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At least 811 records · Page 45

SeekAView: An Intelligent Dimensionality Reduction Strategy for Navigating High-Dimensional Data Spaces

Dealing with the curse of dimensionality is a key challenge in high-dimensional data visualization. We present SeekAView to address three main gaps in the existing research literature. First, automated methods like dimensionality reduction or clustering suffer from a lack of transparency in letting analysts interact with their outputs in real-time to suit their exploration strategies. The results often suffer from a lack of interpretability, especially for domain experts not trained in statistics and machine learning. Second, exploratory visualization techniques like scatter plots or parallel coordinates suffer from a lack of visual scalability: it is difficult to present a coherent overview of interesting combinations of dimensions. Third, the existing techniques do not provide a flexible workflow that allows for multiple perspectives into the analysis process by automatically detecting and suggesting potentially interesting subspaces. In SeekAView we address these issues using suggestion based visual exploration of interesting patterns for building and refining multidimensional subspaces. Compared to the state-of-the-art in subspace search and visualization methods, we achieve higher transparency in showing not only the results of the algorithms, but also interesting dimensions calibrated against different metrics. We integrate a visually scalable design space with an iterative workflow guiding the analysts by choosing the starting points and letting them slice and dice through the data to find interesting subspaces and detect correlations, clusters, and outliers. We present two usage scenarios for demonstrating how SeekAView can be applied in real-world data analysis scenarios.

Krause, Josua↗

Hands-On Computer Science: The Array of Things Experimental Urban Instrument

Chicago's Array of Things (AoT) project is aptly described as a technology experiment or a "smart city" prototype. The concept of such an extensible "instrument" arose within a larger translational research vision applying computer science and engineering research for the multidimensional benefit of people and communities in cities. The AoT project hypothesized that wireless intelligent sensor networks could enable both quantitative social science and urban monitoring while also stimulating youth interest in science and technology. Successful deployment of such sensor networks could provide open data from urban measurements not only in support of diverse research questions-in environmental dynamics, urban architecture, engineering, and social sciences-but also informing community groups and city planners. Further, the AoT project and its successor SAGE project are a computer science and engineering experiment, but its success is inextricably tied to community engagement and experiential education. Simply put, community acceptance is a prerequisite to installing and testing the instrument.

97 MATHEMATICS AND COMPUTING↗

DynaM: Dynamic Multiresolution Data Representation for Large-Scale Scientific Analysis

Fast growing large-scale systems enable scientific applications to run at a much larger scale and accordingly produce gigantic volumes of simulation output. Such data imposes a grand challenge to post-processing tasks such as visualization and data analysis, because these tasks are often performed at a host machine that is remotely located and equipped with much less memory and storage resources. During the simulation runs, it is also desirable for scientists to be able to interactively monitor and steer the progress of simulation. This requires scientific data to be represented in an efficient form for initial exploration and computation steering. In this paper, we propose DynaM a software framework that can represent scientific data in a multiresolution form, and dynamically organize data blocks into an optimized layout for efficient scientific analysis. DynaM supports a convolution-based multiresolution data representation for abstracting scientific data for visualization at a wide spectrum of resolution. To support the efficient generation and retrieval of different data granularities from such representation, a dynamic data organization in DynaM is enabled to cater distinct peculiarities of different size data blocks for efficient and balanced I/O performance. Our experimental results demonstrate that DynaM can efficiently represent large scientific dataset and speed up the visualization of multidimensional scientific data. An up to 29 times speedup is achieved on Jaguar supercomputer at Oak Ridge National Laboratory.

