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At least 55 records · Page 3

On the Information in Spike Timing: Neural Codes Derived from Polychronous Groups

There is growing evidence regarding the importance of spike timing in neural information processing, with even a small number of spikes carrying information, but computational models lag significantly behind those for rate coding. Experimental evidence on neuronal behavior is consistent with the dynamical and state dependent behavior provided by recurrent connections. This motivates the minimalistic abstraction investigated in this paper, aimed at providing insight into information encoding in spike timing via recurrent connections. We employ information-theoretic techniques for a simple reservoir model which encodes input spatiotemporal patterns into a sparse neural code, translating the polychronous groups introduced by Izhike-vich into codewords on which we can perform standard vector operations. Finally, we show that the distance properties of the code are similar to those for (optimal) random codes. In particular, the code meets benchmarks associated with both linear classification and capacity, with the latter scaling exponentially with reservoir size.

computational modeling↗

Dislocation Patterning in Deforming Crystals: Theory, Computational Predictions and Validation (Final Technical Report)

This project was awarded for an initial period of three years, followed by a no-cost extension for one year and a funded one-year renewal. During the first four years, the project focused on investigating the role of dislocation reactions and dislocation correlation in dislocation patterning in FCC metals. During the fifth year, the scope of research was expanded to investigate the effects of composition inhomogeneity on the mesoscale plastic response of Body-Centered Cubic (BCC) alloys. In addition to its impact on metal hardening during deformation, dislocation patterning provides the microstructure information required to understand phenomena like fracture and recrystallization in metals. The Continuum Dislocation Dynamics (CDD) framework was the methodology used during the first four years, followed by the use of Discrete Dislocation Dynamics (DDD) during the fifth year. CDD is a density-based formalism of dislocation dynamics in which the plastic deformation of crystals is predicted together with the mesoscale dislocation patterns by tracking the space-time evolution of dislocations as driven by the applied stress, short-range and long-range interactions of dislocations, and cross slip. CDD is a crystal mechanics approach in which the plastic constitutive part is replaced with the equations of dislocation dynamics, which is driven by the internal stress via a mobility laws, while the evolution of the density gives the eigenstrain required to update the internal stress itself. The governing equations are thus those of crystal mechanics cast as an eigenstrain problem and those of dislocation transport and reactions. Our investigations during the first four years were driven by the hypothesis that that dislocation patterning is triggered by spatiotemporal dislocation density and internal stress fluctuations, and that such fluctuations influence the collective dislocation dynamic through their effects on the short-range reaction rates and the collective dislocation mobility. This hypothesis was tested by modeling the influence of the dislocation reactions and dislocation correlations on collective dislocation dynamics. The main research components during the first four years were: 1) Reformulation of the CDD framework to integrate the dislocation correlations and dislocation reactions. 2) Simulation of the dislocation correlations and quantifying their contribution to the long-range stress of complex dislocation systems. 3) Computational implementation of the updated CDD model for FCC single crystals and development of an efficient CDD code. 4) Investigation of dislocation patterning in FCC crystals based on the updated CDD model. Some key findings from these investigations were: 1) The patterning of dislocations is initiated by cross slip and internal stress fluctuations, and the refinement of the pattern results from junction formation. 2) Patterning is more prominent under high stress. 3) The correlation stress was found to be a significant part of the mean field stress in continuum representations of dislocation dynamics. During the last year of the project, we have established a method for performing dislocation dynamics in inhomogeneous alloys and demonstrated the impact of composition inhomogeneity on the characteristics of initial yielding and dislocation character in BCC alloys. We also tested this method using an irradiated ferritic alloy in which the composition and dislocation loops effects are both present. In doing so, we have considered two aspects of the role of inhomogeneity, the creation of internal coherency stress due to the dependence of the lattice parameter on the local composition, and the dependence of the dislocation mobility on the local composition. These two aspects resulted in an unexpected behavior of the dislocation system, and, in turn, the yielding behavior of BCC alloys. Key findings include: 1) The composition inhomogeneity in BCC alloys alters the well-known role of screw dislocations by forcing a level of waviness on the average dislocation character, thus destroying the screw character dominance in the yielding observed in pure or homogeneous BCC metals. 2) In the case of irradiated alloys, while composition inhomogeneity by itself and dislocation loops by themselves result in some hardening, the superposition of the two mechanisms does not result in the sum of the two contributions via any known rule. The latter result contradicts the classical works related hardening via multiple mechanisms, which state that various hardening mechanisms can be added linearly or using some Pythagorean additive rule. We were able to rationalize this unexpected result by a closer loop at the origin of the hardening mechanisms themselves, which both involved long-range elastic interactions with dislocations. We reached the conclusion that the hardening resulting from the total stress associated with these two mechanisms (current work) differs from the sum of the effects of the individual stress fields (classical literature). We have also found a major flaw in the classical theory of spinodal hardening. The latter theory never considered the impact of composition undulation on the solute hardening. We have built a new general theory accounting for the effect of solute friction together with the composition undulations on the dislocation configuration at Critical Resolved Shear Stress (CRSS), which is yielding a new definition of the spinodal hardening and new different results. This work is the first to recognize the lack of the role of solute in spinodal hardening theory of alloys.

