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GrammarViz 3.0: Interactive Discovery of Variable-Length Time Series Patterns

The problems of recurrent and anomalous pattern discovery in time series, e.g., motifs and discords, respectively, have received a lot of attention from researchers in the past decade. However, since the pattern search space is usually intractable, most existing detection algorithms require that the patterns have discriminative characteristics and have its length known in advance and provided as input, which is an unreasonable requirement for many real-world problems. In addition, patterns of similar structure, but of different lengths may co-exist in a time series. In order to address these issues, we have developed algorithms for variable-length time series pattern discovery that are based on symbolic discretization and grammar inference—two techniques whose combination enables the structured reduction of the search space and discovery of the candidate patterns in linear time. In this work, we present GrammarViz 3.0—a software package that provides implementations of proposed algorithms and graphical user interface for interactive variable-length time series pattern discovery. The current version of the software provides an alternative grammar inference algorithm that improves the time series motif discovery workflow, and introduces an experimental procedure for automated discretization parameter selection that builds upon the minimum cardinality maximum cover principle and aids the time series recurrent and anomalous pattern discovery.

97 MATHEMATICS AND COMPUTING↗

The waiting time problem in a model hominin population

Functional information is normally communicated using specific, context-dependent strings of symbolic characters. This is true within the human realm (texts and computer programs), and also within the biological realm (nucleic acids and proteins). In biology, strings of nucleotides encode much of the information within living cells. How do such information-bearing nucleotide strings arise and become established? This paper uses comprehensive numerical simulation to understand what types of nucleotide strings can realistically be established via the mutation/selection process, given a reasonable timeframe. The program Mendel’s Accountant realistically simulates the mutation/selection process, and was modified so that a starting string of nucleotides could be specified, and a corresponding target string of nucleotides could be specified. We simulated a classic pre-human hominin population of at least 10,000 individuals, with a generation time of 20 years, and with very strong selection (50 % selective elimination). Random point mutations were generated within the starting string. Whenever an instance of the target string arose, all individuals carrying the target string were assigned a specified reproductive advantage. When natural selection had successfully amplified an instance of the target string to the point of fixation, the experiment was halted, and the waiting time statistics were tabulated. Using this methodology we tested the effect of mutation rate, string length, fitness benefit, and population size on waiting time to fixation. Biologically realistic numerical simulations revealed that a population of this type required inordinately long waiting times to establish even the shortest nucleotide strings. To establish a string of two nucleotides required on average 84 million years. To establish a string of five nucleotides required on average 2 billion years. We found that waiting times were reduced by higher mutation rates, stronger fitness benefits, and larger population sizes. However, even using the most generous feasible parameters settings, the waiting time required to establish any specific nucleotide string within this type of population was consistently prohibitive. We show that the waiting time problem is a significant constraint on the macroevolution of the classic hominin population. Routine establishment of specific beneficial strings of two or more nucleotides becomes very problematic.

54 ENVIRONMENTAL SCIENCES↗

Initial experience with a SiPM-based PET/CT scanner: influence of acquisition time on image quality

Background: A newly introduced PET/CT scanner (Discovery Meaningful Insights—DMI, GE Healthcare) includes the silicon photomultiplier (SiPM) with timeof-flight (TOF) technology first used in the GE SIGNA PET/MRI. In this study, we investigated the impact of various acquisition times on image quality using this SiPM-based PET/CT. Methods: We reviewed data from 58 participants with cancer who were scanned using the DMI PET/CT scanner. The administered dosages ranged 295.3–429.9 MBq (mean ± SD 356.3 ± 37.4) and imaging started at 71–142 min (mean ± SD 101.41 ± 17. 52) after administration of the radiopharmaceutical. The patients’ BMI ranged 19.79–46. 16 (mean ± SD 26.55 ± 5.53). We retrospectively reconstructed the raw TOF data at 30, 60, 90, and 120 s/bed and at the standard image acquisition time per clinical protocol (180 or 210 s/bed depending on BMI). Each reconstruction was reviewed blindly by two nuclear medicine physicians and scored 1–5 (1—poor, 5—excellent quality). The liver signal-to-noise ratio (SNR) was used as a quantitative measure of image quality. Results: The average scores ± SD of the readers were 2.61 ± 0.83, 3.70 ± 0.92, 4.36 ± 0.82, 4.82 ± 0.39, and 4.91 ± 0.91 for the 30, 60, 90, and 120 s/bed and at standard acquisition time, respectively. Inter-reader agreement on image quality assessment was good, with a weighted kappa of 0.80 (95% CI 0.72–0.81). In the evaluation of the effects of time per bed acquisition on semi-quantitative measurements, we found that the only time point significantly different from the standard time were 30 and 60 s (both with P < 0.001). The effects of dose and BMI were not statistically significant (P = 0.195 and 0.098, respectively). There was a significant positive effect of time on SNR (P < 0.001), as well as a significant negative effect of weight (P < 0.001). Conclusions: Our results suggest that despite significant delays from injection to imaging (due to comparison with standard PET/CT) compared to standard clinical operations and even in a population with average BMI > 25, images can be acquired as fast as 90 s/bed using the SiPM PET/CT and still result in very good image quality (average score > 4).

