Automatic Coding of Short Text Responses via Clustering in Educational Assessment

ERIC Educational Resources Information Center

Zehner, Fabian; Sälzer, Christine; Goldhammer, Frank

2016-01-01

Automatic coding of short text responses opens new doors in assessment. We implemented and integrated baseline methods of natural language processing and statistical modelling by means of software components that are available under open licenses. The accuracy of automatic text coding is demonstrated by using data collected in the "Programme…

Error threshold for color codes and random three-body Ising models.

PubMed

Katzgraber, Helmut G; Bombin, H; Martin-Delgado, M A

2009-08-28

We study the error threshold of color codes, a class of topological quantum codes that allow a direct implementation of quantum Clifford gates suitable for entanglement distillation, teleportation, and fault-tolerant quantum computation. We map the error-correction process onto a statistical mechanical random three-body Ising model and study its phase diagram via Monte Carlo simulations. The obtained error threshold of p(c) = 0.109(2) is very close to that of Kitaev's toric code, showing that enhanced computational capabilities do not necessarily imply lower resistance to noise.

The statistics of the vestibular input experienced during natural self-motion differ between rodents and primates.

PubMed

Carriot, Jérome; Jamali, Mohsen; Chacron, Maurice J; Cullen, Kathleen E

2017-04-15

In order to understand how the brain's coding strategies are adapted to the statistics of the sensory stimuli experienced during everyday life, the use of animal models is essential. Mice and non-human primates have become common models for furthering our knowledge of the neuronal coding of natural stimuli, but differences in their natural environments and behavioural repertoire may impact optimal coding strategies. Here we investigated the structure and statistics of the vestibular input experienced by mice versus non-human primates during natural behaviours, and found important differences. Our data establish that the structure and statistics of natural signals in non-human primates more closely resemble those observed previously in humans, suggesting similar coding strategies for incoming vestibular input. These results help us understand how the effects of active sensing and biomechanics will differentially shape the statistics of vestibular stimuli across species, and have important implications for sensory coding in other systems. It is widely believed that sensory systems are adapted to the statistical structure of natural stimuli, thereby optimizing coding. Recent evidence suggests that this is also the case for the vestibular system, which senses self-motion and in turn contributes to essential brain functions ranging from the most automatic reflexes to spatial perception and motor coordination. However, little is known about the statistics of self-motion stimuli actually experienced by freely moving animals in their natural environments. Accordingly, here we examined the natural self-motion signals experienced by mice and monkeys: two species commonly used to study vestibular neural coding. First, we found that probability distributions for all six dimensions of motion (three rotations, three translations) in both species deviated from normality due to long tails. Interestingly, the power spectra of natural rotational stimuli displayed similar structure for both species and were not well fitted by power laws. This result contrasts with reports that the natural spectra of other sensory modalities (i.e. vision, auditory and tactile) instead show a power-law relationship with frequency, which indicates scale invariance. Analysis of natural translational stimuli revealed important species differences as power spectra deviated from scale invariance for monkeys but not for mice. By comparing our results to previously published data for humans, we found the statistical structure of natural self-motion stimuli in monkeys and humans more closely resemble one another. Our results thus predict that, overall, neural coding strategies used by vestibular pathways to encode natural self-motion stimuli are fundamentally different in rodents and primates. © 2017 The Authors. The Journal of Physiology © 2017 The Physiological Society.

The statistics of the vestibular input experienced during natural self‐motion differ between rodents and primates

PubMed Central

Carriot, Jérome; Jamali, Mohsen; Chacron, Maurice J.

2017-01-01

Key points In order to understand how the brain's coding strategies are adapted to the statistics of the sensory stimuli experienced during everyday life, the use of animal models is essential.Mice and non‐human primates have become common models for furthering our knowledge of the neuronal coding of natural stimuli, but differences in their natural environments and behavioural repertoire may impact optimal coding strategies.Here we investigated the structure and statistics of the vestibular input experienced by mice versus non‐human primates during natural behaviours, and found important differences.Our data establish that the structure and statistics of natural signals in non‐human primates more closely resemble those observed previously in humans, suggesting similar coding strategies for incoming vestibular input.These results help us understand how the effects of active sensing and biomechanics will differentially shape the statistics of vestibular stimuli across species, and have important implications for sensory coding in other systems. Abstract It is widely believed that sensory systems are adapted to the statistical structure of natural stimuli, thereby optimizing coding. Recent evidence suggests that this is also the case for the vestibular system, which senses self‐motion and in turn contributes to essential brain functions ranging from the most automatic reflexes to spatial perception and motor coordination. However, little is known about the statistics of self‐motion stimuli actually experienced by freely moving animals in their natural environments. Accordingly, here we examined the natural self‐motion signals experienced by mice and monkeys: two species commonly used to study vestibular neural coding. First, we found that probability distributions for all six dimensions of motion (three rotations, three translations) in both species deviated from normality due to long tails. Interestingly, the power spectra of natural rotational stimuli displayed similar structure for both species and were not well fitted by power laws. This result contrasts with reports that the natural spectra of other sensory modalities (i.e. vision, auditory and tactile) instead show a power‐law relationship with frequency, which indicates scale invariance. Analysis of natural translational stimuli revealed important species differences as power spectra deviated from scale invariance for monkeys but not for mice. By comparing our results to previously published data for humans, we found the statistical structure of natural self‐motion stimuli in monkeys and humans more closely resemble one another. Our results thus predict that, overall, neural coding strategies used by vestibular pathways to encode natural self‐motion stimuli are fundamentally different in rodents and primates. PMID:28083981

