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DOE OSTI2025

Provable Security and Resilience in Critical Infrastructure – Next Steps

With the conclusion of the Laboratory Directed Research and Development (LDRD) project on Provable Security and Resilience (PSaR) in Critical Infrastructure, we present forward-looking technical concepts and strategies that build on the project’s outcomes and INL’s long-standing expertise in infrastructure protection. The challenge is to protect critical infrastructure and functions much more efficiently at scale than capable adversaries can attack at scale. After summarizing progress and ongoing work we’ll discuss what are the challenges that remain and what are new/emerging technologies, strategies, and processes to meet those challenges. Finally, we’ll layout concepts that integrate with other protection work in the coming year and beyond. For example, building secure function-specific platforms based on the seL4 microkernel, and considering the successes of Cyber-Informed Engineering as a model for engage, collaboration, and adoption. We look forward to your feedback and collaboration as we refine and expand this vision.

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Vision and Development of a Design, Implementation, and Verification Automation (DIVA) Software Platform for DNA Construction

Abstract DNA construction, while a prerequisite to many biological endeavors, is often a time-consuming distraction from an individual’s primary research objectives. We envisioned that with the right software infrastructure and cultural mindset, a single person could execute in parallel the batched DNA construction tasks of an entire research institute, at scales realizing efficiency gains through process and laboratory automation. In pursuit of this vision, we developed the Design, Implementation, and Verification Automation (DIVA) software platform. DIVA’s web interface enables researchers to design DNA constructs (using visual biological computer-aided design tools and biological parts repositories), submit designs for construction to dedicated staff, and track DNA construction as it progresses. DIVA supports the dedicated staff through the DNA construction process and records both successful and unsuccessful attempts toward improving the overall process. The platform is publicly available at public-diva.jbei.org and its open-source code through github.com/JBEI/DIVA.

Plahar, Hector [DOE Agile BioFoundry , , ,; DOE Jo↗

DOE OSTI2015

Future Directions in Computer Graphics and Visualization: From CG&A's Editorial Board

With many new members joining the CG&A editorial board over the past year, and with a renewed commitment to not only document the state of the art in computer graphics research and applications but to anticipate and where possible foster future areas of scientific discourse and industrial practice, we asked editorial and advisory council members about where they see their fields of expertise going. The answers compiled here aren’t meant to be all encompassing or deterministic when it comes to the opportunities computer graphics and interactive visualization hold for the future. Instead, we aim to accomplish two things: give a more in-depth introduction of members of the editorial board to the CG&A readership and encourage cross-disciplinary discourse toward approaching, complementing, or disputing the visions laid out in this compilation.

Applications, State of Field↗

DOE OSTI2025

Open-Source and FAIR Research Software for Proteomics

Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Leveraging Registers in Vision Transformers for Robust Adaptation

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Computer science↗

DOE OSTI2022

Secure Collaborative Environment for Seamless Sharing of Scientific Knowledge

In a secure collaborative environment, tera-bytes of data generated from powerful scientific instruments are used to train secure machine learning (ML) models on exascale computing systems, which are then securely shared with internal or external collaborators as cloud-based services. Devising such a secure platform is necessary for seamless scientific knowledge sharing without compromising individual, or institute-level, intellectual property and privacy details. By enabling new computing opportunities with sensitive data, we envision a secure collaborative environment that will play a significant role in accelerating scientific discovery. Several recent technological advancements have made it possible to realize these capabilities. In this paper, we present our efforts at ORNL toward developing a secure computation platform. We present a use case where scientific data generated from complex instruments, like those at the Spallation Neutron Source (SNS), are used to train a differential privacy enabled deep learning (DL) network on Summit, which is then hosted as a secure multi-party computation (MPC) service on ORNL’s Compute and Data Environment for Science (CADES) cloud computing platform for third-party inference. In this feasibility study, we discuss the challenges involved, elaborate on leveraged technologies, analyze relevant performance results and present the future vision of our work to establish secure collaboration capabilities within and outside of ORNL.

