosphere can diffuse into large volumes of air downwind from the point of release. The extent of radioactivity can cover thousands of cubic meters of air. For such large volumes, the weather models used to predict the down-wind distribution of the plume and the radiation transport models used to predict the radiation reaching ground-level from the plume can take tens of hours of computer time on multi-node institutional High-Performance Computing facilities. In this paper we focus on the radiation transport aspect of plume modeling. Here, we describe a phenomenological method for approximating the amounts of radiation that reach ground level from large volumes of a static radioactive plume that can be calculated on a stand-alone personal computer in much shorter computation times than those usually needed for such large volume evaluations. We refer to this method as the Density Scaling Approximation (DSA). Its ability to approximate ground-level count rates of large plumes comes from using a small-plume volume with a scaled-up value of air density to simulate the same number of scatterings that occur during transport in larger plume volumes at normal air density. We demonstrate the DSA by using a 100 m-diameter air-filled hemispherical dome geometry with a uniform volumetric activity of 135 Xe gas throughout the air-filled volume. The DSA for a larger dome diameter is obtained by evaluating the 100 m dome with an air density scaled up by the linear ratio of the larger diameter to the 100 m diameter. We find that this approximation works well for dome diameters up to 1200 m – the largest diameter studied and a size more than sufficient for accounting for all the radiation from 135 Xe. Moreover, most of our DSA results can be calculated over 500 times faster than corresponding full-sized geometry with normal air density. To help evaluate the accuracy of the DSA and gain insight into how well it can reproduce different regions of the spectra, we use three, easily understood regions of interest to compare the DSA results to the full-sized geometry at normal air density results. These regions are the full-energy peak, the region of single-Compton scattering, and the region of multiple-Compton scattering. We show how the dominance of the Compton scattering mechanism determines this division and thus provides insight into how Compton scattering is manifested in spectra from photon scattering through air in general, and how well the DSA approximation works.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Grating-based holographic diffraction methods for X-rays and neutrons: phase object approximation and dynamical theory

A method dubbed grating-based holography was recently used to determine the structure of colloidal fluids in the rectangular grooves of a diffraction grating from X-ray scattering measurements. Similar grating-based measurements have also been recently made with neutrons using a technique called spin-echo small-angle neutron scattering. The analysis of the X-ray diffraction data was done using an approximation that treats the X-ray phase change caused by the colloidal structure as a small perturbation to the overall phase pattern generated by the grating. In this paper, the adequacy of this weak phase approximation is explored for both X-ray and neutron grating holography. Additionally, it is found that there are several approximations hidden within the weak phase approximation that can lead to incorrect conclusions from experiments. In particular, the phase contrast for the empty grating is a critical parameter. Finally, while the approximation is found to be perfectly adequate for X-ray grating holography experiments performed to date, it cannot be applied to similar neutron experiments because the latter technique requires much deeper grating channels.

36 MATERIALS SCIENCE↗

Generalized spin σ -SCF method

We introduce a generalization of the σ-SCF method to approximate noncollinear spin ground and excited single-reference electronic states by minimizing the Hamiltonian variance. The new method is based on the σ-SCF method, originally proposed by Ye et al. [J. Chem. Phys. 147, 214104 (2017)], and provides a prescription to determine ground and excited noncollinear spin states on an equal footing. Our implementation was carried out utilizing an initial simulated annealing stage followed by a mean-field iterative self-consistent approach to simplify the cumbersome search introduced by generalizing the spin degrees of freedom. The simulated annealing stage ensures a broad exploration of the Hilbert space spanned by the generalized spin single-reference states with random complex element-wise rotations of the generalized density matrix elements in the simulated annealing stage. The mean-field iterative self-consistent stage employs an effective Fockian derived from the variance, which is utilized to converge tightly to the solutions. This process helps us to easily find complex spin structures, avoiding manipulating the initial guess. As proof-of-concept tests, we present results for Hn (n = 3–7) planar rings and polyhedral clusters with geometrical spin frustration. We show that most of these systems have noncollinear spin excited states that can be interpreted in terms of geometric spin frustration. These states are not directly targeted by energy minimization methods, which are meant to converge to the ground state. This stresses the capability of the σ-SCF methodology to find approximate noncollinear spin structures as mean-field excited states.