Scaling up the evaluation of psychotherapy: evaluating motivational interviewing fidelity via statistical text classification

PubMed Central

2014-01-01

Background Behavioral interventions such as psychotherapy are leading, evidence-based practices for a variety of problems (e.g., substance abuse), but the evaluation of provider fidelity to behavioral interventions is limited by the need for human judgment. The current study evaluated the accuracy of statistical text classification in replicating human-based judgments of provider fidelity in one specific psychotherapy—motivational interviewing (MI). Method Participants (n = 148) came from five previously conducted randomized trials and were either primary care patients at a safety-net hospital or university students. To be eligible for the original studies, participants met criteria for either problematic drug or alcohol use. All participants received a type of brief motivational interview, an evidence-based intervention for alcohol and substance use disorders. The Motivational Interviewing Skills Code is a standard measure of MI provider fidelity based on human ratings that was used to evaluate all therapy sessions. A text classification approach called a labeled topic model was used to learn associations between human-based fidelity ratings and MI session transcripts. It was then used to generate codes for new sessions. The primary comparison was the accuracy of model-based codes with human-based codes. Results Receiver operating characteristic (ROC) analyses of model-based codes showed reasonably strong sensitivity and specificity with those from human raters (range of area under ROC curve (AUC) scores: 0.62 – 0.81; average AUC: 0.72). Agreement with human raters was evaluated based on talk turns as well as code tallies for an entire session. Generated codes had higher reliability with human codes for session tallies and also varied strongly by individual code. Conclusion To scale up the evaluation of behavioral interventions, technological solutions will be required. The current study demonstrated preliminary, encouraging findings regarding the utility of statistical text classification in bridging this methodological gap. PMID:24758152

Applications of statistical physics and information theory to the analysis of DNA sequences

NASA Astrophysics Data System (ADS)

Grosse, Ivo

2000-10-01

DNA carries the genetic information of most living organisms, and the of genome projects is to uncover that genetic information. One basic task in the analysis of DNA sequences is the recognition of protein coding genes. Powerful computer programs for gene recognition have been developed, but most of them are based on statistical patterns that vary from species to species. In this thesis I address the question if there exist universal statistical patterns that are different in coding and noncoding DNA of all living species, regardless of their phylogenetic origin. In search for such species-independent patterns I study the mutual information function of genomic DNA sequences, and find that it shows persistent period-three oscillations. To understand the biological origin of the observed period-three oscillations, I compare the mutual information function of genomic DNA sequences to the mutual information function of stochastic model sequences. I find that the pseudo-exon model is able to reproduce the mutual information function of genomic DNA sequences. Moreover, I find that a generalization of the pseudo-exon model can connect the existence and the functional form of long-range correlations to the presence and the length distributions of coding and noncoding regions. Based on these theoretical studies I am able to find an information-theoretical quantity, the average mutual information (AMI), whose probability distributions are significantly different in coding and noncoding DNA, while they are almost identical in all studied species. These findings show that there exist universal statistical patterns that are different in coding and noncoding DNA of all studied species, and they suggest that the AMI may be used to identify genes in different living species, irrespective of their taxonomic origin.

Statistical Analysis of CFD Solutions From the Fifth AIAA Drag Prediction Workshop

NASA Technical Reports Server (NTRS)

Morrison, Joseph H.

2013-01-01

A graphical framework is used for statistical analysis of the results from an extensive N-version test of a collection of Reynolds-averaged Navier-Stokes computational fluid dynamics codes. The solutions were obtained by code developers and users from North America, Europe, Asia, and South America using a common grid sequence and multiple turbulence models for the June 2012 fifth Drag Prediction Workshop sponsored by the AIAA Applied Aerodynamics Technical Committee. The aerodynamic configuration for this workshop was the Common Research Model subsonic transport wing-body previously used for the 4th Drag Prediction Workshop. This work continues the statistical analysis begun in the earlier workshops and compares the results from the grid convergence study of the most recent workshop with previous workshops.