36 MATERIALS SCIENCE↗

Serpentine Magnet Designs for the Interaction Region of the Electron-Ion Collider (EIC)

The Electron-Ion Collider (EIC), hosted by Brookhaven National Laboratory, is designed to deliver a peak luminosity of 1 × 10 34 cm −2 sec −1 . The interaction region (IR) of the EIC imposes several constraints in terms of field quality, aperture, and spatial layout, which necessitates the development of several unique superconducting serpentine direct wind magnets. These magnets are constructed using either a single strand or a small-diameter 6-around-1 NbTi cable, presenting unique challenges for design and optimization. This paper introduces a new computational code specifically developed to streamline and integrate the design process for these magnets, enabling faster design iterations while addressing their complex requirements. Here, in this paper, we first introduce the code, which builds on established electromagnetic fundamentals. The code incorporates tools for optimizing winding patterns and for correcting magnetic multipoles; additionally, it interfaces with established magnet design software. We also present the design of several serpentine magnets for the EIC IR, demonstrating the code’s capability to deliver precise and efficient solutions. These designs highlight the code’s ability to accelerate the development cycle, ensuring the serpentine magnets meet the demanding specifications of the EIC project.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Special issue: Advanced stencil-code engineering

Here, stencil codes are compute-intensive algorithms, in which data points arranged in a large grid are being recomputed repeatedly from the values of data points in a predefined neighborhood. This fixed neighborhood pattern is called a stencil. Stencils codes see wide-spread use in computing the discrete solutions of partial differential equations and systems composed of such equations.

97 MATHEMATICS AND COMPUTING↗

Power and Limitations of Linear Programming Decoder for Quantum LDPC Codes

Decoding quantum error-correcting codes is a key challenge in enabling fault-tolerant quantum computation. In the classical setting, linear programming (LP) decoders offer provable performance guarantees and can leverage fast practical optimization algorithms. Although LP decoders have been proposed for quantum codes, their performance and limitations remain relatively underexplored. In this work, we uncover a key limitation of LP decoding for quantum low-density parity-check (LDPC) codes: certain constant-weight error patterns lead to ambiguous fractional solutions that cannot be resolved through independent rounding. To address this issue, we incorporate a post-processing technique known as ordered statistics decoding (OSD), which significantly enhances LP decoding performance in practice. Our results show that LP decoding, when augmented with OSD, can outperform belief propagation with the same post-processing for intermediate code sizes of up to hundreds of qubits. These findings suggest that LP-based decoders, equipped with effective post-processing, offer a promising approach for decoding near-term quantum LDPC codes.

Gu, Shouzhen [Yale U.]↗

Power and Limitations of Linear Programming Decoder for Quantum LDPC Codes

Decoding quantum error-correcting codes is a key challenge in enabling fault-tolerant quantum computation. In the classical setting, linear programming (LP) decoders offer provable performance guarantees and can leverage fast practical optimization algorithms. Although LP decoders have been proposed for quantum codes, their performance and limitations remain relatively underexplored. In this work, we uncover a key limitation of LP decoding for quantum low-density parity-check (LDPC) codes: certain constant-weight error patterns lead to ambiguous fractional solutions that cannot be resolved through independent rounding. To address this issue, we incorporate a post-processing technique known as ordered statistics decoding (OSD), which significantly enhances LP decoding performance in practice. Our results show that LP decoding, when augmented with OSD, can outperform belief propagation with the same post-processing for intermediate code sizes of up to hundreds of qubits. These findings suggest that LP-based decoders, equipped with effective post-processing, offer a promising approach for decoding near-term quantum LDPC codes.

