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Scalable computations for nonstationary Gaussian processes
Nonstationary Gaussian process models can capture complex spatially varying dependence structures in spatial datasets. However, the large number of observations in modern datasets makes fitting such models computationally intractable with conventional dense linear algebra. In addition, derivative-free or even first-order optimization methods can be very slow to converge when estimating many spatially varying parameters. In this paper, we present a computational framework which couples an algebraic block diagonal plus low-rank covariance matrix approximation with stochastic trace estimation to facilitate the efficient use of second-order solvers for maximum likelihood estimation of Gaussian process models with many parameters. We demonstrate the effectiveness of these methods by simultaneously fitting 192 parameters in the popular nonstationary model of Paciorek and Schervish using 107,600 sea surface temperature anomaly measurements.
Stochastic Vector Techniques in Ground-State Electronic Structure
Herein we review a suite of stochastic vector computational approaches for studying the electronic structure of extended condensed matter systems. These techniques help reduce algorithmic complexity, facilitate efficient parallelization, simplify computational tasks, accelerate calculations, and diminish memory requirements. While their scope is vast, we limit our study to ground-state and finite temperature density functional theory (DFT) and second-order many-body perturbation theory. More advanced topics, such as quasiparticle (charge) and optical (neutral) excitations and higher-order processes, are covered elsewhere. We start by explaining how to use stochastic vectors in computations, characterizing the associated statistical errors. Next, we show how to estimate the electron density in DFT and discuss effective techniques to reduce statistical errors. Finally, we review the use of stochastic vectors for calculating correlation energies within the second-order Møller-Plesset perturbation theory and its finite temperature variational form. Example calculation results are presented and used to demonstrate the efficacy of the methods.
Probing for the Trace Estimation of a Permuted Matrix Inverse Corresponding to a Lattice Displacement
We report thatpProbing is a general technique that is used to reduce the variance of the Hutchinson stochastic estimator for the trace of the inverse of a large, sparse matrix A. The variance of the estimator is the sum of the squares of the off-diagonal elements of A -1 . Therefore, this technique computes probing vectors that when used in the estimator annihilate the largest off-diagonal elements. For matrices that display decay of the magnitude of |A$^{-1}_{ij}$| with the graph distance between nodes i and j, this is achieved through graph coloring of increasing powers A k . Equivalently, when a matrix stems from a lattice discretization, it is computationally beneficial to find a distance-k coloring of the lattice. Previously, a hierarchical coloring was proposed so that k can be increased at runtime as needed without discarding previous work. In this work, we study probing for the more general problem of computing the trace of a permutation of A -1 , say PA -1 . The motivation comes from lattice quantum chromodynamics (QCD), where we need to construct “disconnected diagrams” to extract flavor-separated generalized parton functions. In lattice QCD, where the matrix has a four-dimensional toroidal lattice structure, these nonlocal operators correspond to a PA -1 , where P is the permutation relating to some displacement $\vec{p}$ in one or more dimensions. We focus on a single dimension displacement (p), but our methods are general. We show that probing on A k or (PA) k does not annihilate the largest magnitude elements. To resolve this issue, our displacement-based probing works on PA k using a new coloring scheme that works directly on appropriately displaced neighborhoods on the lattice. We prove lower bounds on the number of colors needed and study the effect of this scheme on variance reduction, both theoretically and experimentally on a real-world lattice QCD calculation. We achieve orders of magnitude speedup over the unprobed or the naively probed methods.
Machine Learning Assisted HPC Workload Trace Generation for Leadership Scale Storage Systems
Monitoring and analyzing a wide range of I/O activities in an HPC cluster is important in maintaining mission-critical performance in a large-scale, multi-user, parallel storage system. Center-wide I/O traces can provide high-level information and fine-grained activities per application or per user running in the system. Studying such large-scale traces can provide helpful insights into the system. It can be used to develop predictive methods for making predictive decisions, adjusting scheduling policies, or providing decisions for the design of next-generation systems. However, sharing real-world I/O traces to expedite such research efforts leaves a few concerns; i) the cost of sharing the large traces is expensive due to this large size, and ii) privacy concern is an issue.We address such issues by building an end-to-end machine learn- ing (ML) workflow that can generate I/O traces for large-scale HPC applications. We leverage ML based feature selection and gener- ative models for I/O trace generation. The generative models are trained on I/O traces collected by the darshan I/O characterization tool over a period of one year. We present a two-step generation process consisting of two deep-learning models, called the feature generator and the trace generator. The combination of two-step generative models provides robustness by reducing the bias of the model and accounting for the stochastic nature of the I/O traces across different runs of an application. We evaluate the performance of the generative models and show that the two-step model can generate time-series I/O traces with less than 20% root mean square error.
