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At least 685 records · Page 38

Anomaly Detection in Dynamic Networks

Anomaly detection in dynamic communication networks has many important security applications. These networks can be extremely large and so detecting any changes in their structure can be computationally challenging; hence, computationally fast, parallelisable methods for monitoring the network are paramount. For this reason the methods presented here use independent node and edge based models to detect locally anomalous substructures within communication networks. As a first stage, the aim is to detect changes in the data streams arising from node or edge communications. Throughout the thesis simple, conjugate Bayesian models for counting processes are used to model these data streams. A second stage of analysis can then be performed on a much reduced subset of the network comprising nodes and edges which have been identified as potentially anomalous in the first stage. The first method assumes communications in a network arise from an inhomogeneous Poisson process with piecewise constant intensity. Anomaly detection is then treated as a changepoint problem on the intensities. The changepoint model is extended to incorporate seasonal behavior inherent in communication networks. This seasonal behavior is also viewed as a changepoint problem acting on a piecewise constant Poisson process. In a static time frame, inference is made on this extended model via a Gibbs sampling strategy. In a sequential time frame, where the data arrive as a stream, a novel, fast Sequential Monte Carlo (SMC) algorithm is introduced to sample from the sequence of posterior distributions of the change points over time. A second method is considered for monitoring communications in a large scale computer network. The usage patterns in these types of networks are very bursty in nature and don’t fit a Poisson process model. For tractable inference, discrete time models are considered, where the data are aggregated into discrete time periods and probability models are fitted to the communication counts. In a sequential analysis, anomalous behavior is then identified from outlying behavior with respect to the fitted predictive probability models. Seasonality is again incorporated into the model and is treated as a changepoint model on the transition probabilities of a discrete time Markov process. Second stage analytics are then developed which combine anomalous edges to identify anomalous substructures in the network.

97 MATHEMATICS AND COMPUTING↗

A Model Tree Generator (MTG) Framework for Simulating Hydrologic Systems: Application to Reservoir Routing

Data-driven algorithms have been widely used as effective tools to mimic hydrologic systems. Unlike black-box models, decision tree algorithms offer transparent representations of systems and reveal useful information about the underlying process. A popular class of decision tree models is model tree (MT), which is designed for predicting continuous variables. Most MT algorithms employ an exhaustive search mechanism and a pre-defined splitting criterion to generate a piecewise linear model. However, this approach is computationally intensive, and the selection of the splitting criterion can significantly affect the performance of the generated model. These drawbacks can limit the application of MTs to large datasets. To overcome these shortcomings, a new flexible Model Tree Generator (MTG) framework is introduced here. MTG is equipped with several modules to provide a flexible, efficient, and effective tool for generating MTs. The application of the algorithm is demonstrated through simulation of controlled discharge from several reservoirs across the Contiguous United States (CONUS).

54 ENVIRONMENTAL SCIENCES↗

Coupled Electron-Photon Monte Carlo Radiation Transport for Next-Generation Computing Systems

Traditional Monte Carlo particle transport codes are expected to run inefficiently on next-generation architectures as they are memory-intensive and highly divergent. Since electrons and photons also behave differently, the future for coupled electron-photon radiation transport looks even worse. This project describes preliminary efforts to improve the performance of Monte Carlo particle transport codes when using accelerators like the graphics processing unit (GPU). Two key issues are addressed: how to handle memory-intensive tallies, and how to reduce divergence. Tallying on the GPU can be done efficiently by post-processing particle data, or by using a feature called warp shuffle for summing scores in parallel during the simulation. Reducing divergence is possible by using an event-based algorithm for particle tracking instead of the traditional history-based one. Although performance tests presented in this work show that the history-based algorithm generally outperformed the event-based one for simple problems, this outcome will likely change as the complexity of the code increases.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

WinPSSP : a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

The direct-space methods software Powder Structure Solution Program ( PSSP ) [Pagola & Stephens (2010). J. Appl. Cryst. 43 , 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs. WinPSSP is a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinates into the Rietveld analysis software GSAS. WinPSSP performance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.