Assessment of Current Jet Noise Prediction Capabilities

NASA Technical Reports Server (NTRS)

Hunter, Craid A.; Bridges, James E.; Khavaran, Abbas

2008-01-01

An assessment was made of the capability of jet noise prediction codes over a broad range of jet flows, with the objective of quantifying current capabilities and identifying areas requiring future research investment. Three separate codes in NASA s possession, representative of two classes of jet noise prediction codes, were evaluated, one empirical and two statistical. The empirical code is the Stone Jet Noise Module (ST2JET) contained within the ANOPP aircraft noise prediction code. It is well documented, and represents the state of the art in semi-empirical acoustic prediction codes where virtual sources are attributed to various aspects of noise generation in each jet. These sources, in combination, predict the spectral directivity of a jet plume. A total of 258 jet noise cases were examined on the ST2JET code, each run requiring only fractions of a second to complete. Two statistical jet noise prediction codes were also evaluated, JeNo v1, and Jet3D. Fewer cases were run for the statistical prediction methods because they require substantially more resources, typically a Reynolds-Averaged Navier-Stokes solution of the jet, volume integration of the source statistical models over the entire plume, and a numerical solution of the governing propagation equation within the jet. In the evaluation process, substantial justification of experimental datasets used in the evaluations was made. In the end, none of the current codes can predict jet noise within experimental uncertainty. The empirical code came within 2dB on a 1/3 octave spectral basis for a wide range of flows. The statistical code Jet3D was within experimental uncertainty at broadside angles for hot supersonic jets, but errors in peak frequency and amplitude put it out of experimental uncertainty at cooler, lower speed conditions. Jet3D did not predict changes in directivity in the downstream angles. The statistical code JeNo,v1 was within experimental uncertainty predicting noise from cold subsonic jets at all angles, but did not predict changes with heating of the jet and did not account for directivity changes at supersonic conditions. Shortcomings addressed here give direction for future work relevant to the statistical-based prediction methods. A full report will be released as a chapter in a NASA publication assessing the state of the art in aircraft noise prediction.

Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.

PubMed

Mørk, Søren; Holmes, Ian

2012-03-01

Probabilistic logic programming offers a powerful way to describe and evaluate structured statistical models. To investigate the practicality of probabilistic logic programming for structure learning in bioinformatics, we undertook a simplified bacterial gene-finding benchmark in PRISM, a probabilistic dialect of Prolog. We evaluate Hidden Markov Model structures for bacterial protein-coding gene potential, including a simple null model structure, three structures based on existing bacterial gene finders and two novel model structures. We test standard versions as well as ADPH length modeling and three-state versions of the five model structures. The models are all represented as probabilistic logic programs and evaluated using the PRISM machine learning system in terms of statistical information criteria and gene-finding prediction accuracy, in two bacterial genomes. Neither of our implementations of the two currently most used model structures are best performing in terms of statistical information criteria or prediction performances, suggesting that better-fitting models might be achievable. The source code of all PRISM models, data and additional scripts are freely available for download at: http://github.com/somork/codonhmm. Supplementary data are available at Bioinformatics online.

Statistical Analysis of CFD Solutions from the Fourth AIAA Drag Prediction Workshop

NASA Technical Reports Server (NTRS)

Morrison, Joseph H.

2010-01-01

A graphical framework is used for statistical analysis of the results from an extensive N-version test of a collection of Reynolds-averaged Navier-Stokes computational fluid dynamics codes. The solutions were obtained by code developers and users from the U.S., Europe, Asia, and Russia using a variety of grid systems and turbulence models for the June 2009 4th Drag Prediction Workshop sponsored by the AIAA Applied Aerodynamics Technical Committee. The aerodynamic configuration for this workshop was a new subsonic transport model, the Common Research Model, designed using a modern approach for the wing and included a horizontal tail. The fourth workshop focused on the prediction of both absolute and incremental drag levels for wing-body and wing-body-horizontal tail configurations. This work continues the statistical analysis begun in the earlier workshops and compares the results from the grid convergence study of the most recent workshop with earlier workshops using the statistical framework.

Adaptive distributed source coding.

PubMed

Varodayan, David; Lin, Yao-Chung; Girod, Bernd

2012-05-01

We consider distributed source coding in the presence of hidden variables that parameterize the statistical dependence among sources. We derive the Slepian-Wolf bound and devise coding algorithms for a block-candidate model of this problem. The encoder sends, in addition to syndrome bits, a portion of the source to the decoder uncoded as doping bits. The decoder uses the sum-product algorithm to simultaneously recover the source symbols and the hidden statistical dependence variables. We also develop novel techniques based on density evolution (DE) to analyze the coding algorithms. We experimentally confirm that our DE analysis closely approximates practical performance. This result allows us to efficiently optimize parameters of the algorithms. In particular, we show that the system performs close to the Slepian-Wolf bound when an appropriate doping rate is selected. We then apply our coding and analysis techniques to a reduced-reference video quality monitoring system and show a bit rate saving of about 75% compared with fixed-length coding.

Statistical dielectronic recombination rates for multielectron ions in plasma

NASA Astrophysics Data System (ADS)

Demura, A. V.; Leont'iev, D. S.; Lisitsa, V. S.; Shurygin, V. A.

2017-10-01

We describe the general analytic derivation of the dielectronic recombination (DR) rate coefficient for multielectron ions in a plasma based on the statistical theory of an atom in terms of the spatial distribution of the atomic electron density. The dielectronic recombination rates for complex multielectron tungsten ions are calculated numerically in a wide range of variation of the plasma temperature, which is important for modern nuclear fusion studies. The results of statistical theory are compared with the data obtained using level-by-level codes ADPAK, FAC, HULLAC, and experimental results. We consider different statistical DR models based on the Thomas-Fermi distribution, viz., integral and differential with respect to the orbital angular momenta of the ion core and the trapped electron, as well as the Rost model, which is an analog of the Frank-Condon model as applied to atomic structures. In view of its universality and relative simplicity, the statistical approach can be used for obtaining express estimates of the dielectronic recombination rate coefficients in complex calculations of the parameters of the thermonuclear plasmas. The application of statistical methods also provides information for the dielectronic recombination rates with much smaller computer time expenditures as compared to available level-by-level codes.

