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At least 199 records · Page 11

Central California Disasters: Incorporating Satellite-Derived Precipitation and Soil Moisture Products into Flood Preparedness and Emergency Management in California

Atmospheric rivers are a major contributor to extreme precipitation events and flooding in California. This study assessed the feasibility of using Earth observation data to monitor precipitation, soil moisture, and flooding from atmospheric rivers in the Salinas River Watershed in central California during the winter of 2022-2023. The team analyzed satellite derived precipitation estimates from the Global Precipitation Measurement mission, soil moisture data from the Soil Moisture Active Passive radiometer, and synthetic aperture radar imagery from Sentinel-1 to detect flood inundation. Global Precipitation Measurement precipitation estimates were found to underestimate rainfall by 33% to 52% compared to rain gauge data. The team found the Soil Moisture Active Passive dataset to be a valuable flooding indicator that they could visualize through various graphical representations, although its accuracy still needs verification with in situ flood maps. Sentinel-1 synthetic aperture radar imagery provided mapping of flood inundation extent along the Salinas River and surrounding areas and the Blue Spot model appears to be a good predictor of pluvial flood zones. The findings suggest Earth observations can enhance precipitation and flooding monitoring by the California Department of Water Resources, though further verification is needed. Integration of these datasets with vulnerability indices highlighted communities at highest risk during the 2022-2023 flooding events.

Abhinav Banthiya↗

A Visual Analytics Framework for the Detection of Anomalous Call Stack Trees in High Performance Computing Applications

Anomalous runtime behavior detection is one of the most important tasks for performance diagnosis in High Performance Computing (HPC). Most of the existing methods find anomalous executions based on the properties of individual functions, such as execution time. However, it is insufficient to identify abnormal behavior without taking into account the context of the executions, such as the invocations of children functions and the communications with other HPC nodes. We improve upon the existing anomaly detection approaches by utilizing the call stack structures of the executions, which record rich temporal and contextual information. With our call stack tree (CSTree) representation of the executions, we formulate the anomaly detection problem as finding anomalous tree structures in a call stack forest. The CSTrees are converted to vector representations using our proposed stack2vec embedding. Structural and temporal visualizations of CSTrees are provided to support users in the identification and verification of the anomalies during an active anomaly detection process. Furthermore, three case studies of real-world HPC applications demonstrate the capabilities of our approach.

97 MATHEMATICS AND COMPUTING↗

Models of Speed Discrimination

The prime purpose of this project was to investigate various theoretical issues concerning the integration of information across visual space. To date, most of the research efforts in the study of the visual system seem to have been focused in two almost non-overlaping directions. One research focus has been the low level perception as studied by psychophysics. The other focus has been the study of high level vision exemplified by the study of object perception. Most of the effort in psychophysics has been devoted to the search for the fundamental "features" of perception. The general idea is that the most peripheral processes of the visual system decompose the input into features that are then used for classification and recognition. The experimental and theoretical focus has been on finding and describing these analyzers that decompose images into useful components. Various models are then compared to the physiological measurements performed on neurons in the sensory systems. In the study of higher level perception, the work has been focused on the representation of objects and on the connections between various physical effects and object perception. In this category we find the perception of 3D from a variety of physical measurements including motion, shading and other physical phenomena. With few exceptions, there seem to be very limited development of theories describing how the visual system might combine the output of the analyzers to form the representation of visual objects. Therefore, the processes underlying the integration of information over space represent critical aspects of vision system. The understanding of these processes will have implications on our expectations for the underlying physiological mechanisms, as well as for our models of the internal representation for visual percepts. In this project, we explored several mechanisms related to spatial summation, attention, and eye movements. The project comprised three components: 1. Modeling visual search for the detection of speed deviation. 2. Perception of moving objects. 3. Exploring the role of eye movements in various visual tasks.

Source record↗

Stimulus information contaminates summation tests of independent neural representations of features

Many models of visual processing assume that visual information is analyzed into separable and independent neural codes, or features. A common psychophysical test of independent features is known as a summation study, which measures performance in a detection, discrimination, or visual search task as the number of proposed features increases. Improvement in human performance with increasing number of available features is typically attributed to the summation, or combination, of information across independent neural coding of the features. In many instances, however, increasing the number of available features also increases the stimulus information in the task, as assessed by an optimal observer that does not include the independent neural codes. In a visual search task with spatial frequency and orientation as the component features, a particular set of stimuli were chosen so that all searches had equivalent stimulus information, regardless of the number of features. In this case, human performance did not improve with increasing number of features, implying that the improvement observed with additional features may be due to stimulus information and not the combination across independent features.