Gu, Shouzhen [Yale U.]↗

Power and Limitations of Linear Programming Decoder for Quantum LDPC Codes

Decoding quantum error-correcting codes is a key challenge in enabling fault-tolerant quantum computation. In the classical setting, linear programming (LP) decoders offer provable performance guarantees and can leverage fast practical optimization algorithms. Although LP decoders have been proposed for quantum codes, their performance and limitations remain relatively underexplored. In this work, we uncover a key limitation of LP decoding for quantum low-density parity-check (LDPC) codes: certain constant-weight error patterns lead to ambiguous fractional solutions that cannot be resolved through independent rounding. To address this issue, we incorporate a post-processing technique known as ordered statistics decoding (OSD), which significantly enhances LP decoding performance in practice. Our results show that LP decoding, when augmented with OSD, can outperform belief propagation with the same post-processing for intermediate code sizes of up to hundreds of qubits. These findings suggest that LP-based decoders, equipped with effective post-processing, offer a promising approach for decoding near-term quantum LDPC codes.

Gu, Shouzhen [Yale U.]↗

Separatrix-to-Wall Simulations of Impurity Transport with a Fully Three-Dimensional Wall in DIII-D

A novel multi-code workflow to interpret collector probe deposition patterns in DIII-D has been developed. The components of the workflow consist of a detailed computer-aided design (CAD) file of the vessel wall and the scrape-off layer (SOL) codes MAFOT, OSM, DIVIMP and 3DLIM. A special-purpose toolkit enables passing the output of these codes between each other to provide a full-SOL picture of impurity transport. A demonstration of the workflow is described to support evidence of near-SOL tungsten parallel accumulation during trace W impurity experiments on DIII-D. Iteration between simulated deposition patterns in 3DLIM and DIVIMP predicts a region of elevated W density near the separatrix about halfway between the outboard midplane and the top of the plasma. Furthermore, this workflow will be used to better interpret collector probe experiments on DIII-D.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Reverse-Mode Algorithmic Differentiation of an OpenMP-Parallel Compressible Flow Solver

y Reverse-mode algorithmic differentiation (AD) is an established method for obtaining adjoint derivatives of computer simulation applications. In computational fluid dynamics (CFD), adjoint derivatives of a cost function output such as drag or lift with respect to design parameters such as surface coordinates or geometry control points are a key ingredient for shape optimization, uncertainty quantification and flow control. The computational cost of CFD applications and their derivatives makes it essential to use high-performance computing hardware efficiently, including multi- and many-core architectures. Nevertheless, OpenMP is not supported in most AD tools, and previously shown methods achieve poor scalability of the derivative code. We present the AD of an OpenMP-parallelized finite volume compressible flow solver for unstructured meshes. Our approach enables us to reuse the parallelization of the original code in the computation of adjoint derivatives. The method works by identifying code segments that can be differentiated in reverse-mode without changing their memory access pattern. The OpenMP parallelization is integrated into the derivative code during the build process in a way that is robust to modifications of the original code and independent of the OpenMP support of the differentiation tool. We show the scalability of our adjoint CFD solver on test cases ranging from thousands to millions of finite volume mesh cells on CPUs with up to 16 threads as well as on an Intel XeonPhi card with 236 threads. We demonstrate that our approach is more practical to implement for production-sized CFD codes and produces more efficient adjoint derivative code than previously shown AD methods.

Huckelheim, Jan↗

Validation and benchmarking of two particle-in-cell codes for a glow discharge

The two particle-in-cell codes EDIPIC and LSP are benchmarked and validated for a parallel-plate glow discharge in helium, in which the axial electric field had been carefully measured, primarily to investigate and improve the fidelity of their collision models. The scattering anisotropy of electron-impact ionization, as well as the value of the secondary-electron emission yield, are not well known in this case. The experimental uncertainty for the emission yield corresponds to a factor of two variation in the cathode current. If the emission yield is tuned to make the cathode current computed by each code match the experiment, the computed electric fields are in excellent agreement with each other, and within about 10% of the experimental value. The non-monotonic variation of the width of the cathode fa ll with the applied voltage seen in the experiment is reproduced by both codes. The electron temperature in the negative glow is within experimental error bars for both codes, but the density of slow trapped electrons is underestimated. A more detailed code comparison don e for several synthetic cases of electron-beam injection into helium gas shows that the codes are in excellent agreement for ionization rate, as well as for elastic and excitation collisions with isotropic scattering pattern. The remaining significant discrepancies between the two codes are due to differences in their electron binary-collision models, and for anisotropic scattering due to elastic and excitation collisions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Non-convex Multi-species Hopfield Models

In this work we introduce a multi-species generalization of the Hopfield model for associative memory, where neurons are divided into groups and both inter-groups and intra-groups pair-wise interactions are considered, with different intensities. Thus, this system contains two of the main ingredients of modern deep neural-network architectures: Hebbian interactions to store patterns of information and multiple layers coding different levels of correlations. The model is completely solvable in the low-load regime with a suitable generalization of the Hamilton–Jacobi technique, despite the Hamiltonian can be a non-definite quadratic form of the Mattis magnetizations. The family of multi-species Hopfield model includes, as special cases, the 3-layers Restricted Boltzmann Machine with Gaussian hidden layer and the Bidirectional Associative Memory model.

