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At least 235 records · Page 13

Electronic spectra from TDDFT and machine learning in chemical space

Due to its favorable computational efficiency, time-dependent (TD) density functional theory (DFT) enables the prediction of electronic spectra in a high-throughput manner across chemical space. Its predictions, however, can be quite inaccurate. We resolve this issue with machine learning models trained on deviations of reference second-order approximate coupled-cluster (CC2) singles and doubles spectra from TDDFT counterparts, or even from DFT gap. We applied this approach to low-lying singlet-singlet vertical electronic spectra of over 20 000 synthetically feasible small organic molecules with up to eight CONF atoms. The prediction errors decay monotonously as a function of training set size. For a training set of 10 000 molecules, CC2 excitation energies can be reproduced to within ±0.1 eV for the remaining molecules. Analysis of our spectral database via chromophore counting suggests that even higher accuracies can be achieved. Based on the evidence collected, we discuss open challenges associated with data-driven modeling of high-lying spectra and transition intensities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DIRAQ: scalable in situ data- and resource-aware indexing for optimized query performance

Scientific data analytics in high-performance computing environments has been evolving along with the advancement of computing capabilities. With the onset of exascale computing, the increasing gap between compute performance and I/O bandwidth has rendered the traditional post-simulation processing a tedious process. Despite the challenges due to increased data production, there exists an opportunity to benefit from "cheap" computing power to perform query-driven exploration and visualization during simulation time. To accelerate such analyses, applications traditionally augment, post-simulation, raw data with large indexes, which are then repeatedly utilized for data exploration. However, the generation of current state-of-the-art indexes involves a compute- and memory-intensive processing, thus rendering them inapplicable in an in situ context. In this paper we propose DIRAQ, a parallel in situ, in network data encoding and reorganization technique that enables the transformation of simulation output into a query-efficient form, with negligible runtime overhead to the simulation run. DIRAQ's effective core-local, precision-based encoding approach incorporates an embedded compressed index that is 3---6 $$\times $$ ? smaller than current state-of-the-art indexing schemes. Its data-aware index adjustmentation improves performance of group-level index layout creation by up to 35 % and reduces the size of the generated index by up to 27 %. Moreover, DIRAQ's in network index merging strategy enables the creation of aggregated indexes that speed up spatial-context query responses by up to $$10\times $$ 10 ? versus alternative techniques. DIRAQ's topology-, data-, and memory-aware aggregation strategy results in efficient I/O and yields overall end-to-end encoding and I/O time that is less than that required to write the raw data with MPI collective I/O.

Computer Science↗

Coordinative Entities: Forms of Organizing in Data Intensive Science

Scientific collaboration is a long-standing subject of CSCW scholarship that typically focuses on the development and use of computing systems to facilitate research. The research presented in this article investigates the sociality of science by identifying and describing particular, common forms of organizing that researchers in four different scientific realms employ to conduct work in both local contexts and as part of distributed, global projects. This paper introduces five prototypical forms of organizing we categorize as coordinative entities: the Principal Group, Intermittent Exchange, Sustained Aggregation, Federation, and Facility Organization. Coordinative entities as a categorization help specify, articulate, compare, and trace overlapping and evolving arrangements scientists use to facilitate data intensive research. We use this typology to unpack complexities of data intensive scientific collaboration in four cases, showing how scientists invoke different coordinative entities across three types of research activities: data collection, processing, and analysis. Finally, our contribution scrutinizes the sociality of scientific work to illustrate how these actors engage in relational work within and among diverse, dispersed forms of organizing across project, funding, and disciplinary boundaries.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Toward memory-efficient melt pool monitoring: a classification framework using event-based imaging and sparse sensing technique