NASA Discipline Space Human Factors↗

CoordNet: Data Generation and Visualization Generation for Time-Varying Volumes via a Coordinate-Based Neural Network

Although deep learning has demonstrated its capability in solving diverse scientific visualization problems, it still lacks generalization power across different tasks. To address this challenge, we propose CoordNet, a single coordinate-based framework that tackles various tasks relevant to time-varying volumetric data visualization without modifying the network architecture. The core idea of our approach is to decompose diverse task inputs and outputs into a unified representation (i.e., coordinates and values) and learn a function from coordinates to their corresponding values. We achieve this goal using a residual block-based implicit neural representation architecture with periodic activation functions. We evaluate CoordNet on data generation (i.e., temporal super-resolution and spatial super-resolution) and visualization generation (i.e., view synthesis and ambient occlusion prediction) tasks using time-varying volumetric data sets of various characteristics. Here, the experimental results indicate that CoordNet achieves better quantitative and qualitative results than the state-of-the-art approaches across all the evaluated tasks. Source code and pre-trained models are available at https://github.com/stevenhan1991/CoordNet.

97 MATHEMATICS AND COMPUTING↗

Quantifying and connecting atomic and crystallographic grain boundary structure using local environment representation and dimensionality reduction techniques

In this paper, the relationship between grain boundary crystallography and grain boundary atomic structure is examined, using [100] - symmetric tilt grain boundaries in nickel. The structural unit model is used as a benchmark to evaluate the atomic structure description capacities of an emerging structural descriptor, the local environment representation, which itself is a refinement of the Smooth Overlap of Atomic Positions (SOAP) descriptor. We show that the local environment representation encodes both the information of the structural unit model and additional information, such as distortion in the structural units and the arrangement of the structural units at the interface. The use of the local environment representation permits the use of a visualization tool known as SPRING to represent structural similarities between grain boundaries. With the SPRING representation, we produce objective evidence of a relationship between crystallography and atomic structure, at least for [100] - symmetric tilt grain boundaries.

36 MATERIALS SCIENCE↗

A New Default Colormap for ParaView

ParaView is one of the most prominent software tools for scientific visualization used by scientists around the world. Color is a primary conduit to visually map data to its representation and, thus, enable investigation and interpretation of the data. Colormap selection has a significant impact on the data revealed; its design and selection is a critical aspect of scientific data visualization. A common choice for a user is the program’s default colormap, so careful consideration of this default is consequential. Although the current default colormap in ParaView, a succession of hues from cool blue to warm red, has served the community well, research shows that more nuanced colormap configurations increase discriminability while maintaining other critical metrics. These findings inspire us to revisit and update the default colors in ParaView. Here, in this study, we present a new ParaView default colormap, the criteria and methods of development, and example visualizations and analytic metrics.

97 MATHEMATICS AND COMPUTING↗

Ionospheric Simulation System for Satellite Observations and Global Assimilative Modeling Experiments (ISOGAME)

ISOGAME is designed and developed to assess quantitatively the impact of new observation systems on the capability of imaging and modeling the ionosphere. With ISOGAME, one can perform observation system simulation experiments (OSSEs). A typical OSSE using ISOGAME would involve: (1) simulating various ionospheric conditions on global scales; (2) simulating ionospheric measurements made from a constellation of low-Earth-orbiters (LEOs), particularly Global Navigation Satellite System (GNSS) radio occultation data, and from ground-based global GNSS networks; (3) conducting ionospheric data assimilation experiments with the Global Assimilative Ionospheric Model (GAIM); and (4) analyzing modeling results with visualization tools. ISOGAME can provide quantitative assessment of the accuracy of assimilative modeling with the interested observation system. Other observation systems besides those based on GNSS are also possible to analyze. The system is composed of a suite of software that combines the GAIM, including a 4D first-principles ionospheric model and data assimilation modules, an Internal Reference Ionosphere (IRI) model that has been developed by international ionospheric research communities, observation simulator, visualization software, and orbit design, simulation, and optimization software. The core GAIM model used in ISOGAME is based on the GAIM++ code (written in C++) that includes a new high-fidelity geomagnetic field representation (multi-dipole). New visualization tools and analysis algorithms for the OSSEs are now part of ISOGAME.

