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At least 973 records · Page 54

SigTime: Learning and Visually Explaining Time Series Signatures

Understanding and distinguishing temporal patterns in time series data is essential for scientific discovery and decision-making. For example, in biomedical research, uncovering meaningful patterns in physiological signals can improve diagnosis, risk assessment, and patient outcomes. However, existing methods for time series pattern discovery face major challenges, including high computational complexity, limited interpretability, and difficulty in capturing meaningful temporal structures. Here, to address these gaps, we introduce a novel learning framework that jointly trains two Transformer models using complementary time series representations: shapelet-based representations to capture localized temporal structures and traditional feature engineering to encode statistical properties. The learned shapelets serve as interpretable signatures that differentiate time series across classification labels. Additionally, we develop a visual analytics system—SigTime—with coordinated views to facilitate exploration of time series signatures from multiple perspectives, aiding in useful insights generation. We quantitatively evaluate our learning framework on eight publicly available datasets and one proprietary clinical dataset. Additionally, we demonstrate the effectiveness of our system through two usage scenarios along with the domain experts: one involving public ECG data and the other focused on preterm labor analysis.

97 MATHEMATICS AND COMPUTING↗

Exploring Enhanced Dominant Resource Fairness Using Linear Programming Calculated Weights

Maintaining resource fairness while achieving optimization for various performance metrics such as resource utilization, turnaround time and job latency is a well-known resource scheduling challenge in cloud computing. Despite the significant progress made with the introduction of dominant resource fairness by Ghodsi et al., which ensures major allocation properties such as sharing incentive, strategy-proofness, envy-freeness and Pareto efficiency to be achieved

Yan, Bo [Binghamton University]↗

Comparison of Radiation Models for a Turbulent Piloted Methane/Air Jet Flame: A Frozen-Field Study

Numerical modeling of radiative transfer in nongray reacting media is a challenging problem in computational science and engineering. The choice of radiation models is important for accurate and efficient high-fidelity combustion simulations. Different applications usually involve different degrees of complexity, so there is yet no consensus in the community. In this paper, the performance of different radiative transfer equation (RTE) solvers and spectral models for a turbulent piloted methane/air jet flame are studied. The flame is scaled from the Sandia Flame D with a Reynolds number of 22,400. Three classes of RTE solvers, namely the discrete ordinates method, spherical harmonics method, and Monte Carlo method, are examined. The spectral models include the Planck-mean model, the full-spectrum k-distribution (FSK) method, and the line-by-line (LBL) calculation. The performances of different radiation models in terms of accuracy and computational cost are benchmarked. The results have shown that both RTE solvers and spectral models are critical in the prediction of radiative heat source terms for this jet flame. The trade-offs between the accuracy, the computational cost, and the implementation difficulty are discussed in detail. The results can be used as a reference for radiation model selection in combustor simulations.

David, Chloe↗

Geometric deep learning of RNA structure

RNA molecules adopt three-dimensional structures that are critical to their function and of interest in drug discovery. Few RNA structures are known, however, and predicting them computationally has proven challenging. We introduce a machine learning approach that enables identification of accurate structural models without assumptions about their defining characteristics, despite being trained with only 18 known RNA structures. The resulting scoring function, the Atomic Rotationally Equivariant Scorer (ARES), substantially outperforms previous methods and consistently produces the best results in community-wide blind RNA structure prediction challenges. By learning effectively even from a small amount of data, our approach overcomes a major limitation of standard deep neural networks. Because it uses only atomic coordinates as inputs and incorporates no RNA-specific information, this approach is applicable to diverse problems in structural biology, chemistry, materials science, and beyond.

