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At least 397 records · Page 22

Benchmarking of alignment-free sequence comparison methods

Background: Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Results: Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events. Conclusion: The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions

59 BASIC BIOLOGICAL SCIENCES↗

Towards the Development of Real-Time Normalized Burn Ratio (NBR) and Delta NBR Imagery from GOES-16/17 and S-NPP

Burned landscapes present difficult hydrologic forecasting challenges for National Weather Service Offices. Burned soils and landscapes can be conducive to the development of flash flooding and landslides from heavy precipitation events. The severity of the burn scar can be directly related to the risk for debris flows and flash flooding. Burned Area Reflectance Classification (BARC) map is generated to indicate the degree of burn severity, which is generated initially by high-resolution satellite imagery from sources such as Landsat, and later by labor-intensive efforts conducted at the burn scar by Burned Area Emergency Response (BAER) teams. The challenge for operational meteorologists is that these sources of information are not readily available in near real-time. Landsat imagery, for example, may only be available about once every eight days, and cloudy conditions can obstruct the observation of the burn scar during a single pass. BAER teams cannot conduct assessments until the wildfire has been at least 40 percent contained (up to 80 percent in some regions), and the process itself can take further days to weeks to complete depending on a number of factors. To help remedy this lapse in knowledge, NASA SPoRT has developed the generation of NBR imagery in the Advanced Weather Interactive Processing System (AWIPS) using data from the operational GOES 16 and 17 satellites and S-NPP. This presentation will discuss the development of the GOES- and SNPP-derived NBR and dNBR imagery and their initial evaluation by real-time decision makers.

Berndt, Emily↗

A Systematic Exploration of Kilonova Candidates from Neutron Star Mergers during the Third Gravitational-wave Observing Run

We present a comprehensive analysis of 653 optical candidate counterparts reported during the third gravitational-wave (GW) observing run. Our sample concentrates on candidates from the 15 events (published in GWTC-2, GWTC-3, or not retracted on GraceDB) that had a >1% chance of including a neutron star in order to assess their viability as true kilonovae. In particular, we leverage tools available in real time, including pre-merger detections and cross-matching with catalogs (i.e., point-source, variable-star, quasar and host-galaxy redshift data sets), to eliminate 65% of candidates in our sample. We further employ spectroscopic classifications, late-time detections, and light-curve behavior analyses and conclude that 66 candidates remain viable kilonovae. These candidates lack sufficient information to determine their classifications, and the majority would require luminosities greater than that of AT 2017gfo. Pre-merger detections in public photometric survey data and comparison of cataloged host-galaxy redshifts with the GW event distances are critical to incorporate into vetting procedures, as these tools eliminated >20% and >30% of candidates, respectively. We expect that such tools that leverage archival information will significantly reduce the strain on spectroscopic and photometric follow-up resources in future observing runs. Finally, we discuss the critical role prompt updates from GW astronomers to the EM community play in reducing the number of candidates requiring vetting.

79 ASTRONOMY AND ASTROPHYSICS↗

Flood Mapping of Recent Major Hurricane Events with Synthetic Aperture Radar, Commercial Imaging, and Aerial Observations

Floodwater mapping is an important remote sensing process that is used for disaster response, recovery, and damage assessment practices. Developing a system to read in Synthetic Aperture Radar (SAR) data and perform land cover classification will allow for the production of near real-time inundation mapping, enabling government and emergency response entities to get a preliminary idea of the situation. SAR is a unique remote sensing tool. Data in this project was obtained by NASA Jet Propulsion Laboratory’s Uninhabited Aerial Vehicle SAR (UAVSAR), an L-band radar mounted to a Gulfstream III jet. Data collected by UAVSAR is similar to what will be available from the NASA-Indian Space Research Organization (NISAR) mission starting in early 2022. Using Python and ArcGIS applications, a model was developed using training samples taken from NOAA post-event aerial photography and UAVSAR data gathered in the aftermath of Hurricane Florence in September 2018.

