Using Approximate Nearest Neighbor Methods to Rapidly Search Large Seismic Signal Archives.
Abstract not provided.
Slinkard, Megan Elizabeth↗
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Efficient graph representation framework for chemical molecule similarity tasks
Graph data has emerged in numerous scientific domains and machine learning techniques have been widely used for analysis and learning of diverse data for prediction and decision. Machine learning techniques can readily address complex problems by leveraging their structural information. But graphs cannot be directly used for existing machine learning algorithms unless encoded as vectors. The problem of efficient representation of graphs is a substantial challenge in graph machine learning. In this paper, we propose a novel two-stage framework for the representation of chemical molecule graphs based on the strengths of Graph Isomorphism Networks (GINs) and Siamese autoencoders. In the first stage, the GIN model is constructed and trained using the structural information of chemical molecule graphs. Node attributes, edge attributes, and edge indices are used as input data, while graph attributes are used as labels. The GIN model effectively captures the structural characteristics of graphs and can accurately predict graph attributes, i.e., molecular properties. It also generates Graph Embeddings, represented as vectors that encode the structural information of graphs. In the second stage, Graph Embedding vectors are further optimized for downstream similarity tasks while preserving the graph structural information. The Siamese autoencoder is constructed and trained, which reduces the dimensionality of the Graph Embedding vectors, while maximizing the preservation of structural information in the original high-dimensional vectors. The resulting low-dimensional Graph Embeddings can be effectively utilized for tasks such as approximate nearest neighbor search. The experimental results demonstrate the effectiveness of our proposed framework in accurately predicting graph similarity.
Ma, Jiaji↗
The electrostatics of a dusty plasma
The potential distribution in a plasma containing dust grains were derived where the Debye length can be larger or smaller than the average intergrain spacing. Three models were treated for the grain-plasma system, with the assumption that the system of dust and plasma is charge-neutral: a permeable grain model, an impermeable grain model, and a capacitor model that does not require the nearest neighbor approximation of the other two models. A gauge-invariant form of Poisson's equation was used which is linearized about the average potential in the system. The charging currents to a grain are functions of the difference between the grain potential and this average potential. Expressions were obtained for the equilibrium potential of the grain and for the gauge-invariant capacitance between the grain and the plasma. The charge on a grain is determined by the product of this capacitance and the grain-plasma potential difference.
Whipple, E. C.↗
Fast Query-Optimized Kernel-Machine Classification
A recently developed algorithm performs kernel-machine classification via incremental approximate nearest support vectors. The algorithm implements support-vector machines (SVMs) at speeds 10 to 100 times those attainable by use of conventional SVM algorithms. The algorithm offers potential benefits for classification of images, recognition of speech, recognition of handwriting, and diverse other applications in which there are requirements to discern patterns in large sets of data. SVMs constitute a subset of kernel machines (KMs), which have become popular as models for machine learning and, more specifically, for automated classification of input data on the basis of labeled training data. While similar in many ways to k-nearest-neighbors (k-NN) models and artificial neural networks (ANNs), SVMs tend to be more accurate. Using representations that scale only linearly in the numbers of training examples, while exploring nonlinear (kernelized) feature spaces that are exponentially larger than the original input dimensionality, KMs elegantly and practically overcome the classic curse of dimensionality. However, the price that one must pay for the power of KMs is that query-time complexity scales linearly with the number of training examples, making KMs often orders of magnitude more computationally expensive than are ANNs, decision trees, and other popular machine learning alternatives. The present algorithm treats an SVM classifier as a special form of a k-NN. The algorithm is based partly on an empirical observation that one can often achieve the same classification as that of an exact KM by using only small fraction of the nearest support vectors (SVs) of a query. The exact KM output is a weighted sum over the kernel values between the query and the SVs. In this algorithm, the KM output is approximated with a k-NN classifier, the output of which is a weighted sum only over the kernel values involving k selected SVs. Before query time, there are gathered statistics about how misleading the output of the k-NN model can be, relative to the outputs of the exact KM for a representative set of examples, for each possible k from 1 to the total number of SVs. From these statistics, there are derived upper and lower thresholds for each step k. These thresholds identify output levels for which the particular variant of the k-NN model already leans so strongly positively or negatively that a reversal in sign is unlikely, given the weaker SV neighbors still remaining. At query time, the partial output of each query is incrementally updated, stopping as soon as it exceeds the predetermined statistical thresholds of the current step. For an easy query, stopping can occur as early as step k = 1. For more difficult queries, stopping might not occur until nearly all SVs are touched. A key empirical observation is that this approach can tolerate very approximate nearest-neighbor orderings. In experiments, SVs and queries were projected to a subspace comprising the top few principal- component dimensions and neighbor orderings were computed in that subspace. This approach ensured that the overhead of the nearest-neighbor computations was insignificant, relative to that of the exact KM computation.