Townshend, Raphael J. L.↗

Scaling Structured Multigrid to 500K+ Cores Through Coarse-Grid Redistribution

The effcient solution of sparse, linear systems resulting from the discretization of partial differential equations is crucial to the performance of many physics-based simulations. The algorithmic optimality of multilevel approaches for common discretizations makes them a good candidate for an efficient parallel solver. Yet, modern architectures for high-performance computing systems continue to challenge the parallel scalability of multilevel solvers. While algebraic multigrid methods are robust for solving a variety of problems, the increasing importance of data locality and cost of data movement in modern architectures motivates the need to carefully exploit structure in the problem. Robust logically structured variational multigrid methods, such as Black Box Multigrid (BoxMG), maintain structure throughout the multigrid hierarchy. This avoids indirection and increased coarse- grid communication costs typical in parallel algebraic multigrid. Nevertheless, the parallel scalability of structured multigrid is challenged by coarse-grid problems where the overhead in communication dominates computation. In this paper, an algorithm is introduced for redistributing coarse-grid problems through incremental agglomeration. Guided by a predictive performance model, this algorithm provides robust redistribution decisions for structured multilevel solvers. A two-dimensional diffusion problem is used to demonstrate the significant gain in performance of this algorithm over the previous approach that used agglomeration to one processor. In addition, the parallel scalability of this approach

97 MATHEMATICS AND COMPUTING↗

Software Defined Architectures for Data Analytics

Data analytics applications increasingly are complex workflows composed of phases with very different program behaviors (e.g., graph algorithms and machine learning, algorithms operating on sparse an dense data structures, etc). To reach the levels of efficiency required to process these workflows in real time, upcoming architectures will need to leverage even more workload specialization. If, at one end, we may find even more heterogenous processors composed by a myriad of specialized processing elements, at the other end we may see novel reconfigurable architectures, composed of sets of functional units and memories interconnected with (re)configurable on-chip networks, able to adapt dynamically to adapt the workload characteristics. Field Programmable Gate Arrays are more and more used for accelerating various workloads and, in particular, inferencing in machine learning, providing higher efficiency than other solutions. However, their fine grained nature still leads to issues for the design software and still makes dynamic reconfiguration impractical. Future, more coarse-grained architectures could offer the features to execute diverse workloads at high efficiency while providing better reconfiguration mechanisms for dynamic adaptability. Nevertheless, we argue that the challenges for reconfigurable computing remain in the software. In this position paper, we describe a possible toolchain for reconfigurable architectures targeted at data analytics.

FPGA, Dataflow, Reconfigurable Architectures, Soft↗

CoREC: Scalable and Resilient In-memory Data Staging for In-situ Workflows

The dramatic increase in the scale of current and planned high-end HPC systems is leading new challenges, such as the growing costs of data movement and IO, and the reduced mean time between failures (MTBF) of system components. In-situ workflows, i.e., executing the entire application workflows on the HPC system, have emerged as an attractive approach to address data-related challenges by moving computations closer to the data, and staging-based frameworks have been effectively used to support in-situ workflows at scale. However, the resilience of these staging-based solutions has not been addressed, and they remain susceptible to expensive data failures. Furthermore, naive use of data resilience techniques such as n-way replication and erasure codes can impact latency and/or result in significant storage overheads. In this article, we present CoREC, a scalable and resilient in-memory data staging runtime for large-scale in-situ workflows. CoREC uses a novel hybrid approach that combines dynamic replication with erasure coding based on data access patterns. It also leverages multiple levels of replications and erasure coding to support diverse data resiliency requirements. Furthermore, the article presents optimizations for load balancing and conflict-avoiding encoding, and a low overhead, lazy data recovery scheme. We have implemented the CoREC runtime and have deployed with the DataSpaces staging service on leadership class computing machines and present an experimental evaluation in the article. Here, the experiments demonstrate that CoREC can tolerate in-memory data failures while maintaining low latency and sustaining high overall storage efficiency at large scales.

97 MATHEMATICS AND COMPUTING↗

2D-DIC Challenge MATLAB Analysis Code v. 1.0

This code replicates the analysis completed in the published article (see reference below) for the 2D-DIC Challenge (https://sem.org/dic-challenge/), conducted under the auspices of the Society for Experimental Mechanics (SEM). The purpose of the DIC Challenge is to provide a set of vetted and standard images, which all users and developers of Digital Image Correlation (DIC) software can use -DIC Challenge results from Sample 14 and Sample 15 of the DIC-Challenge images, and computes various statistics on the data, such as the noise, bias, and spatial resolution. P.L. Reu, E. Toussaint, E. Jones, H.A. Bruck, M. Iadicola, R. Balcaen, D.Z. Turner, T. Siebert, P. Lava, M. Simonsen (2018) Exp. Mech. 58(7):1067-1099, https://doi.org/10.1007/s11340-017-0349-0.