62 RADIOLOGY AND NUCLEAR MEDICINE↗

A scalable transformer model for real-time decision making in neutron scattering experiments

The U.S. Department of Energy's (DOE's) neutron research facilities at Oak Ridge National Laboratory (ORNL), including the High Flux Isotope Reactor (HFIR) and the Spallation Neutron Source (SNS), are a state-of-the-art neutron scattering facility that allows researchers to study the structure and dynamics of materials at the atomic scale. At the SNS, neutrons are measured using the time-of-flight (TOF) technique as they move through a neutron beamline to interact with a sample. Large volumes of neutron scattering data are collected and recorded in neutron event mode. Optimal productivity of the TOF instrument is limited due to the lack of real-time data analysis tools. The large amount of data generated by the experiments can be challenging to process and analyze in real time, particularly for experiments that require rapid feedback and adjustment of experimental parameters. The regular computer/workstation cannot keep up with the experiment speed to provide real-time feedback to adjust experimental parameters, so connecting the supercomputers available to the neutron facility is necessary to achieve real-time data analysis and experiment steering. To address this challenge, we exploit the Frontier supercomputer at Oak Ridge Leadership Computing Facility (OLCF) to train a scalable temporal fusion transformer model for real-time decision making of TOF neutron scattering experimentation. Here, in this paper, we present the results using Frontier to provide the processing power needed to rapidly process and analyze large volumes of single-crystal diffraction data collected at TOPAZ, a neutron time-of-flight Laue single-crystal diffractometer at the SNS.

97 MATHEMATICS AND COMPUTING↗

Femtosecond timing distribution and control for next generation accelerators and light sources

Femtosecond Timing Distribution At LCLS Free-electron-lasers (FEL) have the capability of producing high photon flux from the IR to the hard x-ray wavelength range and to emit femtosecond and eventually even attosecond pulses. This makes them an ideal tool for fundamental as well as applied re-search. Timing precision at the Stanford Linear Coherent Light Source (LCLS) between the x-ray FEL (XFEL) and ultrafast optical lasers is currently no better than 100 fs RMS. Ideally this precision should be much better and could be limited only by the x-ray pulse duration, which can be as short as a few femtoseconds. An increasing variety of science problems involving electron and nuclear dynamics in chemical and material systems will become accessible as the timing improves to a few femtoseconds. Advanced methods of electron beam conditioning or pulse injection could allow the FEL to achieve pulse durations less than one femtosecond. The objective of the work described in this proposal is to set up an optical timing distribution system based on mode locked Erbium doped fiber lasers at LCLS facility to improve the timing precision in the facility and allow time stamping with a 10 fs precision. The primary commercial applications for optical timing distributions systems are seen in the worldwide accelerator facilities and next generation light sources community. It is reasonable to expect that at least three major XFELs will be built in the next decade. In addition there will be up to 10 smaller machines, such as FERMI in Italy and Maxlab in Sweden, plus the market for upgrading already existing facilities like Jefferson Lab. The total market is estimated to be on the order of a 100 Million US Dollars. The company owns the exclusive rights to the IP covering the technology enabling sub-10 fs synchronization systems. Testing this technology, which has set records in a lab environment, at LCLS, hence in a real world scenario, is an important corner stone of bringing the technology to market.

