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At least 433 records · Page 24

Deep medical image analysis with representation learning and neuromorphic computing

Deep learning is increasingly used in medical imaging, improving many steps of the processing chain, from acquisition to segmentation and anomaly detection to outcome prediction. Yet significant challenges remain: (i) image-based diagnosis depends on the spatial relationships between local patterns, something convolution and pooling often do not capture adequately; (ii) data augmentation, the de facto method for learning three-dimensional pose invariance, requires exponentially many points to achieve robust improvement; (iii) labelled medical images are much less abundant than unlabelled ones, especially for heterogeneous pathological cases; and (iv) scanning technologies such as magnetic resonance imaging can be slow and costly, generally without online learning abilities to focus on regions of clinical interest. To address these challenges, novel algorithmic and hardware approaches are needed for deep learning to reach its full potential in medical imaging.

60 APPLIED LIFE SCIENCES↗

Application of Aura OMI L2G Products Compared with NASA MERRA-2 Assimilation

The Ozone Monitoring Instrument (OMI) is one of the instruments aboard NASA's Aura satellite. It measures ozone total column and vertical profile, aerosols, clouds, and trace gases including NO2, SO2, HCHO, BrO, and OClO using absorption in the ultraviolet electromagnetic spectrum (280 - 400 nm). OMI Level-2G (L2G) products are based on the pixel-level OMI granule satellite measurements stored within global 0.25 deg. X 0.25 deg. grids, therefore they conserve all the Level 2 (L2) spatial and temporal details for 24 hours of scientific data in one file. The second Modern-Era Retrospective analysis for Research and Applications (MERRA-2) is NASA's atmospheric reanalysis, using an upgraded version of Goddard Earth Observing System Model, version 5 (GEOS-5) data assimilation system. MERRA-2 includes aerosol data reanalysis and improved representations of stratospheric ozone, compared with its predecessor MERRA, in both instantaneous and time-averaged collections. It is found that simply comparing satellite Level-3 products might cause biases, due to lack of detailed temporal and original retrieval information. It is therefore preferable to inter-compare or implement satellite derived physical quantities directly with/to model assimilation with as high temporal and spatial resolutions as possible. This study will demonstrate utilization of OMI L2G daily aerosol and ozone products by comparing them with MERRA-2 hourly aerosol/ozone simulations, matched in both space and time aspects. Both OMI and MERRA-2 products are accessible online through NASA Goddard Earth Sciences Data Information Services Center (GES DISC, https://disc.gsfc.nasa.gov/).

OMI L2G products↗

A high accuracy/resolution spectral element/Fourier–Galerkin method for the simulation of shoaling non-linear internal waves and turbulence in long domains with variable bathymetry

A high-order hybrid continuous-Galerkin numerical method, designed for the simulation of non-linear, non -hydrostatic internal waves and turbulence in long computational domains with complex bathymetry, is presented. The spatial discretization in the non-periodic wave-propagating directions, utilizes the nodal spectral element method. Such a high-order element-based discretization allows the highly accurate representation of complex domain geometry along with the flexibility of concentrating resolution in areas of interest. Under the assumption of the normal-to-isobath propagation of non-linear internal waves, a third periodic direction is incorporated via a Fourier-Galerkin discretization. The distinct non-hydrostatic nature of non-linear internal waves and, any instabilities and turbulence therein, necessitates the numerically challenging solution of the pressure Poisson problem. A defining feature of this work is the application of a domain decomposition approach, combined with block-Jacobi/deflation-based preconditioning to the pressure Poisson problem. Such a combined approach is particularly suitable for the long high aspect-ratio complex domains of interest and enables the efficient high-accuracy reproduction of the non-hydrostatic dynamics of non-linear internal waves. Implementation details are also described in the context of the stability of the solver and its parallelization strategy. A series of benchmarks of increasing complexity demonstrate the robustness of the flow solver. The benchmarks culminate with the three-dimensional simulation of a convectively breaking mode-one non-linear internal wave over a realistic South-China-Sea bathymetric transect and background current/stratification profiles.

