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DOE OSTI2024

Analysis and Benchmarking of feature reduction for classification under computational constraints

Abstract Machine learning is most often expensive in terms of computational and memory costs due to training with large volumes of data. Current computational limitations of many computing systems motivate us to investigate practical approaches, such as feature selection and reduction, to reduce the time and memory costs while not sacrificing the accuracy of classification algorithms. In this work, we carefully review, analyze, and identify the feature reduction methods that have low costs/overheads in terms of time and memory. Then, we evaluate the identified reduction methods in terms of their impact on the accuracy, precision, time, and memory costs of traditional classification algorithms. Specifically, we focus on the least resource intensive feature reduction methods that are available in Scikit-Learn library. Since our goal is to identify the best performing low-cost reduction methods, we do not consider complex expensive reduction algorithms in this study. In our evaluation, we find that at quadratic-scale feature reduction, the classification algorithms achieve the best trade-off among competitive performance metrics. Results show that the overall training times are reduced 61%, the model sizes are reduced 6×, and accuracy scores increase 25% compared to the baselines on average with quadratic scale reduction.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Design of functional materials based on new principles of disorder. Final Report

Disorder is present to some extent in every material. The disorder can be sparse and localized – individual defects – or globally such as in a glass. Normally disorder is considered to be detrimental to function. However, this is not necessarily always the case. This project addressed the question: How does disorder provide new potentialities for the behavior of a material that would be absent in a crystalline material of the same composition? We have discovered a new principle for disordered matter: Independence of bond-level response. This work has introduced the possibility of creating new classes of mechanical meta-materials with applications everywhere from microscopic biological molecules (allostery) to large scale architectural disordered networks. During the course of this grant, we have subsequently elaborated on these novel ideas about bond-level independence of properties in disordered materials. In particular, this study has required that we understand the limits of disorder. That is, if crystals are perfect order, is there another diametrically opposed pole which is the most disordered state? We have shown that, in a well-defined way, jamming is one extreme disordered pole of rigid matter. Jamming is a far-from-equilibrium way of creating a rigid solid by rapidly quenching a random distribution of particles to a mechanically stable system at zero temperature. To understand the jammed state of matter, we have elucidated the low-frequency excitation of these systems. This has allowed a new way of understanding materials that cannot be easily classified as crystals or glasses. These ideas can be extended to address the mechanical properties of polycrystalline matter. Memory formation in matter can take inspiration from memory that occurs in a biological context. The issue of memory formation raises another set of questions at the heart of how the energy landscape is organized and how it can be manipulated to store information in a solid. This project has explored how to understand the degree to which multiple memories can be stored in a single system and has created a holistic understanding of how inputs can be used to create a desired response.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Unveiling the nature of Ga-based chalcogenides for electrical switching selectors

Three-dimensional phase-change memory with stackable crossbar architecture is a promising technology to meet the urgent demands for high-density storage and rapid information processing in the era of explosive data growth. The performance depends strongly on the properties of ovonic threshold switching (OTS) selectors, which control the on/off states of memory units. Amorphous GaS serves as an outstanding OTS material, distinguished by its sizable mobility gap and high crystallization temperature, while the underlying mechanism continues to be inadequately comprehended. Here, in this work, we systematically studied the structural and electronic properties of amorphous Ga-X (X = S/Se/Te) using first-principles calculations. The results show that Ga atoms adopt tetrahedral motifs, while S/Se/Te atoms predominantly exhibit the structure of a distorted triangular pyramid. This structural arrangement is ascribed to the substantial dative bonds formed by the lone-pair electrons of the anions and the vacant sp3 orbitals around Ga atoms. Large mobility gaps (e.g., GaS: 2.43 eV, GaSe: 1.76 eV, GaTe: 1.26 eV) and distinct mid-gap states (e.g., ∼0.66 eV above valence band tail) ensure that these three chalcogenide glasses can be switched on under an external electric field while effectively suppressing leakage current without a bias, and the defect electronic states originate from short, robust Ga-Ga bonds due to the formation of distorted chain-like local structures. Our research elucidates the mechanisms of amorphous Ga-X as OTS materials, enriching the spectrum of electrical switching selectors by incorporating III-VI chalcogenides. This inclusion offers novel opportunities for the refinement and optimization of high-density integrated memory systems.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Influence of plateau, slope, and valley on soil hydrology during the dry season in a Central Amazon old‐growth forest

