SEARCH · Engineering Papers

Results for “representation”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 847 records · Page 47

All sources NASA NTRS DOE OSTI

DOE OSTI2025

DOME: Directional medical embedding vectors from Electronic Health Records

Motivation: The increasing availability of Electronic Health Record (EHR) systems has created enormous potential for translational research. Recent developments in representation learning techniques have led to effective large-scale representations of EHR concepts along with knowledge graphs that empower downstream EHR studies. However, most existing methods require training with patient-level data, limiting their abilities to expand the training with multi-institutional EHR data. On the other hand, scalable approaches that only require summary-level data do not incorporate temporal dependencies between concepts. Methods: We introduce a DirectiOnal Medical Embedding (DOME) algorithm to encode temporally directional relationships between medical concepts, using summary-level EHR data. Specifically, DOME first aggregates patient-level EHR data into an asymmetric co-occurrence matrix. Then it computes two Positive Pointwise Mutual Information (PPMI) matrices to correspondingly encode the pairwise prior and posterior dependencies between medical concepts. Following that, a joint matrix factorization is performed on the two PPMI matrices, which results in three vectors for each concept: a semantic embedding and two directional context embeddings. They collectively provide a comprehensive depiction of the temporal relationship between EHR concepts. Results: We highlight the advantages and translational potential of DOME through three sets of validation studies. First, DOME consistently improves existing direction-agnostic embedding vectors for disease risk prediction in several diseases, for example achieving a relative gain of 5.5% in the area under the receiver operating characteristic (AUROC) for lung cancer. Second, DOME excels in directional drug-disease relationship inference by successfully differentiating between drug side effects and indications, correspondingly achieving relative AUROC gain over the state-of-the-art methods by 10.8% and 6.6%. Finally, DOME effectively constructs directional knowledge graphs, which distinguish disease risk factors from comorbidities, thereby revealing disease progression trajectories. The source codes are provided at https://github.com/celehs/Directional-EHRembedding.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

A velocity space hybridization-based Boltzmann equation solver

In the present research, a new method for simulation of rarefied gas flows is proposed, a velocity-space hybrid of both a DSMC representation of particles and a discrete velocity quasi-particle representation of the distribution function. The hybridization scheme is discussed in detail, and is numerically verified for two test-cases: the BKW relaxation problem and a stationary Maxwellian distribution. It is demonstrated that such a velocity-space hybridization can provide computational benefits when compared to a pure discrete velocity method or pure DSMC approach, while retaining some of the more attractive properties of discrete velocity methods. Further possible improvements to the velocity-space hybrid approach are discussed.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Pass-efficient methods for compression of high-dimensional turbulent flow data

The future of high-performance computing, specifically on future Exascale computers, will presumably see memory capacity and bandwidth fail to keep pace with data generated, for instance, from massively parallel partial differential equation (PDE) systems. Current strategies proposed to address this bottleneck entail the omission of large fractions of data, as well as the incorporation of in situ compression algorithms to avoid overuse of memory. To ensure that post-processing operations are successful, this must be done in a way that a sufficiently accurate representation of the solution is stored. Moreover, in situations where the input/output system becomes a bottleneck in analysis, visualization, etc., or the execution of the PDE solver is expensive, the number of passes made over the data must be minimized. In the interest of addressing this problem, this work focuses on the utility of pass-efficient, parallelizable, low-rank, matrix decomposition methods in compressing high-dimensional simulation data from turbulent flows. Additionally, a particular emphasis is placed on using coarse representation of the data – compatible with the PDE discretization grid – to accelerate the construction of the low-rank factorization. This includes the presentation of a novel single-pass matrix decomposition algorithm for computing the so-called interpolative decomposition. The methods are described extensively and numerical experiments on two turbulent channel flow data are performed. In the first (unladen) channel flow case, compression factors exceeding 400 are achieved while maintaining accuracy with respect to first- and second-order flow statistics. In the particle-laden case, compression factors of 100 are achieved and the compressed data is used to recover particle velocities. These results show that these compression methods can enable efficient computation of various quantities of interest in both the carrier and disperse phases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Neural-network learning of SPOD latent dynamics