Ionospheric gravity wave measurements with the USU dynasonde
A method for the measurement of ionospheric Gravity Wave (GW) using the USU Dynasonde is outlined. This method consists of a series of individual procedures, which includes functions for data acquisition, adaptive scaling, polarization discrimination, interpolation and extrapolation, digital filtering, windowing, spectrum analysis, GW detection, and graphics display. Concepts of system theory are applied to treat the ionosphere as a system. An adaptive ionogram scaling method was developed for automatically extracting ionogram echo traces from noisy raw sounding data. The method uses the well known Least Mean Square (LMS) algorithm to form a stochastic optimal estimate of the echo trace which is then used to control a moving window. The window tracks the echo trace, simultaneously eliminating the noise and interference. Experimental results show that the proposed method functions as designed. Case studies which extract GW from ionosonde measurements were carried out using the techniques described. Geophysically significant events were detected and the resultant processed results are illustrated graphically. This method was also developed for real time implementation in mind.
Developing a Nuclear Quality Assurance Compliant Design Methodology for Neutronic Analysis of Xe-100 Design
The primary objective of this work is to develop a design methodology compliant with nuclear quality assurance standards for the Xe-100 neutronic design verification studies. To achieve this, a Monte Carlo model of the Xe-100 reactor was constructed using the exclusion principle, transformation technique, and universe-based level specification following Idaho National Laboratory (INL) NQA level-1 compliant standards and an NQA-1 compliant version of MCNP6. The model encompasses the entire reactor core structures, including the upper plenum, core region, and lower plenum sections, along with all sub-components. The active core section was represented using the spectral regions, each comprising a particular fuel composition and temperature averaged over the considered zone, calculated by X-energy using Very Superior Old Programs (VSOP). Additionally, a component-wise temperature map was implemented into the model, not only for the core region but also for the structural components. Temperature-dependent cross-section libraries, along with thermal scattering law libraries, generated using INL NQA-1 compliant version of NJOY21, were utilized for each isotope in the burnt fuel and the structural materials. Furthermore, the volume of each modeled component was estimated using a stochastic approach with the ray tracing method in MCNP and criticality calculations were performed.
Diagonal state designs with reconfigurable real-time circuits
Unitary designs are widely used in quantum computation, but in many practical settings it suffices to construct a diagonal state design generated with unitary gates diagonal in the computational basis. In this work, we introduce a simple and efficient diagonal state 3-design based on real-time evolutions under 2-local Hamiltonians. Our construction is inspired by the classical Girard-Hutchinson trace estimator in that it involves the stochastic preparation of many random-phase states. Though the exact Girard-Hutchinson states are not tractably implementable on a quantum computer, we can construct states that match the statistical moments of the Girard-Hutchinson states with real-time evolution. Importantly, our random states are all generated using the same Hamiltonians for real-time evolution, with the randomness arising solely from stochastic variations in the durations of the evolutions. In this sense, the circuit is fully reconfigurable and thus suited for near-term realizations on both digital and analog platforms. Moreover, we show how to extend our construction to achieve diagonal state designs of arbitrarily high order.
Hierarchical Multi-agent Large Language Model Reasoning for Autonomous Heterogeneous Catalyst Discovery
Artificial intelligence is reshaping scientific exploration, but most methods automate procedural tasks without engaging in scientific reasoning, limiting autonomy in discovery. We demonstrate that hierarchical agentic large language model reasoning can efficiently drive simulation and scientific exploration. Across two chemical applications, CO adsorption on Cu surface transition metal adatoms and on M–N–C catalysts, reasoning-guided exploration reduces required atomistic simulations by up to 90% relative to heuristic or random selection. Comparisons across single-agent, multi-agent, and stochastic baselines show that hierarchical strategies yield more coherent and information-efficient search trajectories. Reasoning traces reveal chemically grounded decisions that cannot be explained by semantic bias or stochastic sampling. We realize these agentic reasoning strategies in Materials Agents for Simulation and Theory in Electronic-structure Reasoning (MASTER), a multimodal system that translates natural language into density functional theory workflows. Altogether, multi-agent collaboration accelerates heterogeneous catalyst discovery and marks a step toward more autonomous, reasoning-guided scientific exploration.
BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets
BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. Furthermore, we observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.
Optimizing shift selection in multilevel Monte Carlo for disconnected diagrams in lattice QCD
The calculation of disconnected diagram contributions to physical signals is a computationally expensive task in Lattice QCD. To extract the physical signal, the trace of the inverse Lattice Dirac operator, a large sparse matrix, must be stochastically estimated. Because the variance of the stochastic estimator is typically large, variance reduction techniques must be employed. Multilevel Monte Carlo (MLMC) methods reduce the variance of the trace estimator by utilizing a telescoping sequence of estimators. Frequency Splitting is one such method that uses a sequence of inverses of shifted operators to estimate the trace of the inverse lattice Dirac operator, however there is no a priori way to select the shifts that minimize the cost of the multilevel trace estimation. Here we present a sampling and interpolation scheme that is able to predict the variances associated with Frequency Splitting under displacements of the underlying space time lattice. The interpolation scheme is able to predict the variances to high accuracy and therefore chooses shifts that correspond to an approximate minimum of the cost for the trace estimation. We show that Frequency Splitting with the chosen shifts displays significant speedups over multigrid deflation, and that these shifts can be used for multiple configurations within the same ensemble with no penalty to performance.
Interpolation as a means of shift selection for multilevel Monte Carlo with lattice displacements
The calculation of disconnected diagram contributions to physical signals is a computationally expensive task in Lattice QCD. To extract the physical signal, the trace of the inverse Lattice Dirac operator, a large sparse matrix, must be stochastically estimated. Because the variance of the stochastic estimator is typically large, variance reduction techniques must be employed. Multilevel Monte Carlo (MLMC) methods reduce the variance of the trace estimator by utilizing a telescoping sequence of estimators. Frequency Splitting is one such method that uses a sequence of inverses of shifted operators to estimate the trace of the inverse of the lattice Dirac operator, however there is no a priori way to select the shifts that minimize the cost of the multilevel trace estimation. We present a sampling and interpolation scheme that is able to predict the variances associated with Frequency Splitting under displacements of the underlying space time lattice. The interpolation scheme is able to predict the variances to high accuracy and therefore choose shifts that correspond to an approximate minimum of the cost for the trace estimation. We show that Frequency Splitting with the chosen shifts displays significant speedups over multigrid deflation
Stochastic Averaging of Radiative Transfer Coefficients for Relativistic Electrons
Abstract Synchrotron emissivities, absorptivities, and Faraday rotation and conversion coefficients are needed in modeling a variety of astrophysical sources, including Event Horizon Telescope (EHT) sources. We develop a method for estimating transfer coefficients that exploits their linear dependence on the electron distribution function, decomposing the distribution function into a sum of parts each of whose emissivity can be calculated easily. We refer to this procedure as stochastic averaging and apply it in two contexts. First, we use it to estimate the emissivity of an isotropicκdistribution function with a high-energy cutoff. The resulting coefficients can be evaluated efficiently enough to be used directly in ray-tracing calculations, and we provide an example calculation. Second, we use stochastic averaging to assess the effect of subgrid turbulence on the volume-averaged emissivity and along the way provide a prescription for a turbulent emissivity. We find that for parameters appropriate to EHT sources turbulence reduces the emissivity slightly. In the infrared, turbulence can dramatically increase the emissivity.
Optimization of nonlinear turbulence in stellarators
We present new stellarator equilibria that have been optimized for reduced turbulent transport using nonlinear gyrokinetic simulations within the optimization loop. The optimization routine involves coupling the pseudo-spectral GPU-native gyrokinetic code GX with the stellarator equilibrium and optimization code DESC . Since using GX allows for fast nonlinear simulations, we directly optimize for reduced nonlinear heat fluxes. To handle the noisy heat flux traces returned by these simulations, we employ the simultaneous perturbation stochastic approximation (SPSA) method that only uses two objective function evaluations for a simple estimate of the gradient. We show several examples that optimize for both reduced heat fluxes and good quasi-symmetry as a proxy for low neoclassical transport. Finally, we run full transport simulations using the T3D stellarator transport code to evaluate the changes in the macroscopic profiles.