60 APPLIED LIFE SCIENCES↗

CMed: Crowd Analytics for Medical Imaging Data

In this work, we present a visual analytics framework, CMed, for exploring medical image data annotations acquired from crowdsourcing. CMed can be used to visualize, classify, and filter crowdsourced clinical data based on a number of different metrics such as detection rate, logged events, and clustering of the annotations. CMed provides several interactive linked visualization components to analyze the crowd annotation results for a particular video and the associated workers. Additionally, all results of an individual worker can be inspected using multiple linked views in our CMed framework. We allow a crowdsourcing application analyst to observe patterns and gather insights into the crowdsourced medical data, helping him/her design future crowdsourcing applications for optimal output from the workers. We demonstrate the efficacy of our framework with two medical crowdsourcing studies: polyp detection in virtual colonoscopy videos and lung nodule detection in CT thin-slab maximum intensity projection videos. We also provide experts' feedback to show the effectiveness of our framework. Lastly, we share the lessons we learned from our framework with suggestions for integrating our framework into a clinical workflow.

97 MATHEMATICS AND COMPUTING↗

Robust Machine Learning Inference from X-ray Absorption Near Edge Spectra through Featurization

X-ray absorption spectroscopy (XAS) is a commonly employed technique for characterizing functional materials. In particular, X-ray absorption near edge spectra (XANES) encode local coordination and electronic information, and machine learning approaches to extract this information are of significant interest. To date, most ML approaches for XANES have primarily focused on using the raw spectral intensities as input, overlooking the potential benefits of incorporating spectral transformations and dimensionality reduction techniques into ML predictions. Here, in this work, we focused on systematically comparing the impact of different featurization methods on the performance of ML models for XAS analysis. We evaluated the classification and regression capabilities of these models on computed data sets and validated their performance on previously unseen experimental data sets. Our analysis revealed an intriguing discovery: the cumulative distribution function feature achieves both high prediction accuracy and exceptional transferability. This remarkably robust performance can be attributed to its tolerance to horizontal shifts in the spectra, which is crucial when validating models using experimental data. While this work exclusively focuses on XANES analysis, we anticipate that the methodology presented here will hold promise as a versatile asset to the broader spectroscopy community.

36 MATERIALS SCIENCE↗

Mn IV -Oxo complex of a bis(benzimidazolyl)-containing N5 ligand reveals different reactivity trends for Mn IV -oxo than Fe IV -oxo species

Using the pentadentate ligand (N-bis(1-methyl-2-benzimidazolyl)methyl-N-(bis-2-pyridylmethyl)amine, 2pyN2B), presenting two pyridyl and two (N-methyl)benzimidazolyl donor moieties in addition to a central tertiary amine, new Mn II and Mn IV -oxo complexes were generated and characterized. The [Mn IV (O)(2pyN2B)] 2+ complex showed spectroscopic signatures (i.e., electronic absorption band maxima and intensities, EPR signals, and Mn K-edge X-ray absorption edge and near-edge data) similar to those observed for other MnIV-oxo complexes with neutral, pentadentate N 5 supporting ligands. The near-IR electronic absorption band maximum of [Mn IV (O)(2pyN2B)] 2+ , as well as DFT-computed metric parameters, are consistent with the equatorial (N-methyl)benzimidazolyl ligands being stronger donors to the MnIV center than the pyridyl and quinolinyl ligands found in analogous MnIV-oxo complexes. The hydrogen- and oxygen-atom transfer reactivities of [Mn IV (O)(2pyN2B)] 2+ were assessed through reactions with hydrocarbons and thioanisole, respectively. When compared with related Mn IV -oxo adducts, [Mn IV (O)(2pyN2B)] 2+ showed muted reactivity in hydrogen-atom transfer reactions with hydrocarbons. This result stands in contrast to observations for the analogous Fe IV -oxo complexes, where [Fe IV (O)(2pyN2B)] 2+ was found to be one of the more reactive members of its class.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Constraint methods that accelerate free-energy simulations of biomolecules

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann’s law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

IMG/M: integrated genome and metagenome comparative data analysis system

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review(ER) companion system (IMG/M ER: https://img.jgi.doe.gov/ mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.