97 MATHEMATICS AND COMPUTING↗

Evolution of microstructures in radiation fields using a coupled binary-collision Monte Carlo phase field approach

The simulation of radiation effects in materials broadly falls into two categories. At short time and length scales lies the modeling of primary radiation damage, such as point defect creation, energy deposition, and ballistic mixing. This is followed by the modeling at longer time scales of thermally activated microstructure evolution and defect reactions, such as recombination, clustering, and coarsening. The binary collision Monte Carlo method is an established, numerically efficient method for the computation of primary radiation damage. Conversely, the phase field method is a state of the art method for microstructure evolution on longer time and length scales. Here we present a concurrent coupling of these two methods, overcoming the difference between the discrete object Monte Carlo paradigm for primary radiation damage and the continuum field variable approach for microstructure evolution. The coupling is bidirectional, in which the microstructure evolution in the MOOSE finite element frame- work provides the spatial scattering data set for the charged particle trans- port and receives point defect, mass transport, and heat source terms from the simulated collision cascades that contribute to the field variable evolution. The concurrent coupling scheme is implemented in the code Magpie and demonstrated by investigating patterning for a model irradiated immiscible binary alloy. The results from the coupled binary collision Monte Carlo/phase field simulations reproduce the results of analytical models for phase separation, phase mixing, and patterning, supporting the approach and indicating its utility for modeling real materials systems.

36 MATERIALS SCIENCE↗

High-speed quantitative X-ray multi-contrast imaging with deep learning based modulated pattern analysis

The advent of X-ray multi-contrast imaging methods, providing absorption, phase, and dark-field images, holds tremendous promise for complementary and non-destructive visualization of inner structures within materials and bio-samples. However, the low efficiency in measuring and analyzing X-ray modulated patterns has hindered their application in high-resolution in situ imaging. In this work, the Enhanced Scanning Pattern-based Imaging Neural Network (ESPINNet) is introduced as a powerful tool for achieving high-speed, high-resolution quantitative imaging. ESPINNet is faster than correlation-based speckle tracking methods such as XSVT and UMPA, and provides a balanced performance in terms of resolution and speed for data collection by using fewer scanning images. In comparison with our previously developed neural network, ESPINNet introduces the capability to generate dark-field images, further enhancing its versatility. By leveraging scanning patterns, ESPINNet significantly improves resolution and measurement precision. Furthermore, its adaptability to various modulation patterns, including those produced by sandpaper, coded masks, or gratings, ensures broad applicability. These features enable real-time 2D and 3D multi-contrast imaging, positioning ESPINNet as a transformative solution for applications in materials science and biomedical research, particularly for high-speed and in situ measurements.

X-ray at-wavelength metrology↗

Analysis of Threading Libraries for High Performance Computing

With the appearance of multi-/many core machines, applications and runtime systems have evolved in order to exploit the new on-node concurrency brought by new software paradigms. POSIX threads (Pthreads) was widely-adopted for that purpose and it remains as the most used threading solution in current hardware. Lightweight thread (LWT) libraries emerged as an alternative offering lighter mechanisms to tackle the massive concurrency of current hardware. In this article, we analyze in detail the most representative threading libraries including Pthread- and LWT-based solutions. In addition, to examine the suitability of LWTs for different use cases, we develop a set of microbenchmarks consisting of OpenMP patterns commonly found in current parallel codes, and we compare the results using threading libraries and OpenMP implementations. Moreover, we study the semantics offered by threading libraries in order to expose the similarities among different LWT application programming interfaces and their advantages over Pthreads. This article exposes that LWT libraries outperform solutions based on operating system threads when tasks and nested parallelism are required.

