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At least 253 records · Page 14

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

Text mining in the biomedical sciences is rapidly transitioning from small-scale evaluation to large-scale application. In this article, we argue that text-mining technologies have become essential tools in real-world biomedical research. We describe four large scale applications of text mining, as showcased during a recent panel discussion at the BioCreative V Challenge Workshop. We draw on these applications as case studies to characterize common requirements for successfully applying text-mining techniques to practical biocuration needs. We note that system ‘accuracy’ remains a challenge and identify several additional common difficulties and potential research directions including (i) the ‘scalability’ issue due to the increasing need of mining information from millions of full-text articles, (ii) the ‘interoperability’ issue of integrating various text-mining systems into existing curation workflows and (iii) the ‘reusability’ issue on the difficulty of applying trained systems to text genres that are not seen previously during development. We then describe related efforts within the text-mining community, with a special focus on the BioCreative series of challenge workshops. We believe that focusing on the near-term challenges identified in this work will amplify the opportunities afforded by the continued adoption of text-mining tools. In conclusion, in order to sustain the curation ecosystem and have text-mining systems adopted for practical benefits, we call for increased collaboration between text-mining researchers and various stakeholders, including researchers, publishers and biocurators.

59 BASIC BIOLOGICAL SCIENCES↗

"Experimental Research at the Energy Frontier in High Energy Physics" (Final Technical Report)

Recent developments in particle physics and cosmology raise the exciting prospect that we are on the threshold of a major step forward in our understanding of the universe. This proposal describes a research program at the University of Illinois in experimental high-energy physics on the ATLAS experiment at CERN’s Large Hadron Collider (LHC). Our group actively collaborates with the Theory Group and other experimental efforts within the Office of Science frontiers (energy, intensity, and cosmic) to search broadly in the ATLAS data to maximize our potential for scientifc discovery. The thrust of this proposal is to search for new physics using ATLAS data. Emphasis is placed on novel use of the Higgs boson as a tool to search for new particles and interactions and development of fast particle tracking systems for use in triggering. We propose to continue our strong role in FTK commissioning and operations. To maximize the impact and vitality of the proposed physics program through the HL-LHC running, we will lead firmware efforts in the HWTT Phase-II TDAQ upgrade, leveraging our expertise acquired through development of fast tracking hardware and firmware for the FTK system.

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Quantum Computing Strategy 2026

Quantum computing (QC) is a rapidly maturing technology with the potential for revolutionary impacts on stockpile stewardship science and national security. Recent developments in fault-tolerant architectures have compressed vendor roadmaps, and predictions of a production-ready quantum computer by the mid-2030s are becoming increasingly credible. This strategy provides a roadmap for integrating QC into the Advanced Simulation and Computing (ASC) program by investing in four strategic focus areas: 1. Develop Capabilities in Mission-Relevant Quantum Applications: ASC will prioritize developing quantum-ready applications in mission areas that have shown significant promise for quantum advantage, including simulations of materials in extreme environments, nuclear dynamics, solving linear and nonlinear partial differential equations, and uncertainty quantification. These applications directly support stockpile stewardship science and modernization objectives. 2. Conduct R&D in Algorithms, Software, and Hardware: Sustained research into quantum algorithms, robust software tools, and quantum hardware is essential. ASC will develop efficient quantum algorithms; invest in quantum compilers, debuggers, and performance tools; and explore specialized quantum hardware tailored to NNSA’s unique requirements. 3. Engage with Vendors and Partners: Early and active collaboration with commercial quantum hardware vendors and academic partners is critical. Through testbeds, co-design agreements, and quantum demonstration facilities, ASC will influence hardware design, gain early access to emerging technologies, and ensure that quantum platforms evolve to meet mission needs. 4. Build Knowledge, Experience, and Workforce: Expanding and upskilling the quantum-trained workforce is essential to long-term success. This includes hiring, internal training, university outreach, and postdoctoral support to ensure ASC maintains the expertise required to operate, program, and integrate quantum systems as they become available. While quantum computing will never replace classical computing, it has the potential to solve certain problems with speed and accuracy that would be unachievable using any conceivable classical high-performance computing (HPC) system. By investing strategically in QC, ASC will help propel the emergent QC industry, maintain U.S. technological leadership, ensure mission readiness, and position itself to rapidly adopt quantum technologies as they mature.