Deflation↗

Implementation and Evaluation of Emission‐Driven Land‐Atmosphere Coupled Simulation in E3SMv2.1

Emissions-driven (prognostic CO 2 ) simulations are essential for representing two-way carbon-climate feedback in Earth System Models. We present an emissions-driven land–atmosphere coupled biogeochemistry (BGC) configuration (BGCLNDATM_progCO2) in version 2.1 of the Energy Exascale Earth System Model (E3SMv2.1). This is the first E3SM configuration that performs land-atmosphere emission-hindcasts. Here, we document its implementation, evaluate the model's performance against observations and other models, and propose a structured evaluation protocol for such emissions-driven simulations. We conducted transient historical simulations (1850–2014) with BGCLNDATM_progCO2 and compare them to reference simulations—a land-atmosphere coupled simulation without BGC and a standalone land simulation with BGC, both using prescribed CO 2 concentrations—and to observations. BGCLNDATM_progCO2 overestimates atmospheric CO 2 concentrations by 11–23 ppm yet stays within the 40-ppm spread CMIP6 emission-driven models and retains physical climate properties comparable to the reference runs. The CO 2 biases are partly attributed to underrepresented oceanic CO 2 uptake and inadequate representations of some terrestrial processes. In general, introducing prognostic CO 2 did not change physical climate metrics at the global scale but had larger regional effects, particularly over land where spatially heterogeneous CO 2 and prognostic leaf area index influenced surface energy balance. Finally, we propose a general evaluation protocol including spin-up assessment, atmospheric CO 2 benchmarking, physical climate evaluation, and land biogeochemical analysis to support scientific rigor and facilitate inter-model comparisons. The new configuration lays the groundwork for future enhancements, including improved terrestrial biogeochemical processes, integrated marine biogeochemistry, and additional human–Earth system interactions. These developments advance E3SM toward fully coupled emissions-driven simulations, enabling more accurate carbon–climate feedback projections and informing mitigation policy by providing physically consistent carbon-budget metrics for mitigation scenarios.

54 ENVIRONMENTAL SCIENCES↗

A Predictor-Corrector Strategy for Adaptivity in Dynamical Low-Rank Approximations

Here, in this paper, we present a predictor-corrector strategy for constructing rank-adaptive, dynamical low-rank approximations (DLRAs) of matrix-valued ODE systems. The strategy is a compromise between (i) low-rank step-truncation approaches that alternately evolve and compress solutions and (ii) strict DLRA approaches that augment the low-rank manifold using subspaces generated locally in time by the DLRA integrator. The strategy is based on an analysis of the error between a forward temporal update into the ambient full-rank space, which is typically computed in a step-truncation approach before recompressing, and the standard DLRA update, which is forced to live in a low-rank manifold. We use this error, without requiring its full-rank representation, to correct the DLRA solution. A key ingredient for maintaining a low-rank representation of the error is a randomized SVD, which introduces some degree of stochastic variability into the implementation. The strategy is formulated and implemented in the context of discontinuous Galerkin spatial discretizations of PDEs and applied to several versions of DLRA methods found in the literature as well as a new variant. Numerical experiments comparing the predictor-corrector strategy to other methods demonstrate robustness to overcome shortcomings of step truncation or strict DLRA approaches: The former may require more memory than is strictly needed, while the latter may miss transients solution features that cannot be recovered. The effect of randomization, tolerances, and other implementation parameters is also explored.

97 MATHEMATICS AND COMPUTING↗

MLMOD: Machine Learning Methods for Data-Driven Modeling in LAMMPS

MLMOD is a software package for incorporating machine learning approaches and models into simulations of microscale mechanics and molecular dynamics in LAMMPS. Recent machine learning approaches provide promising data-driven approaches for learning representations for system behaviors from experimental data and high fidelity simulations. The package facilitates learning and using data-driven models for (i) dynamics of the system at larger spatial-temporal scales (ii) interactions between system components, (iii) features yielding coarser degrees of freedom, and (iv) features for new quantities of interest characterizing system behaviors. MLMOD provides hooks in LAMMPS for (i) modeling dynamics and time-step integration, (ii) modeling interactions, and (iii) computing quantities of interest characterizing system states. The package allows for use of machine learning methods with general model classes including Neural Networks, Gaussian Process Regression, Kernel Models, and other approaches. Here we discuss our prototype C++/Python package, aims, and example usage. For related papers, examples, updates, and additional information see https://github.com/atzberg/mlmod and http://atzberger.org/.

97 MATHEMATICS AND COMPUTING↗

Lattice Clifford fractons and their Chern-Simons-like theory

We use Dirac matrix representations of the Clifford algebra to build fracton models on the lattice and their effective Chern-Simons-like theory. As an example, we build lattice fractons in odd D spatial dimensions and their (D+1) spacetime dimensional effective theory. The model possesses an anti-symmetric K matrix resembling that of hierarchical quantum Hall states. The gauge charges are conserved in sub-dimensional manifolds which ensures the fractonic behavior. The construction extends to any lattice fracton model built from commuting projectors and with tensor products of spin-1/2 degrees of freedom at the sites.