Here, we aim to reconstruct the latent space dynamics of high dimensional, quasi-stationary systems using model order reduction via the spectral proper orthogonal decomposition (SPOD). The proposed method is based on three fundamental steps: in the first, once that the mean flow field has been subtracted from the realizations (also referred to as snapshots), we compress the data from a high-dimensional representation to a lower dimensional one by constructing the SPOD latent space; in the second, we build the time-dependent coefficients by projecting the snapshots containing the fluctuations onto the SPOD basis and we learn their evolution in time with the aid of recurrent neural networks; in the third, we reconstruct the high-dimensional data from the learnt lower -dimensional representation. The proposed method is demonstrated on two different test cases, namely, a compressible jet flow, and a geophysical problem known as the Madden-Julian Oscillation. An extensive comparison between SPOD and the equivalent POD-based counterpart is provided and differences between the two approaches are highlighted. The numerical results suggest that the proposed model is able to provide low rank predictions of complex statistically stationary data and to provide insights into the evolution of phenomena characterized by specific range of frequencies. The comparison between POD and SPOD surrogate strategies highlights the need for further work on the characterization of the interplay of error between data reduction techniques and neural network forecasts.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Residual-based error correction for neural operator accelerated infinite-dimensional Bayesian inverse problems

We explore using neural operators, or neural network representations of nonlinear maps between function spaces, to accelerate infinite-dimensional Bayesian inverse problems (BIPs) with models governed by nonlinear parametric partial differential equations (PDEs). Neural operators have gained significant attention in recent years for their ability to approximate the parameter-to-solution maps defined by PDEs using as training data solutions of PDEs at a limited number of parameter samples. The computational cost of BIPs can be drastically reduced if the large number of PDE solves required for posterior characterization are replaced with evaluations of trained neural operators. However, reducing error in the resulting BIP solutions via reducing the approximation error of the neural operators in training can be challenging and unreliable. We provide an a priori error bound result that implies certain BIPs can be ill-conditioned to the approximation error of neural operators, thus leading to inaccessible accuracy requirements in training. To reliably deploy neural operators in BIPs, we consider a strategy for enhancing the performance of neural operators: correcting the prediction of a trained neural operator by solving a linear variational problem based on the PDE residual. We show that a trained neural operator with error correction can achieve a quadratic reduction of its approximation error, all while retaining substantial computational speedups of posterior sampling when models are governed by highly nonlinear PDEs. The strategy is applied to two numerical examples of BIPs based on a nonlinear reaction–diffusion problem and deformation of hyperelastic materials. We demonstrate that posterior representations of the two BIPs produced using trained neural operators are greatly and consistently enhanced by error correction.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

A sharp interface Lagrangian-Eulerian method for flexible-body fluid-structure interaction

This paper introduces a sharp-interface approach to simulating fluid-structure interaction (FSI) involving flexible bodies described by general nonlinear material models and across a broad range of mass density ratios. This new flexible-body immersed Lagrangian-Eulerian (ILE) scheme extends our prior work on integrating partitioned and immersed approaches to rigid-body FSI. Our numerical approach incorporates the geometrical and domain solution flexibility of the immersed boundary (IB) method with an accuracy comparable to body-fitted approaches that sharply resolve flows and stresses up to the fluid-structure interface. Unlike many IB methods, our ILE formulation uses distinct momentum equations for the fluid and solid subregions with a Dirichlet-Neumann coupling strategy that connects fluid and solid subproblems through simple interface conditions. As in earlier work, we use approximate Lagrange multiplier forces to treat the kinematic interface conditions along the fluid-structure interface. This penalty approach simplifies the linear solvers needed by our formulation by introducing two representations of the fluid-structure interface, one that moves with the fluid and another that moves with the structure, that are connected by stiff springs. This approach also enables the use of multi-rate time stepping, which allows us to use different time step sizes for the fluid and structure subproblems. Our fluid solver relies on an immersed interface method (IIM) for discrete surfaces to impose stress jump conditions along complex interfaces while enabling the use of fast structured-grid solvers for the incompressible Navier-Stokes equations. The dynamics of the volumetric structural mesh are determined using a standard finite element approach to large-deformation nonlinear elasticity via a nearly incompressible solid mechanics formulation. This formulation also readily accommodates compressible structures with a constant total volume, and it can handle fully compressible solid structures for cases in which at least part of the solid boundary does not contact the incompressible fluid. Selected grid convergence studies demonstrate second-order convergence in volume conservation and in the pointwise discrepancies between corresponding positions of the two interface representations as well as between first and second-order convergence in the structural displacements. The time stepping scheme is also demonstrated to yield second-order convergence. To assess and validate the robustness and accuracy of the new algorithm, comparisons are made with computational and experimental FSI benchmarks. Test cases include both smooth and sharp geometries in various flow conditions. Furthermore, we also demonstrate the capabilities of this methodology by applying it to model the transport and capture of a geometrically realistic, deformable blood clot in an inferior vena cava filter.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