97 MATHEMATICS AND COMPUTING↗

Project Accomplishments Summary - SC03/01672.04.0. Flow, Thermal Evolution, and Electrochemistry in Layered Poroelastic Materials

Sandia National Laboratories (SNL) and the Procter and Gamble Company (P&G), which eventually spun off The Duracell Company (Duracell) to Berkshire Hathaway, collaborated to develop a computational tool that predicts the in-use and manufacturing-process performance of consumer electrical energy storage devices. This computational tool was particularly useful in exploring the effects of material microstructure, device configuration/geometry, manufacturing and manufacturing defects on product performance.

36 MATERIALS SCIENCE↗

Satellites as Sentinels for Health

Remotely-sensed data and observations are providing powerful new tools for addressing the human health aspects of sustainability by enabling improved understanding of the relationships and linkages between health-related environmental parameters and society as well as techniques for early warning of potential health problems. Remote sensing, geographic information systems, improved computational capabilities, and interdisciplinary research between the Earth and health science communities are being combined in rich collaborative efforts resulting in more rapid problem-solving, early warning, and prevention in global health issues. This paper provides a number of recent examples of applications of these technologies to health issues related to the following: infectious and vector-borne diseases; urban, regional and global air pollution; heat stress; UV radiation; water-borne disease; extreme weather; contaminant pathways (ocean, atmosphere, ice).

Maynard, Nancy G.↗

Interactive Learning During Solar Maximum

The goal of this project is to develop and distribute e-educational material for space science during times of solar activity that emphasizes underlying basic science principles of solar disturbances and their effects on Earth. This includes materials such as simulations, animations, group projects and other on-line materials to be used by students either in high school or at the introductory college level. The on-line delivery tool originally intended to be used is known as Interactive Multimedia Education at a Distance (IMED), which is a web-based software system used at UCLA for interactive distance learning. IMED is a password controlled system that allows students to access text, images, bulletin boards, chat rooms, animation, simulations and individual student web sites to study science and to collaborate on group projects.

Ashour-Abdalla, Maha↗

Modeling for Integrated Science Management and Resilient Systems Development

Many physiological, environmental, and operational risks exist for crewmembers during spaceflight. An understanding of these risks from an integrated perspective is required to provide effective and efficient mitigations during future exploration missions that typically have stringent limitations on resources available, such as mass, power, and crew time. The Human Research Program (HRP) is in the early stages of developing collaborative modeling approaches for the purposes of managing its science portfolio in an integrated manner to support cross-disciplinary risk mitigation strategies and to enable resilient human and engineered systems in the spaceflight environment. In this talk, we will share ideas being explored from fields such as network science, complexity theory, and system-of-systems modeling. Initial work on tools to support these explorations will be discussed briefly, along with ideas for future efforts.

Shelhamer, M.↗

Virtualized Multi-Mission Operations Center (vMMOC) and its Cloud Services

His presentation will cover, the current and future, technical and organizational opportunities and challenges with virtualizing a multi-mission operations center. The full deployment of Goddard Space Flight Centers (GSFC) Virtualized Multi-Mission Operations Center (vMMOC) is nearly complete. The Space Science Mission Operations (SSMO) organizations spacecraft ACE, Fermi, LRO, MMS(4), OSIRIS-REx, SDO, SOHO, Swift, and Wind are in the process of being fully migrated to the vMMOC. The benefits of the vMMOC will be the normalization and the standardization of IT services, mission operations, maintenance, and development as well as ancillary services and policies such as collaboration tools, change management systems, and IT Security. The vMMOC will also provide operational efficiencies regarding hardware, IT domain expertise, training, maintenance and support.The presentation will also cover SSMO's secure Situational Awareness Dashboard in an integrated, fleet centric, cloud based web services fashion. Additionally the SSMO Telemetry as a Service (TaaS) will be covered, which allows authorized users and processes to access telemetry for the entire SSMO fleet, and for the entirety of each spacecrafts history. Both services leverage cloud services in a secure FISMA High and FedRamp environment, and also leverage distributed object stores in order to house and provide the telemetry. The services are also in the process of leveraging the cloud computing services elasticity and horizontal scalability. In the design phase is the Navigation as a Service (NaaS) which will provide a standardized, efficient, and normalized service for the fleet's space flight dynamics operations. Additional future services that may be considered are Ground Segment as a Service (GSaaS), Telemetry and Command as a Service (TCaaS), Flight Software Simulation as a Service, etc.