43 PARTICLE ACCELERATORS↗

Time-Gated Raman Spectroscopy (Intern Final Report)

Time-gated Raman spectroscopy is a powerful tool for rapid non-destructive analysis of chemical compounds, particularly when combined with other investigative methods. Time-gating the signal obtained from a sample during Raman spectroscopy allows for the removal of background emission and black body radiation, improving clarity and accuracy of scans. The main objectives of this project were to prove the lab’s time-gated Raman spectroscopy system works as proof of concept and to make select improvements to the in-house LabVIEW software used to run the time-gated system. This time-gated system will be added to the CTK’s TAP reactors in the future, but this is out of the scope of this internship project. This research is important, as understanding the mechanisms behind catalysts leads to designing better systems/materials and the perfection of catalysts, and energy-efficient chemical manufacturing is key when designing a greener future. The research for this project was done with samples at both ambient conditions in sample holders and at operando conditions (i.e., high temperature, unsteady-state) inside a small-volume chemical reactor. Numerous spectro-kinetic scans of the catalysts were obtained, but the advanced dynamics of these systems are still being interpreted. There is data that demonstrates that the time-gated system is correctly rejecting emission from samples, and one can observe real-time changes in the signal from the sample, due to coking or changes induced by redox chemistry. Chemical manufacturers and the planet are the main beneficiaries of catalysis research, as better catalysts will reduce carbon emissions.

36 MATERIALS SCIENCE↗

Visualizations of Travel Time Performance Based on Vehicle Reidentification Data

This paper provides a visual reference of the breadth of arterial performance phenomena based on travel time measures obtained from reidentification technology that has proliferated in the past 5 years. These graphical performance measures are revealed through overlay charts and statistical distribution as revealed through cumulative frequency diagrams (CFDs). With overlays of vehicle travel times from multiple days, dominant traffic patterns over a 24-h period are reinforced and reveal the traffic behavior induced primarily by the operation of traffic control at signalized intersections. A cumulative distribution function in the statistical literature provides a method for comparing traffic patterns from various time frames or locations in a compact visual format that provides intuitive feedback on arterial performance. The CFD may be accumulated hourly, by peak periods, or by time periods specific to signal timing plans that are in effect. Combined, overlay charts and CFDs provide visual tools with which to assess the quality and consistency of traffic movement for various periods throughout the day efficiently, without sacrificing detail, which is a typical byproduct of numeric-based performance measures. These methods are particularly effective for comparing before-and-after median travel times, as well as changes in interquartile range, to assess travel time reliability.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Time-resolved Neutron-gamma-ray Data Acquisition for in Situ Subsurface Planetary Geochemistry

The current gamma-ray/neutron instrumentation development effort at NASA Goddard Space Flight Center aims to extend the use of active pulsed neutron interrogation techniques to probe the subsurface elemental composition of planetary bodies in situ. Previous NASA planetary science missions, that used neutron and/or gamma-ray spectroscopy instruments, have relied on neutrons produced from galactic cosmic rays. One of the distinguishing features of this effort is the inclusion of a high intensity 14.1 MeV pulsed neutron generator synchronized with a custom data acquisition system to time each event relative to the pulse. With usually only one opportunity to collect data, it is difficult to set a priori time-gating windows to obtain the best possible results. Acquiring time-tagged, event-by-event data from nuclear induced reactions provides raw data sets containing channel/energy, and event time for each gamma ray or neutron detected. The resulting data set can be plotted as a function of time or energy using optimized analysis windows after the data are acquired. Time windows can now be chosen to produce energy spectra that yield the most statistically significant and accurate elemental composition results that can be derived from the complete data set. The advantages of post-processing gamma-ray time-tagged event-by-event data in experimental tests using our prototype instrument will be demonstrated.