High-order limiting methods using maximum principle bounds derived from the Boltzmann equation I: Euler equations

The use of limiting methods for high-order numerical approximations of hyperbolic conservation laws generally requires defining an admissible region/bounds for the solution. In this work, we present a novel approach for computing solution bounds and limiting for the Euler equations through the kinetic representation provided by the Boltzmann equation, which allows for extending limiters designed for linear advection directly to the Euler equations. Given an arbitrary set of solution values to compute bounds over (e.g., numerical stencil) and a desired linear advection limiter, the proposed approach yields an analytic expression for the admissible region of particle distribution function values, which may be numerically integrated to yield a set of bounds for the density, momentum, and total energy. Further, these solution bounds are shown to preserve positivity of density/pressure/internal energy and, when paired with a limiting technique, can robustly resolve strong discontinuities while recovering high-order accuracy in smooth regions without any ad hoc corrections (e.g., relaxing the bounds). This approach is demonstrated in the context of an explicit unstructured high-order discontinuous Galerkin/flux reconstruction scheme for a variety of difficult problems in gas dynamics, including cases with extreme shocks and shock-vortex interactions. Furthermore, this work presents a foundation for limiting techniques for more complex macroscopic governing equations that can be derived from an underlying kinetic representation for which admissible solution bounds are not well-understood.

42 ENGINEERING↗

DOE OSTI2026

Identifying stochastic dynamics via finite expression methods

Modeling stochastic differential equations (SDEs) is crucial for understanding complex dynamical systems in various scientific fields. Recent methods often employ neural network-based models, which typically represent SDEs through a combination of deterministic and stochastic terms. However, these models usually lack interpretability and have difficulty in generalizing beyond their training domain. Here, this paper introduces the Finite Expression Method (FEX), a symbolic learning approach designed to derive interpretable mathematical representations of the deterministic component of SDEs. For the stochastic component, we integrate FEX with advanced generative modeling techniques to provide a comprehensive representation of SDEs. The numerical experiments on linear, nonlinear, and multidimensional SDEs demonstrate that FEX generalizes well beyond the training domain and delivers more accurate long-term predictions compared to neural network-based methods. The symbolic expressions identified by FEX not only improve prediction accuracy but also offer valuable scientific insights into the underlying dynamics of the systems.

Complex dynamical systems↗

DOE OSTI2026

Quantum mechanical closure of partial differential equations with symmetries

We develop a statistical framework for the dynamical closure of spatiotemporal dynamics governed by partial differential equations. Employing the mathematical framework of quantum mechanics to embed the original classical dynamics into a quantum mechanical representation, we use the space of quantum density operators to model the unresolved degrees of freedom of the original dynamics in a statistical sense, and the framework of quantum measurement to predict their contributions to the resolved dynamics. The embedded dynamics is discretized by a positivity preserving process, leading to a compressed representation that is invariant under the dynamical symmetries of the resolved dynamics. We present a data based formulation of the closure scheme and apply it to a closure problem for the shallow water equations. The numerical results demonstrate that our closure model can accurately predict the main features of the true dynamics, including for out of sample initial conditions.

Delay embedding↗

DOE OSTI2022

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Magnetic structure of topological nodal-line semimetal EuSb 2

Here, we investigated the magnetic structure of the magnetic topological nodal-line semimetal EuSb 2 using x-ray resonant magnetic scattering at the Eu 𝐿 3 absorption edge. Forbidden magnetic reflections confirm antiferromagnetic ordering with propagation vector 𝐪 = (0.5,0,0) below 𝑇 N ≈ 27 K. Azimuthal-angle-dependent measurements reveal that the Eu moments are aligned along the monoclinic 𝑏 axis. Comparison between the measured 𝐐-dependent magnetic Bragg peak intensities and calculations based on representation analysis identifies the magnetic structure as the A-type antiferromagnetic 𝛤 4 representation with a (++−−) arrangement along the 𝑎 direction. These results establish the microscopic magnetic structure of EuSb 2 and provide a basis for understanding the interplay between antiferromagnetism and topological electronic states in this system.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Thermodynamic modeling of the U 3 O 8-x solid solution phase