Vision sensors like CMOS and CCD cameras are often used for in-process monitoring of melt pools in laser-based additive and welding processes, but they require transferring large amounts of data and computational processing resources. Event-based neuromorphic imagery, on the other hand, detects only the change in pixel intensity, thus potentially reducing the data amount and latency. With an event imager, this study develops a framework for melt pool condition classification, including image construction, time scale selection, optimal pixel selection, and sparse classification, to achieve a highly memory-efficient scheme. These are based on sparse sensing techniques with singular value decomposition (SVD) and QR pivoting, the two fundamental matrix transformations for linear dimensionality reduction. The framework is then validated by classifying a controlled experiment by exciting various mode shapes of liquid gallium pools of varying depths (3, 6, and 8 mm). At 200 pixels, the classifier can reach overall accuracy of 75%, while at 2000 pixels (0.013% of the total possible pixels), the accuracy is nearly 90% (89.86%). At the same number of pixels, random selection can only achieve 46% and 67%, respectively. The memory savings of the sparsely sampled event data compared to a conventional imager is about 500 times. In addition to performance, implementation and limitations of the framework are also discussed.

42 ENGINEERING↗

PoPLAR: Portal for Petascale Lifescience Applications and Research

Background: We are focusing specifically on fast data analysis and retrieval in bioinformatics that will have a direct impact on the quality of human health and the environment. The exponential growth of data generated in biology research, from small atoms to big ecosystems, necessitates an increasingly large computational component to perform analyses. Novel DNA sequencing technologies and complementary high-throughput approaches–such as proteomics, genomics, metabolomics, and meta-genomics–drive data-intensive bioinformatics. While individual research centers or universities could once provide for these applications, this is no longer the case. Today, only specialized national centers can deliver the level of computing resources required to meet the challenges posed by rapid data growth and the resulting computational demand. Consequently, we are developing massively parallel applications to analyze the growing flood of biological data and contribute to the rapid discovery of novel knowledge. Methods: The efforts of previous National Science Foundation (NSF) projects provided for the generation of parallel modules for widely used bioinformatics applications on the Kraken supercomputer. We have profiled and optimized the code of some of the scientific community’s most widely used desktop and small-cluster-based applications, including BLAST from the National Center for Biotechnology Information (NCBI), HMMER, and MUSCLE; scaled them to tens of thousands of cores on high-performance computing (HPC) architectures; made them robust and portable to next-generation architectures; and incorporated these parallel applications in science gateways with a web-based portal. Results: This paper will discuss the various developmental stages, challenges, and solutions involved in taking bioinformatics applications from the desktop to petascale with a front-end portal for very-large-scale data analysis in the life sciences. Conclusions: This research will help to bridge the gap between the rate of data generation and the speed at which scientists can study this data. The ability to rapidly analyze data at such a large scale is having a significant, direct impact on science achieved by collaborators who are currently using these tools on supercomputers.

59 BASIC BIOLOGICAL SCIENCES↗

Filament-Free Bulk Resistive Memory Enables Deterministic Analogue Switching

Digital computing is nearing its physical limits as computing needs and energy consumption rapidly increase. Analogue-memory-based neuromorphic computing can be orders of magnitude more energy efficient at data-intensive tasks like deep neural networks, but has been limited by the inaccurate and unpredictable switching of analogue resistive memory. Filamentary resistive random access memory (RRAM) suffers from stochastic switching due to the random kinetic motion of discrete defects in the nanometer-sized filament. Here, this stochasticity is overcome by incorporating a solid electrolyte interlayer, in this case, yttria-stabilized zirconia (YSZ), toward eliminating filaments. Filament-free, bulk-RRAM cells instead store analogue states using the bulk point defect concentration, yielding predictable switching because the statistical ensemble behavior of oxygen vacancy defects is deterministic even when individual defects are stochastic. Both experiments and modeling show bulk-RRAM devices using TiO2-X switching layers and YSZ electrolytes yield deterministic and linear analogue switching for efficient inference and training. Bulk-RRAM solves many outstanding issues with memristor unpredictability that have inhibited commercialization, and can, therefore, enable unprecedented new applications for energy-efficient neuromorphic computing. Beyond RRAM, this work shows how harnessing bulk point defects in ionic materials can be used to engineer deterministic nanoelectronic materials and devices.