59 BASIC BIOLOGICAL SCIENCES↗

SU-D-18A-02: Towards Real-Time On-Board Volumetric Image Reconstruction for Intrafraction Target Verification in Radiation Therapy

Purpose: To expedite on-board volumetric image reconstruction from limited-angle kV—MV projections for intrafraction verification. Methods: A limited-angle intrafraction verification (LIVE) system has recently been developed for real-time volumetric verification of moving targets, using limited-angle kV—MV projections. Currently, it is challenged by the intensive computational load of the prior-knowledge-based reconstruction method. To accelerate LIVE, we restructure the software pipeline to make it adaptable to model and algorithm parameter changes, while enabling efficient utilization of rapidly advancing, modern computer architectures. In particular, an innovative two-level parallelization scheme has been designed: At the macroscopic level, data and operations are adaptively partitioned, taking into account algorithmic parameters and the processing capacity or constraints of underlying hardware. The control and data flows of the pipeline are scheduled in such a way as to maximize operation concurrency and minimize total processing time. At the microscopic level, the partitioned functions act as independent modules, operating on data partitions in parallel. Each module is pre-parallelized and optimized for multi-core processors (CPUs) and graphics processing units (GPUs). Results: We present results from a parallel prototype, where most of the controls and module parallelization are carried out via Matlab and its Parallel Computing Toolbox. The reconstruction is 5 times faster on a data-set of twice the size, compared to recently reported results, without compromising on algorithmic optimization control. Conclusion: The prototype implementation and its results have served to assess the efficacy of our system concept. While a production implementation will yield much higher processing rates by approaching full-capacity utilization of CPUs and GPUs, some mutual constraints between algorithmic flow and architecture specifics remain. Based on a careful analysis of the prototype performance, it will be feasible to resolve such issues through appropriate algorithmic modifications or special-purpose hardware, thus enabling target verification in seconds with the LIVE system. This work was partially supported by a research grant from Varian Medical Systems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Non-Exchangeability of Running vs. Other Exercise in Their Association with Adiposity, and Its Implications for Public Health Recommendations

Current physical activity recommendations assume that different activities can be exchanged to produce the same weight-control benefits so long as total energy expended remains the same (exchangeability premise). To this end, they recommend calculating energy expenditure as the product of the time spent performing each activity and the activity’s metabolic equivalents (MET), which may be summed to achieve target levels. The validity of the exchangeability premise was assessed using data from the National Runners’ Health Study. Physical activity dose was compared to body mass index (BMI) and body circumferences in 33,374 runners who reported usual distance run and pace, and usual times spent running and other exercises per week. MET hours per day (METhr/d) from running was computed from: a) time and intensity, and b) reported distance run (1.02 MET ∙hours per km). When computed from time and intensity, the declines (slope±SE) per METhr/d were significantly greater (P<10 -15 ) for running than non-running exercise for BMI (slopes±SE, male: -0.12±0.00 vs. 0.00±0.00; female: -0.12±0.00 vs. -0.01±0.01 kg/m 2 per METhr/d) and waist circumference (male: -0.28±0.01 vs. -0.07±0.01; female: -0. 31±0.01 vs. -0.05±0.01 cm per METhr/d). Reported METhr/d of running was 38% to 43% greater when calculated from time and intensity than distance. Moreover, the declines per METhr/d run were significantly greater when estimated from reported distance for BMI (males: -0.29±0.01; females: -0.27±0.01 kg/m 2 per METhr/d) and waist circumference (males: -0.67±0.02; females: -0.69±0.02 cm per METhr/d) than when computed from time and intensity (cited above). The exchangeability premise was not supported for running vs. non-running exercise. Moreover, distancebased running prescriptions may provide better weight control than time-based prescriptions for running or other activities. Additional longitudinal studies and randomized clinical trials are required to verify these results prospectively.

59 BASIC BIOLOGICAL SCIENCES↗

Bio-Inspired Approaches to Moving-Target Defense Strategies (Final Report)