Jones, Elizabeth↗

Logic in Memory Emulator

Logic in Memory Emulator (LiME) is a hardware/software tool specially designed for memory system evaluation and experiment. Emerging memories display a wide range of bandwidths, latencies, and capacities, making it challenging for the computer architect to navigate the design space of potential memory configurations, and for the application developer to assess performance implications of using such memories. With the LiME framework, architectural ideas can be prototyped in great detail yet with sufficient performance to support realistic evaluation on long running applications. LiME consists of two fundamental components: 1) the hardware and OS infrastructure for the emulator, and 2) a suite of benchmark applications to assist in characterizing the performance of current and future computer architectures. Some of the applications have been collected from other open source projects. Uses: Logging, replay and analysis of an application's memory behavior Evaluate impact of emerging memory technology on application performance. Emulate complex memory interactions in whole applications orders of magnitude faster than software simulation. Emulate acceleration hardware co-located with the memory subsystem. Features: Capture and log external memory accesses to a separate off-chip memory device without affecting application execution. Memory traces include the address, length, timestamp, and optionally the data for each transaction. Captured trace data can be saved to an SD card for off-line analysis. Configure a wide range of memory latencies in sub-nanosecond increments that encompass highbandwidth and storage class memories. Specify regions of interest (ROI) in applications to reduce the amount of trace data captured for analysis. Currently supports execution on Xilinx Zynq SoC which integrates an ARM processor with FPGA logic on a single device. Applications can be run under Linux or in bare metal mode on the ARM cores.

Jain, AbhishekK↗

Earth System Reanalysis in Support of Climate Model Improvements

Recent climate model developments, established through increased model resolution, have led to substantial improvements in model simulations of the time-evolving, coupled Earth system and its subcomponents. However, regardless of resolution, climate models will always produce climate features and variability that differ from the real world and will be prone to biases. This is due to many remaining uncertainties, such as in parametric and structural model uncertainty, in the initial conditions prescribed, and in the prescribed (scenario) forcing which varies on decadal to centennial timescales. Further model improvements are expected to arise specifically from improved representation of physical processes realized through model-data fusion. This will create an unprecedented opportunity to better exploit a large array of Earth observations, from in situ measurements to weather radars and satellite observations, as the resolved scales of the models approach those of the observations. For this, climate DA will be the central tool to bring models and observations into consistency, by improving initial conditions, inferring uncertain model parameters and structure, and quantifying uncertainty. Generally, there will be advantages and complementarities of adjoint-based smoother approaches, ensemble-based filter approaches, or new ML-inspired approaches. Yet, the ever-increasing model resolution will present growing challenges arising from computational cost, calling for new ways of performing data assimilation and model optimization. Using the complementarity in a hybrid approach, blending tools and concepts from variational, ensemble and ML methods might be what is required in the future. In this context ML could be important to handle non-linear responses, and to better approximate non-Gaussian distributions.

54 ENVIRONMENTAL SCIENCES↗

Combining de novo and reference-guided assembly with scaffold_builder

Genome sequencing has become routine, however genome assembly still remains a challenge despite the computational advances in the last decade. In particular, the abundance of repeat elements in genomes makes it difficult to assemble them into a single complete sequence. Identical repeats shorter than the average read length can generally be assembled without issue. However, longer repeats such as ribosomal RNA operons cannot be accurately assembled using existing tools. The application Scaffold_builder was designed to generate scaffolds – super contigs of sequences joined by N-bases – based on the similarity to a closely related reference sequence. This is independent of mate-pair information and can be used complementarily for genome assembly, e.g. when matepairs are not available or have already been exploited. Scaffold_builder was evaluated using simulated pyrosequencing reads of the bacterial genomes Escherichia coli 042, Lactobacillus salivarius UCC118 and Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12. Moreover, we sequenced two genomes from Salmonella enterica serovar Typhimurium LT2 G455 and Salmonella enterica serovar Typhimurium SDT1291 and show that Scaffold_builder decreases the number of contig sequences by 53% while more than doubling their average length. Scaffold_builder is written in Python and is available at http://edwards.sdsu.edu/scaffold_builder. A web-based implementation is additionally provided to allow users to submit a reference genome and a set of contigs to be scaffolded.