Soil moisture regulates plant water supply and drought sensitivity in tropical forests, yet its vertical and topographic variation remains poorly characterized. We combined high-frequency time-domain reflectometry measurements from 5 to 100 cm across plateau, slope, and valley landforms at the Zona Florestal 2 research site north of Manaus, Central Amazonia, to quantify how soil moisture memory, timing of responses to rainfall, dry-down rates (τ), and soil–water depletion vary across these contrasting landforms. Landform-specific soil moisture calibration curves ensured accurate volumetric water content estimates in these highly weathered soils. During the 2023 dry-to-wet transition (August–November), soil moisture memory showed strong topographic contrasts, with valley profiles increasing from ∼47 h at 5 cm to ∼154 h at 100 cm, while plateaus exhibited higher near-surface persistence (∼124 h at 5 cm) but weaker memory at depth. Dry-down behavior reinforced these differences as valley soils exhibited τ values exceeding ∼200 h, more than double the characteristic τ of plateau soils (∼90 h). Rainfall–soil moisture correlations indicated immediate responses at shallow depths in valleys and progressively longer lags with depth on plateaus and slopes. These hydrologic patterns were mirrored in depletion profiles, which declined sharply below 30 cm on plateaus but remained high and sustained throughout the upper meter in slopes and valleys. Together, these findings provide the first depth-resolved field measurements of soil moisture memory, rainfall coupling, dry-down constants, and depletion dynamics across major upland landforms in Central Amazonia and offer clear observational benchmarks for improving land-surface and ecosystem model representations of soil–water processes.

Hillslope↗

DOE OSTI2022

$χ$-$MeRA$: Computationally efficient adaptive mesh refinement of Monte Carlo mesh based tallies

Here, the reactor physics community is always focused on reducing the computational time and memory required for simulations. $χ$-$MeRA$, which stands for flux-based-($χ$)-Mesh tally Refinement Adaptively, was built to reduce the computational time and memory required to solve the neutronics side of a multiphysics problem when compared to traditional methods for mesh based tallies in Monte Carlo (MC) simulations. $χ$-$MeRA$ couples a MC code with an adaptive mesh refinement (AMR) algorithm to take advantage of the accuracy of a MC code and the efficiency of an AMR algorithm. Also developed within $χ$-$MeRA$ was a set of metrics to assess the effects of the refinement on various parameters in the simulation space. For a plutonium sphere, $χ$-$MeRA$ shows a reduction in memory usage and computation time when compared to a fully refined mesh by a factor of 14.7 and 6.7, respectively. When compared to an unstructured mesh, improvement of 1.3 and 4.8 was achieved for memory usage and computation time. The development of $χ$-$MeRA$ helps solve the neutronics side of a multiphysics problem in a faster, more computationally efficient manner than traditional methods, and the final mesh created contains accurate results that can be passed onto the next physics code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Conditional Point Sampling: A Monte Carlo Method for Radiation Transport in Stochastic Media.

Current methods for stochastic media transport are either computationally expensive or, by nature, approximate. Moreover, none of the well-developed, benchmarked approximate methods can compute the variance caused by the stochastic mixing, a quantity especially important to safety calculations. Therefore, we derive and apply a new conditional probability function (CPF) for use in the recently developed stochastic media transport algorithm Conditional Point Sampling (CoPS), which 1) leverages the full intra-particle memory of CoPS to yield errorless computation of stochastic media outputs in 1D, binary, Markovian-mixed media, and 2) leverages the full inter-particle memory of CoPS and the recently developed Embedded Variance Deconvolution method to yield computation of the variance in transport outputs caused by stochastic material mixing. Numerical results demonstrate errorless stochastic media transport as compared to reference benchmark solutions with the new CPF for this class of stochastic mixing as well as the ability to compute the variance caused by the stochastic mixing via CoPS. Using previously derived, non-errorless CPFs, CoPS is further found to be more accurate than the atomic mix approximation, Chord Length Sampling (CLS), and most of memory-enhanced versions of CLS surveyed. In addition, we study the compounding behavior of CPF error as a function of cohort size (where a cohort is a group of histories that share intra-particle memory) and recommend that small cohorts be used when computing the variance in transport outputs caused by stochastic mixing.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2025