Yoginath, Srikanth↗

DOE OSTI2024

Exploiting universal nonlocal dispersion in optically active materials for spectro-polarimetric computational imaging

Recent years have seen significant advancements in exploring novel light-matter interactions such as hyperbolic dispersion within natural crystals. However, current studies have predominantly concentrated on local optical response of materials characterized by a dielectric tensor without spatial dispersion. Here, we investigate the nonlocal response in optically-active crystals with screw symmetries, revealing their lossless, super-dispersive properties compared to traditional optical response functions. We leverage this universal nonlocal dispersion, i.e. the dispersion of optical rotatory power, to explore a novel spectral de-multiplexing scheme compared to conventional gratings, prisms and metasurfaces. We design and demonstrate an ‘Nonlocal-Cam’ - a camera that exploits nonlocal dispersion through sampling of polarized spectral states and the application of computational spectral reconstruction algorithms. The Nonlocal-Cam captures information in both laboratory and outdoor field experiments which is unavailable to traditional intensity cameras - the spectral texture of polarization. Merging the fields of nonlocal electrodynamics and computational imaging, our work paves the way for exploiting nonlocal optics of optically active materials in a variety of applications, from biological microscopy to physics-driven machine vision and remote sensing.

Wang, Xueji [Purdue Univ., West Lafayette, IN (Uni↗

DOE OSTI2011

Collaborative Visualization: Definition, Challenges, and Research Agenda

Collaborative visualization has emerged as a new research direction which offers the opportunity to reach new audiences and application areas for visualization tools and techniques. Technology now allows us to easily connect and collaborate with one another - in settings as diverse as over networked computers, across mobile devices, or using shared displays such as interactive walls and tabletop surfaces. Any of these collaborative settings carries a set of challenges and opportunities for visualization research. Digital information is already regularly accessed by multiple people together in order to share information, to view it together, to analyze it, or to form decisions. However, research on how to best support collaboration with and around visualizations is still in its infancy and has so far focused only on a small subset of possible application scenarios. The purpose of this article is (1) to provide a clear scope, definition, and overview of the evolving field of collaborative visualization, (2) to help pinpoint the unique focus of collaborative visualization with its specific aspects, challenges, and requirements within the intersection of general computer-supported collaborative work (CSCW) and visualization research, and (3) to draw attention to important future research questions to be addressed by the community. Thus, the goal of the paper is to discuss a research agenda for future work on collaborative visualization, including our vision for how to meet the grand challenge and to urge for a new generation of visualization tools that were designed with collaboration in mind from their very inception.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