Salmonella enterica serovar typhimurium↗

Solving multiphysics-based inverse problems with learned surrogates and constraints

Abstract Solving multiphysics-based inverse problems for geological carbon storage monitoring can be challenging when multimodal time-lapse data are expensive to collect and costly to simulate numerically. We overcome these challenges by combining computationally cheap learned surrogates with learned constraints. Not only does this combination lead to vastly improved inversions for the important fluid-flow property, permeability, it also provides a natural platform for inverting multimodal data including well measurements and active-source time-lapse seismic data. By adding a learned constraint, we arrive at a computationally feasible inversion approach that remains accurate. This is accomplished by including a trained deep neural network, known as a normalizing flow, which forces the model iterates to remain in-distribution, thereby safeguarding the accuracy of trained Fourier neural operators that act as surrogates for the computationally expensive multiphase flow simulations involving partial differential equation solves. By means of carefully selected experiments, centered around the problem of geological carbon storage, we demonstrate the efficacy of the proposed constrained optimization method on two different data modalities, namely time-lapse well and time-lapse seismic data. While permeability inversions from both these two modalities have their pluses and minuses, their joint inversion benefits from either, yielding valuable superior permeability inversions and CO 2 plume predictions near, and far away, from the monitoring wells.

Yin, Ziyi (ORCID:0000000250248771)↗

Changes in short- and medium-range order in metallic liquids during undercooling

It has been widely speculated that dominant motifs, such as short-range icosahedral order, can influence glass formation and the properties of glasses. Experimental data on both fragile and strong undercooled liquids demonstrate corresponding changes in their thermophysical properties consistent with increasing development of a network of interconnect motifs based on molecular dynamics. Describing these regions of local order, how they connect, and how they are related to property changes have been challenging issues, both computationally and experimentally. Yet the consensus is that metallic liquids develop interconnected medium-range order consisting of some regions with lower mobility with deeper undercooling. Less well understood is how these motifs (or “crystal genes”) in the liquid can inhibit nucleation in the deeply undercooled liquid or influence phase selection upon devitrification. These motifs tend to have local packing unlike stable compounds with icosahedral order tending to dominate the best glass formers. The underlying kinetic and thermodynamic forces that guide the formation of these motifs and how they interconnect during undercooling remain open questions.

36 MATERIALS SCIENCE↗

A Hybrid Reduced-Order Model of Fine-Resolution Hydrologic Simulations at a Polygonal Tundra Site

High-resolution predictions of land surface hydrological dynamics are desirable for improved investigations of regional- and watershed-scale processes. Direct deterministic simulations of fine-resolution land surface variables present many challenges, including high computational cost. We therefore propose the use of reduced-order modeling techniques to facilitate emulation of fine-resolution simulations. We use an emulator, Gaussian process regression, to approximate fine-resolution four-dimensional soil moisture fields predicted using a three-dimensional surface-subsurface hydrological simulator (PFLOTRAN). A dimension-reduction technique known as “proper orthogonal decomposition” is further used to improve the efficiency of the resulting reduced-order model (ROM). The ROM reduces simulation computational demand to negligible levels compared to the underlying fine-resolution model. In addition, the ROM that we constructed is equipped with an uncertainty estimate, allowing modelers to construct a ROM consistent with uncertainty in the measured data. The ROM is also capable of constructing statistically equivalent analogs that can be used in uncertainty and sensitivity analyses. We apply the technique to four polygonal tundra sites near Barrow, Alaska that are part of the Department of Energy’s Next-Generation Ecosystem Experiments (NGEE)-Arctic project. The ROM is trained for each site using simulated soil moisture from 1998-2000 and validated using the simulated data for 2002 and 2006. The average relative RMSEs of the ROMs are under 1%.