Melancon, Alexander M.↗

PAIReD jet: A multi-pronged resonance tagging strategy across all Lorentz boosts

We propose a new approach of jet-based event reconstruction that aims to optimally exploit correlations between the products of a hadronic multi-pronged decay across all Lorentz boost regimes. The new approach utilizes clustered small-radius jets as seeds to define unconventional jets, referred to as PAIReD jets. The constituents of these jets are subsequently used as inputs to machine learning-based algorithms to identify the flavor content of the jet. We demonstrate that this approach achieves higher efficiencies in the reconstruction of signal events containing heavy-flavor jets compared to other event reconstruction strategies at all Lorentz boost regimes. Classifiers trained on PAIReD jets also have significantly better background rejections compared to those based on traditional event reconstruction approaches using small-radius jets at low Lorentz boost regimes. The combined effect of a higher signal reconstruction efficiency and better classification performance results in a two to four times stronger rejection of light-flavor jets compared to conventional strategies at low Lorentz-boosts, and rejection rates similar to classifiers based on large-radius multi-pronged jets at high Lorentz-boost regimes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A hybrid neural architecture: Online attosecond x-ray characterization

The emergence of high-repetition-rate x-ray free-electron lasers (XFELs), such as SLAC’s LCLS-II, serves as our canonical example for autonomous controls that necessitate high-throughput diagnostics paired with streaming computational pipelines capable of single-shot analysis with extremely low latency. We present the deterministic characterization with an integrated parallelizable hybrid resolver architecture, a hybrid machine learning framework designed for fast, accurate analysis of XFEL diagnostics using angular streaking-based sinogram images. This architecture integrates convolutional neural networks and bidirectional long short-term memory models to denoise input, identify x-ray sub-spike features, and extract sub-spike relative delays with sub-30 attosecond temporal resolution. Deployed on low-latency hardware, it achieves over 10 kHz throughput with 168.3 μs inference latency, indicating scalability to 14 kHz with field-programmable gate array integration. By transforming regression tasks into classification problems and leveraging optimized error encoding, we achieve high precision with low-latency performance that is critical for real-time streaming event selection and experimental control feedback signals. This represents a key development in real-time control pipelines for next-generation autonomous science, generally, and high repetition-rate x-ray experiments in particular.

Accelerator Physics (physics.acc-ph)↗

A simple framework to characterize land aridity based on surface energy partitioning regimes

Land aridity is often characterized by the aridity index (AI), which does not account for land surface water-energy interactions that are crucially important in determining regional climate. Such interactions can be captured by the evaporative fraction (EF, ratio of evapotranspiration to available energy) regimes. As EF is subject to energy and water limitations in humid and dry areas, respectively, EF regimes may be used to characterize land aridity to account for the influence of complex land characteristics and their impact on water availability. Here, we propose a simple framework to characterize land aridity by statistically ranking the coupling strength between EF and surface energy and water terms. The framework is demonstrated using gridded data and compared with AI over the U.S. and China. Results show that regionalization of aridity zones based on EF regimes and a two-tiered classification scheme may provide information such as surface energy and water variability complementary to the background aridity depicted by AI, with implications for extreme events.

54 ENVIRONMENTAL SCIENCES↗

Air Classification of Forest Residue for Tissue and Ash Separation Efficiency

The goal of this Case Study was to evaluate the performance of air classification of logging residues toward meeting conversion CMAs for carbon and ash contents, as compared to the static status quo Base Case system in which the residues are first dried and then ground in a hammer mill with a 6 mm screen and fines less than 1.18 mm are removed. Also considered were moisture and ash impacts on throughput and Overall Operating Effectiveness (OOE), as well as delivered feedstock cost and minimum fuel selling price (MFSP). Laboratory data on the impacts of fan speed and moisture content on the separation efficiency of soil ash, needles and bark from white wood were received from FCIC Subtask 5.2: Preprocessing, High Temperature Conversion Preprocessing (Jordan Klinger and Tiasha Bhattacharjee, INL). Average throughput and energy consumption data were obtained from the Bioenergy Feedstock National User Facility (BFNUF) (Neal Yancey, INL) for the same air classifier. These data were utilized to develop the necessary response surface equations to perform throughput analysis using discrete event simulation. Feedstock-Conversion Interface Consortium. Because the Base Case status quo system utilizes drying prior to grinding, we modeled the Case Study with drying prior to air classification and subsequent grinding of the separated white wood to isolate the individual quality and cost impacts of air classification relative to the Base Case system.