Angular-spatial hp -adaptivity for radiative transfer with discontinuous Galerkin spectral element methods

Radiative transfer is important for many science and engineering applications, and numerical simulations of radiative transfer can be challenging. For instance, the radiation field is seven-dimensional – three spatial, two angular, one wavelength, and one temporal – and often features steep gradients. Therefore, memory usage is a key issue. To reduce memory, some past work has investigated the use of adaptive mesh refinement (AMR), typically for either the spatial or angular coordinate, and typically for only h -adaptivity. Here, we propose the use of AMR for the spatial and angular coordinates together, and the use of h - and p -adaptivity together as hp -AMR for the potential for further memory savings. We implemented the proposed method for several test cases in two spatial and one angular dimension, with the discontinuous Galerkin spectral element method. These test cases featured highly anisotropic angular radiation, with or without steep spatial gradients. Our primary findings from these test cases were: (1) Angular hp -adaptivity can deliver the radiation solution with the same accuracy as, and with much less computational memory than, uniform angular h - or p -refinements, or angular h -adaptivity alone. This is most obvious when the incoming radiation is highly anisotropic, in which case the savings can be orders of magnitude. (2) Full spatial-angular hp -adaptivity is more efficient in solution representation, compared to solely spatial or solely angular -adaptivity. This is most evident when steep gradients are present in both the spatial and angular distribution. These results suggest that adaptive spatial- hp angular-refinement may perform well in large-scale seven-dimensional applications.

Adaptive refinement↗

DOE OSTI2026

Memsensing by surface ion migration within Debye length

Integration between electronics and biology is often facilitated by iontronics, where ion migration in aqueous media governs sensing and memory. However, the Debye screening effect limits electric fields to the Debye length, the distance over which mobile ions screen electrostatic interactions, necessitating external voltages that constrain the operation speed and device design. Here we report a high-speed in-memory sensor based on vanadium dioxide (VO2) that operates without an external voltage by leveraging built-in electric fields within the Debye length. When VO2 contacts a low-work-function metal (for example, indium) in a salt solution, electrochemical reactions generate indium ions that migrate into the VO2 surface under the native electric field, inducing a surface insulator-to-metal phase transition of VO2. The VO2 conductance increase rate reflects the salt concentration, enabling in-memory sensing, or memsensing of the solution. The memsensor mimics Caenorhabditis elegans chemosensory plasticity to guide a miniature boat for adaptive chemotaxis, illustrating low-power aquatic neurorobotics with fewer memory units.

Guo, Ruihan↗

DOE OSTI2020

Jamming, fragility and pinning phenomena in superconducting vortex systems

Abstract We examine driven superconducting vortices interacting with quenched disorder under a sequence of perpendicular drive pulses. As a function of disorder strength, we find four types of behavior distinguished by the presence or absence of memory effects. The fragile and jammed states exhibit memory, while the elastic and pinning dominated regimes do not. In the fragile regime, the system organizes into a pinned state during the first pulse, flows during the second perpendicular pulse, and then returns to a pinned state during the third pulse which is parallel to the first pulse. This behavior is the hallmark of the fragility proposed for jamming in particulate matter. For stronger disorder, we observe a robust jamming state with memory where the system reaches a pinned or reduced flow state during the perpendicular drive pulse, similar to the shear jamming of granular systems. We show signatures of the different states in the spatial vortex configurations, and find that memory effects arise from coexisting elastic and pinned components of the vortex assembly. The sequential perpendicular driving protocol we propose for distinguishing fragile, jammed, and pinned phases should be general to the broader class of driven interacting particles in the presence of quenched disorder.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Collective neural network behavior in a dynamically driven disordered system of superconducting loops