Fontana, Weslei↗

A Lagrangian method for a two layer shallow water model

One of the biggest drawbacks of Eulerian methods is the presence of the nonlinear convective terms which leads to inaccurate representations of advection and fronts. An alternative and conceptually simpler approach is the Lagrangian approach in which the fluid particles themselves are tracked and equations are derived based on local spatial interaction. In this formulation the nonlinear convective terms do not appear. The main drawback with the Lagrangian formulation, however, is that the local spatial interactions are time dependent. That is, at each time level, one must know the current neighbors of a given particle to accurately compute the forces acting on the particle. The Voroni Mesh which is continuously deforming and always linking nearest neighbors is needed. The effectiveness of a simple Lagrangian method for simulating the onset of a Kelvin-Helmholtz instability in a 2 layer fluid is demonstrated.

Augenbaum, J. M.↗

The solution of non-linear hyperbolic equation systems by the finite element method

A finite-element method for the solution of nonlinear hyperbolic systems of equations, such as those encountered in non-self-adjoint problems of transient phenomena in convection-diffusion or in the mixed representation of wave problems, is developed and demonstrated. The problem is rewritten in moving coordinates and reinterpolated to the original mesh by a Taylor expansion prior to a standard Galerkin spatial discretization, and it is shown that this procedure is equivalent to the time-discretization approach of Donea (1984). Numerical results for sample problems are presented graphically, including such shallow-water problems as the breaking of a dam, the shoaling of a wave, and the outflow of a river; compressible flows such as the isothermal flow in a nozzle and the Riemann shock-tube problem; and the two-dimensional scalar-advection, nonlinear-shallow-water, and Euler equations.

Loehner, R.↗

Finite Element Model Development and Validation for Aircraft Fuselage Structures

The ability to extend the valid frequency range for finite element based structural dynamic predictions using detailed models of the structural components and attachment interfaces is examined for several stiffened aircraft fuselage structures. This extended dynamic prediction capability is needed for the integration of mid-frequency noise control technology. Beam, plate and solid element models of the stiffener components are evaluated. Attachment models between the stiffener and panel skin range from a line along the rivets of the physical structure to a constraint over the entire contact surface. The finite element models are validated using experimental modal analysis results. The increased frequency range results in a corresponding increase in the number of modes, modal density and spatial resolution requirements. In this study, conventional modal tests using accelerometers are complemented with Scanning Laser Doppler Velocimetry and Electro-Optic Holography measurements to further resolve the spatial response characteristics. Whenever possible, component and subassembly modal tests are used to validate the finite element models at lower levels of assembly. Normal mode predictions for different finite element representations of components and assemblies are compared with experimental results to assess the most accurate techniques for modeling aircraft fuselage type structures.

Buehrle, Ralph D.↗

A Large Dataset of Fluvial Hydraulic and Geometry Attributes Derived From USGS Field Measurement Records

Accurate representation of river channel geometry is important for hydrologic and hydraulic modeling of fluvial systems. Often, channel geometry is estimated using simple rating curves that can be applied across various spatial scales. However, such methods are limited to power law relations that do not employ many potentially relevant catchment and river attributes. This paper introduce a new dataset, IFMHA (Inventory of Field Measurement of Hydraulic Attributes), to enable research studies on channel geometry and streamflow characteristics. IFMHA is derived from the National Water Information System (NWIS) site inventory for surface water field measurements and stream attributes from the National Hydrography Dataset (NHD). IFMHA includes 2,802,532 records from 10,050 sites (NWIS streamgaging stations). The dataset utility is demonstrated here by presenting a series of conceptual models for estimating channel geometry parameters (i.e., channel mean depth, channel maximum depth, wetted perimeter, and roughness) based on the available field attributes within IFMHA. Such a dataset and attributed channel geometry parameters can enhance the performance of operational flood forecasting frameworks (e.g. National Water Model) by providing more accurate initial conditions used in hydrologic and hydraulic routing models.

Hydrology↗

Euler-Rodrigues Parameters: A Quantum Circuit to Calculate Rigid-Body Rotations

The use of vectorial parameterization to create geometrical representations in computational models has a large number of applications. One particular application is the calculation of the 3D rotational motion of rigid bodies, that could be used for the spatial location estimation from objects. Provided the algebraic nature of this problem, it could benefit from Quantum Computing, in particular several vectors could be superposed to be transformed with a single operation, providing a quantum processing advantage. In this article, we propose an implementation of a Quantum Computing algorithm to compute Euler-Rodrigues Parameters to model rigid body rotations to transform arbitrary functions, rotating multiple vectors in superposition. We developed this algorithm using Qiskit, taking into account the limitations imposed by the current Noisy Intermediate Scale Quantum (NISQ) devices, such as the reduced number of qubits available and the limited coherence time.