CMA↗

Self-Organizing Map-Based Resilience Quantification and Resilient Control of Distribution Systems Under Extreme Events

Due to climate change, extreme weather events are occurring more frequently and with increasing impact. This trend poses a significant challenge for distribution system operators (DSO) to ensure that there is uninterrupted power supply to critical loads in their networks. To embed resilience into DSO's decision-making, resilience needs to be first quantified and then integrated into the system-level optimization. Therefore, this paper first develops a novel self-organizing map (SOM) based method (called SomRes) to quantify the time-varying resilience index of a system that can leverage the powerful classification property of SOMs and removes some of the disadvantages of subjective weight assignment methods. Using SomRes, a resilient resource allocation and operational dispatch algorithm is further developed to enhance system resilience against extreme events by considering the SomRes resilience index directly as the feedback. Here, the proposed resilience quantification approach is benchmarked with a state-of-the-art approach and the efficacy of the proposed resilient dispatch algorithm is demonstrated through several deterministic and statistical case studies on the IEEE 123-bus distribution system. Simulation studies show that the proposed SomRes quantification method is an appropriate indicator of system resilience, and the resilient resource allocation and dispatch strategy can significantly reduce critical load shedding under varying event propagation scenarios.

24 POWER TRANSMISSION AND DISTRIBUTION↗

The Heraklion Extragalactic Catalogue (HECATE): A Value-added Galaxy Catalogue for Multimessenger Astrophysics

We present the Heraklion Extragalactic Catalogue, or HECATE, an all-sky value-added galaxy catalogue, aiming to facilitate present and future multiwavelength and multi messenger studies in the local Universe. It contains 204 733 galaxies up to a red shift of 0.047 (D200 Mpc), and it is>50 per cent complete in terms of the B-band luminosity density at distances in the0–170 Mpc range. By incorporating and homogenizing data from astronomical data bases and multiwavelength surveys, the catalogue offers positions, sizes, distances, morphological classifications, star formation rates, stellar masses, metallicities, and nuclear activity classifications. This wealth of information can enable a wide range of applications, such as (i) demographic studies of extragalactic sources, (ii) initial characterization of transient events, and (iii) searches for electromagnetic counterparts of gravitational-wave events. The catalogue is publicly available to the community at a dedicated portal, which will also host future extensions in terms of the covered volume and data products.

K Kovlakas↗

Assessing the Effectiveness of Generalized Likelihood Ratio Test Detector Schemes in Seismic Event Detection and the Avoidance of Nontarget Signals

Cross-correlation techniques have played a long-standing and pivotal role in seismic event monitoring. However, the performance of correlation-based detectors is challenged by nuisance seismicity, or nontarget signals. Such detections are a problem when the mission is to automatically map events to the correct source region. Using aftershocks of the 2014 $M_w$ 6.0 South Napa, California, earthquake, we demonstrate the effectiveness of utilizing a dynamic correlation processor framework in a generalized likelihood ratio test (GLRT) detector configuration to minimize nontarget detections. A GLRT maximizes a detection statistic with respect to one or more unknown parameters. In this case, the detection statistic is a template signal match against the waveform in a window sliding over a data stream, and the unknown parameter is an index variable indicating group membership of the template event or events. Detected events are assigned to the event group that yields the largest detection statistic. In this work, our results show that a GLRT detector will outperform a suite of independently operating correlation and subspace detectors in terms of having a lower nontarget detection rate at a given missed detection rate. We also show that a GLRT detector composed of a few high-rank subspace detectors has a slightly higher nontarget detection rate, but a significantly lower missed detection rate, than a GLRT detector composed of many low-rank subspace detectors. The high-rank GLRT configuration produced impressive results even with marginal data (single channel, single station, and very low time bandwidth product), which bodes well for the utility of building efficient aftershock classification systems and global monitoring systems at larger scales. However, future work is required to assess performance at the regional scale and to assess the performance of the system at detecting target events not used in the detector template creation.