It is important to accurately characterize the equilibrium behavior of U 3 O 8 during UO 2 nuclear fuel fabrication as the determination of the oxygen to uranium ratio in UO 2 powders and pellets is dependent on U 3 O 8 stoichiometry. Prior thermodynamic modeling efforts have treated U 3 O 8 as stoichiometric; however, it is experimentally known that the phase exhibits hypostoichiometric behavior at temperatures >850 K. The goal of this work was to model U 3 O 8 as a solid solution using the compound energy formalism and optimize the model to experimental data according to the CALPHAD methodology. Results of the U 3 O 8-x model assessment were visualized by recalculating the previously assessed U–O binary phase diagram replacing a stoichiometric representation of U 3 O 8 with a U 3 O 8-x solid solution model. Moreover, a recommendation is made to revise the U 3 O 8 to U conversion factor used in the ASTM C 1453 standard based on the literature and updated thermodynamic representation for U 3 O 8-x presented in this work.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Demonstrating the viability of Lagrangian in situ reduction on supercomputers

Performing exploratory analysis and visualization of large-scale time-varying computational science applications is challenging due to inaccuracies that arise from under-resolved data. In recent years, Lagrangian representations of the vector field computed using in situ processing are being increasingly researched and have emerged as a potential solution to enable exploration. However, prior works have offered limited estimates of the encumbrance on the simulation code as they consider “theoretical” in situ environments. Further, the effectiveness of this approach varies based on the nature of the vector field, benefitting from an in-depth investigation for each application area. With this study, an extended version of Sane et al. (2021), we contribute an evaluation of Lagrangian analysis viability and efficacy for simulation codes executing at scale on a supercomputer. We investigated previously unexplored cosmology and seismology applications as well as conducted a performance benchmarking study by using a hydrodynamics mini-application targeting exascale computing. Here, to inform encumbrance, we integrated in situ infrastructure with simulation codes, and evaluated Lagrangian in situ reduction in representative homogeneous and heterogeneous HPC environments. To inform post hoc accuracy, we conducted a statistical analysis across a range of spatiotemporal configurations as well as a qualitative evaluation. Additionally, our study contributes cost estimates for distributed-memory post hoc reconstruction. In all, we demonstrate viability for each application — data reduction to less than 1% of the total data via Lagrangian representations, while maintaining accurate reconstruction and requiring under 10% of total execution time in over 90% of our experiments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Exploiting Kronecker structure in exponential integrators: Fast approximation of the action of φ $-$functions of matrices via quadrature

Here, in this article, we propose an algorithm for approximating the action of φ $-$ functions of matrices against vectors, which is a key operation in exponential time integrators. In particular, we consider matrices with Kronecker sum structure, which arise from problems admitting a tensor product representation. The method is based on quadrature approximations of the integral form of the φ $-$ functions combined with a scaling and modified squaring method. Owing to the Kronecker sum representation, only actions of 1D matrix exponentials are needed at each quadrature node and assembly of the full matrix can be avoided. Additionally, we derive a priori bounds for the quadrature error, which show that, as expected by classical theory, the rate of convergence of our method is supergeometric. Guided by our analysis, we construct a fast and robust method for estimating the optimal scaling factor and number of quadrature nodes that minimizes the total cost for a prescribed error tolerance. We investigate the performance of our algorithm by solving several linear and semilinear time-dependent problems in 2D and 3D. The results show that our method is accurate and orders of magnitude faster than the current state-of-the-art.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Quantifying the Influence of Size, Shape, and Density of Microplastics on Their Transport Modes: A Modeling Approach

Microplastics (MPs) pose significant risks to marine ecosystems and human health, necessitating accurate predictions of their distributions in aquatic environments for effective risk mitigation. However, understanding MP transport dynamics is challenging because of the inadequate representation of MP characteristics such as size, shape, and density in numerical models. Further, the accuracy of the MP vertical profiles in existing models has not been thoroughly validated. Thus, we developed an MP transport model within the Finite Volume Community Ocean Model framework (FVCOM-MP) by integrating MP characteristics. We validated FVCOM-MP against experimental and analytical data, focusing on various MP transport modes and transitions. FVCOM-MP successfully replicates MP profiles in different transport modes, including the bedload, surface-load, suspended-load, and mixed-load modes. Additionally, we introduce phase diagrams for classifying MP transport modes based on particle characteristics, enhancing our understanding of MP dynamics in aquatic systems. The transport modes for a number of real-world MP particles, including fishing line, plastic bag/bottle fragments, synthetic fibers, tire wear particles, polyvinyl chloride and expanded polystyrene pellets, were analyzed with these phase diagrams.

