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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

Abstract Motivation Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task. Results We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D. Availability and implementation Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

CDvist: A webserver for identification and visualization of conserved domains in protein sequences

Identification of domains in protein sequences allows their assigning to biological functions. Several webservers exist for identification of protein domains using similarity searches against various databases of protein domain models. However, none of them provides comprehensive domain coverage while allowing bulk querying and their visualization schemes can be improved. To address these issues, we developed CDvist (a comprehensive domain visualization tool), which combines the best available search algorithms and databases into a user-friendly framework. First, a given protein sequence is matched to domain models using high-specificity tools and only then unmatched segments are subjected to more sensitive algorithms resulting in a best possible comprehensive coverage. In conclusion, bulk querying and rich visualization and download options provide improved functionality to domain architecture analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Abstract Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.

Sehnal, David↗
DOE OSTI2015

Immersive visualization for materials science data analysis using the Oculus Rift

In this paper, we propose strategies and objectives for immersive data visualization with applications in materials science using the Oculus Rift virtual reality headset. We provide background on currently available analysis tools for neutron scattering data and other large-scale materials science projects. In the context of the current challenges facing scientists, we discuss immersive virtual reality visualization as a potentially powerful solution. We introduce a prototype immersive visualization system, developed in conjunction with materials scientists at the Spallation Neutron Source, which we have used to explore large crystal structures and neutron scattering data. Finally, we offer our perspective on the greatest challenges that must be addressed to build effective and intuitive virtual reality analysis tools that will be useful for scientists in a wide range of fields.

Drouhard, Margaret↗
DOE OSTI2019

Visual Analytics for Deep Embeddings of Large Scale Molecular Dynamics Simulations

Molecular Dynamics (MD) simulation have been emerging as an excellent candidate for understanding complex atomic and molecular scale mechanism of bio-molecules that control essential bio-physical phenomenon in a living organism. But this MD technique produces large-size and long-timescale data that are inherently high-dimensional and occupies many terabytes of data. Processing this immense amount of data in a meaningful way is becoming increasingly difficult. Therefore, specific dimensionality reduction algorithm using deep learning technique has been employed here to embed the high-dimensional data in a lower-dimension latent space that still preserves the inherent molecular characteristics i.e. retains biologically meaningful information. Subsequently, the results of the embedding models are visualized for model evaluation and analysis of the extracted underlying features. However, most of the existing visualizations for embeddings have limitations in evaluating the embedding models and understanding the complex simulation data. We propose an interactive visual analytics system for embeddings of MD simulations to not only evaluate and explain an embedding model but also analyze various characteristics of the simulations. Our system enables exploration and discovery of meaningful and semantic embedding results and supports the understanding and evaluation of results by the quantitatively described features of the MD simulations (even without specific labels).

Chae, Junghoon↗
DOE OSTI2021

Visual Understanding of COVID-19 Knowledge Graph for Predictive Analysis

This study aims to effectively analyze and visualize the concept to concept network derived from the COVID-19 Open Research Dataset (CORD-19) dataset, where we have more than 48,000 concepts with more than 300,000 relationships between concepts. In analyzing networks, we focus on finding relationship patterns between the coronavirus disease 2019 (COVID-19) concepts and other concepts. Given the node and edge datasets, we construct directional graphs and calculate all pair shortest paths based on multiple edge weight schemes. However, statistical metrics are not sufficient to identify specific relationships represented in the network. Therefore, we also propose a visual analytics approach to effectively understand the knowledge graph. Our highly interactive visual analytics allows users to effectively analyze the evolving graphs and (COVID-19) concept nodes and other nodes related to the COVID-19 nodes. We envision that this study will pave the path to develop strategies to provide more accurate and scalable predictive analysis on knowledge graphs related to CORD19 and other biomedical knowledge graphs.

Lim, Seung-Hwan↗
DOE OSTI2024

Top Research Challenges and Opportunities for Near Real-Time Extreme-Scale Visualization of Scientific Data

The rapid advancement in scientific simulations and experimental facilities has resulted in the generation of vast amounts of data at unprecedented scales. The analysis and visualization of large amounts of data is a challenge in and of itself, but the requirements for timeliness significantly magnify these difficulties. Near real-time visualization is critical to monitor and analyze the data produced by these large facilities, but current production tools are not well-suited to these requirements. In this position paper, we share our perspective on some of the challenges, and thus, opportunities for research that stand in the way of near-real-time visualization of large scientific data.

Pugmire, Dave↗
DOE OSTI2012

Visualization of High Resolution Spatial Mass Spectrometric Data during Acquisition

Mass Spectrometric Imaging (IMS) allows the generation of 2D ion density maps that help visualize molecules present in sections of tissues and cells. The combination of spatial and mass resolution results in large and complex data sets that require powerful and efficient analysis and interpretation. In this paper, a graphical user interface (GUI) that can visualize the large data during data acquisition itself is presented. The program also has the ability to perform processing and analysis of the dataset. The various functions of the GUI including visualization of mass spectra, generation of 2D maps for selected species, manipulation of the heat maps, and peak identification are also presented.