58 GEOSCIENCES↗

Precipitation regime classification for the Mojave Desert: Implications for fire occurrence

Mojave Desert ecosystem processes are dependent upon the amount and seasonality of precipitation. Multi-decadal periods of drought or above-average rainfall affect landscape vegetation condition, biomass and susceptibility to fire. The seasonality of precipitation events can also affect the likelihood of lightning, a key ignition source for fires. To develop an understanding of precipitation regimes and fire patterns we used monthly average precipitation data and GIS data representing burned areas from 1971-2010. We applied a K-means cluster analysis to the monthly precipitation data identifying three distinct precipitation seasons; winter (October – March), spring (April-June) and summer (July-September) and four discrete precipitation regimes within the Mojave ecoregion.

classification↗

Long-Term Retrievals of Cloud Type and Fair-Weather Shallow Cumulus Events at the ARM SGP Site

Abstract A long-term climatology of classified cloud types has been generated for 13 years (1997–2009) over the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) site for seven cloud categories: low clouds, congestus, deep convection, altocumulus, altostratus, cirrostratus/anvil, and cirrus. The classification was based on the cloud macrophysical quantities of cloud top, cloud base, and physical thickness of cloud layers, as measured by active sensors such as the millimeter-wavelength cloud radar (MMCR) and micropulse lidar (MPL). Climate variability of cloud characteristics has been examined using the 13-yr cloud-type retrieval. Low clouds and cirrus showed distinct diurnal and seasonal cycles. Total cloud occurrence followed the variation of low clouds, with a diurnal peak in early afternoon and a seasonal maximum in late winter. Additionally, further work has been done to identify fair-weather shallow cumulus (FWSC) events for 9 years (2000–08). Periods containing FWSC, a subcategory of clouds classified as low clouds, were produced using cloud fraction information from a total-sky imager and ceilometer. The identified FWSC periods in our study show good agreement with manually identified FWSC, missing only 6 cases out of 70 possible events during the spring to summer seasons (May–August).

54 ENVIRONMENTAL SCIENCES↗

Frequency of Fast, Narrow Gamma-ray Bursts and Burst Classification

Evidence from the Vela satellites that very brief, approximately 0.1 s, gamma-ray bursts constitute a class distinct from the longer, highly structured bursts has been strengthened by the results of the Venera 11 and 12 KKONUS experiments. The Goodard ISEE-3 gamma-ray burst spectrometer, utilizing a trigger criterion which is more likely to be independent of duration than previous experiments, detected a sample of events which enhances this bimodal distribution. The ISEE-3 result is corroborated by an increase in the frequency of detection of short bursts in the KONUS 13/14 database over KONUS 11/12, an effect attributable to the use of a shorter trigger integration time in the later experiments. Considerations such as repeating bursters complicate a simple dichotomous classification of gamma-ray bursts.

Norris, J. P.↗

Example of Occupational Surveillance in a Telemedicine Setting: Application of Epidemiologic Methods at NASA Johnson Space Center

In 2010, NASA implemented Lifetime Surveillance of Astronaut Health, a formal occupational surveillance program for the U.S. astronaut corps. Because of the nature of the space environment, space medicine presents unique challenges and opportunities for epidemiologists. One such example is the use of telemedicine while crewmembers are in flight, where the primary source of information about crew health is verbal communication between physicians and their crewmembers. Due to restricted medical capabilities, the available health information is primarily crewmember report of signs and symptoms, rather than diagnoses. As epidemiologists at NASA, Johnson Space Center, we have shifted our paradigm from tracking diagnoses based on traditional terrestrial clinical practice to one in which we also incorporate reported symptomology as potential antecedents of disease. In this presentation we describe how characterization of reported signs and symptoms can be used to establish incidence rates for inflight immunologic events. We describe interdisciplinary data sources of information that are used in combination with medical information to analyze the data. We also delineate criteria for symptom classification inclusion. Finally, we present incidence tables and graphs to illustrate the final outcomes. Using signs and symptoms reported via telemedicine, the epidemiologists provide summary evidence regarding incidence of potential inflight medical conditions. These results inform our NASA physicians and scientists, and support evaluation of the occupational health risks associated with spaceflight.