Modeling rarefied gas chemistry with QuiPS, a novel quasi-particle method
The goal of this work is to build up the capability of quasi-particle simulation (QuiPS), a novel flow solver, such that it can adequately model the rarefied portion of an atmospheric reentry trajectory. Direct simulation Monte Carlo (DSMC) is the conventional solver for such conditions, but struggles to resolve transient flows, trace species, and high-level internal energy states due to stochastic noise. Quasi-particle simulation (QuiPS) is a novel Boltzmann solver that describes a system with a discretized, truncated velocity distribution function. The resulting fixed-velocity, variable weight quasi-particles enable smooth variation of macroscopic properties. The distribution function description enables the use of a variance-reduced collision model, greatly minimizing expense near equilibrium. This work presents the addition of a neutral air chemistry model to QuiPS and some demonstrative 0D simulations. The explicit representation of internal distributions in QuiPS reveals some of the flaws in existing physics models. Overall, variance reduction, a key feature of QuiPS, can greatly reduce expense of multi-dimensional calculations, but is only cheaper when the gas composition is near chemical equilibrium.
DIISC-II: Unveiling the Connections between Star Formation and Interstellar Medium in the Extended Ultraviolet Disk of NGC 3344
We present our investigation of the extended ultraviolet (XUV) disk galaxy, NGC 3344, conducted as part of Deciphering the Interplay between the Interstellar medium, Stars, and the Circumgalactic medium survey. We use surface and aperture photometry of individual young stellar complexes to study star formation and its effect on the physical properties of the interstellar medium. We measure the specific star formation rate (sSFR) and find it to increase from 10 –10 yr –1 in the inner disk to >10 –8 yr –1 in the extended disk. This provides evidence for inside-out disk growth. If these sSFRs are maintained, the XUV disk stellar mass can double in ~0.5 Gyr, suggesting a burst of star formation. The XUV disk will continue forming stars for a long time due to the high gas depletion times (τ dep ). The stellar complexes in the XUV disk have high-Σ H I and low-Σ SFR with τ dep ~ 10 Gyr, marking the onset of a deviation from the traditional Kennicutt–Schmidt law. We find that both far-ultraviolet (FUV) and a combination of FUV and 24 μm effectively trace star formation in the XUV disk. Hα is weaker in general and prone to stochasticities in the formation of massive stars. Investigation of the circumgalactic medium at 29.5 kpc resulted in the detection of two absorbing systems with metal-line species: the stronger absorption component is consistent with gas flows around the disk, most likely tracing inflow, while the weaker component is likely tracing corotating circumgalactic gas.
Stochastic Models of Human Errors
Humans play an important role in the overall reliability of engineering systems. More often accidents and systems failure are traced to human errors. Therefore, in order to have meaningful system risk analysis, the reliability of the human element must be taken into consideration. Describing the human error process by mathematical models is a key to analyzing contributing factors. Therefore, the objective of this research effort is to establish stochastic models substantiated by sound theoretic foundation to address the occurrence of human errors in the processing of the space shuttle.
Energetic electron transport in magnetic fields with island chains and stochastic regions
This paper investigates energetic electron transport in magnetized toroidal plasmas with magnetic fields characterized by island chains and regions of stochastic field lines produced by coil perturbations. We report on experiments performed in the DIII-D tokamak, which utilize electron cyclotron heating and current drive pulses to ‘tag’ electron populations within different locations across the discharge. The cross-field transport of these populations is then inferred from electron cyclotron emission measurements and gamma emission signals from scintillator detectors. Two types of energetic particles are distinguished and discussed: non-relativistic suprathermal electrons and relativistic runaway electrons. The magnetic field topology in each discharge is reconstructed with field-line tracing codes, which are also used to determine the location and scale of magnetic islands and stochastic regions. Comparison of simulations and experiments suggests that suprathermal transport is suppressed when the tagging is performed at a smaller radial location than the location of the $q = 1$ island chain and enhanced otherwise. Here q is the safety factor. We further demonstrate that increasing the width of the stochastic region within the edge plasma yields enhancement of the suprathermal electron transport.