S4PST: Sustainability for Programming Systems and Tools: May Workshop Report

The US Department of Energy (DOE) Exascale Computing Project (ECP) has fostered and strengthened the use of modern software engineering practices for developing applications and libraries, and this effort has resulted in the coordinated and interoperable E4S1 and xSDK2 ecosystems. Although this approach is cost-effective, it relies on robust programming systems and tools (PST) as the underlying foundation for our HPC software. At present, our primary PST stack consists of traditional high-performance computing (HPC) languages, namely Fortran, C, C++, and the popular Python language for data analysis and AI workflows. These languages support various programming frameworks and run-time abstractions that enable parallelism and concurrency across multiple node architectures and thousands of nodes through a variety of interconnect systems. However, to accommodate users’ diverse needs, certain aspects of the HPC ecosystem are delegated to vendor-specific or third-party implementations that extend beyond a particular scientific domain. This broader scope results in a multitude of specifications and variations, which leads to a complex orchestration of many-ecosystems. Unfortunately, this complexity in the ecosystem imposes additional overhead costs on consumers during the latter stages of the development cycle. In addition to the software ecosystem challenge, the upcoming conclusion of the ECP by December 2023 has raised significant concerns within the HPC programming systems community, from both the economic and social perspectives. The ECP has implemented a management structure for software development and funding decisions across all ECP participants by following a conventional hierarchical and centralized approach. However, this structure has prompted certain considerations within the community, particularly in anticipation of the Software Sustainability initiative by the DOE’s Advanced Scientific Computing Research Program (ASCR). For the success of this new initiative, it is of utmost importance to secure consistent funding and foster close engagement with researchers and core developers of existing programming-system products. This collaboration is vital to maintaining the critical capabilities of the current software during the transition phase while proactively adapting to future technology and workforce trends. The community recognizes the significance of adapting to emerging trends and is aware of the inherent fragility of the HPC software ecosystem, particularly in relation to programming systems that cater to all users. The ability to adapt and evolve is essential to staying relevant and effectively addressing these technical, economic, and social challenges. The S4PST team, which represents one of the six ASCR Software Sustainability seedling projects, is dedicated to tackling these challenges through community-based approaches that go beyond the scope of the DOE. This involves collaboration between national laboratories with academia, non-DOE institutions, hardware and system vendors, and international partners. By fostering these partnerships, we aim to create a robust and sustainable HPC software ecosystem that can effectively meet the needs of the community. This new community effort, driven by the eight DOE labs, will take on the responsibility of guiding funding decisions for programming-systems development and maintenance with transparency and consistency across all decisions. Additionally, the team will offer common technical services to the programming systems community, irrespective of their funding situations, and facilitate community-wide incubation to proactively nurture the software ecosystem. By actively engaging with stakeholders and employing a collaborative approach, we can collectively shape the future of programming systems and ensure a robust and thriving HPC software landscape. On May 11–12, 2023, the S4PST team conducted its inaugural kick-off workshop at the Innovative Computing Laboratory (ICL) in the University of Tennessee, Knoxville, hosted by Hartwig Anzt. The workshop encompassed various sessions dedicated to presentations and discussions, with the aim of comprehending the team members’ perspectives on the vision of software sustainability. Additionally, the workshop aimed to identify the technical, economic, and social requirements for sustaining the programming-systems community in the field of HPC. This report provides a summary of the S4PST effort by highlighting five major thrust areas discussed during the workshop: (i) community, (ii) technical support, (iii) training and diversity, (iv) verification, validation and correctness, and (v) emerging technologies. It also encompasses an overview of the presentations and discussions held throughout the event, our views and potential synergies with other seedling efforts, along with the outcomes and key takeaways from our initial discussions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Vision-Guided Automation and Assistance

Robotic automation and assistance is an excellent way to increase efficiency and safety when working in a potentially hazardous workspace. However, many traditional automation approaches rely on the precise placement of items to be manipulated. The scope of such automated tasks is also limited to the manipulation of one type of object since there is no way to distinguish between different objects. The addition of a vision pipeline, where robot vision is used to localize and recognize objects, can allow the robot to perform more complex tasks in a variable workspace. In my vision pipeline, a depth camera is used to generate a 3D point cloud of the workspace. Objects to be manipulated are isolated in the point cloud by filtering out shared surfaces and using Euclidean cluster extraction to group clusters of points. The locations of the objects are then estimated from the point cloud of the isolated objects. The localization of objects with robot vision allows for variable workspaces, reducing the overhead associated with requiring all objects to be precisely placed in the workspace. For object recognition, deep learning is used to train a neural network that classifies objects from the raw point clouds. More complex tasks that require multiple objects to be manipulated differently can be achieved through the vision pipeline. Through its ability to visualize the workspace, robot vision greatly improves efficiency and safety of automated and assistive tasks.