Microplastic transport, Settling velocity, Rising ↗

DOE OSTI2020

Database development and exploration of process–microstructure relationships using variational autoencoders

The paper demonstrates graphical representation of a large database containing process–microstructure relationships using an unsupervised machine learning algorithm. Correlating microstructural features to processing is an essential first step to answer the difficult problem of process sequence design. Here, a large database of 346,200 orientation distribution functions resulting from a variety of process sequences is constructed, where each sequence comprises up to four stages of tension, compression and rolling along different directions in various permutations. This open-source database is constructed for collaborative development of process design algorithms. The paper demonstrates a novel application of the large database: graphical representation of texture–process relationships. A variational autoencoder is used to reduce the entire database to a two dimensional latent space where variations in processes and properties can be visualized. Using proximity analysis in this latent space, we can quickly unearth multiple process solutions to the problem of texture or property design.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Dense autoencoders, clustering techniques, and semi-supervised learning for HPGe $γ$-spectra

Classifying high-resolution gamma spectra by their isotopic content is an essential task in nuclear forensics and other applications. Traditional analysis methods are often time-intensive, but machine learning (ML) may help analysts quickly process many spectra. Such methods tend to rely on abundant, well-labeled data for training. Historical gamma data exists in various fields but is not uniformly useful for supervised ML due to inconsistent labeling. Here, to address some of these challenges, we present a method to classify and organize unlabeled data from high-purity germanium detectors using an autoencoding neural network (autoencoder). We trained dense autoencoders to compress gamma data into latent representations that enable efficient data characterization. By clustering the encoded spectra or lower-dimensional mappings of them, we identified and removed portions of over-abundant data categories, resulting in a more balanced dataset and improved autoencoder performance. This encoding and clustering pipeline also enabled the organization of spectra into self-consistent categories. Finally, we found that encoded representations showed potential as inputs for semi-supervised learning of nuclide identification (NID) labels, achieving an average F1 score of 0.85 ± 0.03 when mapping encodings to a set of 65 isotope labels.

Autoencoders↗

DOE OSTI2019

A framework for assessment of predictive capability maturity and its application in nuclear thermal hydraulics

Here this work presents a formalized and computerized framework for the assessment of decision regarding the adequacy of a simulation tool for a nuclear reactor application. The decision regarding a code’s adequacy for an application is dependent on the assessment of different attributes that govern verification, validation, and uncertainty quantification of the code. In this work, the focus is on code validation. Therefore, the framework is developed and illustrated from the perspective of decision regarding the validation assessment of a code. Code validation assessment is performed based on the validation test results, data applicability, and process quality assurance factors. The process quality assurance factors warrant the trustworthiness of the evidence and help in checking people and process compliance with respect to the standard requirements. The proposed framework is developed using an argument modeling technique called Goal Structuring Notation (GSN). Goal structuring notation facilitates structural knowledge representation, information abstraction, evidence incorporation, and provides a skeletal structure for quantitative maturity assessment. The decision schema for the development of the decision model is based on the Predictive Capability Maturity Model (PCMM) and Analytic Hierarchy Process (AHP) and formalized using Goal structuring notation. Each decision attribute is formulated as a claim, where the degree of validity of the claim (attribute’s assessment) is expressed using different maturity levels. The GSN representation of the decision model is transformed into a confidence network to provide evidence-based quantitative maturity assessment using the Bayesian network. A metric based on the expected utility of maturity levels, called expected distance metric, is proposed to measure the distance between target maturity and achieved maturity on a scale of zero to one. Expected distance metric helps in comparing the assessment of different attributes and identification of major areas of concern in terms of modeling capability, data needs, and quality of assessment process. The practical application of the framework is demonstrated by a case study on validation assessment of a thermal-hydraulic code for a challenge problem called Departure from Nucleate Boiling (DNB).

42 ENGINEERING↗