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At least 1,279 records · Page 71

A Knowledge Graph Approach for the Secondary Use of Cancer Registry Data

Population-based central cancer registries collect valuable structured and unstructured data primarily for cancer surveillance and research, enhancing insights into clinical features associated with cancer occurrence, cancer treatment, and cancer outcomes to guide interventions which reduce the cancer burden. Cancer registries primarily collect data on (1) cancer type (case or tumor); (2) patient demographics such as age, gender, and residential address at time of diagnosis; (3) planned first course of treatment; and (4) date of last contact, vital status, and cause of death. Cancer registry data is dynamic, structured data, which is extracted from many unstructured sources such as electronic healthcare records, and consolidated for reporting and other purposes. While available advanced analytic tools such as SEER*Stat have the ability to build SAS queries, we, however, explore an innovative knowledge graph approach to organizing cancer registry data for advanced analytics and visualization, which has unique advantages over approaches of existing tools. This innovative knowledge graph approach semantically enriches the data and easily enables linkage with third-party data, which can better explain variation in outcomes. We have developed a prototype knowledge graph based on data from the Louisiana Tumor Registry and other publicly available datasets including Behavioral Risk Factor Surveillance System, Clinical Trials, DBpedia, GeoNames, Rural-Urban Continuum Codes, and Semantic MEDLINE. The resource description framework (RDF) data model was selected to represent our knowledge graph, which contains more than 25 billion triples and is ~4TB in storage size. To exhibit the benefits of the knowledge graph approach, we used scenario specific queries, which find the relationships between cancer treatment sequences and outcomes. To illustrate its ease of use in iterative analysis, the knowledge graph was linked to external datasets for performing complex queries across multiple datasets. In addition, we used knowledge graphs to identify data discrepancies and to handle schema changes. Finally, we visualized the knowledge graph to discover data patterns. Our results demonstrate this graph-based solution enables cancer researchers to execute complex queries and more easily perform iterative analyses to improve understanding of cancer registry data. In the future, we would like to use high-performance computing (HPC) resources for faster-generating hypotheses with clinical potential from our knowledge graph.

Hasan, S M Shamimul↗

Argonne broadens understanding of America’s transportation and mobility systems

Mobility in America is changing fast. To understand where it’s headed, Argonne caught up with Michael Berube, the acting deputy assistant secretary for transportation in the U.S. Department of Energy’s Office of Energy Efficiency and Renewable Energy. While at the laboratory, Berube took time to highlight the ways in which technology and consumer demand are shaping transportation, and the insights national laboratories like Argonne can provide about the future.

97 MATHEMATICS AND COMPUTING↗

CMSSW Scaling Limits on Many-Core Machines

Today the LHC offline computing relies heavily on CPU resources, despite the interest in compute accelerators, such as GPUs, for the longer term future. The number of cores per CPU socket has continued to increase steadily, reaching the levels of 64 cores (128 threads) with recent AMD EPYC processors, and 128 cores on Ampere Altra Max ARM processors. Over the course of the past decade, the CMS data processing framework, CMSSW, has been transformed from a single-threaded framework into a highly concurrent one. The first multithreaded version was brought into production by the start of the LHC Run 2 in 2015. Since then, the framework's threading efficiency has gradually been improved by adding more levels of concurrency and reducing the amount of serial code paths. The latest addition was support for concurrent Runs. In this work we review the concurrency model of the CMSSW, and measure its scalability with real CMS applications, such as simulation and reconstruction, on mode rn many-core machines. We show metrics such as event processing throughput and application memory usage with and without the contribution of I/O, as I/O has been the major scaling limitation for the CMS applications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

MPF X-Ray Module Setup for 2018

The Mobile Plutonium Facility (MPF) is a portable module design facility that can be deployed anywhere in the world for the safe recovery, packaging, and shipment of a nations legacy, or excess plutonium stockpile. All of the modules of MPF have specific purposes for operating in a mission if one were to ever come up. For my past four internships here at SRNL I have been working on the support of the X-Ray module for MPF. This year I installed new equipment I had purchased last year for the X-Ray Module and made sure the module was mission ready for the chance that the team deploys in the future for plutonium recovery. Using digital radiography (DR) and computed tomography (CT) provides the MPF team the ability to verify the contents of containers that would be holding material. This also ensures the safety of the team members in the glovebox facilities by verifying that there are no sharps, liquids, or other items that may harm the workers or glovebox operations when working with radioactive material. X-Ray imaging can also pick up low density objects like plastic bags and tape. Note how the DR image hides the puncture in the inner can while the CT image shows the damage. New DR and CT computers with upgraded software, New imaging panel, NOVO Portable X-Ray System. Because of the new upgrades to the X-Ray module system containers can be scanned and evaluated quicker than before. With the last system the 3D model reconstruction alone would take anywhere from 10-12 minutes, now with the new system that time has been brought down to just shy of 1 minute 30 seconds. The new portable system also can 1,2 or 4 images of an object and stitch them together into a mosaic for scanning of larger containers.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Quasiclassical sampling and Wigner sampling of initial vibrational coordinates and momenta for polyatomic molecules in Monte Carlo molecular dynamics simulations