36 MATERIALS SCIENCE↗

Multi-level Layout Optimization for Efficient Spatio-temporal Queries on ISABELA-compressed Data

The size and scope of cutting-edge scientific simulations are growing much faster than the I/O subsystems of their runtime environments, not only making I/O the primary bottleneck, but also consuming space that pushes the storage capacities of many computing facilities. These problems are exacerbated by the need to perform data-intensive analytics applications, such as querying the dataset by variable and spatio-temporal constraints, for what current database technologies commonly build query indices of size greater than that of the raw data. To help solve these problems, we present a parallel query-processing engine that can handle both range queries and queries with spatio-temporal constraints, on B-spline compressed data with user-controlled accuracy. Our method adapts to widening gaps between computation and I/O performance by querying on compressed metadata separated into bins by variable values, utilizing Hilbert space-filling curves to optimize for spatial constraints and aggregating data access to improve locality of per-bin stored data, reducing the false positive rate and latency bound I/O operations (such as seek) substantially. We show our method to be efficient with respect to storage, computation, and I/O compared to existing database technologies optimized for query processing on scientific data.

Computer Science↗

Experiences with string matching on the Fermi Architecture

String matching is at the core of many real-world applications, such as security, bioinformatic, data mining. All these applications requires the ability to match always growing data sets against large dictionaries effectively, fastly and possibly in real time. Unfortunately, string matching is a computationally intensive procedure which poses significant challenges on current software and hardware implementations. Graphic Processing Units (GPU) have become an interesting target for such high-throughput applications, but the algorithms and the data structures need to be redesigned to be parallelized and adapted to the underlining hardware, coping with the limitations imposed by these architectures. In this paper we present an efficient implementation of the Aho-Corasick string matching algorithm on GPU, showing how we progressively redesigned the algorithm and the data structures to fit on the architecture. We then evaluate the implementation on single and multiple Tesla C2050 (T20 ``Fermi'' based) boards, comparing them to the previous Tesla C1060 (T10 based) solutions and equivalent multicore implementations on x86 CPUs. We discuss the various tradeoffs of the different architectures.

99 GENERAL AND MISCELLANEOUS↗

DataSpaces: an interaction and coordination framework for coupled simulation workflows

Emerging high-performance distributed computing environments are enabling new end-to-end formulations in science and engineering that involve multiple interacting processes and data-intensive application workflows. For example, current fusion simulation efforts are exploring coupled models and codes that simultaneously simulate separate application processes, such as the core and the edge turbulence. These components run on different high performance computing resources, need to interact at runtime with each other and with services for data monitoring, data analysis and visualization, and data archiving. As a result, they require efficient and scalable support for dynamic and flexible couplings and interactions, which remains a challenge. This paper presents DataSpaces a flexible interaction and coordination substrate that addresses this challenge. DataSpaces essentially implements a semantically specialized virtual shared space abstraction that can be associatively accessed by all components and services in the application workflow. It enables live data to be extracted from running simulation components, indexes this data online, and then allows it to be monitored, queried and accessed by other components and services via the space using semantically meaningful operators. The underlying data transport is asynchronous, low-overhead and largely memory-to-memory. The design, implementation, and experimental evaluation of DataSpaces using a coupled fusion simulation workflow is presented.

Computer Science↗

SU-E-J-177: A Computational Approach for Determination of Anisotropic PTV Margins Based On Statistical Shape Analysis for Prostate Cancer Radiotherapy