Tian, Yuan↗

Rethinking Sensitivity Analysis of Nuclear Simulations with Topology

In nuclear engineering, understanding the safety margins of the nuclear reactor via simulations is arguably of paramount importance in predicting and preventing nuclear accidents. It is therefore crucial to perform sensitivity analysis to understand how changes in the model inputs affect the outputs. Modern nuclear simulation tools rely on numerical representations of the sensitivity information -- inherently lacking in visual encodings -- offering limited effectiveness in communicating and exploring the generated data. In this paper, we design a framework for sensitivity analysis and visualization of multidimensional nuclear simulation data using partition-based, topology-inspired regression models and report on its efficacy. We rely on the established Morse-Smale regression technique, which allows us to partition the domain into monotonic regions where easily interpretable linear models can be used to assess the influence of inputs on the output variability. The underlying computation is augmented with an intuitive and interactive visual design to effectively communicate sensitivity information to the nuclear scientists. Our framework is being deployed into the multi-purpose probabilistic risk assessment and uncertainty quantification framework RAVEN (Reactor Analysis and Virtual Control Environment). We evaluate our framework using an simulation dataset studying nuclear fuel performance.

computational topology↗

A PEPS Plugin for TNQVM

This work introduces an extension to the Tensor Network Quantum Virtual Machine (TNQVM) tool, enhancing the existing stack of ExaScale Tensor Network (ExaTN), ExaScale Accelerator (XACC), and TNQVM. It features a new plugin that enables efficient simulation of a Projected Entangled Pair State (PEPS), a 2D tensor network. To improve simulation efficiency for PEPS, we have implemented the snake boundary contraction algorithm. By integrating this capability into the existing stack, we enhance the overall functionality and versatility of the framework. We tested this new PEPS topology for a simple GHZ bell-pair generation quantum circuit and saw that its runtime is very close to that of the MPS topology. We estimate that the real potential of the PEPS topology becomes discernible when quantum circuits with multidimensional entanglement are simulated using tensor networks. In such cases, 1D tensor networks fail to represent or contract them efficiently.

Chundury, Srikar↗

OpenACC offloading of the MFC compressible multiphase flow solver on AMD and NVIDIA GPUs

GPUs are the heart of the latest generations of supercomputers. We efficiently accelerate a compressible multiphase flow solver via OpenACC on NVIDIA and AMD Instinct GPUs. Optimization is accomplished by specifying the directive clauses gang vector and collapse. Further speedups of six and ten times are achieved by packing user-defined types into coalesced multidimensional arrays and manual inlining via metaprogramming. Additional optimizations yield seven-times speedup of array packing and thirty-times speedup of select kernels on Frontier. Weak scaling efficiencies of 97% and 95% are observed when scaling to 50% of Summit and 87% of Frontier. Strong scaling efficiencies of 84% and 81% are observed when increasing the device count by a factor of 8 and 16 on V100 and MI250X hardware. The strong scaling efficiency of AMD’s MI250X increases to 92% when increasing the device count by a factor of 16 when GPU-aware MPI is used for communication.

Wilfong, Benjamin↗

On the Configuration of the US Western Interconnection Voltage Stability Boundary

Abstract—Stability limits are considered in power system planning and operations to estimate the available stability margins and, if possible, to maximize the utilization of transmission facilities. These important tasks are influenced by configuration of the stability boundary. The paper introduces a new fast approach to explore the voltage stability boundary of a large system and reveal its detailed multidimensional structure. The 17939-bus U.S. Western Interconnection planning model was used to illustrate the method. Significant peculiarities of the boundary’s configuration were identified, including its nonconvexity, discontinuity, branching and internal singularities (“holes”) that were not known before and could not been found by traditional methods. Experiments using WECC system are performed to evaluate the computation time using different methods. Our results show that the proposed methods are very promising in reducing calculation time and complexity

Makarov, Yuri V.↗

Improving the Performance of Integrated Power-Hardware-in-the-Loop and Quasi-Static Time-Series Simulations