This report records the work and contributions of the NITRD-funded Bio-Inspired Approaches to Moving-Target Defense Strategies project performed by Pacific Northwest National Laboratory under the technical guidance of the National Security Agency’s R6 division. The project has incorporated a number of bio-inspired cyber defensive technologies within an elastic framework provided by the Digital Ants. This project has created the first scalable, real-world prototype of the Digital Ants Framework (DAF) and integrated five technologies into this flexible, decentralized framework: (1) Ant-Based Cyber Defense (ABCD), (2) Behavioral Indicators, (3) Bioinformatic Classification, (4) Moving-Target Reconfiguration, and (5) Ambient Collaboration. The DAF can be used operationally to decentralize many such data intensive applications that normally rely on collection of large amounts of data in a central repository. In this work, we have shown how these component applications may be decentralized and may perform analysis at the edge. Operationally, this will enable analytics to scale far beyond current limitations while not suffering from the bandwidth or computational limitations of centralized analysis. This effort has advanced the R6 Cyber Security research program to secure digital infrastructures by developing a dynamic means to adaptively defend complex cyber systems. We hope that this work will benefit both our client’s efforts in system behavior modeling and cyber security to the overall benefit of the nation.

Bioinformatic Classification↗

Relative Hausdorff distance for network analysis

Similarity measures are used extensively in machine learning and data science algorithms. The newly proposed graph Relative Hausdorff (RH) distance is a lightweight yet nuanced similarity measure for quantifying the closeness of two graphs. In this work we study the effectiveness of RH distance as a tool for detecting anomalies in time-evolving graph sequences. We apply RH to cyber data with given red team events, as well to synthetically generated sequences of graphs with planted attacks. In our experiments, the performance of RH distance is at times comparable, and sometimes superior, to graph edit distance in detecting anomalous phenomena. Furthermore, our results suggest that in appropriate contexts, RH distance has advantages over more computationally intensive similarity measures.

97 MATHEMATICS AND COMPUTING↗

Enhancing approximate modular Bayesian inference by emulating the conditional posterior

In modular Bayesian analyses, complex models are composed of distinct modules, each representing different aspects of the data or prior information. In this context, fully Bayesian approaches can sometimes lead to undesirable feedback between modules, compromising the integrity of the inference. The “cut-distribution” prevents unwanted influence between modules by “cutting” feedback. The direct sampling (DS) algorithm is standard practice for approximating the cut-distribution, but it can be computationally intensive, especially when the number of imputations required is large. An enhanced method is proposed, the Emulating the Conditional Posterior (ECP) algorithm, which leverages emulation to increase the number of imputations. Through numerical experiment it is demonstrated that the ECP algorithm outperforms the traditional DS approach in terms of accuracy and computational efficiency, particularly when resources are constrained. Here, it is also shown how the DS algorithm can be improved using ideas from design of experiments. Some practical recommendations are given for algorithm choice in modular Bayesian analyses.

97 MATHEMATICS AND COMPUTING↗

Functional Image-Guided Radiotherapy Planning in Respiratory-Gated Intensity-Modulated Radiotherapy for Lung Cancer Patients With Chronic Obstructive Pulmonary Disease

Purpose: To investigate the incorporation of functional lung image-derived low attenuation area (LAA) based on four-dimensional computed tomography (4D-CT) into respiratory-gated intensity-modulated radiotherapy (IMRT) or volumetric modulated arc therapy (VMAT) in treatment planning for lung cancer patients with chronic obstructive pulmonary disease (COPD). Methods and Materials: Eight lung cancer patients with COPD were the subjects of this study. LAA was generated from 4D-CT data sets according to CT values of less than than -860 Hounsfield units (HU) as a threshold. The functional lung image was defined as the area where LAA was excluded from the image of the total lung. Two respiratory-gated radiotherapy plans (70 Gy/35 fractions) were designed and compared in each patient as follows: Plan A was an anatomical IMRT or VMAT plan based on the total lung; Plan F was a functional IMRT or VMAT plan based on the functional lung. Dosimetric parameters (percentage of total lung volume irradiated with {>=}20 Gy [V20], and mean dose of total lung [MLD]) of the two plans were compared. Results: V20 was lower in Plan F than in Plan A (mean 1.5%, p = 0.025 in IMRT, mean 1.6%, p = 0.044 in VMAT) achieved by a reduction in MLD (mean 0.23 Gy, p = 0.083 in IMRT, mean 0.5 Gy, p = 0.042 in VMAT). No differences were noted in target volume coverage and organ-at-risk doses. Conclusions: Functional IGRT planning based on LAA in respiratory-guided IMRT or VMAT appears to be effective in preserving a functional lung in lung cancer patients with COPD.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Microwave and Millimeter-Wave Radiometric Studies of Temperature, Water Vapor and Clouds