58 GEOSCIENCES↗

Performance Engineering Research Institute SciDAC-2 Enabling Technologies Institute Final Report

Enhancing the performance of SciDAC applications on petascale systems has high priority within DOE SC. As we look to the future, achieving expected levels of performance on high-end com-puting (HEC) systems is growing ever more challenging due to enormous scale, increasing archi-tectural complexity, and increasing application complexity. To address these challenges, PERI has implemented a unified, tripartite research plan encompassing: (1) performance modeling and prediction; (2) automatic performance tuning; and (3) performance engineering of high profile applications. The PERI performance modeling and prediction activity is developing and refining performance models, significantly reducing the cost of collecting the data upon which the models are based, and increasing model fidelity, speed and generality. Our primary research activity is automatic tuning (autotuning) of scientific software. This activity is spurred by the strong user preference for automatic tools and is based on previous successful activities such as ATLAS, which has automatically tuned components of the LAPACK linear algebra library, and other re-cent work on autotuning domain-specific libraries. Our third major component is application en-gagement, to which we are devoting approximately 30% of our effort to work directly with Sci-DAC-2 applications. This last activity not only helps DOE scientists meet their near-term per-formance goals, but also helps keep PERI research focused on the real challenges facing DOE computational scientists as they enter the Petascale Era.

97 MATHEMATICS AND COMPUTING↗

Enabling Predictive Simulation and UQ of Complex Multiphysics PDE Systems by the Development of Goal-Oriented Variational Sensitivity Analysis and a-Posteriori Error Estimation Methods

This project addressed the challenge of predictive computational analysis of strongly coupled, highly nonlinear multiphysics systems characterized by multiple physical phenomena that span a large range of length- and time-scales. Specifically, the project was focused on computational estimation of numerical error and sensitivity analysis of computational solutions with respect to variations in parameters and data. In addition, the project investigated the use of accurate computational estimates to guide efficient adaptive discretization. The project developed, analyzed and evaluated new variational adjoint-based techniques for integration, model, and data error estimation/control and sensitivity analysis, in evolutionary multiphysics multiscale simulations.

97 MATHEMATICS AND COMPUTING↗

DEGAS: Dynamic Exascale Global Address Space Programming Environments

The Dynamic, Exascale Global Address Space programming environment (DEGAS) project will develop the next generation of programming models and runtime systems to meet the challenges of Exascale computing. The Berkeley part of the project concentrated on communication-optimal code generation to optimize speed and energy efficiency by reducing data movement. Our work developed communication lower bounds, and/or communication avoiding algorithms (that either meet the lower bound, or do much less communication than their conventional counterparts) for a variety of algorithms, including linear algebra, machine learning and genomics. The Berkeley part of the project concentrated on communication-optimal code generation to optimize speed and energy efficiency by reducing data movement. Our work developed communication lower bounds, and/or communication avoiding algorithms (that either meet the lower bound, or do much less communication than their conventional counterparts) for a variety of algorithms, including linear algebra, machine learning and genomics.

97 MATHEMATICS AND COMPUTING↗

Multiscale Approach to Fast ModSim for Laser Processing of Metals for Future Nuclear Deterrence Environments

Predicting performance of parts produced using laser-metal processing remains an out- standing challenge. While many computational models exist, they are generally too computationally expensive to simulate the build of an engineering-scale part. This work develops a reduced order thermal model of a laser-metal system using analytical Green's function solutions to the linear heat equation, representing a step towards achieving a full part performance prediction in an "overnight" time frame. The developed model is able to calculate a thermal history for an example problem 72 times faster than a traditional FEM method. The model parameters are calibrated using a non-linear solution and microstructures and residual stresses calculated and compared to a non-linear case. The calibrated model shows promising agreement with a non-linear solution.

36 MATERIALS SCIENCE↗