This paper introduces a novel multirate cosimulation architecture that overcomes previous challenges integrating faster real-time, microseconds-scale, power-hardware-in-the-loop (PHIL) with larger scale but slower, real-time, seconds-scale, quasi-static time-series (QSTS) simulation. Specifically, an intermediate reduced-equivalent electromagnetic transient (EMT) model duplicates the key power system topology to capture high-speed dynamics and converge hardware-power system interactions between QSTS updates. Exchanging multidimensional parameter vectors (loads, control status, etc.) between the QSTS and EMT models enables capturing the interactions of the rich, high-node-count (thousands of electrical nodes) QSTS model with the hardware. This architecture offers full spatial resolution from QSTS, including individual load dynamics, actual distribution management system controls, and nodal voltages. Simultaneously, the intermediate EMT model provides more detailed high-speed transients of key distributed energy resource hardware interactions. In addition, we use careful PHIL interface design and the exchange of complex power data, rather than current, to further improve performance. This cosimulation architecture is demonstrated by testing a simulated distribution system with an interconnected 500-kVA advanced photovoltaic (PV) inverter in PHIL. In conclusion, the architecture successfully captured PV local volt-volt ampere reactive (volt-VAR) control interactions with the larger network under time-varying electrical and weather conditions.

42 ENGINEERING↗

Multi-jagged: A scalable parallel spatial partitioning algorithm

Geometric partitioning is fast and effective for load-balancing dynamic applications, particularly those requiring geometric locality of data (particle methods, crash simulations). We present, to our knowledge, the first parallel implementation of a multidimensional-jagged geometric partitioner. In contrast to the traditional recursive coordinate bisection algorithm (RCB), which recursively bisects subdomains perpendicular to their longest dimension until the desired number of parts is obtained, our algorithm does recursive multi-section with a given number of parts in each dimension. By computing multiple cut lines concurrently and intelligently deciding when to migrate data while computing the partition, we minimize data movement compared to efficient implementations of recursive bisection. We demonstrate the algorithm's scalability and quality relative to the RCB implementation in Zoltan on both real and synthetic datasets. Our experiments show that the proposed algorithm performs and scales better than RCB in terms of run-time without degrading the load balance. Lastly, our implementation partitions 24 billion points into 65,536 parts within a few seconds and exhibits near perfect weak scaling up to 6K cores.

97 MATHEMATICS AND COMPUTING↗

Ion Number Density Quantification Utilizing Pulsing Frequency in Negative Differential Resistance (NDR) Regime of Microplasma Operation

A mathematical model is presented for quantifying the ion number density over a range of discharge current in microplasma discharges. The ion number density is determined from measured discharge voltage, current, pulsing frequency, and trace impurity that is injected into the system deliberately. Experiments are conducted in pure helium with nitrogen being introduced as the trace species. The ion number density is estimated over a range of discharge current and is compared with multidimensional simulation results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A Framework for Robust Long-Term Voltage Stability of Distribution Systems

Power injection uncertainties in distribution power grids, which are mostly induced by aggressive introduction of intermittent renewable sources, may drive the system away from normal operating regimes and potentially lead to the loss of long-term voltage stability (LTVS). Naturally, there is an ever increasing need for a tool for assessing the LTVS of a distribution system. This paper presents a fast and reliable tool for constructing inner approximations of LTVS regions in multidimensional injection space such that every point in our constructed region is guaranteed to be solvable. Numerical simulations demonstrate that our approach outperforms all existing inner approximation methods in most cases. Furthermore, the constructed regions are shown to cover substantial fractions of the true voltage stability region. In conclusion, the paper will later discuss a number of important applications of the proposed technique, including fast screening for viable injection changes, constructing an effective solvability index and rigorously certified loadability limits.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Temporal Summary Images: An Approach to Narrative Visualization via Interactive Annotation Generation and Placement

Visualization is a powerful technique for analysis and communication of complex, multidimensional, and time-varying data. However, it can be difficult to manually synthesize a coherent narrative in a chart or graph due to the quantity of visualized attributes, a variety of salient features, and the awareness required to interpret points of interest (POIs). We present Temporal Summary Images (TSIs) as an approach for both exploring this data and creating stories from it. As a visualization, a TSI is composed of three common components: (1) a temporal layout, (2) comic strip-style data snapshots, and (3) textual annotations. To augment user analysis and exploration, we have developed a number of interactive techniques that recommend relevant data features and design choices, including an automatic annotations workflow. As the analysis and visual design processes converge, the resultant image becomes appropriate for data storytelling. For validation, we use a prototype implementation for TSIs to conduct two case studies with large-scale, scientific simulation datasets.