Collective properties of complex systems composed of many interacting components such as neurons in our brain can be modeled by artificial networks based on disordered systems. We show that a disordered neural network of superconducting loops with Josephson junctions can exhibit computational properties like categorization and associative memory in the time evolution of its state in response to information from external excitations. Superconducting loops can trap multiples of fluxons in many discrete memory configurations defined by the local free energy minima in the configuration space of all possible states. A memory state can be updated by exciting the Josephson junctions to fire or allow the movement of fluxons through the network as the current through them surpasses their critical current thresholds. Simulations performed with a lumped element circuit model of a 4-loop network show that information written through excitations is translated into stable states of trapped flux and their time evolution. Experimental implementation on a high-Tc superconductor YBCO-based 4-loop network shows dynamically stable flux flow in each pathway characterized by the correlations between junction firing statistics. Neural network behavior is observed as energy barriers separating state categories in simulations in response to multiple excitations, and experimentally as junction responses characterizing different flux flow patterns in the network. The state categories that produce these patterns have different temporal stabilities relative to each other and the excitations. This provides strong evidence for time-dependent (short-to-long-term) memories, that are dependent on the geometrical and junction parameters of the loops, as described with a network model.

Josephson junctions↗

DOE OSTI2023

Integration of Ag-CBRAM crossbars and Mott ReLU neurons for efficient implementation of deep neural networks in hardware

In-memory computing with emerging non-volatile memory devices (eNVMs) has shown promising results in accelerating matrix-vector multiplications. However, activation function calculations are still being implemented with general processors or large and complex neuron peripheral circuits. Here, we present the integration of Ag-based conductive bridge random access memory (Ag-CBRAM) crossbar arrays with Mott rectified linear unit (ReLU) activation neurons for scalable, energy and area-efficient hardware (HW) implementation of deep neural networks. We develop Ag-CBRAM devices that can achieve a high ON/OFF ratio and multi-level programmability. Compact and energy-efficient Mott ReLU neuron devices implementing ReLU activation function are directly connected to the columns of Ag-CBRAM crossbars to compute the output from the weighted sum current. We implement convolution filters and activations for VGG-16 using our integrated HW and demonstrate the successful generation of feature maps for CIFAR-10 images in HW. Our approach paves a new way toward building a highly compact and energy-efficient eNVMs-based in-memory computing system.

Mott insulators↗

DOE OSTI2026

Linear complexity

We present factorization and solution phases for a new linear complexity direct solver designed for concurrent batch operations on fine-grained parallel architectures, for matrices amenable to hierarchical representation. We focus on the strong-admissibility-based $\mathscr{H}^{2}$ format, where strong recursive skeletonization factorization compresses remote interactions. We build upon previous implementations of $\mathscr{H}^{2}$ matrix construction for efficient factorization and solution algorithm design, which are illustrated graphically in stepwise detail. The algorithms are ‘blackbox’ in the sense that the only inputs are the matrix and right-hand side, without analytical or geometrical information about the origin of the system. We demonstrate linear complexity scaling in both time and memory on four representative families of dense matrices up to one million in size. Parallel scaling up to 16 threads is enabled by a multi-level matrix graph coloring and avoidance of dynamic memory allocations thanks to prefix-sum memory management. An experimental backward error analysis is included. We break down the timings of different phases, identify phases that are memory-bandwidth limited, and discuss alternatives for phases that may be sensitive to the trend to employ lower precisions for performance.