Pulsed neutrongenerator↗

Taxi-Out Time Prediction for Departures at Charlotte Airport Using Machine Learning Techniques

Predicting the taxi-out times of departures accurately is important for improving airport efficiency and takeoff time predictability. In this paper, we attempt to apply machine learning techniques to actual traffic data at Charlotte Douglas International Airport for taxi-out time prediction. To find the key factors affecting aircraft taxi times, surface surveillance data is first analyzed. From this data analysis, several variables, including terminal concourse, spot, runway, departure fix and weight class, are selected for taxi time prediction. Then, various machine learning methods such as linear regression, support vector machines, k-nearest neighbors, random forest, and neural networks model are applied to actual flight data. Different traffic flow and weather conditions at Charlotte airport are also taken into account for more accurate prediction. The taxi-out time prediction results show that linear regression and random forest techniques can provide the most accurate prediction in terms of root-mean-square errors. We also discuss the operational complexity and uncertainties that make it difficult to predict the taxi times accurately.

Safe and efficient surface operations↗

Time-dependent Photoionization Modeling of Warm Absorbers: High-resolution Spectra and Response to Flaring Light Curves

Time-dependent photoionization modeling of warm absorber (WA) outflows in active galactic nuclei can play an important role in understanding the interaction between WAs and the central black hole. The WA may be out of the equilibrium state because of the variable nature of the central continuum. In this paper, with the help of time dependent photoionization modeling, we study how the WA gas properties change with time and how it reacts to changing radiation fields. Incorporating a flaring incident light curve, we investigate the behavior of WAs using a photoionization code that simultaneously and consistently solves the time-dependent equations of level population, heating and cooling, and radiative transfer. We simulate the physical processes in the gas clouds, such as ionization, recombination, heating, cooling, and the transfer of ionizing radiation through the cloud and present high-resolution time-resolved absorption spectra. We demonstrate that time-dependent radiative transfer is important and the calculations that omit this effect quantitatively and systematically underestimate the absorption. Time-dependent photoionization models provide crucial insights into the characteristics of WAs and can be used to constrain their density and spatial distribution.

Astrophysicists↗

Reducing EnergyPlus Run Time For Code Compliance Tools

Integration of the EnergyPlus ™ simulation engine into performance-based code compliance software raises a concern about simulation run time, which impacts timely feedback of compliance results to the user. EnergyPlus annual simulations for proposed and code baseline building models, and mechanical equipment sizing result in simulation run times beyond acceptable limits. This paper presents a study that compares the results of a shortened simulation time period using 4 weeks of hourly weather data (one per quarter), to an annual simulation using full 52 weeks of hourly weather data. Three representative building types based on DOE Prototype Building Models and three climate zones were used for determining the validity of using a shortened simulation run period. Further sensitivity analysis and run time comparisons were made to evaluate the robustness and run time savings of using this approach. The results of this analysis show that the shortened simulation run period provides compliance index calculations within 1% of those predicted using annual simulation results, and typically saves about 75% of simulation run time.

energyplus, simulation, runtime, run time, comchec↗

Time Scale Effects on the Temperature Coefficient of Reactivity

For a nuclear reactor, the temperature coefficient of reactivity (TCR) is of significance for both power control and safety analysis, but it is not always a constant. For example, the TCR may be dependent upon temperature due to Doppler broadening, and may be also dependent upon time scale due to heat transfer and thermal expansion. A fast burst reactor is a favorable nuclear facility to simulate the time scale effects on the TCR. Fast burst reactors are generally unmoderated research reactors of enriched uranium metal or uranium alloys. The neutrons are fast and the Doppler broadening effects can be neglected, and the TCR is mainly contributed by fuel thermal expansion. Fast burst reactors can operate on both steady state power mode and burst power mode. In steady state power mode, the systems are assumed to be in thermal equilibrium. In burst mode, the full width at half maximum (FWHM) of the power is from tens of microseconds to a few milliseconds, and the heat transfer is generally neglected. If FWHM is short enough, thermal expansion will have a time delay due to inertial effect. This paper is aimed to study the exact time scale effects on the TCR due to thermal expansion. The TCR contributed by the Doppler broadening effects was neglected, because it is relatively small (The k{sub eff} as a function of temperature was also calculated using the Monte Carlo particle transport code JMCT by our group, and no definite difference due to the temperature change was obtained near room temperature), and there is no method to evaluate the time scale dependence of the Doppler broadening effects yet. In the time scale from 1 x 10{sup -6} s to 1 x 10{sup 5} s, the TCR of a Godiva-like spherical fast burst reactor was calculated with perturbation theory. A Godiva-like spherical fast burst reactor was studied, the calculation of the time scale effects on TCR involved thermal conduction, thermoelasticity and reactivity variation analysis. Both the thermal and the thermoelastic problems were solved using ANSYS software. ANSYS is software implementation of finite element simulations, which is widely used in engineering field. The reactivity variation due to thermal expansion was calculated with perturbation theory.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Linking age, survival, and transit time distributions