In a quasiclassical trajectory simulation, the vibrational modes are initialised with quantised vibrational energies, but vibrational phases are sampled by Monte Carlo. This requires an algorithm to assign coordinates and momenta to the various atoms. In this work, we present two methods for implementing this for nonrotating polyatomic molecules, namely, fixed-energy vibrational-state-selected initial conditions and thermal initial conditions. We also present a method for initiating classical trajectories with a ground-state Wigner distribution. These vibrational treatments are sufficient to initialise trajectories for unimolecular processes, and we also show how they can be applied to simulate bimolecular collision processes. The treatments of unimolecular and bimolecular collision processes are available in two Python codes called wigner_state_selected.py and bimolecular_collision.py, respectively, which will generate initial condition files that are recognisable by the SHARC and SHARC-MN computer programs for dynamics calculations. Both codes are available as standalone programs, as well as being included in SHARC-MN, and they will be included in future versions of SHARC. Here, the methods implemented in these codes are mostly also available in the ANT computer program, and those that are not available in ANT will be incorporated in future versions of ANT.

Wigner distribution↗

Performance of a geometric deep learning pipeline for HL-LHC particle tracking

The Exa.TrkX project has applied geometric learning concepts such as metric learning and graph neural networks to HEP particle tracking. Exa.TrkX’s tracking pipeline groups detector measurements to form track candidates and filters them. The pipeline, originally developed using the TrackML dataset (a simulation of an LHC-inspired tracking detector), has been demonstrated on other detectors, including DUNE Liquid Argon TPC and CMS High-Granularity Calorimeter. This paper documents new developments needed to study the physics and computing performance of the Exa.TrkX pipeline on the full TrackML dataset, a first step towards validating the pipeline using ATLAS and CMS data. The pipeline achieves tracking efficiency and purity similar to production tracking algorithms. Crucially for future HEP applications, the pipeline benefits significantly from GPU acceleration, and its computational requirements scale close to linearly with the number of particles in the event.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A Long History of Supercomputing

As part of its national security science mission, Los Alamos National Laboratory and HPC have a long, entwined history dating back to the earliest days of computing. From bringing the first problem to the nation’s first computer to building the first machine to break the petaflop barrier, Los Alamos holds many “firsts” in HPC breakthroughs. Today, supercomputers are integral to stockpile stewardship and the Laboratory continues to work with vendors in developing the future of HPC.

97 MATHEMATICS AND COMPUTING↗

An Uncertainty Quantification Framework for Prognostics and Condition-Based Monitoring

This paper presents a computational framework for uncertainty quantification in prognostics in the context of condition-based monitoring of aerospace systems. The different sources of uncertainty and the various uncertainty quantification activities in condition-based prognostics are outlined in detail, and it is demonstrated that the Bayesian subjective approach is suitable for interpreting uncertainty in online monitoring. A state-space model-based framework for prognostics, that can rigorously account for the various sources of uncertainty, is presented. Prognostics consists of two important steps. First, the state of the system is estimated using Bayesian tracking, and then, the future states of the system are predicted until failure, thereby computing the remaining useful life of the system. The proposed framework is illustrated using the power system of a planetary rover test-bed, which is being developed and studied at NASA Ames Research Center.

Health Monitoring↗

The MSFC Solar Activity Future Estimation (MSAFE) Model

The Natural Environments Branch of the Engineering Directorate at Marshall Space Flight Center (MSFC) provides solar cycle forecasts for NASA space flight programs and the aerospace community. These forecasts provide future statistical estimates of sunspot number, solar radio 10.7 cm flux (F10.7), and the geomagnetic planetary index, Ap, for input to various space environment models. For example, many thermosphere density computer models used in spacecraft operations, orbital lifetime analysis, and the planning of future spacecraft missions require as inputs the F10.7 and Ap. The solar forecast is updated each month by executing MSAFE using historical and the latest month's observed solar indices to provide estimates for the balance of the current solar cycle. The forecasted solar indices represent the 13-month smoothed values consisting of a best estimate value stated as a 50 percentile value along with approximate +/- 2 sigma values stated as 95 and 5 percentile statistical values. This presentation will give an overview of the MSAFE model and the forecast for the current solar cycle.