Purpose: Our aim of this study was to propose a computational approach for determination of anisotropic planning target volume (PTV) margins based on statistical shape analysis with taking into account time variations of clinical target volume (CTV) shapes for the prostate cancer radiation treatment planning (RTP). Methods: Systematic and random setup errors were measured using orthogonal projection and cone beam computed tomography (CBCT) images for data of 20 patients, who underwent the intensity modulated radiation therapy for prostate cancer. The low-risk, intermediate-risk, and high-risk CTVs were defined as only a prostate, a prostate plus proximal 1-cm seminal vesicles, and a prostate plus proximal 2-cm seminal vesicles, respectively. All CTV regions were registered with a reference CTV region with a median volume to remove the effect of the setup errors, and converted to a point distribution models. The systematic and random errors for translations of CTV regions were automatically evaluated by analyzing the movements of centroids of CTV regions. The random and systematic errors for shape variations of CTV regions were obtained from covariance matrices based on point distributions for the CTV contours on CBCT images of 72 fractions of 10 patients. Anisotropic PTV margins for 6 directions (right, left, anterior, posterior, superior and inferior) were derived by using Yoda’s PTV margin model. Results: PTV margins with and without shape variations were 5.75 to 8.03 mm and 5.23 to 7.67 mm for low-risk group, 5.87 to 8.33 mm and 5.23 to 7.67 mm for intermediate-risk group, and 5.88 to 8.25 mm and 5.29 to 7.82 mm for highrisk group, respectively. Conclusion: The proposed computational approach could be feasible for determination of the anisotropic PTV margins with taking into account CTV shape variations for the RTP.

60 APPLIED LIFE SCIENCES↗

Hyperplane decision trees as piecewise linear surrogate models for chemical process design

Recent trends in chemical engineering research point towards an increasing reliance on data-driven modeling approaches. Neural networks, for instance, have proven to be accurate when data is plentiful and high-dimensional, but in many cases, they require computationally-intensive training procedures. Here, in this work, we describe hyperplane decision trees (HT) as a highly expressive and low-compute machine learning model architecture. These models are locally linear and have linear decision boundaries, resulting in a piecewise linear model of the data. This property allows them to be converted into mixed-integer linear constraints which can be globally optimized. Our open-source PyTorch implementation of this method is a fast, flexible, and accessible way to build accurate piecewise linear models of data.

Decision trees↗

Simulation of kinematic Kikuchi diffraction patterns from atomistic structures

One of the limitations of atomistic simulations is that many of the computational tools used to extract structural information from atomic trajectories provide metrics that are not directly compatible with experiments for validation. In this work, to bridge between simulation and experiment, a method is presented to produce simulated Kikuchi diffraction patterns using data from atomistic simulations, without requiring a priori specification of the crystal structure or defect periodicity. The Kikuchi pattern simulation is based on the kinematic theory of diffraction, with Kikuchi line intensities computed via a discrete structure factor calculation. Reciprocal lattice points are mapped to Kikuchi lines using a geometric projection of the reciprocal space data. This method is validated using single crystal atomistic models, and the novelty of this approach is emphasized by simulating kinematic Kikuchi diffraction patterns from an atomistic model containing a nanoscale dislocation loop. Deviations in kinematic Kikuchi line intensities are explained considering the displacement field of the dislocation loop, as is done in diffraction contrast theory.

42 ENGINEERING↗

Brochure on the 2024 ASCR Workshop on Analog Computing for Science

Analog computing fundamentally differs from digital by representing data with fully continuous physical quantities, such as voltages, probabilities, chemical concentrations, or light intensities, rather than encoding values in discrete binary states. While digital computing has historically excelled in precision, scalability, and noise resistance, newer analog approaches are gaining interest for their potential to dramatically improve energy efficiency and processing speed. Analog systems can inherently solve mathematical problems through their physical behavior and offer distinct advantages in scenarios where continuous operations are more effective than Boolean logic.

97 MATHEMATICS AND COMPUTING↗

Measuring the impact of burst buffers on data-intensive scientific workflows

Science applications frequently produce and consume large volumes of data, but delivering this data to and from compute resources can be concerning, as parallel file system performance is not keeping up with compute and memory performance. To alter this I/O bottleneck, some systems have deployed burst buffers, but their impact on performance for real-world scientific workflow applications is still not clear. In this paper, we examine the impact of burst buffers through the remote-shared, allocatable burst buffers on the Cori system at NERSC. By running two data-intensive workflows, a high-throughput genome analysis workflow, and a subset of the SCEC high-performance CyberShake workflow, a production seismic hazard analysis workflow, we find that using burst buffers offers read and write improvements of an order of magnitude, and these improvements lead to increased job performance, and thereby increased overall workflow performance, even for long-running CPU-bound jobs.