Mazzoni, Dominic↗
An Algorithm to Generate Synthetic 3D Microstructures from 2D Exemplars
The inverse problem of constructing 3D microstructures from 2D data is an area of active research within the materials science community. This paper presents the implementation of a robust, computationally efficient algorithm, Hierarchical Algorithm for the Reconstruction of Exemplars (HARE), written in Python to reconstruct 3D features in a given microstructure from up to three orthogonal 2D exemplars using nearest neighbor matching to reproduce feature qualities, such as shape, size, and distribution. HARE’s feature sampling implements histogram reweighting to avoid both over- and undersampling. A neighborhood voting scheme allows each pixel to provisionally affect its neighbors according to its weight. Finally, the algorithm is presently configured for two-phase materials and is being extended to accommodate multiple phases. HARE is a convenient and robust base from which to generate statistically representative synthetic microstructures for use in multi-scale modeling or machine learning applications to support advanced manufacturing and materials discovery.
36 MATERIALS SCIENCE↗
Online multimedia retrieval on CPU–GPU platforms with adaptive work partition
Nearest neighbors search is a core operation found in several online multimedia services. These services have to handle very large databases, while, at the same time, they must minimize the query response times observed by users. This is specially complex because those services deal with fluctuating query workloads (rates). Consequently, they must adapt at run-time to minimize the response times as the load varies. In this paper, we address the aforementioned challenges with a distributed memory parallelization of the product quantization nearest neighbor search, also known as IVFADC, for hybrid CPU–GPU machines. Overall, our parallel IVFADC implements an out-of-GPU memory execution scheme to use the GPU for databases in which the index does not fit in its memory, which is crucial for searching in very large databases. The careful use of CPU and GPU with work stealing led to an average response time reduction of 2.4 as compared to using the GPU only. Also, our approach to adapt the system to fluctuating loads, called Dynamic Query Processing Policy (DQPP), attained a response time reduction of up to 5 vs. the best static (BS) policy for moderate loads. The system has attained high query processing rates and near-linear scalability in all experiments. We have evaluated our system on a machine with up to 256 NVIDIA V100 GPUs processing a database of 256 billion SIFT features vectors.
97 MATHEMATICS AND COMPUTING↗
The Application of New Software Technology to the Architecture of the National Cycle Program
As part of the Numerical Propulsion System Simulation (NPSS) effort of NASA Lewis in conjunction with the United States aeropropulsion industry, a new system simulation framework, the National Cycle Program (NCP), capable of combining existing empirical engine models with new detailed component-based computational models is being developed. The software architecture of the NCP program involves a generalized object- oriented framework and a base-set of engine component models along with supporting tool kits which will support engine simulation in a distributed environment. As the models are extended to contain two and three dimensions the computing load increases rapidly and it is intended that this load be distributed across multiple work stations executing concurrently in order to get acceptably fast results. The research carried out was directed toward performance analysis of the distributed object system. More specifically, the performance of the actor-based distributed object design I created earlier was desired. To this end, the research was directed toward the design and implementation of suitable performance-analysis techniques and software to demonstrate those techniques. There were three specific results which are reported in two separate reports submitted separately as NASA Technical Memoranda. The results are: (1) Design, implementation, and testing of a performance analysis program for a set of active objects (actor based objects) which allowed the individual actors to be assigned to arbitrary processes on an arbitrary set of machines. (2) The global-balance-equation approach has the fundamental limitation that the number of equations increases exponentially with the number of actors. Hence, unlike many approximate approaches to this problem, the nearest-neighbor approach allows checking of the solution and an estimate of the error. The technique was demonstrated in a prototype analysis program as part of this research. The results of the program were checked against the global-balance solution discussed above. Late during the grant, a much better approximation was developed and this is discussed in result below. As a consequence, a proposal was submitted to continue the research by developing the new approximation including development of a complete program from the prototype. (3) The source of approximation in the nearest-neighbor algorithm is the requirement for estimating some joint probabilities from some marginal distributions. A completely ad hoc estimate was used in the prototype.