GLT↗

BuildingsBench: A Benchmark for Universal Building Load Forecasting [SWR-23-51]

The residential and commercial building stock in the United States is responsible for a significant percentage of energy consumption and greenhouse gas emissions. Electrification of end-uses, as well as decarbonizing the electrical grid through renewable energy sources such as solar and wind, constitutes the pathway to zero-emission buildings. Forecasting day-ahead building energy consumption is an integral part of this solution. Currently, specialized forecasting models are hand-made for each individual building, which is time-consuming, expensive, and leads to duplicated efforts. BuildingsBench is a Python software framework for training and comparing generalized machine learning models for universal building load forecasting. This challenge tasks a single foundational model to generalize its forecasts for a wide variety of buildings, across geographic regions, building types, weather patterns, and more. This software provide code for pre-training such models and subsequently evaluating their performance on a suite of hundreds of diverse real and synthetic buildings. BuildingsBench is a platform for: - Large-scale pretraining with the synthetic Buildings-900K dataset for short-term load forecasting (STLF). Buildings-900K is statistically representative of the entire U.S. building stock and is extracted from the NREL End-Use Load Profiles database. - Benchmarking on two tasks evaluating generalization: zero-shot STLF and transfer learning for STLF. We provide an index-based PyTorch Dataset for large-scale pretraining, easy data loading for multiple real building energy consumption datasets as PyTorch Tensors or Pandas DataFrames, simple (persistence) to advanced (transformer) baselines, metrics management, and more.

Emami, Patrick↗

Block-Parallel Data Analysis with DIY2

DIY2 is a programming model and runtime for block-parallel analytics on distributed-memory machines. Its main abstraction is block-structured data parallelism: data are decomposed into blocks; blocks are assigned to processing elements (processes or threads); computation is described as iterations over these blocks, and communication between blocks is defined by reusable patterns. By expressing computation in this general form, the DIY2 runtime is free to optimize the movement of blocks between slow and fast memories (disk and flash vs. DRAM) and to concurrently execute blocks residing in memory with multiple threads. This enables the same program to execute in-core, out-of-core, serial, parallel, single-threaded, multithreaded, or combinations thereof. This paper describes the implementation of the main features of the DIY2 programming model and optimizations to improve performance. DIY2 is evaluated on benchmark test cases to establish baseline performance for several common patterns and on larger complete analysis codes running on large-scale HPC machines.

97 MATHEMATICS AND COMPUTING↗

Impact of Misclassification Rates on Compression Efficiency of Red Blood Cell Images of Malaria Infection Using Deep Learning

Malaria is a severe public health problem worldwide, with some developing countries being most affected. Reliable remote diagnosis of malaria infection will benefit from efficient compression of high-resolution microscopic images. This paper addresses a lossless compression of malaria-infected red blood cell images using deep learning. Specifically, we investigate a practical approach where images are first classified before being compressed using stacked autoencoders. We provide probabilistic analysis on the impact of misclassification rates on compression performance in terms of the information-theoretic measure of entropy. We then use malaria infection image datasets to evaluate the relations between misclassification rates and actually obtainable compressed bit rates using Golomb–Rice codes. Simulation results show that the joint pattern classification/compression method provides more efficient compression than several mainstream lossless compression techniques, such as JPEG2000, JPEG-LS, CALIC, and WebP, by exploiting common features extracted by deep learning on large datasets. This study provides new insight into the interplay between classification accuracy and compression bitrates. The proposed compression method can find useful telemedicine applications where efficient storage and rapid transfer of large image datasets is desirable.

59 BASIC BIOLOGICAL SCIENCES↗

GOTHIC Aerosol Source Depletion Studies

Pacific Northwest National Laboratory has continued work to develop an aerosol-laden flow modeling capability with the Generation of Thermal Hydraulic Information in Containment (GOTHIC TM ) computer code to perform simulations for thermal hydraulic conditions and aerosol transport and deposition in spent fuel casks. This report describes our recent work to expand our model that was originally developed in 2019 to allow for thermal characterization, carrier gas flow determination, and tracking of particulate behavior throughout the entire canister volume. This was achieved through conversion of decay heat source in all fuel tubes within the model from heaters to thermal conductors in GOTHIC as well as remeshing the internal volume of the canister. These model improvements allowed for simulations of base case scenarios for comparison of similar efforts by our collaborators with alternative tools at Sandia and Oak Ridge. Several characteristics of the GOTHIC code were elucidated by this effort and were documented for consideration in how the code is used for this effort moving forward. For instance, treatment of particle size distributions, initial spatial distributions, mesh gradients, and minimum volume concentrations were identified as important issues for consideration. Ultimately, the current version of the code is capable of tracking temperatures, flow rates, and particle behavior throughout the canister internal volume. This report presents predicted depletion times and preferred deposition patterns within the canister. Additionally, this report documents code performance and insights for further model development and use for comparisons to other codes and for predicting system behavior in experiments being performed and planned by our collaborators.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