The adaption and use of research codes for performance assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liebetrau, A.M.

1987-05-01

Models of real-world phenomena are developed for many reasons. The models are usually, if not always, implemented in the form of a computer code. The characteristics of a code are determined largely by its intended use. Realizations or implementations of detailed mathematical models of complex physical and/or chemical processes are often referred to as research or scientific (RS) codes. Research codes typically require large amounts of computing time. One example of an RS code is a finite-element code for solving complex systems of differential equations that describe mass transfer through some geologic medium. Considerable computing time is required because computationsmore » are done at many points in time and/or space. Codes used to evaluate the overall performance of real-world physical systems are called performance assessment (PA) codes. Performance assessment codes are used to conduct simulated experiments involving systems that cannot be directly observed. Thus, PA codes usually involve repeated simulations of system performance in situations that preclude the use of conventional experimental and statistical methods. 3 figs.« less

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of {sup 64}Cu and {sup 67}Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nasrabadi, M. N., E-mail: mnnasrabadi@ast.ui.ac.ir; Sepiani, M.

2015-03-30

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE and LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of 64Cu and 67Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

NASA Astrophysics Data System (ADS)

Nasrabadi, M. N.; Sepiani, M.

2015-03-01

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE & LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

Analysis of multi-fragmentation reactions induced by relativistic heavy ions using the statistical multi-fragmentation model

NASA Astrophysics Data System (ADS)

Ogawa, T.; Sato, T.; Hashimoto, S.; Niita, K.

2013-09-01

The fragmentation cross-sections of relativistic energy nucleus-nucleus collisions were analyzed using the statistical multi-fragmentation model (SMM) incorporated with the Monte-Carlo radiation transport simulation code particle and heavy ion transport code system (PHITS). Comparison with the literature data showed that PHITS-SMM reproduces fragmentation cross-sections of heavy nuclei at relativistic energies better than the original PHITS by up to two orders of magnitude. It was also found that SMM does not degrade the neutron production cross-sections in heavy ion collisions or the fragmentation cross-sections of light nuclei, for which SMM has not been benchmarked. Therefore, SMM is a robust model that can supplement conventional nucleus-nucleus reaction models, enabling more accurate prediction of fragmentation cross-sections.

Statistical core design methodology using the VIPRE thermal-hydraulics code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lloyd, M.W.; Feltus, M.A.

1994-12-31

This Penn State Statistical Core Design Methodology (PSSCDM) is unique because it not only includes the EPRI correlation/test data standard deviation but also the computational uncertainty for the VIPRE code model and the new composite box design correlation. The resultant PSSCDM equation mimics the EPRI DNBR correlation results well, with an uncertainty of 0.0389. The combined uncertainty yields a new DNBR limit of 1.18 that will provide more plant operational flexibility. This methodology and its associated correlation and uniqe coefficients are for a very particular VIPRE model; thus, the correlation will be specifically linked with the lumped channel and subchannelmore » layout. The results of this research and methodology, however, can be applied to plant-specific VIPRE models.« less

Three-Dimensional Algebraic Models of the tRNA Code and 12 Graphs for Representing the Amino Acids.

PubMed

José, Marco V; Morgado, Eberto R; Guimarães, Romeu Cardoso; Zamudio, Gabriel S; de Farías, Sávio Torres; Bobadilla, Juan R; Sosa, Daniela

2014-08-11

Three-dimensional algebraic models, also called Genetic Hotels, are developed to represent the Standard Genetic Code, the Standard tRNA Code (S-tRNA-C), and the Human tRNA code (H-tRNA-C). New algebraic concepts are introduced to be able to describe these models, to wit, the generalization of the 2n-Klein Group and the concept of a subgroup coset with a tail. We found that the H-tRNA-C displayed broken symmetries in regard to the S-tRNA-C, which is highly symmetric. We also show that there are only 12 ways to represent each of the corresponding phenotypic graphs of amino acids. The averages of statistical centrality measures of the 12 graphs for each of the three codes are carried out and they are statistically compared. The phenotypic graphs of the S-tRNA-C display a common triangular prism of amino acids in 10 out of the 12 graphs, whilst the corresponding graphs for the H-tRNA-C display only two triangular prisms. The graphs exhibit disjoint clusters of amino acids when their polar requirement values are used. We contend that the S-tRNA-C is in a frozen-like state, whereas the H-tRNA-C may be in an evolving state.

Reliability-based criteria for load and resistance factor design code for wood bridges

Treesearch

Chris Eamon; Andrzej S. Nowak; Michael A. Ritter; Joe Murphy

2000-01-01

Recently AASHTO adopted a load and resistance factor design code for highway bridges. The new code provides a rational basis for the design of steel and concrete structures. However, the calibration was not done for wood bridges. Therefore, there is a need to fill this gap. The development of statistical models for wood bridge structures is discussed. Recent test...