Ido, Haisam Kassim↗

Lunar Instrument Data Integration Into the Virtual Reality Mission Simulation System for Decision Communication and Situational Awareness

In situ resource utilization (ISRU) technologies are a key advancement required to make human habitation on the Moon and Mars viable. The upcoming Volatiles Investigating Polar Exploration Rover (VIPER) mission will provide crucial correlations between volatiles and lunar geology to understand the water content available for ISRU on the moon. The mission will require the coordination of multi-disciplinary teams across the country making real time decisions based on rover instrument data. The virtual reality Mission Simulation System (vMSS) is a virtual reality platform designed at MIT by the Resource Exploration and Science of our Cosmic Environment (RESOURCE) team to provide teams with a collaboration interface for planetary missions like VIPER. Herein we determine the integration pathway for analog based datasets that are examples of VIPER's two main instruments, the near-infrared volatile spectrometer subsystem (NIRVSS) and the neutron spectrometer subsystem (NSS), into vMSS to provide the most valuable visualization tools. Focusing on improving situational awareness, decision making, reducing task load and incorporating comments from scientists working previous analogs and on the current VIPER mission, we recommend critical elements to implement into vMSS and the best approaches for data visualization. We present a review of relevant analogs and state of the art mission software. We have developed a design concept and path to flight of analysed instrument data integrated with data maps that allow for virtual manipulation and annotation between non-co-located team members. We focus on pre-mission mapping of a priori data for improved situational awareness, layering of analysed instrument data, correlative mapping and interactive capabilities for in-mission decision making, as well as archiving and annotation tools for post-mission analysis. Finally, we lay out the roadmap for the future development of immersive sample site visualization capabilities and the use of integrated instrument data in vMSS with automated temporal and geospatial planning.

Cody Alison Paige↗

Computational Modeling to Advance Novel Medical Isotopes for Radiotheranostics: A DOE-NIH Joint Workshop Executive Summary

The DOE-NIH Joint Workshop on Computational Modeling to Advance Novel Medical Isotopes for Radiotheranostics, held on September 27, 2024, brought together experts from government, academia, and industry to address critical challenges in radionuclide production and clinical translation. Here, the workshop emphasized interdisciplinary collaboration, particularly between the Department of Energy (DOE) and the National Institutes of Health (NIH), to strengthen the domestic isotope supply, streamline regulatory pathways, and further integrate computational tools into radiopharmaceutical therapy (RPT). Key discussions explored the role of AI-driven modeling, machine learning, and digital twin technologies in optimizing dosimetry, dynamically personalizing treatments, and reducing time to clinical adoption. Advances in predictive computational modeling were highlighted as essential for improving radionuclide yield, purity, and synthesis efficiency. Regulatory considerations and equitable access were central themes, with participants advocating for harmonized global standards, adaptive trial designs, and expanded infrastructure for clinical implementation. DOE computational and production infrastructure was emphasized. Future priorities identified include increased investment in radionuclide production infrastructure, expanded workforce development in radiopharmaceutical sciences and computational modeling, and the creation of robust public-private partnerships. The workshop concluded that continued strategic collaboration and sustained resources will be vital for advancing next-generation radiotheranostics, ensuring safe and effective therapies accessible to all patients.