Abstract Although the concepts of age, survival, and transit time have been widely used in many fields, including population dynamics, chemical engineering, and hydrology, a comprehensive mathematical framework is still missing. Here we discuss several relationships among these quantities by starting from the evolution equation for the joint distribution of age and survival, from which the equations for age and survival time readily follow. It also becomes apparent how the statistical dependence between age and survival is directly related to either the age dependence of the loss function or the survival‐time dependence of the input function. The solution of the joint distribution equation also allows us to obtain the relationships between the age at exit (or death) and the survival time at input (or birth), as well as to stress the symmetries of the various distributions under time reversal. The transit time is then obtained as a sum of the age and survival time, and its properties are discussed along with the general relationships between their mean values. The special case of steady state case is analyzed in detail. Some examples, inspired by hydrologic applications, are presented to illustrate the theory with the specific results.

Calabrese, Salvatore↗

Perioperative Timing of Infliximab and the Risk of Serious Infection After Elective Hip and Knee Arthroplasty

Objective The optimal timing of tumor necrosis factor antagonists before elective surgery is unknown. This study evaluated the association between infliximab timing and serious infection after elective hip or knee arthroplasty. Methods A retrospective cohort study evaluated US Medicare patients with rheumatoid arthritis, inflammatory bowel disease, psoriasis, psoriatic arthritis, or ankylosing spondylitis who received infliximab within 6 months of elective knee or hip arthroplasty from 2007 to 2013. Propensity‐adjusted analyses examined whether infliximab stop timing (time between the most recent infusion and surgery) was associated with hospitalized infection within 30 days or prosthetic joint infection ( PJI ) within 1 year. Results Hospitalized infection within 30 days occurred after 270 of 4,288 surgeries (6.3%). Infliximab stop timing <4 weeks versus 8–12 weeks was not associated with an increase in infection within 30 days (propensity‐adjusted odds ratio [ OR ] 0.90 [95% confidence interval (95% CI ) 0.60–1.34]). The rate of PJI was 2.9 per 100 person‐years and was not increased in patients with stop timing <4 weeks versus 8–12 weeks (hazard ratio [ HR ] 0.98 [95% CI 0.52–1.87]). Glucocorticoid dosage >10 mg/day was associated with increased risk of 30‐day infection ( OR 2.11 [95% CI 1.30–3.40]) and PJI ( HR 2.70 [95% CI 1.30–5.60]). Other risk factors for infection included elderly age, comorbidities, revision surgery, and previous hospitalized infection. Conclusion Administering infliximab within 4 weeks of elective knee or hip arthroplasty was not associated with a higher risk of short‐ or long‐term serious infection compared to withholding infliximab for longer time periods. Glucocorticoid use, especially >10 mg/day, was associated with an increased infection risk.

George, Michael D.↗

Quantum complexity of time evolution with chaotic Hamiltonians

We study the quantum complexity of time evolution in large-N chaotic systems, with the SYK model as our main example. This complexity is expected to increase linearly for exponential time prior to saturating at its maximum value, and is related to the length of minimal geodesics on the manifold of unitary operators that act on Hilbert space. Using the Euler-Arnold formalism, we demonstrate that there is always a geodesic between the identity and the time evolution operator e -iHt whose length grows linearly with time. This geodesic is minimal until there is an obstruction to its minimality, after which it can fail to be a minimum either locally or globally. We identify a criterion — the Eigenstate Complexity Hypothesis (ECH) — which bounds the overlap between offdiagonal energy eigenstate projectors and the k-local operators of the theory, and use it to argue that the linear geodesic will at least be a local minimum for exponential time. We show numerically that the large-N SYK model (which is chaotic) satisfies ECH and thus has no local obstructions to linear growth of complexity for exponential time, as expected from holographic duality. In contrast, we also study the case with N = 2 fermions (which is integrable) and find short-time linear complexity growth followed by oscillations. Our analysis relates complexity to familiar properties of physical theories like their spectra and the structure of energy eigenstates and has implications for the hypothesized computational complexity class separations PSPACE * BQP/poly and PSPACE * BQSUBEXP/subexp, and the “fast-forwarding” of quantum Hamiltonians.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Space-time generalization of mutual information