Boukaram, Wajih↗

DOE OSTI2023

Efficient GPU Implementation of Automatic Differentiation for Computational Fluid Dynamics

Many scientific and engineering applications require repeated calculations of derivatives of output functions with respect to input parameters. Automatic Differentiation (AD) is a method that automates derivative calculations and can significantly speed up code development. In Computational Fluid Dynamics (CFD), derivatives of flux functions with respect to state variables (Jacobian) are needed for efficient solutions of the nonlinear governing equations. AD of flux functions on graphics processing units (GPUs) is challenging as flux computations involve many intermediate variables that create high register pressure and require significant memory traffic because of the need to store the derivatives. This paper presents a forward-mode AD method based on multivariate dual numbers that addresses these challenges and simultaneously reduces the floating-point operation count. The dimension of the multivariate dual numbers is optimized for performance. The flux computations are restructured to minimize the number of temporary variables and reduce register pressure. For effective utilization of memory bandwidth, shared memory is used to store the local flux Jacobian. This AD implementation is compared with several other Jacobian implementations on an NVIDIA V100 GPU (V100). For three-dimensional perfect-gas compressible-flow equations implemented in a practical CFD code, the AD implementation of a flux Jacobian based on multivariate dual numbers of dimension 5 outperforms all other GPU AD implementations on V100. Its performance is comparable with the optimized hand-differentiated version. Finally, the implementation achieves 75% of the peak floating-point throughput and 61 % of the peak global device memory bandwidth usage.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

A High-Throughput Solver for Marginalized Graph Kernels on GPU

Here, we present the design and optimization of a solver for efficient and high-throughput computation of the marginalized graph kernel on General Purpose GPUs. The graph kernel is computed using the conjugate gradient method to solve a generalized Laplacian of the tensor product between a pair of graphs. To cope with the large gap between the instruction throughput and the memory bandwidth of the GPUs, our solver forms the graph tensor product on-the-fly without storing it in memory. This is achieved by using threads in a warp cooperatively to stream the adjacency and edge label matrices of individual graphs by small square matrix blocks called tiles, which are then staged in registers and the shared memory for later reuse. Warps across a thread block can further share tiles via the shared memory to increase data reuse. We exploit the sparsity of the graphs hierarchically by storing only non-empty tiles using a coordinate format and nonzero elements within each tile using bitmaps. We propose a new partition-based reordering algorithm for aggregating nonzero elements of the graphs into fewer but denser tiles to further exploit sparsity. We carry out extensive theoretical analyses on the graph tensor product primitives for tiles of various density and evaluate their performance on synthetic and real-world datasets. Our solver delivers three to four orders of magnitude speedup over existing CPU-based solvers such as GraKeL and GraphKernels. The capability of the solver enables kernel-based learning tasks at unprecedented scales.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies overlapping sequences, simplifies their layout, and creates consensus. Despite many algorithms developed in the literature, the efficient assembly of large genomes is still an open problem. In this work, we introduce new distributed-memory parallel algorithms for overlap detection and layout simplification steps of de novo genome assembly, and implement them in the diBELLA 2D pipeline. Our distributed memory algorithms for both overlap detection and layout simplification are based on linear-algebra operations over semirings using 2D distributed sparse matrices. Our layout step consists of performing a transitive reduction from the overlap graph to a string graph. We provide a detailed communication analysis of the main stages of our new algorithms. diBELLA 2D achieves near linear scaling with over 80% parallel efficiency for the human genome, reducing the runtime for overlap detection by 1.2-1.3× for the human genome and 1.5-1.9× for C.elegans compared to the state-of-the-art. Our transitive reduction algorithm outperforms an existing distributed-memory implementation by 10.5-13.3× for the human genome and 18-29× for the C. elegans. Our work paves the way for efficient de novo assembly of large genomes using long reads in distributed memory.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Design of Hopfield Networks Based on Superconducting Coupled Oscillators