Pi, Xiaoqing↗

Three-Dimensional Structure and Modeling of a Normal Bifurcated Shock Train from Experimental Measurements

An asymmetric, bifurcated normal shock train in a Mach 2 constant area, rectangular duct is investigated in the University of Michigan Direct Connect Isolator facility. High-speed schlieren imaging, wall static pressure measurements, surface oil flow visualization, and particle image velocimetry of a shock train are synthesized into a three-dimensional representation of shock train structure. This visualization is then used to inform the underlying flow physics of the distributed fluid dynamical processes along the structure. The detailed, three-dimensional morphology of the flow profile entering the shock train is shown to have a significant impact on the separated flow morphology of the shock train. This results in skewed supersonic core flow with alternating separation bubbles in the surrounding boundary layers. Finally, the efficacy of the prevailing pseudo-shock models in the literature is analyzed with the support of the available flow measurements. None are found to simultaneously model both the pressure and streamwise Mach number profile of the UMDCI pseudo-shock.

Hypersonics↗

Bioinspired engineering of exploration systems for NASA and DoD

A new approach called bioinspired engineering of exploration systems (BEES) and its value for solving pressing NASA and DoD needs are described. Insects (for example honeybees and dragonflies) cope remarkably well with their world, despite possessing a brain containing less than 0.01% as many neurons as the human brain. Although most insects have immobile eyes with fixed focus optics and lack stereo vision, they use a number of ingenious, computationally simple strategies for perceiving their world in three dimensions and navigating successfully within it. We are distilling selected insect-inspired strategies to obtain novel solutions for navigation, hazard avoidance, altitude hold, stable flight, terrain following, and gentle deployment of payload. Such functionality provides potential solutions for future autonomous robotic space and planetary explorers. A BEES approach to developing lightweight low-power autonomous flight systems should be useful for flight control of such biomorphic flyers for both NASA and DoD needs. Recent biological studies of mammalian retinas confirm that representations of multiple features of the visual world are systematically parsed and processed in parallel. Features are mapped to a stack of cellular strata within the retina. Each of these representations can be efficiently modeled in semiconductor cellular nonlinear network (CNN) chips. We describe recent breakthroughs in exploring the feasibility of the unique blending of insect strategies of navigation with mammalian visual search, pattern recognition, and image understanding into hybrid biomorphic flyers for future planetary and terrestrial applications. We describe a few future mission scenarios for Mars exploration, uniquely enabled by these newly developed biomorphic flyers.

Space Flight↗

Configuration space representation in parallel coordinates

By means of a system of parallel coordinates, a nonprojective mapping from R exp N to R squared is obtained for any positive integer N. In this way multivariate data and relations can be represented in the Euclidean plane (embedded in the projective plane). Basically, R squared with Cartesian coordinates is augmented by N parallel axes, one for each variable. The N joint variables of a robotic device can be represented graphically by using parallel coordinates. It is pointed out that some properties of the relation are better perceived visually from the parallel coordinate representation, and that new algorithms and data structures can be obtained from this representation. The main features of parallel coordinates are described, and an example is presented of their use for configuration space representation of a mechanical arm (where Cartesian coordinates cannot be used).

Fiorini, Paolo↗

Wavelet-Based Interpolation and Representation of Non-Uniformly Sampled Spacecraft Mission Data

A well-documented problem in the analysis of data collected by spacecraft instruments is the need for an accurate, efficient representation of the data set. The data may suffer from several problems, including additive noise, data dropouts, an irregularly-spaced sampling grid, and time-delayed sampling. These data irregularities render most traditional signal processing techniques unusable, and thus the data must be interpolated onto an even grid before scientific analysis techniques can be applied. In addition, the extremely large volume of data collected by scientific instrumentation presents many challenging problems in the area of compression, visualization, and analysis. Therefore, a representation of the data is needed which provides a structure which is conducive to these applications. Wavelet representations of data have already been shown to possess excellent characteristics for compression, data analysis, and imaging. The main goal of this project is to develop a new adaptive filtering algorithm for image restoration and compression. The algorithm should have low computational complexity and a fast convergence rate. This will make the algorithm suitable for real-time applications. The algorithm should be able to remove additive noise and reconstruct lost data samples from images.