42 ENGINEERING↗

DOE OSTI2018

Vanguard Astra and ATSE – an ARM-based Advanced Architecture Prototype System and Software Environment (FY18 L2 Milestone #8759 Report)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

FY18 L2 Milestone #6360 Report: Initial Capability of an Arm-based Advanced Architecture Prototype System and Software Environment

The Vanguard program informally began in January 2017 with the submission of a white paper entitled "Sandia's Vision for a 2019 Arm Testbed" to NNSA headquarters. The program proceeded in earnest in May 2017 with an announcement by Doug Wade (Director, Office of Advanced Simulation and Computing and Institutional R&D at NNSA) that Sandia National Laboratories (Sandia) would host the first Advanced Architecture Prototype platform based on the Arm architecture. In August 2017, Sandia formed a Tri-lab team chartered to develop a robust HPC software stack for Astra to support the Vanguard program goal of demonstrating the viability of Arm in supporting ASC production computing workloads. This document describes the high-level Vanguard program goals, the Vanguard-Astra project acquisition plan and procurement up to contract placement, the initial software stack environment planned for the Vanguard-Astra platform (Astra), a description of how the communities of users will utilize the platform during the transition from the open network to the classified network, and initial performance results.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Quantum Vision Transformers for Quark–Gluon Classification

We introduce a hybrid quantum-classical vision transformer architecture, notable for its integration of variational quantum circuits within both the attention mechanism and the multi-layer perceptrons. The research addresses the critical challenge of computational efficiency and resource constraints in analyzing data from the upcoming High Luminosity Large Hadron Collider, presenting the architecture as a potential solution. In particular, we evaluate our method by applying the model to multi-detector jet images from CMS Open Data. The goal is to distinguish quark-initiated from gluon-initiated jets. We successfully train the quantum model and evaluate it via numerical simulations. Using this approach, we achieve classification performance almost on par with the one obtained with the completely classical architecture, considering a similar number of parameters.

Comajoan Cara, Marçal (ORCID:0009000126263752)↗

DOE OSTI2021

Scoreboard

Emerging HPC machines have given rise to enhanced compute power that far outstrips the machine's ability to save large scale results for post-processing. To combat this, in situ data analysis techniques are slowly being adopted. With in situ data management favoring workflows composed of multiple simulations and analyses connected in transit on heterogeneous machines, scientists and engineers need a tool that enables them to create data extracts, visualizations, and interactively monitor and steer their simulations. Scoreboard Phase II is a next generation analysis software that supports composite in transit workflows on heterogeneous architectures and restores interactivity to in situ data analysis through simulation monitoring and computational steering. Scoreboard provides a simulation dashboard with graphs of metrics over time, controls for setting custom simulation steering parameters, controls for managing the set of data extracts being produced in the simulation, as well as the ability to explore data extracts, all from a web browser. Realizing the vision outlined in this project required research into making a system that integrates end to end from simulations all the way to the user. In situ tools generally suffer from complexity and excessive software dependencies. Scoreboard, by contrast, is easy to build and integrate into simulation codes and it provides first class FORTRAN support. The Scoreboard library is capable of in situ and in transit data analysis that can produce data extracts commonly needed for Computational Fluid Dynamics (CFD) analysis. Simulations can transparently stage data in transit to a Scoreboard Endpoint program, which can accept their data and produce the requested data extracts. This lets simulations return to their work while the Endpoint works on the analysis. Efficiently staging the data at scale was a topic of this research. Scoreboard provides the means to let the user manage data extracts and monitor/steer many simulations from a web browser. This area of the research focused on discovery of in transit network components to expose and control their steering parameters within an interactive browser-based user interface that includes: system topology, gathered metrics, notifications, dynamically-generated steering controls, and exploration of visualization data products.