Suggs, Ron↗

The MSFC Solar Activity Future Estimation (MSAFE) Model

The Natural Environments Branch of the Engineering Directorate at Marshall Space Flight Center (MSFC) provides solar cycle forecasts for NASA space flight programs and the aerospace community. These forecasts provide future statistical estimates of sunspot number, solar radio 10.7 cm flux (F10.7), and the geomagnetic planetary index, Ap, for input to various space environment models. For example, many thermosphere density computer models used in spacecraft operations, orbital lifetime analysis, and the planning of future spacecraft missions require as inputs the F10.7 and Ap. The solar forecast is updated each month by executing MSAFE using historical and the latest month's observed solar indices to provide estimates for the balance of the current solar cycle. The forecasted solar indices represent the 13-month smoothed values consisting of a best estimate value stated as a 50 percentile value along with approximate +/- 2 sigma values stated as 95 and 5 percentile statistical values. This presentation will give an overview of the MSAFE model and the forecast for the current solar cycle.

Suggs, Ron↗

The MSFC Solar Activity Future Estimation (MSAFE) Model

The Natural Environments Branch of the Engineering Directorate at Marshall Space Flight Center (MSFC) provides solar cycle forecasts for NASA space flight programs and the aerospace community. These forecasts provide future statistical estimates of sunspot number, solar radio 10.7 cm flux (F10.7), and the geomagnetic planetary index, Ap, for input to various space environment models. For example, many thermosphere density computer models used in spacecraft operations, orbital lifetime analysis, and the planning of future spacecraft missions require as inputs the F10.7 and Ap. The solar forecast is updated each month by executing MSAFE using historical and the latest month's observed solar indices to provide estimates for the balance of the current solar cycle. The forecasted solar indices represent the 13-month smoothed values consisting of a best estimate value stated as a 50 percentile value along with approximate +/- 2 sigma values stated as 95 and 5 percentile statistical values. This presentation will give an overview of the MSAFE model and the forecast for the current solar cycle.

Suggs, Ron↗

Memo regarding the Final Review of FY21 ASC L2 Milestone 7840: Neural Mini-Apps for Future Heterogeneous HPC Systems

The final review for the FY21 Advanced Simulation and Computing (ASC) Computational Systems and Software Environments (CSSE) L2 Milestone #7840 was conducted on August 25th, 2021 at Sandia National Laboratories in Albuquerque, New Mexico. The review committee/panel unanimously agreed that the milestone has been successfully completed, exceeding expectations on several of the key deliverables.

97 MATHEMATICS AND COMPUTING↗

Implementation and extension of the impulse transfer function method for future application to the space shuttle project. Volume 1: Analysis and correlation studies

Computer programming, data processing, and a correlation study that employed data collected in the first phase test were used to demonstrate that standard test procedures and equipment could be used to collect a significant number of transfer functions from tests of the Lunar Module test article LTA-11. The testing consisted of suspending the vehicle from the apex fittings of the outrigger trusses through a set of air springs to simulate the free-free state. Impulsive loadings were delivered, one at a time, at each of the landing gear's attachment points, in three mutually perpendicular directions; thus a total of 36 impulses were applied to the vehicle. Time histories of each pulse were recorded on magnetic tape along with 40 channels of strain gage response and 28 channels of accelerometer response. Since an automated data processing system was not available, oscillograph playbacks were made of all 2400 time histories as a check on the validity of the data taken. In addition, one channel of instrumentation was processed to determine its response to a set of forcing functions from a prior LTA-11 drop test. This prediction was compared with drop test results as a first measure of accuracy.

Mantus, M.↗

IBM PC enhances the world's future

Although the purpose of this research is to illustrate the importance of computers to the public, particularly the IBM PC, present examinations will include computers developed before the IBM PC was brought into use. IBM, as well as other computing facilities, began serving the public years ago, and is continuing to find ways to enhance the existence of man. With new developments in supercomputers like the Cray-2, and the recent advances in artificial intelligence programming, the human race is gaining knowledge at a rapid pace. All have benefited from the development of computers in the world; not only have they brought new assets to life, but have made life more and more of a challenge everyday.