The mutual information characterizes correlations between spatially separated regions of a system. Yet, in experiments we often measure dynamical correlations, which involve probing operators that are also separated in time. Here, we introduce a space-time generalization of mutual information which, by construction, satisfies several natural properties of the mutual information and at the same time characterizes correlations across subsystems that are separated in time. In particular, this quantity, that we call the space-time mutual information, bounds all dynamical correlations. We construct this quantity based on the idea of the quantum hypothesis testing. As a by-product, our definition provides a transparent interpretation in terms of an experimentally accessible setup. We draw connections with other notions in quantum information theory, such as quantum channel discrimination. Finally, we study the behavior of the space-time mutual information in several settings and contrast its long-time behavior in many-body localizing and thermalizing systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Constant-Momentum Acceleration Time-of-Flight Mass Spectrometry with Energy Focusing

Fundamental aspects of constant--momentum acceleration time-­of-­flight mass spectrometry (CMA-TOFMS) are explored as a means to improve mass resolution. By accelerating all ions to the same momentum, rather than to the same energy, the effects of the initial ion spatial and energy distributions upon the total ion flight time are decoupled. This decoupling permits the initial spatial distribution of ions in the acceleration region to be optimized independently and energy focus, including ion turn-around-time error, to be accomplished with a linear-field reflectron. Constant-momentum acceleration also linearly disperses ions across time according to mass-to-change (m/z) ratio, instead of the quadratic relationship between flight time and m/z found in conventional TOFMS. Here, CMA-TOFMS is shown to achieve simultaneous spatial and energy focusing over a selected portion of the mass spectrum. An orthogonal-acceleration time-of-flight outfitted with a reduced-pressure dc glow discharge (GD) ionization source is used to demonstrate CMA-TOFMS with atomic ions. The influence of experimental parameters such as the amplitude and width of the time-dependent CMA pulse on mass resolution is investigated, and a useful CMA-TOFMS focusing window of 2 to 18 Da is found for GD-CMA-TOFMS.

Dennis, Elise A.↗

Substrate-Coated Illumination Droplet Spray Ionization: Real-Time Monitoring of Photocatalytic Reactions

Real-time monitoring of photocatalytic reactions facilitates the elucidation of the mechanisms of the reactions. However, suitable tools for real-time monitoring are lacking. Herein, a novel method based on droplet spray ionization named substrate-coated illumination droplet spray ionization (SCI-DSI) for direct analysis of photocatalytic reaction solution is reported. SCI-DSI addresses many of the analytical limitations of electrospray ionization (ESI) for analysis of photocatalytic-reaction intermediates, and has potential for both in situ analysis and real-time monitoring of photocatalytic reactions. In SCI-DSI-mass spectrometry (MS), a photocatalytic reaction occurs by loading sample solutions onto the substrate-coated cover slip and by applying UV light above the modified slip; one corner of this slip adjacent to the inlet of a mass spectrometer is the high-electric-field location for launching a charged-droplet spray. After both testing and optimizing the performance of SCI-DSI, the value of this method for in situ analysis and real-time monitoring of photocatalytic reactions was demonstrated by the removal of cyclophosphamide (CP) in TiO{sub 2}/UV. Reaction times ranged from seconds to minutes, and the proposed reaction intermediates were captured and identified by tandem mass spectrometry. Moreover, the free hydroxyl radical (·OH) was identified as the main radicals for CP removal. These results show that SCI-DSI is suitable for in situ analysis and real-time monitoring of CP removal under TiO{sub 2}-based photocatalytic reactions. SCI-DSI is also a potential tool for in situ analysis and real-time assessment of the roles of radicals during CP removal under TiO{sub 2}-based photocatalytic reactions.Graphical Abstract .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