Thomas, Mathew↗
DOE OSTI2013

ADIOS Visualization Schema: A First Step Towards Improving Interdisciplinary Collaboration in High Performance Computing

Scientific communities have benefitted from a significant increase of available computing and storage resources in the last few decades. For science projects that have access to leadership scale computing resources, the capacity to produce data has been growing exponentially. Teams working on such projects must now include, in addition to the traditional application scientists, experts in various disciplines including applied mathematicians for development of algorithms, visualization specialists for large data, and I/O specialists. Sharing of knowledge and data is becoming a requirement for scientific discovery, providing useful mechanisms to facilitate this sharing is a key challenge for e-Science. Our hypothesis is that in order to decrease the time to solution for application scientists we need to lower the barrier of entry into related computing fields. We aim at improving users' experience when interacting with a vast software ecosystem and/or huge amount of data, while maintaining focus on their primary research field. In this context we present our approach to bridge the gap between the application scientists and the visualization experts through a visualization schema as a first step and proof of concept for a new way to look at interdisciplinary collaboration among scientists dealing with big data. The key to our approach is recognizing that our users are scientists who mostly work as islands. They tend to work in very specialized environment but occasionally have to collaborate with other researchers in order to take full advantage of computing innovations and get insight from big data. We present an example of identifying the connecting elements between one of such relationships and offer a liaison schema to facilitate their collaboration.

Computer Science↗
DOE OSTI2016

Visualization and Analysis Requirements for In Situ Processing for a Large-Scale Fusion Simulation Code

In situ techniques have become a very active research area since they have been shown to be an effective way to combat the issues associated with the ever growing gap between computation and I/O bandwidth. In order to take full advantage of in situ techniques with a large-scale simulation code, it is critical to understand the breadth and depth of its analysis requirements. In this paper, we present the results of a survey done with members of the XGC1 fusion simulation code team in order to gather their requirements for analysis and visualization. We look at these requirements from the perspective of in situ processing and present a list of XGC1 analysis tasks performed by its physicists, engineers, and visualization specialists. This analysis of the specific needs and use cases of a single code is important in understanding the nature of the needs that simulations have in terms of data movement and usage for visualization and analysis, now and in the future.

Kress, James M.↗
DOE OSTI2024

Forte: An Interactive Visual Analytic Tool for Trust-Augmented Net-Load Forecasting

Accurate net-load forecasting is vital for energy planning, aiding decisions on trade and load distribution. However, assessing the performance of forecasting models across diverse input variables, like temperature and humidity, remains challenging, particularly for eliciting a high degree of trust in the model outcomes. In this context, there is a growing need for data-driven technological interventions to aid scientists in comprehending how models react to both noisy and clean input variables, thus shedding light on complex behaviors and fostering confidence in the outcomes. In this paper, we present Forte, a visual analytics-based application to explore deep probabilistic net-load forecasting models across various input variables and understand the error rates for different scenarios. With carefully designed visual interventions, this web-based interface empowers scientists to derive insights about model performance by simulating diverse scenarios, facilitating an informed decision-making process. We discuss observations made using Forte and demonstrate the effectiveness of visualization techniques to provide valuable insights into the correlation between weather inputs and net-load forecasts, ultimately advancing grid capabilities by improving trust in forecasting models.

Bhattacharjee, Kaustav↗
DOE OSTI2024

Visual Analytics of Performance of Quantum Computing Systems and Circuit Optimization

Driven by potential exponential speedups in business, security, and scientific scenarios, interest in quantum computing is surging. This interest feeds the development of quantum computing hardware, but several challenges arise in optimizing application performance for hardware metrics (e.g., qubit coherence and gate fidelity). In this work, we describe a visual analytics approach for analyzing the performance properties of quantum devices and quantum circuit optimization. Our approach allows users to explore spatial and temporal patterns in quantum device performance data and it computes similarities and variances in key performance metrics. Detailed analysis of the error properties characterizing individual qubits is also supported. We also describe a method for visualizing the optimization of quantum circuits. The resulting visualization tool allows researchers to design more efficient quantum algorithms and applications by increasing the interpretability of quantum computations.

Chae, Junghoon↗
DOE OSTI2021

Beyond Visual Analytics: Human-Machine Teaming for AI-Driven Data Sensemaking

"Detect the expected, discover the unexpected" was the founding principle of the field of visual analytics. This mantra implies that human stakeholders, like a domain expert or data analyst, could leverage visual analytics techniques to seek answers to known unknowns and discover unknown unknowns in the course of the data sensemaking process. We argue that in the era of AI-driven automation, we need to recalibrate the roles of humans and machines (e.g., a machine learning model) as teammates. We posit that by realizing human-machine teams as a stakeholder unit, we can better achieve the best of both worlds: automation transparency and human reasoning efficacy. However, this also increases the burden on analysts and domain experts towards performing more cognitively demanding tasks than what they are used to. In this paper, we reflect on the complementary roles in a human-machine team through the lens of cognitive psychology and map them to existing and emerging research in the visual analytics community. We discuss open questions and challenges around the nature of human agency and analyze the shared responsibilities in human-machine teams.