Bose, Tamal↗

Modeling of three-dimensional surfaces using high-level canonical piecewise-linear functions in cylindrical coordinates

In this paper, the potential application of the high-level canonical piecewise-linear model in the field of three-dimensional visualization is proposed. This idea emerges from the premise that a three-dimensional surface can be modeled by a continuous two-dimensional function. In this regard, the main contribution consists in providing a methodology for the construction of such function. For this purpose, the well-known algorithm used in the high-level canonical piecewise-linear model has been modified to achieve functions with greater graphing capability. One of the most notorious changes made with respect to the traditional methodology is the use of a new scheme of function domain partition. Contrary to the simplicial partitioning, in our proposal, an equally distributed angular partitioning is considered. With this, the resulting approximate function is expressed in cylindrical coordinates which overcome the typical limitation of graphs in Cartesian coordinates of only representing single-valued surfaces. Another remarkable change can be found in the range of evaluation of the function. Instead of using an open interval, in our approach, a closed interval from 0 to 2π is adopted. To support this proposal, illustrative case studies are reported. Numerical simulations demonstrate the effectiveness of this type of representation model not only in visual perception of three-dimensional surfaces, but also in more complex tasks like volume estimation.

97 MATHEMATICS AND COMPUTING↗

Two memories for geographical slant: separation and interdependence of action and awareness

The present study extended previous findings of geographical slant perception, in which verbal judgments of the incline of hills were greatly overestimated but motoric (haptic) adjustments were much more accurate. In judging slant from memory following a brief or extended time delay, subjects' verbal judgments were greater than those given when viewing hills. Motoric estimates differed depending on the length of the delay and place of response. With a short delay, motoric adjustments made in the proximity of the hill did not differ from those evoked during perception. When given a longer delay or when taken away from the hill, subjects' motoric responses increased along with the increase in verbal reports. These results suggest two different memorial influences on action. With a short delay at the hill, memory for visual guidance is separate from the explicit memory informing the conscious response. With short or long delays away from the hill, short-term visual guidance memory no longer persists, and both motor and verbal responses are driven by an explicit representation. These results support recent research involving visual guidance from memory, where actions become influenced by conscious awareness, and provide evidence for communication between the "what" and "how" visual processing systems.

NASA Discipline Space Human Factors↗

A Julia Framework for Graph-Structured Nonlinear Optimization

Graph theory provides a convenient framework for modeling and solving structured optimization problems. Under this framework, the modeler can arrange/assemble the components of an optimization model (variables, constraints, objective functions, and data) within nodes and edges of a graph, and this representation can be used to visualize, manipulate, and solve the problem. In this work, we present a Julia framework for modeling and solving graph-structured nonlinear optimization problems. Our framework integrates the modeling package Plasmo.jl (which facilitates the construction and manipulation of graph models) and the nonlinear optimization solver MadNLP.jl (which provides capabilities for exploiting graph structures to accelerate solution). We illustrate with a simple example how model construction and manipulation can be performed in an intuitive manner using Plasmo.jl and how the model structure can be exploited by MadNLP.jl. We also demonstrate the scalability of the framework by targeting a large-scale, stochastic gas network problem that contains over 1.7 million variables.

Cole, David↗

Production Operations Management System (POMS) for Fermilab Experiments

The Production Operations Management System (POMS) software allows production teams and analysis groups across multiple Fermilab experiments to launch, modify and monitor large scale campaigns of related Monte Carlo or data processing jobs, and currently manages the majority of production computing of experiments at Fermilab.POMS provides a web service interface that enables automated job submission on distributed resources according to customers’ requests, as well as subsequent monitoring of those submissions as well as recovery of failed submissions, debugging and record keeping.POMS interfaces with existing HEP data access, processing, movement and monitoring tools at Fermilab, including Jobsub (for job submission), SAM (for data management), and Landscape (for monitoring), and in combination with them handles the creation of intermediate datasets of files for multistage campaigns.POMS visualizes these campaigns with an interactive GUI interface. An important feature of POMS is a one-to-one connection between the GUI campaign visualizer and a text based representation of the complete campaign configuration. An extensible library of template campaign configurations is available. The templates are user modifiable and map cleanly to and from the GUI description of the campaign.This paper will discuss the current usage, history, and some technical details of POMS, as well as planned future extensions, particularly interfacing with Rucio as well as SAM for file movement.

Mengel, Marc↗

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