42 ENGINEERING↗

Volumetric-modulated arc therapy vs conventional fixed-field intensity-modulated radiotherapy in a whole-ventricular irradiation: A planning comparison study

This study evaluated the dosimetric difference between volumetric-modulated arc therapy (VMAT) and conventional fixed-field intensity-modulated radiotherapy (cIMRT) in whole-ventricular irradiation. Computed tomography simulation data for 13 patients were acquired to create plans for VMAT and cIMRT. In both plans, the same median dose (100% = 24 Gy) was prescribed to the planning target volume (PTV), which comprised a tumor bed and whole ventricles. During optimization, doses to the normal brain and body were reduced, provided that the dose constraints of the target coverage were satisfied. The dose-volume indices of the PTV, normal brain, and body as well as monitor units were compared between the 2 techniques by using paired t-tests. The results showed no significant difference in the homogeneity index (0.064 vs 0.065; p = 0.824) of the PTV and conformation number (0.78 vs 0.77; p = 0.065) between the 2 techniques. In the normal brain and body, the dose-volume indices showed no significant difference between the 2 techniques, except for an increase in the volume receiving a low dose in VMAT; the absolute volume of the normal brain and body receiving 1 Gy of radiation significantly increased in VMAT by 1.6% and 8.3%, respectively, compared with that in cIMRT (1044 vs 1028 mL for the normal brain and 3079.2 vs 2823.3 mL for the body; p<0.001). The number of monitor units to deliver a 2.0-Gy fraction was significantly reduced in VMAT compared with that in cIMRT (354 vs 873, respectively; p<0.001). In conclusion, VMAT delivers IMRT to complex target volumes such as whole ventricles with fewer monitor units, while maintaining target coverage and conformal isodose distribution comparable to cIMRT; however, in addition to those characteristics, the fact that the volume of the normal brain and body receiving a low dose would increase in VMAT should be considered.

61 RADIATION PROTECTION AND DOSIMETRY↗

Estimating statistical isotropy violation in CMB due to non-circular beam and complex scan in minutes

Mild, unavoidable deviations from circular-symmetry of instrumental beams along with scan strategy can give rise to measurable Statistical Isotropy (SI) violation in Cosmic Microwave Background (CMB) experiments. If not accounted properly, this spurious signal can complicate the extraction of other SI violation signals (if any) in the data. However, estimation of this effect through exact numerical simulation is computationally intensive and time consuming. A generalized analytical formalism not only provides a quick way of estimating this signal, but also gives a detailed understanding connecting the leading beam anisotropy components to a measurable BipoSH characterisation of SI violation. In this paper, we provide an approximate generic analytical method for estimating the SI violation generated due to a non-circular (NC) beam and arbitrary scan strategy, in terms of the Bipolar Spherical Harmonic (BipoSH) spectra. Our analytical method can predict almost all the features introduced by a NC beam in a complex scan and thus reduces the need for extensive numerical simulation worth tens of thousands of CPU hours into minutes long calculations. As an illustrative example, we use WMAP beams and scanning strategy to demonstrate the easability, usability and efficiency of our method. We test all our analytical results against that from exact numerical simulations.

79 ASTRONOMY AND ASTROPHYSICS↗

Phase-change heterostructure enables ultralow noise and drift for memory operation

Artificial intelligence and other data-intensive applications have escalated the demand for data storage and processing. New computing devices, such as phase-change random access memory (PCRAM)–based neuro-inspired devices, are promising options for breaking the von Neumann barrier by unifying storage with computing in memory cells. However, current PCRAM devices have considerable noise and drift in electrical resistance that erodes the precision and consistency of these devices. We designed a phase-change heterostructure (PCH) that consists of alternately stacked phase-change and confinement nanolayers to suppress the noise and drift, allowing reliable iterative RESET and cumulative SET operations for high-performance neuro-inspired computing. Our PCH architecture is amenable to industrial production as an intrinsic materials solution, without complex manufacturing procedure or much increased fabrication cost.

Science & Technology - Other Topics↗