Statistical Analysis of CFD Solutions from the 6th AIAA CFD Drag Prediction Workshop

NASA Technical Reports Server (NTRS)

Derlaga, Joseph M.; Morrison, Joseph H.

2017-01-01

A graphical framework is used for statistical analysis of the results from an extensive N- version test of a collection of Reynolds-averaged Navier-Stokes computational uid dynam- ics codes. The solutions were obtained by code developers and users from North America, Europe, Asia, and South America using both common and custom grid sequencees as well as multiple turbulence models for the June 2016 6th AIAA CFD Drag Prediction Workshop sponsored by the AIAA Applied Aerodynamics Technical Committee. The aerodynamic con guration for this workshop was the Common Research Model subsonic transport wing- body previously used for both the 4th and 5th Drag Prediction Workshops. This work continues the statistical analysis begun in the earlier workshops and compares the results from the grid convergence study of the most recent workshop with previous workshops.

The Increased Sensitivity of Irregular Peripheral Canal and Otolith Vestibular Afferents Optimizes their Encoding of Natural Stimuli

PubMed Central

Schneider, Adam D.; Jamali, Mohsen; Carriot, Jerome; Chacron, Maurice J.

2015-01-01

Efficient processing of incoming sensory input is essential for an organism's survival. A growing body of evidence suggests that sensory systems have developed coding strategies that are constrained by the statistics of the natural environment. Consequently, it is necessary to first characterize neural responses to natural stimuli to uncover the coding strategies used by a given sensory system. Here we report for the first time the statistics of vestibular rotational and translational stimuli experienced by rhesus monkeys during natural (e.g., walking, grooming) behaviors. We find that these stimuli can reach intensities as high as 1500 deg/s and 8 G. Recordings from afferents during naturalistic rotational and linear motion further revealed strongly nonlinear responses in the form of rectification and saturation, which could not be accurately predicted by traditional linear models of vestibular processing. Accordingly, we used linear–nonlinear cascade models and found that these could accurately predict responses to naturalistic stimuli. Finally, we tested whether the statistics of natural vestibular signals constrain the neural coding strategies used by peripheral afferents. We found that both irregular otolith and semicircular canal afferents, because of their higher sensitivities, were more optimized for processing natural vestibular stimuli as compared with their regular counterparts. Our results therefore provide the first evidence supporting the hypothesis that the neural coding strategies used by the vestibular system are matched to the statistics of natural stimuli. PMID:25855169

Finding the Root Causes of Statistical Inconsistency in Community Earth System Model Output

NASA Astrophysics Data System (ADS)

Milroy, D.; Hammerling, D.; Baker, A. H.

2017-12-01

Baker et al (2015) developed the Community Earth System Model Ensemble Consistency Test (CESM-ECT) to provide a metric for software quality assurance by determining statistical consistency between an ensemble of CESM outputs and new test runs. The test has proved useful for detecting statistical difference caused by compiler bugs and errors in physical modules. However, detection is only the necessary first step in finding the causes of statistical difference. The CESM is a vastly complex model comprised of millions of lines of code which is developed and maintained by a large community of software engineers and scientists. Any root cause analysis is correspondingly challenging. We propose a new capability for CESM-ECT: identifying the sections of code that cause statistical distinguishability. The first step is to discover CESM variables that cause CESM-ECT to classify new runs as statistically distinct, which we achieve via Randomized Logistic Regression. Next we use a tool developed to identify CESM components that define or compute the variables found in the first step. Finally, we employ the application Kernel GENerator (KGEN) created in Kim et al (2016) to detect fine-grained floating point differences. We demonstrate an example of the procedure and advance a plan to automate this process in our future work.

Assessment of the Effects of Entrainment and Wind Shear on Nuclear Cloud Rise Modeling

NASA Astrophysics Data System (ADS)

Zalewski, Daniel; Jodoin, Vincent

2001-04-01

Accurate modeling of nuclear cloud rise is critical in hazard prediction following a nuclear detonation. This thesis recommends improvements to the model currently used by DOD. It considers a single-term versus a three-term entrainment equation, the value of the entrainment and eddy viscous drag parameters, as well as the effect of wind shear in the cloud rise following a nuclear detonation. It examines departures from the 1979 version of the Department of Defense Land Fallout Interpretive Code (DELFIC) with the current code used in the Hazard Prediction and Assessment Capability (HPAC) code version 3.2. The recommendation for a single-term entrainment equation, with constant value parameters, without wind shear corrections, and without cloud oscillations is based on both a statistical analysis using 67 U.S. nuclear atmospheric test shots and the physical representation of the modeling. The statistical analysis optimized the parameter values of interest for four cases: the three-term entrainment equation with wind shear and without wind shear as well as the single-term entrainment equation with and without wind shear. The thesis then examines the effect of cloud oscillations as a significant departure in the code. Modifications to user input atmospheric tables are identified as a potential problem in the calculation of stabilized cloud dimensions in HPAC.