Whitlock, BradJoseph [Intelligent Light] (00000001↗

DOE OSTI2013

Information and Perception of Meaningful Patterns

The visual system needs to extract the most important elements of the external world from a large flux of information in a short time for survival purposes. It is widely believed that in performing this task, it operates a strong data reduction at an early stage, by creating a compact summary of relevant information that can be handled by further levels of processing. In this work we formulate a model of early vision based on a pattern-filtering architecture, partly inspired by high-speed digital data reduction in experimental high-energy physics (HEP). This allows a much stronger data reduction than models based just on redundancy reduction. We show that optimizing this model for best information preservation under tight constraints on computational resources yields surprisingly specific a-priori predictions for the shape of biologically plausible features, and for experimental observations on fast extraction of salient visual features by human observers. Interestingly, applying the same optimized model to HEP data acquisition systems based on pattern-filtering architectures leads to specific a-priori predictions for the relevant data patterns that these devices extract from their inputs. These results suggest that the limitedness of computing resources can play an important role in shaping the nature of perception, by determining what is perceived as ‘‘meaningful features’’ in the input data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

Funding Student Scholarships to the Richard Tapia Celebration of Diversity in Computing Conference 2013, February 7-10, 2013

This Basic Award allowed for the funding of student scholarships to the Richard Tapia Celebration of Diversity in Computing Conference which took place in Washington, D.C. from February 7-10, 2013. The conference was the seventh in a series and included a stellar array of invited speakers, compelling panel discussions, a student poster competition, a daylong Doctoral Consortium, a session featuring a choice of attractions unique to Washington, D.C., a gala banquet and dance, and many exciting networking opportunities. The conference created a welcoming environment for STEM students, especially underrepresented minority and female students, who were provided the highest quality of learning, networking, and social experiences to empower their educational experience and enhance their ability to succeed with a rigorous STEM degree. The networking and mentoring opportunities available at the conference were also designed to empower students to succeed in STEM careers and ultimately serve in leadership in industry and the professoriate. A key step in attracting underrepresented students into STEM fields and paving the way for their success in influential positions is to create a nurturing and supportive network and community for them to rely upon. It is also critical to educate leaders in corporations, government and academia about the benefits to be gained from increasing the percentage of STEM professionals from underrepresented groups. To this end, The Tapia Conference serves both functions, as it connects STEM students with STEM professionals, leaders, and academics who share the vision of a STEM workforce and community that is truly representative of the community in which we live.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Summarizing the interoperabilities between xSDK members

Rapid, efficient production of high-quality, sustainable extreme-scale scientific applications is best accomplished using a rich ecosystem of state-of-the art reusable libraries, tools, lightweight frameworks, and defined software methodologies, developed by a community of scientists who are striving to identify, adapt, and adopt best practices in software engineering. The vision of the xSDK is to provide infrastructure for and interoperability of a collection of related and complementary software elements — developed by diverse, independent teams throughout the high-performance computing (HPC) community — that provide the building blocks, tools, models, processes, and related artifacts for rapid and efficient development of high-quality applications. A primary component, and challenge, of the xSDK is to improve interoperability among software libraries and domain components. This document summarizes the current and planned interoperabilities of the twenty-three xSDK member packages as of March 2021. Additionally, the status of the xSDK example codes that demonstrate and test the interoperabilities within the xSDK is provided.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

A Survey on Sustainable Software Ecosystems to Support Experimental and Observational Science at Oak Ridge National Laboratory

In the search for a sustainable approach for software ecosystems that supports experimental and observational science (EOS) across Oak Ridge National Laboratory (ORNL), we conducted a survey to understand the current and future landscape of EOS software and data. This paper describes the survey design we used to identify significant areas of interest, gaps, and potential opportunities, followed by a discussion on the obtained responses. The survey formulates questions about project demographics, technical approach, and skills required for the present and the next five years. The study was conducted among 38 ORNL participants between June and July of 2021 and followed the required guidelines for human subjects training. We plan to use the collected information to help guide a vision for sustainable, community-based, and reusable scientific software ecosystems that need to adapt effectively to: i) the evolving landscape of heterogeneous hardware in the next generation of instruments and computing (e.g. edge, distributed, accelerators), and ii) data management requirements for data-driven science using artificial intelligence.

Bernholdt, David↗