digital twins↗

Algorithms and Statistical Models for Scientific Discovery in the Petabyte Era

The field of astronomy has arrived at a turning point in terms of size and complexity of both datasets and scientific collaboration. Commensurately, algorithms and statistical models have begun to adapt --- e.g., via the onset of artificial intelligence --- which itself presents new challenges and opportunities for growth. This white paper aims to offer guidance and ideas for how we can evolve our technical and collaborative frameworks to promote efficient algorithmic development and take advantage of opportunities for scientific discovery in the petabyte era. We discuss challenges for discovery in large and complex data sets; challenges and requirements for the next stage of development of statistical methodologies and algorithmic tool sets; how we might change our paradigms of collaboration and education; and the ethical implications of scientists' contributions to widely applicable algorithms and computational modeling. We start with six distinct recommendations that are supported by the commentary following them. This white paper is related to a larger corpus of effort that has taken place within and around the Petabytes to Science Workshops (https://petabytestoscience.github.io/).

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Climate Informatics

The impacts of present and potential future climate change will be one of the most important scientific and societal challenges in the 21st century. Given observed changes in temperature, sea ice, and sea level, improving our understanding of the climate system is an international priority. This system is characterized by complex phenomena that are imperfectly observed and even more imperfectly simulated. But with an ever-growing supply of climate data from satellites and environmental sensors, the magnitude of data and climate model output is beginning to overwhelm the relatively simple tools currently used to analyze them. A computational approach will therefore be indispensable for these analysis challenges. This chapter introduces the fledgling research discipline climate informatics: collaborations between climate scientists and machine learning researchers in order to bridge this gap between data and understanding. We hope that the study of climate informatics will accelerate discovery in answering pressing questions in climate science.

Climate change↗

Hybridized Agile Software Development of Flight Control Team Tools for International Space Station's Payload Operations Integration Center

Ground systems operations at the National Aeronautics and Space Administration's (NASA) Payload Operations and Integration Center (POIC) at Marshall Space Flight Center (MSFC) recently increased via a High Operations Tempo (HOT) initiative, in order to support more science activities with a fourth crew member on the International Space Station (ISS). The Flight Control Team's (FCT) need to support this increasing pace of payload science operations was the impetus for creating a series of new tools. While their need was clear, the full scope and user experience for each tool was not as well-understood, thus establishing a fixed set of initial requirements was not feasible. A hybridized Agile Software Development (ASD) paradigm was created to take advantage of this uncertainty, plan for it, permit the exploration of novel concepts, and also facilitate a rapid and flexible response to inevitably changing requirements. The POIC's hybridized ASD approach places preeminent focus on providing customer value through the delivery of high quality, customer-focused solutions in short timeframes. This has been successfully achieved through creating unprecedented modes of cooperation and collaboration between operations and software development teams, frequent user evaluations of the software with well-defined feedback mechanisms, increased human factors involvement, and a dedication to successful outcomes by the whole of the POIC. Since space science operations and software development are not typically so closely linked, this paper discusses an approach that offers an optimal way to provide an increased return on investment and a faster time-to-completion than traditional software development paradigms, while aiming at delivering high quality products and customer-driven value.

Albers, Cerese M.↗

NNSA/CEA Workflow Workshop Report 2021

Researchers from three NNSA labs plus CEA recently met for a half-day workshop on scientific and engineering workflows in March of 2021. Tools, projects and use cases from each institution were described. A wide range of unique capabilities and requirements were represented. The workshop highlights the fact that the CEA/NNSA workflows space mirrors the broader open science workflows community, with multiple technologies under development in a number of science domains and under a number of funding streams, with differing capabilities and focuses. Despite the number of tools, presentations and discussions have shown that these tools cover specific mission spaces at the four labs, each with distinctive capabilities that do not completely overlap with each other. We believe there is a strong interest in the short term for sharing lessons learned and collaborating on benchmarks and site evaluation of projects. This report, prepared by the NNSA/CEA Workflows Working Group, briefly summarizes the presentations in the areas of domain specific workflows, end user environments, data management, job and resource management, and infrastructure, and then identifies six broad areas for potential collaboration. A key finding is that users could benefit from greater interoperability, compatibility, and composability of the workflow technologies under development and that point-to-point collaboration opportunities should be identified to explore these aspects.