Data Assimilation - Advances and Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Brian J.

2014-07-30

This presentation provides an overview of data assimilation (model calibration) for complex computer experiments. Calibration refers to the process of probabilistically constraining uncertain physics/engineering model inputs to be consistent with observed experimental data. An initial probability distribution for these parameters is updated using the experimental information. Utilization of surrogate models and empirical adjustment for model form error in code calibration form the basis for the statistical methodology considered. The role of probabilistic code calibration in supporting code validation is discussed. Incorporation of model form uncertainty in rigorous uncertainty quantification (UQ) analyses is also addressed. Design criteria used within a batchmore » sequential design algorithm are introduced for efficiently achieving predictive maturity and improved code calibration. Predictive maturity refers to obtaining stable predictive inference with calibrated computer codes. These approaches allow for augmentation of initial experiment designs for collecting new physical data. A standard framework for data assimilation is presented and techniques for updating the posterior distribution of the state variables based on particle filtering and the ensemble Kalman filter are introduced.« less

BeiDou Geostationary Satellite Code Bias Modeling Using Fengyun-3C Onboard Measurements.

PubMed

Jiang, Kecai; Li, Min; Zhao, Qile; Li, Wenwen; Guo, Xiang

2017-10-27

This study validated and investigated elevation- and frequency-dependent systematic biases observed in ground-based code measurements of the Chinese BeiDou navigation satellite system, using the onboard BeiDou code measurement data from the Chinese meteorological satellite Fengyun-3C. Particularly for geostationary earth orbit satellites, sky-view coverage can be achieved over the entire elevation and azimuth angle ranges with the available onboard tracking data, which is more favorable to modeling code biases. Apart from the BeiDou-satellite-induced biases, the onboard BeiDou code multipath effects also indicate pronounced near-field systematic biases that depend only on signal frequency and the line-of-sight directions. To correct these biases, we developed a proposed code correction model by estimating the BeiDou-satellite-induced biases as linear piece-wise functions in different satellite groups and the near-field systematic biases in a grid approach. To validate the code bias model, we carried out orbit determination using single-frequency BeiDou data with and without code bias corrections applied. Orbit precision statistics indicate that those code biases can seriously degrade single-frequency orbit determination. After the correction model was applied, the orbit position errors, 3D root mean square, were reduced from 150.6 to 56.3 cm.

BeiDou Geostationary Satellite Code Bias Modeling Using Fengyun-3C Onboard Measurements

PubMed Central

Jiang, Kecai; Li, Min; Zhao, Qile; Li, Wenwen; Guo, Xiang

2017-01-01

This study validated and investigated elevation- and frequency-dependent systematic biases observed in ground-based code measurements of the Chinese BeiDou navigation satellite system, using the onboard BeiDou code measurement data from the Chinese meteorological satellite Fengyun-3C. Particularly for geostationary earth orbit satellites, sky-view coverage can be achieved over the entire elevation and azimuth angle ranges with the available onboard tracking data, which is more favorable to modeling code biases. Apart from the BeiDou-satellite-induced biases, the onboard BeiDou code multipath effects also indicate pronounced near-field systematic biases that depend only on signal frequency and the line-of-sight directions. To correct these biases, we developed a proposed code correction model by estimating the BeiDou-satellite-induced biases as linear piece-wise functions in different satellite groups and the near-field systematic biases in a grid approach. To validate the code bias model, we carried out orbit determination using single-frequency BeiDou data with and without code bias corrections applied. Orbit precision statistics indicate that those code biases can seriously degrade single-frequency orbit determination. After the correction model was applied, the orbit position errors, 3D root mean square, were reduced from 150.6 to 56.3 cm. PMID:29076998

Statistical Analysis of the AIAA Drag Prediction Workshop CFD Solutions

NASA Technical Reports Server (NTRS)

Morrison, Joseph H.; Hemsch, Michael J.

2007-01-01

The first AIAA Drag Prediction Workshop (DPW), held in June 2001, evaluated the results from an extensive N-version test of a collection of Reynolds-Averaged Navier-Stokes CFD codes. The code-to-code scatter was more than an order of magnitude larger than desired for design and experimental validation of cruise conditions for a subsonic transport configuration. The second AIAA Drag Prediction Workshop, held in June 2003, emphasized the determination of installed pylon-nacelle drag increments and grid refinement studies. The code-to-code scatter was significantly reduced compared to the first DPW, but still larger than desired. However, grid refinement studies showed no significant improvement in code-to-code scatter with increasing grid refinement. The third AIAA Drag Prediction Workshop, held in June 2006, focused on the determination of installed side-of-body fairing drag increments and grid refinement studies for clean attached flow on wing alone configurations and for separated flow on the DLR-F6 subsonic transport model. This report compares the transonic cruise prediction results of the second and third workshops using statistical analysis.