Schoeffler, James D.↗
Polynomial approximation of Poincare maps for Hamiltonian system
Different methods are proposed and tested for transforming a non-linear differential system, and more particularly a Hamiltonian one, into a map without integrating the whole orbit as in the well-known Poincare return map technique. We construct piecewise polynomial maps by coarse-graining the phase-space surface of section into parallelograms and using either only values of the Poincare maps at the vertices or also the gradient information at the nearest neighbors to define a polynomial approximation within each cell. The numerical experiments are in good agreement with both the real symplectic and Poincare maps.
Froeschle, Claude↗
Machine Learning Surrogates of a Fuel Matrix Degradation Process Model for Performance Assessment of a Nuclear Waste Repository
Spent nuclear fuel repository simulations are currently not able to incorporate detailed fuel matrix degradation (FMD) process models due to their computational cost, especially when large numbers of waste packages breach. The current paper uses machine learning to develop artificial neural network and k-nearest neighbor regression surrogate models that approximate the detailed FMD process model while being computationally much faster to evaluate. Further, using fuel cask temperature, dose rate, and the environmental concentrations of CO 3 2- , O 2 , Fe 2+ , and H 2 as inputs, these surrogates show good agreement with the FMD process model predictions of the UO 2 degradation rate for conditions within the range of the training data. A demonstration in a full-scale shale repository reference case simulation shows that the incorporation of the surrogate models captures local and temporal environmental effects on fuel degradation rates while retaining good computational efficiency.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Frustrated magnetic interactions in FeSe
The structurally simplest high-temperature superconductor FeSe exhibits an intriguing superconducting nematic paramagnetic phase with unusual spin excitation spectra that are different from typical spin waves; thus, determining its effective magnetic exchange interactions is challenging. In this work, we report neutron scattering measurements of spin fluctuations of FeSe in the tetragonal paramagnetic phase. We show that the equal-time magnetic structure factor, S(Q), can be effectively modeled using the self-consistent Gaussian approximation calculation with highly frustrated nearest-neighbor (J 1 ) and next-nearest-neighbor (J 2 ) exchange couplings, and very weak further neighbor exchange interaction. Our results elucidate the frustrated magnetism in FeSe, which provides a natural explanation for the highly tunable superconductivity and nematicity in FeSe and related materials.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Accelerating Multivariate Functional Approximation Computation with Domain Decomposition Techniques⋆
Modeling large datasets through Multivariate Functional Approximations (MFA) provide an elegant way to handle many visualization and scientific analysis workflows. The process necessitates scalable data partitioning methods to compute MFA representations efficiently without compromising the accuracy or continuity of the reconstructed solution. We propose a domain -decomposed method for computing the MFA with B -spline bases, which reduces the total work per task and uses a restricted Additive Schwarz (RAS) method to converge the control point data degrees -of -freedom along subdomain boundaries. We provide an in-depth analysis of the parallel approach with domain decomposition solvers, aiming to minimize local subdomain error residuals and recover high -order continuity at subdomain interfaces with appropriate choices of knot overlaps. The communication cost, determined by the overlap regions in the RAS implementation, is optimized to recover the numerical error profile of the single subdomain case. Our proposed method stands in contrast to previous methods, which typically only recover either C 0 or at best C 1 continuity for arbitrary B -spline degree expansions, or those that require post -processing to blend discontinuities in the reconstructed data. We demonstrate the effectiveness of our approach using analytical and real -world datasets in 1D, 2D, and 3D through both strong and weak scaling studies. The performance results indicate that the overall cost of computing the approximation is directly proportional to the underlying nearest -neighbor communication implementation, and is only weakly dependent on the overlap region size that determines the size of the messages. This finding underscores the efficiency and scalability of our proposed method, making it a promising solution for handling large datasets in scientific workflows.