97 MATHEMATICS AND COMPUTING↗

Improving Property Graph Layouts by Leveraging Attribute Similarity for Structurally Equivalent Nodes

Many real-world networks contain structurally-equivalent nodes. These are defined as vertices that share the same set of neighboring nodes, making them interchangeable with a traditional graph layout approach. However, many real-world graphs also have properties associated with nodes, adding additional meaning to them. We present an approach for swapping locations of structurally-equivalent nodes in graph layout so that those with more similar properties have closer proximity to each other. This improves the usefulness of the visualization from an attribute perspective without negatively impacting the visualization from a structural perspective. We include an algorithm for finding these sets of nodes in linear time, as well as methodologies for ordering nodes based on their attribute similarity, which works for scalar, ordinal, multidimensional, and categorical data.

graph drawing, network visualization, property gra↗

Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture

Propionate accumulation is a common indicator of process imbalances in anaerobic bioreactor systems. The accumulation of propionate can occur due to low retention rates, hydrogen accumulation, or mechanical changes affecting the proximity between propionate oxidizers and partner species, thereby preventing necessary electron transfer. Few studies, however, have observed the changes in microbial community structure during propionate accumulation. We used 454 pyrosequencing of 16S rDNA to evaluate the community membership during propionate accumulations in replicate bioreactors with rumen based cultures. Half of the culture volume from a parent reactor was transferred to a sterile “daughter” reactor, and both systems were run identically. Both reactors experienced a propionate accumulation after roughly 10 days, with the propionate accumulation being less pronounced in the parent reactor as compared to the daughter reactor. Non-metric multidimensional scaling (NMDS) was used to determine clustering patterns of the samples, and correlative methods were used to determine which OTUs were significantly associated with the movements of samples along the NMDS axes. The presence of Saccharofermentans characterized the position of early samples, whereas the presence of Ruminococcus and Succiniclasticum were more indicative of the positions of later samples. Hydrogen accumulation and low sequence counts indicated low methanogen activity. Although both reactor systems were closed to microbial inputs due to the sterilization of influent media, we recorded significant increases in reactor diversity over time. This suggests that changes in the abundances of dominant community members may affect the sequencing of rare taxa within samples.

59 BASIC BIOLOGICAL SCIENCES↗

Bioenergy harvest impacts to biodiversity and resilience vary across aspen‐dominated forest ecosystems in the Lake States region, USA

Abstract Questions Does the increase in disturbance associated with removing harvest residues negatively impact biodiversity and resilience in aspen‐dominated forest ecosystems? How do responses of functional diversity measures relate to community recovery and standing biomass? Location Aspen ( Populus tremuloides, Michx.) mixedwood forests in Minnesota and Michigan, USA. Methods Three levels for two factors, organic matter removal and compaction, were fully crossed, resulting in nine experimental treatments that spanned a range of disturbance severity. Each treatment was replicated three times at each of three sites dominated by the same tree species but having different soil textures (clay, silty loam, sandy). Community composition and taxonomic diversity (species richness, species evenness, Shannon diversity index) were quantified based on woody species abundance sampled 5, 10 and 15 yr after disturbance. Community composition response was assessed using non‐metric multidimensional scaling. Functional diversity (functional richness, evenness, dispersion and divergence) was also estimated using eight species effect and response traits. Finally, we examined community recovery as well as responses of species and functional diversity to disturbance severity over time using repeated measures ANOVA. Results Two responses indicated a potentially negative impact of whole‐tree harvest relative to conventional, stem‐only harvest: functional richness on silty loam soils and species evenness on clayey soils. Otherwise, negative impacts were restricted to forest floor removal or increased compaction. Recovery in community composition was reduced by the most severe treatments, particularly forest floor removal, across the study, but the responses of functional and taxonomic diversity varied among sites, with some measures increasing as a result of severe disturbance. Conclusions Maximization of standing biomass may mean a short‐term sacrifice in species and functional diversity. Also, examinations of forest management impacts on species and functional diversity and composition should apply multiple metrics and indices to ensure potential impacts are not obscured by the reliance on a single approach.