Pelaez, Emilio↗

A 2-D Interface Element for Coupled Analysis of Independently Modeled 3-D Finite Element Subdomains

Over the past few years, the development of the interface technology has provided an analysis framework for embedding detailed finite element models within finite element models which are less refined. This development has enabled the use of cascading substructure domains without the constraint of coincident nodes along substructure boundaries. The approach used for the interface element is based on an alternate variational principle often used in deriving hybrid finite elements. The resulting system of equations exhibits a high degree of sparsity but gives rise to a non-positive definite system which causes difficulties with many of the equation solvers in general-purpose finite element codes. Hence the global system of equations is generally solved using, a decomposition procedure with pivoting. The research reported to-date for the interface element includes the one-dimensional line interface element and two-dimensional surface interface element. Several large-scale simulations, including geometrically nonlinear problems, have been reported using the one-dimensional interface element technology; however, only limited applications are available for the surface interface element. In the applications reported to-date, the geometry of the interfaced domains exactly match each other even though the spatial discretization within each domain may be different. As such, the spatial modeling of each domain, the interface elements and the assembled system is still laborious. The present research is focused on developing a rapid modeling procedure based on a parametric interface representation of independently defined subdomains which are also independently discretized.

Kandil, Osama A.↗

Satellite Derived Land Surface Temperature for Model Assimilation

Studies have shown that land surface temperature (LST) tendencies are sensitive to the surface moisture availability which is a function of soil moisture and vegetation. The assimilation of satellite derived LST tendencies into the surface energy budget of mesoscale models has shown promise in improving the representation of the complex effects of both soil moisture and vegetation within the models for short term simulations. LST derived from geostationary satellites has the potential of providing the temporal and spatial resolution needed for an LST assimilation process. This paper presents an analysis comparing the LST derived from GOES-8 infrared measurements with LST calculated by the MM5 numerical model. The satellite derived LSTs are calculated using a physical split window approach using channels 4 and 5 of GOES-8. The differences in the LST data sets, especially the tendencies, are presented and examined. Quantifying the differences between the data sets provide insight of possible weaknesses in the model parameterizations affecting the surface energy budget calculations and an indication of the potential effectiveness o f assimilating LST into the models.

Suggs, Ronnie J.↗

From primal sketches to the recovery of intensity and reflectance representations

A local change in intensity (edge) is a characteristic that is preserved when an image is filtered through a bandpass filter. Primal sketch representations of images, using the bandpass-filtered data, have become a common process since Marr proposed his model for early human vision. Here, researchers move beyond the primal sketch extraction to the recovery of intensity and reflectance representations using only the bandpass-filtered data. Assessing the response of an ideal step edge to the Laplacian of Gaussian (NAb/A squared G) filter, they found that the resulting filtered data preserves the original change of intensity that created the edge in addition to the edge location. Using the filtered data, they can construct the primal sketches and recover the original (relative) intensity levels between the boundaries. It was found that the result of filtering an ideal step edge with the Intensity-Dependent Spatial Summation (IDS) filter preserves the actual intensity on both sides of the edge, in addition to the edge location. The IDS filter also preserves the reflectance ratio at the edge location. Therefore, one can recover the intensity levels between the edge boundaries as well as the (relative) reflectance representation. The recovery of the reflectance representation is of special interest as it erases shadowing degradations and other dependencies on temporal illumination. This method offers a new approach to low-level vision processing as well as to high data-compression coding. High compression can be gained by transmitting only the information associated with the edge location (edge primitives) that is necessary for the recovery

Alter-Gartenberg, Rachel↗

Dual spectra and mixed energy cascade of turbulence in the wavelet representation

The wavelet-transformed Navier-Stokes equations are used to define quantities such as the transfer of kinetic energy and the flux of kinetic energy through scale r at position x. Direct numerical simulations of turbulent shear flow reveal that although their mean spatial values agree with their traditional counterparts in Fourier space, their spatial variability at every scale is very large, exhibiting non-Gaussian statistics. The local flux of energy involving scales smaller than some r also exhibits large spatial intermittency, and it is negative quite often, indicative of local inverse cascades.