additive Schwarz solvers↗
Clustering at Massive Scale
ClaMS provides hierarchical clustering technology for use on massive, high-dimensional datasets that require distributed memory for processing. The algorithm employed is inspired by the popular HDBSCAN algorithm but makes use of computational kernels better suited for distributed computing. ClaMS is built on scalable nearest neighbor graph construction, metric forest completion, and approximate minimum spanning tree techniques.
Stanley, ThomasA [Lawrence Livermore National Labo↗
Thermodynamic modeling with uncertainty quantification using the modified quasichemical model in quadruplet approximation: Implementation into PyCalphad and ESPEI
The modified quasichemical model in the quadruplet approximation (MQMQA) considers the first- and the second-nearest-neighbor coordination and interactions, particularly useful in describing short-range ordering (SRO) in complex liquids such as molten salts, slag in metal processing, and electrolytic solutions. Here, the present work implements the MQMQA into the Python based open-source software PyCalphad for thermodynamic calculations. This endeavor facilitates the development of MQMQA-based thermodynamic database with uncertainty quantification (UQ) and propagation (UP) using the open-source software ESPEI. A new database structure based on Extensible Markup Language (XML) is proposed for ESPEI evaluation of MQMQA model parameters. Using the KF-NiF 2 , KCl-NaCl-MgCl 2 , and CaCl 2 -CaF 2 -LiCl-LiF salt systems as examples, we demonstrate the successful implementation of MQMQA in PyCalphad through thermodynamic calculations of Gibbs energy, equilibrium quadruplet fractions, and phase diagram, as well as database development with UQ and UP using ESPEI. Furthermore, as an application of the present implementation, both the LiF–TbF 3 and LiF-HoF 3 systems have been modeled by MQMQA for the first time, which are in good agreement with experiments. The present implementation hence offers an open-source capability for performing CALPHAD modeling for complex liquids with SRO using MQMQA plus a new XML database structure.
36 MATERIALS SCIENCE↗
Classification of multispectral image data by the Binary Diamond neural network and by nonparametric, pixel-by-pixel methods
The classification of multispectral image data obtained from satellites has become an important tool for generating ground cover maps. This study deals with the application of nonparametric pixel-by-pixel classification methods in the classification of pixels, based on their multispectral data. A new neural network, the Binary Diamond, is introduced, and its performance is compared with a nearest neighbor algorithm and a back-propagation network. The Binary Diamond is a multilayer, feed-forward neural network, which learns from examples in unsupervised, 'one-shot' mode. It recruits its neurons according to the actual training set, as it learns. The comparisons of the algorithms were done by using a realistic data base, consisting of approximately 90,000 Landsat 4 Thematic Mapper pixels. The Binary Diamond and the nearest neighbor performances were close, with some advantages to the Binary Diamond. The performance of the back-propagation network lagged behind. An efficient nearest neighbor algorithm, the binned nearest neighbor, is described. Ways for improving the performances, such as merging categories, and analyzing nonboundary pixels, are addressed and evaluated.