The importance of accurate measurements of column amounts of water vapor and cloud liquid has been well documented by scientists within the Atmospheric Radiation Measurement (ARM) Program. At the North Slope of Alaska (NSA), both microwave radiometers (MWR) and the MWRProfiler (MWRP), been used operationally by ARM for passive retrievals of the quantities: Precipitable Water Vapor (PWV) and Liquid Water Path (LWP). However, it has been convincingly shown that these instruments are inadequate to measure low amounts of PWV and LWP. In the case of water vapor, this is especially important during the Arctic winter, when PWV is frequently less than 2 mm. For low amounts of LWP (< 50 g/m{sup 2}), the MWR and MWRP retrievals have an accuracy that is also not acceptable. To address some of these needs, in March-April 2004, NOAA and ARM conducted the NSA Arctic Winter Radiometric Experiment - Water Vapor Intensive Operational Period at the ARM NSA/Adjacent Arctic Ocean (NSA/AAO) site. After this experiment, the radiometer group at NOAA moved to the Center for Environmental Technology (CET) of the Department of Electrical and Computer Engineering of the University of Colorado at Boulder. During this 2004 experiment, a total of 220 radiosondes were launched, and radiometric data from 22.235 to 380 GHz were obtained. Primary instruments included the ARM MWR and MWRP, a Global Positioning System (GPS), as well as the CET Ground-based Scanning Radiometer (GSR). We have analyzed data from these instruments to answer several questions of importance to ARM, including: (a) techniques for improved water vapor measurements; (b) improved calibration techniques during cloudy conditions; (c) the spectral response of radiometers to a variety of conditions: clear, liquid, ice, and mixed phase clouds; and (d) forward modeling of microwave and millimeter wave brightness temperatures from 22 to 380 GHz. Many of these results have been published in the open literature. During the third year of this contract, we participated in another ARM-sponsored experiment at the NSA during February-March 2007. This experiment is called the Radiative Heating in Underexplored Bands Campaign (RHUBC) and the GSR was operated successfully for the duration of the campaign. One of the principal goals of the experiment was to provide retrievals of water vapor during PWV amounts less than 2 mm and to compare GSR data with ARM radiometers and radiosondes. A secondary goal was to compare the radiometric response of the microwave and millimeter wavelength radiometers to water and ice clouds. In this final report, we will include the separate progress reports for each of the three years of the project and follow with a section on major accomplishments of the project.

54 ENVIRONMENTAL SCIENCES↗

Implementation and testing of the GPT sensitivities in TRIPOLI-4

Computing the sensitivity of given reactor parameters with respect to nuclear data is mandatory in key applications such as the assessment of reactor safety or core design. In recent years, the development of Monte Carlo methods capable of estimating sensitivity coefficients based on the Standard or Generalized Perturbation Theory (SPT and GPT, respectively) has attracted intensive research efforts, especially in view of having reference golden standard simulations to be compared to faster but approximate deterministic calculations. Following our previous implementation and validation of the SPT functionalities in the Monte Carlo TRIPOLI-4, devoted to the sensitivity of the k eigenvalue, in this work we detail the development of GPT methods for ratios of reaction rates, and validate them against a few relevant benchmark results. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

High-intensity positron microprobe at the Thomas Jefferson National Accelerator Facility

We present a conceptual design for a novel continuous wave electron-linac based high-intensity high-brightness slow-positron production source with a projected intensity on the order of 10{sup 10 }e{sup +}/s. Reaching this intensity in our design relies on the transport of positrons (T{sub +} below 600 keV) from the electron-positron pair production converter target to a low-radiation and low-temperature area for moderation in a high-efficiency cryogenic rare gas moderator, solid Ne. This design progressed through Monte Carlo optimizations of: electron/positron beam energies and converter target thickness, transport of the e{sup +} beam from the converter to the moderator, extraction of the e{sup +} beam from the magnetic channel, a synchronized raster system, and moderator efficiency calculations. For the extraction of e{sup +} from the magnetic channel, a magnetic field terminator plug prototype has been built and experimental results on the effectiveness of the prototype are presented. The dissipation of the heat away from the converter target and radiation protection measures are also discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