Cox, Jozelle↗

Differential surface models for tactile perception of shape and on-line tracking of features

Tactile perception of shape involves an on-line controller and a shape perceptor. The purpose of the on-line controller is to maintain gliding or rolling contact with the surface, and collect information, or track specific features of the surface such as edges of a certain sharpness. The shape perceptor uses the information to perceive, estimate the parameters of, or recognize the shape. The differential surface model depends on the information collected and on the a priori information known about the robot and its physical parameters. These differential models are certain functionals that are projections of the dynamics of the robot onto the surface gradient or onto the tangent plane. A number of differential properties may be directly measured from present day tactile sensors. Others may have to be indirectly computed from measurements. Others may constitute design objectives for distributed tactile sensors of the future. A parameterization of the surface leads to linear and nonlinear sequential parameter estimation techniques for identification of the surface. Many interesting compromises between measurement and computation are possible.

Hemami, H.↗

International Space Station (ISS) Payload Autonomous Operations Past, Present and Future

Draper Laboratorys Timeliner is a scripting and automation system that runs onboard computers in the International Space Station (ISS). Timeliner is fully integrated with ISS and can be used to automate ISS operations tasks. Some of the most challenging aspects of operating a payload in low earth orbit are communication delays, ground equipment failures, and human errors. How does a Payload Developer (PD) know their equipment is operating nominally and collecting science in the most efficient way possible or even powered at any given time? During a ground Loss of Signal (LOS) data outage, PDs have no insight into their experiments state, and benefit greatly from Timeliner scripts executing on ISS to perform telemetry monitoring and commanding operations. This paper will discuss current software designs, and new operational uses for Timeliner. Existing Timeliner capabilities discussed will include: autonomous EXPRESS Rack activation and deactivation; autonomous science data downlinks; Minus Eighty Degree Freezer (MELFI) Dewar autonomous safing; JAXA and ESA module autonomous payload facility safing; as well as many others. New operational concepts discussed will include allowing Timeliner on the payload computer to issue core commands (Thermal, Power, Fire Detection), creation of new ground tools that will monitor the current status of Payload Racks as well as all the messaging from autonomous scripts executing, decreasing approval time for Timeliner bundles, and opening up the Payload MDM Enhanced Processor Integrated Communications Card (EPIC) interface. The EPIC interface could provide a new crew interface for PL Timeliner execution. The new interface could operate on either a Payload Computer System (PCS) or a Station Support Computer (SSC) that is plugged into either the Payload LAN or the Operations LAN which will make communicating to the PL MDM more flexible and greatly increase band width for communication.

Space Mission Automation↗

Turbine Technology Team - An overview of current and planned activities relevant to the National Launch System (NLS)

The current status of the activities and future plans of the Turbine Technology Team of the Consortium for Computational Fluid Dynamics is reviewed. The activities of the Turbine Team focus on developing and enhancing codes and models, obtaining data for code validation and general understanding of flows through turbines, and developing and analyzing the aerodynamic designs of turbines suitable for use in the Space Transportation Main Engine fuel and oxidizer turbopumps. Future work will include the experimental evaluation of the oxidizer turbine configuration, the development, analysis, and experimental verification of concepts to control secondary and tip losses, and the aerodynamic design, analysis, and experimental evaluation of turbine volutes.

Griffin, Lisa W.↗

Heatshield Erosion Due to Dust Particle Impacts on the Schiaparelli Capsule During Martian Entry

On October 2016, a capsule known as Schiaparelli, part of the European Space Agency (ESA) ExoMars mission, entered the Martian atmosphere. Measurements taken during the Schiaparelli descent will be used to validate computational models used to design the thermal protection system (TPS) of future Mars missions. One of the unique features of Schiaparelli entry was the possibility of a major dust storm occurring during the entry. Major dust storms are unpredictable but more likely during the Northern Autumn timeframe. In 2001, for example, regional dust storms merged into a global dust storm that blanketed much of the planet. Even though Schiaparelli did not enter during a major dust storm, future Mars missions will have to account for the possibility of dust erosion (depending on the time of year) when estimating the thickness of the TPS. Because weight is always a critical factor in designing entry vehicles, accurate assessment of dust erosion is necessary to avoid over-design of the TPS. This study will present computational results of heatshield erosion due to dust particle impacts on the Schiaparelli capsule if it had encountered a dust storm during entry.

thermal protection system↗