The global energy shortage has driven the development of many energy-efficient computational platforms beyond Moore's law, among which brain-inspired neuromorphic computing is one of the promising solutions. Associative memory and pattern recognition are important computations solved by brain-inspired Hopfield networks. Classical Hopfield networks store memories via fixed point attractors of their dynamics. In oscillatory Hopfield networks, these attractors are replaced by periodic orbits. Here, we design an oscillatory Hopfield network based on coupled superconducting oscillators. We first employ a mathematical phase reduction approach to map networks of coupled superconducting rapid single flux quantum (RSFQ) ring oscillators to coupled Kuramoto phase-oscillator networks. We use this theory to numerically optimize the hardware's mutual inductances in order to directly match the phase-reduced superconducting oscillators to a model of phase-oscillator-based Hopfield networks. The resulting network can store multiple oscillatory phase-locked memory patterns and recover the patterns based on the initial phase conditions. As different pattern recognition tasks, or learning, require tunable connectivity strengths between the oscillatory nodes, we further employ a coupler circuit that enables tuning the coupling strength between two oscillators by applying an external flux. We demonstrate the functionality of our design through numerical simulations of a small example network with oscillators operating at 86 GHz and recognizing patterns within 10 ns. Our approach enables the learning and retrieval of dynamical memory patterns with a wide range of applications where rhythmic dynamic output is beneficial.

Cheng, Ran↗

DOE OSTI2021

Analysis of GPU Data Access Patterns on Complex Geometries for the D3Q19 Lattice Boltzmann Algorithm

GPU performance of the lattice Boltzmann method (LBM) depends heavily on memory access patterns. When implemented with GPUs on complex domains, typically, geometric data is accessed indirectly and lattice data is accessed lexicographically. Although there are a variety of other options, no study has examined the relative efficacy between them. Here, we examine a suite of memory access schemes via empirical testing and performance modeling. We find strong evidence that semi-direct is often better suited than the more common indirect addressing, providing increased computational speed and reducing memory consumption. For the layout, we find that the Collected Structure of Arrays (CSoA) and bundling layouts outperform the common Structure of Array layout; on V100 and P100 devices, CSoA consistently outperforms bundling, however the relationship is more complicated on K40 devices. When compared to state-of-the-art practices, our recommendations lead to speedups of 10–40 percent and reduce memory consumption up to 17 percent. Using performance modeling and computational experimentation, we determine the mechanisms behind the accelerations. We demonstrate that our results hold across multiple GPUs on two leadership class systems, and present the first near-optimal strong results for LBM with arterial geometries run on GPUs.

42 ENGINEERING↗

DOE OSTI2021

MemXCT: Design, Optimization, Scaling, and Reproducibility of X-Ray Tomography Imaging

Here, this work extends our previous research entitled "MemXCT: Memory-centric X-ray CT Reconstruction with Massive Parallelization" that was originally published at SC19 conference (Hidayetoglu et al., 2019) with reproducibility of the computational imaging performance. X-ray computed tomography (XCT) is regularly used at synchrotron light sources to study the internal morphology of materials at high resolution. However, experimental constraints, such as radiation sensitivity, can result in noisy or undersampled measurements. Further, depending on the resolution, sample size and data acquisition rates, the resulting noisy dataset can be in the order of terabytes. Advanced iterative reconstruction techniques can produce high-quality images from noisy measurements, but their computational requirements have made their use an exception rather than the rule. We propose a novel memory-centric approach that avoids redundant computations at the expense of additional memory complexity. We develop a memory-centric iterative reconstruction system, MemXCT, that uses an optimized SpMV implementation with two-level pseudo-Hilbert ordering and multi-stage input buffering. We evaluate MemXCT on various supercomputer architectures involving KNL and GPU. MemXCT can reconstruct a large (11Kx11K) mouse brain tomogram in 10 seconds using 4096 KNL nodes (256K cores). The results presented in our original article at the SC19 were based on large-scale supercomputing resources. The MemXCT application was selected for the Student Cluster Competition (SCC) Reproducibility Challenge and evaluated on a variety of cloud computing resources by universities around the world in the SC20 conference. We summarize the results of the top-ranked SCC Reproducibility Challenge teams and identify the most pertinent measures for ensuring the reproducibility of our experiments in this article.

47 OTHER INSTRUMENTATION↗