Meneveau, Charles↗

GIS-Based Modeling of Contaminated Soil Volumes at Multiple Sites in the Formerly Utilized Sites Remedial Action Program - 20149

The remediation of hazardous, toxic, and radioactive waste (HTRW) sites produces cost-related risks associated with the estimation of contaminated soil or debris volumes. Historical risk-management techniques include cost contingencies to cover volume uncertainties that affect project budgeting and decision-making. The Buffalo District teamed with project partners to lessen volume uncertainty and reduce project risks at multiple HTRW sites managed under the Formerly Utilized Sites Remedial Action Program (FUSRAP). Historical remedial investigations under FUSRAP commonly identified the presence of radiological material in site media, the associated human health risk, and then areas of remediation. To manage remedial execution and reduce risk, pre-design or remediation-phase sampling essentially 'chased' contamination, which was not conducive to efficient predictive budgeting derived from Feasibility Study (FS) cost analyses. The Buffalo District first optimized their approach to better understand volume uncertainty by utilizing the Argonne National Laboratory's Bayesian Approaches for Adaptive Spatial Sampling (BAASS) software [1]. BAASS processed soft data (e.g., gamma walk-over data) and spatial sampling data to estimate the lateral extent of contaminated soil irrespective of depth (i.e., gross contamination extent) and define areas of contaminant uncertainty. The software performed a binary transformation of contaminant concentrations at all sampling points based upon remedial action goals or a sum of ratios approach (i.e., clean, impacted, or range of impacts in soil). The model produced two-dimensional (horizontal) contaminant probability contours and statistical uncertainty in the sampling coverage and resulting contaminant extents. This method was translated vertically by partitioning the sampling data into depth brackets that produced a stacked representation of contaminant extents and uncertainty in the subsurface (i.e., similar to construction lifts). The results commonly led to a better understanding of project uncertainty and the need for sampling strategies that produce high-confidence soil volumes, which control costs. The BAASS-based delineations were eventually replaced by Empirical Bayesian Kriging (EBK) methods available in ArcGIS Spatial or 3D Analysts [2]. The EBK method calculates contaminant probability zones derived from user-controlled semivariograms of the spatial datasets. The resulting probability zones (e.g., 50% or 80% of contaminant probability) represent the two-dimensional surface delineation of the overall horizontal remedial area, similarly to BAASS. However, unlike BAASS, the vertical sampling data within these probability zones became vertical control points to contour a subterranean surface that connects subsurface points to the land-surface delineations of contamination. The resulting representation of horizontal and vertical impacts within an enclosed envelop (volume) of soil included uncertainty distributions that are used to plan uncertainty-reduction sampling. These data-driven and math-based models of three-dimensional sampling results produced well-bounded remedial volumes for project planning and better uncertainty predictions during project budgeting. The EBK method was applied to several FUSRAP sites managed by the Buffalo District and compared to less rigorously modeled sites previously remediated by the District. The comparison of modeled to actual remediated volumes provide a basis for validating the volume-estimation method. This comparison is important to ensure modeled volumes match physical boundaries of site remediation. FUSRAP sites with denser investigative sampling and lesser volume uncertainty proved useful in remedial planning and contracting. The Buffalo District noted that historical sites with sparser sampling arrays had greater disparity between estimated volumes and final remedial volumes. The benefit achieved over the cost of detailed soil sampling appears positive for FUSRAP projects, especially where impacts vary widely and appear unbounded by investigation-phase sampling. The subsequent Empirical Bayesian Kriging of contamination coupled with vertical contouring for soil estimations reduces uncertainty in soil volumes or indicates where sampling is required to reduce uncertainty, which together optimize remedial planning and budgeting. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

A field–particle correlation analysis of a perpendicular magnetized collisionless shock

Using the field–particle correlation technique, we examine the particle energization in a three-dimensional (one spatial dimension and two velocity dimensions; 1D-2V) continuum Vlasov–Maxwell simulation of a perpendicular magnetized collisionless shock. The combination of the field–particle correlation technique with the high-fidelity representation of the particle distribution function provided by a direct discretization of the Vlasov equation allows us to ascertain the details of the exchange of energy between the electromagnetic fields and the particles in phase space. We identify the velocity-space signatures of shock-drift acceleration of the ions and adiabatic heating of the electrons arising from the perpendicular collisionless shock by constructing a simplified model with the minimum ingredients necessary to produce the observed energization signatures in the self-consistent Vlasov–Maxwell simulation. We are thus able to completely characterize the energy transfer in the perpendicular collisionless shock considered here and provide predictions for the application of the field–particle correlation technique to spacecraft measurements of collisionless shocks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