Salu, Yehuda↗
Enhanced Diffusive Transport in Fluctuating Porous Media
Mass transport within porous structures is a ubiquitous process in biological, geological, and technological systems. Despite the importance of these phenomena, there is no comprehensive theory that describes the complex and diverse transport behavior within porous environments. While the porous matrix itself is generally considered a static and passive participant, many porous environments are in fact dynamic, with fluctuating walls, pores that open and close, and dynamically changing cross-links. While diffusion has been measured in fluctuating structures, notably in model biological systems, it is rarely possible to isolate the effect of fluctuations because of the absence of control experiments involving an identical static counterpart, and it is generally impossible to observe the dynamics of the structure. In this paper, we present a direct comparison of the diffusion of nanoparticles of various sizes within a trackable, fluctuating porous matrix and a geometrically equivalent static matrix, in conditions spanning a range of regimes from obstructed to highly confined. The experimental system comprised a close-packed layer of colloidal spheres that were either immobilized to a planar surface or allowed to fluctuate locally, within the space defined by their nearest neighbors. Interestingly, the effective long-time diffusion coefficient was approximately 35–65% greater in the fluctuating porous matrix than in the static one (depending on the size of the nanoparticle probes), regardless of the geometric regime. This was explained by considering the enhancing effects of matrix fluctuations on the short-time diffusion coefficient and cooperative “gate-opening” motions of matrix particles and nanoparticle probes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Continuous Spin Excitations in the Three-Dimensional Frustrated Magnet K 2 Ni 2 (SO 4 ) 3
Continuous spin excitations are widely recognized as one of the hallmarks of novel spin states in quantum magnets, such as quantum spin liquids (QSLs). Here, we report the observation of such kind of excitations in K 2 Ni 2 (SO 4 ) 3 , which consists of two sets of intersected spin-1 (Ni 2+ ) trillium lattices. Our inelastic neutron scattering measurement on single crystals clearly shows a dominant excitation continuum, which exhibits a distinct temperature-dependent behavior from that of spin waves and is rooted in strong quantum spin fluctuations. Further using the self-consistent-Gaussian-approximation method, we determine that the fourth- and fifth nearest-neighbor exchange interactions are dominant. These two bonds together form a unique three-dimensional network of corner-sharing tetrahedra, which we name as a “hypertrillium” lattice. In conclusion, our results provide direct evidence for the existence of QSL features in K 2 Ni 2 (SO 4 ) 3 and highlight the potential for the hypertrillium lattice to host frustrated quantum magnetism.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Developing Practical Models of Complex Salts for Molten Salt Reactors
Molten salt reactors (MSRs) utilize salts as coolant or as the fuel and coolant together with fissile isotopes dissolved in the salt. It is necessary to therefore understand the behavior of the salts to effectively design, operate, and regulate such reactors, and thus there is a need for thermodynamic models for the salt systems. Molten salts, however, are difficult to represent as they exhibit short-range order that is dependent on both composition and temperature. A widely useful approach is the modified quasichemical model in the quadruplet approximation that provides for consideration of first- and second-nearest-neighbor coordination and interactions. Its use in the CALPHAD approach to system modeling requires fitting parameters using standard thermodynamic data such as phase equilibria, heat capacity, and others. A shortcoming of the model is its inability to directly vary coordination numbers with composition or temperature. Another issue is the difficulty in fitting model parameters using regression methods without already having very good initial values. The proposed paper will discuss these issues and note some practical methods for the effective generation of useful models.
Besmann, Theodore M. (ORCID:0000000155980550)↗
Study of beyond nearest-neighbor environment and intermediate-range order in a sodium aluminosilicate geopolymer using Reverse Monte Carlo modeling
A large scale three-dimensional structural model of a geopolymer with an approximate composition of NaAlSi 2 O 6 .5.5H 2 O obtained by Reverse Monte Carlo (RMC) modeling based on experimental high-energy x-ray diffraction is presented for the first time in order to obtain information regarding beyond nearest-neighbor environment and intermediate-range order (IRO). RMC model exhibits a three-dimensional network consisting of randomly cross-linked AlO 4 and SiO 4 tetrahedral units with uniformly distributed Na atoms and H 2 O molecules. The bond angle distributions, i.e. T-O-T, O-T-O and Na-O-Na angles, are somewhat distorted with lower values compared to analogous crystal systems. The origin of the first peak in the structure factor indicating IRO is investigated using the partial structure factors; Na-Na, Si-Na, Al-Si, O-H, and H-H atom pairs are found to be the main contributors. Ring size distribution analysis demonstrates that the structure mainly involves 6-, 7- and 8-membered rings. Finally, the coherence length of these IRO characteristics is ~10.3 Å.
36 MATERIALS SCIENCE↗