Babiak-Vazquez, Adriana↗

Iterative Strategies for Aftershock Classification in Automatic Seismic Processing Pipelines

We report aftershock sequences following very large earthquakes present enormous challenges to near-real-time generation of seismic bulletins. The increase in analyst resources needed to relocate an inflated number of events is compounded by failures of phase-association algorithms and a significant deterioration in the quality of underlying, fully automatic event bulletins. Current processing pipelines were designed a generation ago, and, due to computational limitations of the time, are usually limited to single passes over the raw data. With current processing capability, multiple passes over the data are feasible. Processing the raw data at each station currently generates parametric data streams that are then scanned by a phase-association algorithm to form event hypotheses. We consider the scenario in which a large earthquake has occurred and propose to define a region of likely aftershock activity in which events are detected and accurately located, using a separate specially targeted semiautomatic process. This effort may focus on so-called pattern detectors, but here we demonstrate a more general grid-search algorithm that may cover wider source regions without requiring waveform similarity. Given many well-located aftershocks within our source region, we may remove all associated phases from the original detection lists prior to a new iteration of the phase-association algorithm. We provide a proof-of-concept example for the 2015 Gorkha sequence, Nepal, recorded on seismic arrays of the International Monitoring System. Even with very conservative conditions for defining event hypotheses within the aftershock source region, we can automatically remove about half of the original detections that could have been generated by Nepal earthquakes and reduce the likelihood of false associations and spurious event hypotheses. Lastly, further reductions in the number of detections in the parametric data streams are likely, using correlation and subspace detectors and/or empirical matched field processing.

58 GEOSCIENCES↗

SU-E-T-630: Predictive Modeling of Mortality, Tumor Control, and Normal Tissue Complications After Stereotactic Body Radiotherapy for Stage I Non-Small Cell Lung Cancer

Purpose: While rates of local control have been well characterized after stereotactic body radiotherapy (SBRT) for stage I non-small cell lung cancer (NSCLC), less data are available characterizing survival and normal tissue toxicities, and no validated models exist assessing these parameters after SBRT. We evaluate the reliability of various machine learning techniques when applied to radiation oncology datasets to create predictive models of mortality, tumor control, and normal tissue complications. Methods: A dataset of 204 consecutive patients with stage I non-small cell lung cancer (NSCLC) treated with stereotactic body radiotherapy (SBRT) at the University of Pennsylvania between 2009 and 2013 was used to create predictive models of tumor control, normal tissue complications, and mortality in this IRB-approved study. Nearly 200 data fields of detailed patient- and tumor-specific information, radiotherapy dosimetric measurements, and clinical outcomes data were collected. Predictive models were created for local tumor control, 1- and 3-year overall survival, and nodal failure using 60% of the data (leaving the remainder as a test set). After applying feature selection and dimensionality reduction, nonlinear support vector classification was applied to the resulting features. Models were evaluated for accuracy and area under ROC curve on the 81-patient test set. Results: Models for common events in the dataset (such as mortality at one year) had the highest predictive power (AUC = .67, p < 0.05). For rare occurrences such as radiation pneumonitis and local failure (each occurring in less than 10% of patients), too few events were present to create reliable models. Conclusion: Although this study demonstrates the validity of predictive analytics using information extracted from patient medical records and can most reliably predict for survival after SBRT, larger sample sizes are needed to develop predictive models for normal tissue toxicities and more advanced machine learning methodologies need be consider in the future.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Thermal Evolution and Radiative Output of Solar Flares Observed by the EUV Variability Experiment (EVE)

This paper describes the methods used to obtain the thermal evolution and radiative output during solar flares as observed by the Extreme u ltraviolet Variability Experiment (EVE) onboard the Solar Dynamics Ob servatory (SDO). Presented and discussed in detail are how EVE measur ements, due to its temporal cadence, spectral resolution and spectral range, can be used to determine how the thermal plasma radiates at v arious temperatures throughout the impulsive and gradual phase of fla res. EVE can very accurately determine the radiative output of flares due to pre- and in-flight calibrations. Events are presented that sh ow the total radiated output of flares depends more on the flare duration than the typical GOES X-ray peak magnitude classification. With S DO observing every flare throughout its entire duration and over a la rge temperature range, new insights into flare heating and cooling as well as the radiative energy release in EUV wavelengths support exis ting research into understanding the evolution of solar flares.

Chamberlin, P. C.↗