Sensemaking, human-machine teaming, agency, artifi↗
DOE OSTI2013

An Interactive Visual Analytics Framework for Multi-Field Data in a Geo-Spatial Context

Climate research produces a wealth of multivariate data. These data often have a geospatial reference and so it is of interest to show them within their geospatial context. One can consider this configuration as a multi field visualization problem, where the geospace provides the expanse of the field. However, there is a limit on the amount of multivariate information that can be fit within a certain spatial location, and the use of linked multivari ate information displays has previously been devised to bridge this gap. In this paper we focus on the interactions in the geographical display, present an implementation that uses Google Earth, and demonstrate it within a tightly linked parallel coordinates display. Several other visual representations, such as pie and bar charts are integrated into the Google Earth display and can be interactively manipulated. Further, we also demonstrate new brushing and visualization techniques for parallel coordinates, such as fixedwindow brushing and correlationenhanced display. We conceived our system with a team of climate researchers, who already made a few important discov eries using it. This demonstrates our system’s great potential to enable scientific discoveries, possibly also in oth er domains where data have a geospatial reference.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2012

Visual Data Analysis as an Integral Part of Environmental Management

The U.S. Department of Energy's (DOE) Office of Environmental Management (DOE/EM) currently supports an effort to understand and predict contaminant fate and transport in natural and engineered systems. Geologists, hydrologists, physicists and computer scientists are working together to create models of existing contaminated sites and to simulate their behavior. Simulation results are verified based on historical data and extrapolated into the future. Visualization is used for model setup verification, visual analysis of high-performance computing simulation results, and uncertainty quantification. This article describes the challenges and solutions for visual data analysis, which impacts the decision-making process for each of the contaminated sites. Lessons learned from these simulations will also have an impact on deciding on treatment measures for other, similarly contaminated areas, including those affected by more recent events, such as Chernobyl and Fukushima.

Meyer, Joerg↗
DOE OSTI2016

Characterizing Provenance in Visualization and Data Analysis: An Organizational Framework of Provenance Types and Purposes

While the primary goal of visual analytics research is to improve the quality of insights and findings, a substantial amount of research in provenance has focused on the history of changes and advances throughout the analysis process. The term, provenance, has been used in a variety of ways to describe different types of records and histories related to visualization. The existing body of provenance research has grown to a point where the consolidation of design knowledge requires cross-referencing a variety of projects and studies spanning multiple domain areas. We present an organizational framework of the different types of provenance information and purposes for why they are desired in the field of visual analytics. Our organization is intended to serve as a framework to help researchers specify types of provenance and coordinate design knowledge across projects. We also discuss the relationships between these factors and the methods used to capture provenance information. In addition, our organization can be used to guide the selection of evaluation methodology and the comparison of study outcomes in provenance research

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Visual Exploration of Semantic Relationships in Neural Word Embeddings

Constructing distributed representations for words through neural language models and using the resulting vector spaces for analysis has become a crucial component of natural language processing (NLP). But, despite their widespread application, little is known about the structure and properties of these spaces. To gain insights into the relationship between words, the NLP community has begun to adapt high-dimensional visualization techniques. Particularly, researchers commonly use t-distributed stochastic neighbor embeddings (t-SNE) and principal component analysis (PCA) to create two-dimensional embeddings for assessing the overall structure and exploring linear relationships (e.g., word analogies), respectively. Unfortunately, these techniques often produce mediocre or even misleading results and cannot address domain-specific visualization challenges that are crucial for understanding semantic relationships in word embeddings. We introduce new embedding techniques for visualizing semantic and syntactic analogies, and the corresponding tests to determine whether the resulting views capture salient structures. Additionally, we introduce two novel views for a comprehensive study of analogy relationships. Finally, we augment t-SNE embeddings to convey uncertainty information in order to allow a reliable interpretation. Combined, the different views address a number of domain-specific tasks difficult to solve with existing tools.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Distributed Neural Representation for Reactive In Situ Visualization

Implicit neural representations (INRs) have emerged as a powerful tool for compressing large-scale volume data. This opens up new possibilities for in situ visualization. However, the efficient application of INRs to distributed data remains an underexplored area. Here, in this work, we develop a distributed volumetric neural representation and optimize it for in situ visualization. Our technique eliminates data exchanges between processes, achieving state-of-the-art compression speed, quality and ratios. Our technique also enables the implementation of an efficient strategy for caching large-scale simulation data in high temporal frequencies, further facilitating the use of reactive in situ visualization in a wider range of scientific problems. We integrate this system with the Ascent infrastructure and evaluate its performance and usability using real-world simulations.

Wu, Qi↗