Curzon, Miranda T.↗

Statistical generic design of glass and optimization: Selective review on oxide glasses

Designing a single glass composition for a multidimensional property space is challenging, and the difficulty increases with the number of design criteria. Traditionally, the task is accomplished using multiple statistical models that describe the relationships between composition (C) and property (P) values, i.e., C-P models. Recently, the structure (S)-property (P) statistical modeling has emerged as a complementary approach. The S-P modeling approach has also been shown to be a preferred method for modeling glass properties, particularly when a small data set is available, such as in single-component studies, or when strong nonlinearities exist between composition and properties. The combined model package, C-S-P, implements the concept of generic glass design, i.e., designing glass for performance by first selecting a specific or optimized set of glass network structural groups using S-P models and then transferring the designed structures (genes) to a particular composition using C-S models. This article reviews a set of supporting cases from the previous C-S-P modeling studies of phosphate, silicate, and borosilicate glasses, which are relevant for many critical commercial applications. The methodology for developing the statistical C-S-P database is presented, enabling the application of P?S?C to achieve a generic glass design and optimization, targeting multiple design criteria for both performance and processing properties simultaneously.

Network structure↗

A cell wall reference profile for Miscanthus bioenergy crops highlights compositional and structural variations associated with development and organ origin

Summary Miscanthus spp. are promising lignocellulosic energy crops, but cell wall recalcitrance to deconstruction still hinders their widespread use as bioenergy and biomaterial feedstocks. Identification of cell wall characteristics desirable for biorefining applications is crucial for lignocellulosic biomass improvement. However, the task of scoring biomass quality is often complicated by the lack of a reference for a given feedstock. A multidimensional cell wall analysis was performed to generate a reference profile for leaf and stem biomass from several miscanthus genotypes harvested at three developmentally distinct time points. A comprehensive suite of 155 monoclonal antibodies was used to monitor changes in distribution, structure and extractability of noncellulosic cell wall matrix glycans. Glycan microarrays complemented with immunohistochemistry elucidated the nature of compositional variation, and in situ distribution of carbohydrate epitopes. Key observations demonstrated that there are crucial differences in miscanthus cell wall glycomes, which may impact biomass amenability to deconstruction. For the first time, variations in miscanthus cell wall glycan components were comprehensively characterized across different harvests, organs and genotypes, to generate a representative reference profile for miscanthus cell wall biomass. Ultimately, this portrait of the miscanthus cell wall will help to steer breeding and genetic engineering strategies for the development of superior energy crops.

Plant Sciences↗

An integrated framework of plant form and function: the belowground perspective

Summary Plant trait variation drives plant function, community composition and ecosystem processes. However, our current understanding of trait variation disproportionately relies on aboveground observations. Here we integrate root traits into the global framework of plant form and function. We developed and tested an overarching conceptual framework that integrates two recently identified root trait gradients with a well‐established aboveground plant trait framework. We confronted our novel framework with published relationships between above‐ and belowground trait analogues and with multivariate analyses of above‐ and belowground traits of 2510 species. Our traits represent the leaf and root conservation gradients (specific leaf area, leaf and root nitrogen concentration, and root tissue density), the root collaboration gradient (root diameter and specific root length) and the plant size gradient (plant height and rooting depth). We found that an integrated, whole‐plant trait space required as much as four axes. The two main axes represented the fast–slow ‘conservation’ gradient on which leaf and fine‐root traits were well aligned, and the ‘collaboration’ gradient in roots. The two additional axes were separate, orthogonal plant size axes for height and rooting depth. This perspective on the multidimensional nature of plant trait variation better encompasses plant function and influence on the surrounding environment.

59 BASIC BIOLOGICAL SCIENCES↗