Three-Dimensional Algebraic Models of the tRNA Code and 12 Graphs for Representing the Amino Acids

PubMed Central

José, Marco V.; Morgado, Eberto R.; Guimarães, Romeu Cardoso; Zamudio, Gabriel S.; de Farías, Sávio Torres; Bobadilla, Juan R.; Sosa, Daniela

2014-01-01

Three-dimensional algebraic models, also called Genetic Hotels, are developed to represent the Standard Genetic Code, the Standard tRNA Code (S-tRNA-C), and the Human tRNA code (H-tRNA-C). New algebraic concepts are introduced to be able to describe these models, to wit, the generalization of the 2n-Klein Group and the concept of a subgroup coset with a tail. We found that the H-tRNA-C displayed broken symmetries in regard to the S-tRNA-C, which is highly symmetric. We also show that there are only 12 ways to represent each of the corresponding phenotypic graphs of amino acids. The averages of statistical centrality measures of the 12 graphs for each of the three codes are carried out and they are statistically compared. The phenotypic graphs of the S-tRNA-C display a common triangular prism of amino acids in 10 out of the 12 graphs, whilst the corresponding graphs for the H-tRNA-C display only two triangular prisms. The graphs exhibit disjoint clusters of amino acids when their polar requirement values are used. We contend that the S-tRNA-C is in a frozen-like state, whereas the H-tRNA-C may be in an evolving state. PMID:25370377

Signatures of criticality arise from random subsampling in simple population models.

PubMed

Nonnenmacher, Marcel; Behrens, Christian; Berens, Philipp; Bethge, Matthias; Macke, Jakob H

2017-10-01

The rise of large-scale recordings of neuronal activity has fueled the hope to gain new insights into the collective activity of neural ensembles. How can one link the statistics of neural population activity to underlying principles and theories? One attempt to interpret such data builds upon analogies to the behaviour of collective systems in statistical physics. Divergence of the specific heat-a measure of population statistics derived from thermodynamics-has been used to suggest that neural populations are optimized to operate at a "critical point". However, these findings have been challenged by theoretical studies which have shown that common inputs can lead to diverging specific heat. Here, we connect "signatures of criticality", and in particular the divergence of specific heat, back to statistics of neural population activity commonly studied in neural coding: firing rates and pairwise correlations. We show that the specific heat diverges whenever the average correlation strength does not depend on population size. This is necessarily true when data with correlations is randomly subsampled during the analysis process, irrespective of the detailed structure or origin of correlations. We also show how the characteristic shape of specific heat capacity curves depends on firing rates and correlations, using both analytically tractable models and numerical simulations of a canonical feed-forward population model. To analyze these simulations, we develop efficient methods for characterizing large-scale neural population activity with maximum entropy models. We find that, consistent with experimental findings, increases in firing rates and correlation directly lead to more pronounced signatures. Thus, previous reports of thermodynamical criticality in neural populations based on the analysis of specific heat can be explained by average firing rates and correlations, and are not indicative of an optimized coding strategy. We conclude that a reliable interpretation of statistical tests for theories of neural coding is possible only in reference to relevant ground-truth models.

ecode - Electron Transport Algorithm Testing v. 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Franke, Brian C.; Olson, Aaron J.; Bruss, Donald Eugene

2016-10-05

ecode is a Monte Carlo code used for testing algorithms related to electron transport. The code can read basic physics parameters, such as energy-dependent stopping powers and screening parameters. The code permits simple planar geometries of slabs or cubes. Parallelization consists of domain replication, with work distributed at the start of the calculation and statistical results gathered at the end of the calculation. Some basic routines (such as input parsing, random number generation, and statistics processing) are shared with the Integrated Tiger Series codes. A variety of algorithms for uncertainty propagation are incorporated based on the stochastic collocation and stochasticmore » Galerkin methods. These permit uncertainty only in the total and angular scattering cross sections. The code contains algorithms for simulating stochastic mixtures of two materials. The physics is approximate, ranging from mono-energetic and isotropic scattering to screened Rutherford angular scattering and Rutherford energy-loss scattering (simple electron transport models). No production of secondary particles is implemented, and no photon physics is implemented.« less

Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics

NASA Technical Reports Server (NTRS)

Mantegna, R. N.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Peng, C. K.; Simons, M.; Stanley, H. E.

1995-01-01

We compare the statistical properties of coding and noncoding regions in eukaryotic and viral DNA sequences by adapting two tests developed for the analysis of natural languages and symbolic sequences. The data set comprises all 30 sequences of length above 50 000 base pairs in GenBank Release No. 81.0, as well as the recently published sequences of C. elegans chromosome III (2.2 Mbp) and yeast chromosome XI (661 Kbp). We find that for the three chromosomes we studied the statistical properties of noncoding regions appear to be closer to those observed in natural languages than those of coding regions. In particular, (i) a n-tuple Zipf analysis of noncoding regions reveals a regime close to power-law behavior while the coding regions show logarithmic behavior over a wide interval, while (ii) an n-gram entropy measurement shows that the noncoding regions have a lower n-gram entropy (and hence a larger "n-gram redundancy") than the coding regions. In contrast to the three chromosomes, we find that for vertebrates such as primates and rodents and for viral DNA, the difference between the statistical properties of coding and noncoding regions is not pronounced and therefore the results of the analyses of the investigated sequences are less conclusive. After noting the intrinsic limitations of the n-gram redundancy analysis, we also briefly discuss the failure of the zeroth- and first-order Markovian models or simple nucleotide repeats to account fully for these "linguistic" features of DNA. Finally, we emphasize that our results by no means prove the existence of a "language" in noncoding DNA.