97 MATHEMATICS AND COMPUTING↗

High Energy Physics Network Requirements Review (Final Report, July-October 2020)

Throughout 2020, ESnet and the Office of High Energy Physics (HEP) of the DOE SC organized an ESnet requirements review of HEP-supported activities. Preparation for this event included identification of key stakeholders: program and facility management, research groups, technology providers, and a number of external observers. These individuals were asked to prepare formal case study documents about their relationship to the HEP program to build a complete understanding of the current, near-term, and long-term status, expectations, and processes that will support the science going forward. A series of pre-planning meetings better prepared case study authors for this task, along with guidance on how the review would proceed in a virtual fashion.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

New developments in space radiation research at NASA: Annotating data using a novel radiation biology ontology

Like many interdisciplinary sciences, data producers and consumers in the field of radiation biology often use a wide variety of terminology to describe their experiments and data. Furthermore, space systems and technologies are rapidly evolving, and a shared understanding and common terminology for these is also lacking. The efficiency of research organizations can be enhanced by standardizing metadata through the use of knowledge resources like ontologies. Employing a sophisticated model such as a formal ontology to standardize metadata enables automated data acquisition processes and supports more complete, accurate meta-analysis through more efficient and complete data discovery and retrieval, particularly when using multiple data sources. Thus, we developed the Radiation Biology Ontology (RBO) in order to improved radiation biology metadata uniformity and transparency. We used open-source software (the Ontology Development Kit, Protégé and WebProtégé) and worked within the OBO Foundry framework, which includes a set of ontology development principles and practices for ontology consistency, uniformity, and accountability. The RBO has now been incorporated into two radiation research data repositories, NASA’s GeneLab omics database (https://genelab.nasa.gov), and the European Commission STORE database (https://www.storedb.org/). Continuous build integration tools allowed our international RBO collaboration to be more efficient and focus its efforts on semantic model design. Currently, the RBO contains over 300 annotated classes and individuals specific to the study of radiation on biological systems, as well as imports of many additional classes from other OBO Foundry ontologies that relate to and/or provide context for these RBO entities. We publish the RBO through the OBO Foundry, so that it is available for browsing, download, and querying through NCBI Bioportal web site and application programming interface. The NASA Ames Life Science Data Archive (ALSDA) is also in the process of adopting use of the RBO, taking NASA one step closer to a knowledge-based system for space biology data. It is our hope that the global communities of radiation research Investigators, data curators and data analysts can similarly leverage the RBO and will contribute to its further development.

radiation↗

PROSPECT-II physics opportunities

We report the precision reactor oscillation and spectrum experiment, PROSPECT, has made world-leading measurements of reactor antineutrinos at short baselines. In its first phase, conducted at the high flux isotope reactor (HFIR) at Oak Ridge National Laboratory, PROSPECT produced some of the strongest limits on eV-scale sterile neutrinos, made a precision measurement of the reactor antineutrino spectrum from 235 U, and demonstrated the observation of reactor antineutrinos in an aboveground detector with good energy resolution and well-controlled backgrounds. The PROSPECT collaboration is now preparing an upgraded detector, PROSPECT-II, to probe yet unexplored parameter space for sterile neutrinos and contribute to a full resolution of the reactor antineutrino anomaly, a longstanding puzzle in neutrino physics. By pressing forward on the world’s most precise measurement of the 235 U antineutrino spectrum and measuring the absolute flux of antineutrinos from 235 U, PROSPECT-II will sharpen a tool with potential value for basic neutrino science, nuclear data validation, and nuclear security applications. Following a two-year deployment at HFIR, an additional PROSPECT-II deployment at a low enriched uranium reactor could make complementary measurements of the neutrino yield from other fission isotopes. PROSPECT-II provides a unique opportunity to continue the study of reactor antineutrinos at short baselines, taking advantage of demonstrated elements of the original PROSPECT design and close access to a highly enriched uranium reactor core.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