Chemistry↗

Coupled Cluster and Density Functional Studies of Atomic Fluorine Chemisorption on Coronene as Model Systems for Graphene Fluorination

Potential energy curves (PECs) of atomic fluorine adsorption on coronene as a model for graphene or nanocarbon surfaces have been computed. The PECs were obtained by scanning the fluorine atom distance to one of the center carbon atoms of the coronene molecule as model system in a “top” position from 4.0 to1.0 Å in intervals of 0.1 Å using a variety of quantum chemical methods. Various density functional theory (DFT) functionals, such as B3LYP, PBE, PBE0, CAM-B3LYP, and LC-ωPBE; approximate DFT methods such as several levels of the density-functional tight-binding (DFTB) method, as well as ab initio wave function theory methods such as MP2, CCSD, CCSD(T), and G2MS extrapolations, were used to evaluate energies for B3LYP/cc-pVDZ PEC geometries. G2MS is an approximation to the highly accurate CCSD(T)/cc-pVTZ level of theory in our work. We found that fluorine is chemically adsorbed on coronene with a binding energy of 22.9 and 23.3 kcal/mol at the B3LYP/cc-pVDZ and G2MS levels of theory, respectively, and 18.3 and 19.3 kcal/mol after counterpoise correction. Here, we found that pure DFT functionals and their DFTB approximations fail to predict the correct dissociation limit due to the DFT-inherent self-interaction error and various limitations in the DFTB approximation itself.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Introducing the embedded random phase approximation: H 2 dissociative adsorption on Cu(111) as an exemplar

The random phase approximation (RPA) as a means of treating electron correlation recently has been shown to outperform standard density functional theory (DFT) approximations in a variety of cases. However, the computational cost of the RPA is substantially more than DFT, especially when aiming to study extended surfaces. Properly accounting for sufficient surface ensemble size, Brillouin zone sampling, and vacuum separation of periodic images in standard periodic-planewave-based DFT code raises the cost to achieve converged results. Here, we show that sub-system embedding schemes enable use of the RPA for modeling heterogeneous reactions at reduced computational cost. Further, we explore two different embedded RPA (emb-RPA) approaches, periodic emb-RPA and cluster emb-RPA. We use the (experimentally and theoretically) well-studied H 2 dissociative adsorption on Cu(111) as our exemplar, and first perform full periodic RPA calculations as a benchmark. The full RPA results match well the semi-empirical barrier fit to experimental observables and others derived from high-level computations, e.g., from recent embedded n-electron valence second order perturbation theory [Zhao et al., J. Chem. Theory Comput. 16(11), 7078–7088 (2020)] and quantum Monte Carlo [Doblhoff-Dier et al., J. Chem. Theory Comput. 13(7), 3208–3219 (2017)] simulations. Among the two emb-RPA approaches tested, the cluster emb-RPA accurately reproduces the energy profile (maximum error of 50 meV along the reaction pathway) while reducing the computational cost by approximately two orders of magnitude. We therefore expect that the embedded cluster approach will enable wider RPA implementation in heterogeneous catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Method for estimating optimal spectral and energy parameters of laser irradiation in photodynamic therapy of biological tissue

We have solved the problem of layer-by-layer laser-light dosimetry in biological tissues and of selecting an individual therapeutic dose in laser therapy. A method is proposed for real-time monitoring of the radiation density in tissue layers in vivo, concentrations of its endogenous (natural) and exogenous (specially administered) chromophores, as well as in-depth distributions of the spectrum of light action on these chromophores. As the background information use is made of the spectrum of diffuse light reflected from a patient's tissue, measured by a fibre-optic spectrophotometer. The measured spectrum is quantitatively analysed by the method of approximating functions for fluxes of light multiply scattered in tissue and by a semi-analytical method for calculating the in-depth distribution of the light flux in a multi-layered medium. We have shown the possibility of employing the developed method for monitoring photosensitizer and oxyhaemoglobin concentrations in tissue, light power absorbed by chromophores in tissue layers at different depths and laser-induced changes in the tissue morphology (vascular volume content and ratios of various forms of haemoglobin) during photodynamic therapy. (biophotonics)

60 APPLIED LIFE SCIENCES↗