Correction of the significance level when attempting multiple transformations of an explanatory variable in generalized linear models

PubMed Central

2013-01-01

Background In statistical modeling, finding the most favorable coding for an exploratory quantitative variable involves many tests. This process involves multiple testing problems and requires the correction of the significance level. Methods For each coding, a test on the nullity of the coefficient associated with the new coded variable is computed. The selected coding corresponds to that associated with the largest statistical test (or equivalently the smallest pvalue). In the context of the Generalized Linear Model, Liquet and Commenges (Stat Probability Lett,71:33–38,2005) proposed an asymptotic correction of the significance level. This procedure, based on the score test, has been developed for dichotomous and Box-Cox transformations. In this paper, we suggest the use of resampling methods to estimate the significance level for categorical transformations with more than two levels and, by definition those that involve more than one parameter in the model. The categorical transformation is a more flexible way to explore the unknown shape of the effect between an explanatory and a dependent variable. Results The simulations we ran in this study showed good performances of the proposed methods. These methods were illustrated using the data from a study of the relationship between cholesterol and dementia. Conclusion The algorithms were implemented using R, and the associated CPMCGLM R package is available on the CRAN. PMID:23758852

Function modeling improves the efficiency of spatial modeling using big data from remote sensing

Treesearch

John Hogland; Nathaniel Anderson

2017-01-01

Spatial modeling is an integral component of most geographic information systems (GISs). However, conventional GIS modeling techniques can require substantial processing time and storage space and have limited statistical and machine learning functionality. To address these limitations, many have parallelized spatial models using multiple coding libraries and have...

AGARD Bulletin. Technical Programme, 1981.

DTIC Science & Technology

1980-08-01

ionospheric effect models and their associated codes. Physical, statistical , and nybrid models will be described in a comprehensive manner. Descriptions...will be to review: The various conventional modes of optical correction required either by ametropias or by normal or pathological drops in visual

Do code of conduct audits improve chemical safety in garment factories? Lessons on corporate social responsibility in the supply chain from Fair Wear Foundation.

PubMed

Lindholm, Henrik; Egels-Zandén, Niklas; Rudén, Christina

2016-10-01

In managing chemical risks to the environment and human health in supply chains, voluntary corporate social responsibility (CSR) measures, such as auditing code of conduct compliance, play an important role. To examine how well suppliers' chemical health and safety performance complies with buyers' CSR policies and whether audited factories improve their performance. CSR audits (n = 288) of garment factories conducted by Fair Wear Foundation (FWF), an independent non-profit organization, were analyzed using descriptive statistics and statistical modeling. Forty-three per cent of factories did not comply with the FWF code of conduct, i.e. received remarks on chemical safety. Only among factories audited 10 or more times was there a significant increase in the number of factories receiving no remarks. Compliance with chemical safety requirements in garment supply chains is low and auditing is statistically correlated with improvements only at factories that have undergone numerous audits.

Do code of conduct audits improve chemical safety in garment factories? Lessons on corporate social responsibility in the supply chain from Fair Wear Foundation

PubMed Central

2016-01-01

Background In managing chemical risks to the environment and human health in supply chains, voluntary corporate social responsibility (CSR) measures, such as auditing code of conduct compliance, play an important role. Objectives To examine how well suppliers’ chemical health and safety performance complies with buyers’ CSR policies and whether audited factories improve their performance. Methods CSR audits (n = 288) of garment factories conducted by Fair Wear Foundation (FWF), an independent non-profit organization, were analyzed using descriptive statistics and statistical modeling. Results Forty-three per cent of factories did not comply with the FWF code of conduct, i.e. received remarks on chemical safety. Only among factories audited 10 or more times was there a significant increase in the number of factories receiving no remarks. Conclusions Compliance with chemical safety requirements in garment supply chains is low and auditing is statistically correlated with improvements only at factories that have undergone numerous audits. PMID:27611103

LIDT-DD: A New Self-Consistent Debris Disc Model Including Radiation Pressure and Coupling Dynamical and Collisional Evolution

NASA Astrophysics Data System (ADS)

Kral, Q.; Thebault, P.; Charnoz, S.

2014-01-01

The first attempt at developing a fully self-consistent code coupling dynamics and collisions to study debris discs (Kral et al. 2013) is presented. So far, these two crucial mechanisms were studied separately, with N-body and statistical collisional codes respectively, because of stringent computational constraints. We present a new model named LIDT-DD which is able to follow over long timescales the coupled evolution of dynamics (including radiation forces) and collisions in a self-consistent way.

Jet Noise Diagnostics Supporting Statistical Noise Prediction Methods

NASA Technical Reports Server (NTRS)

Bridges, James E.

2006-01-01

The primary focus of my presentation is the development of the jet noise prediction code JeNo with most examples coming from the experimental work that drove the theoretical development and validation. JeNo is a statistical jet noise prediction code, based upon the Lilley acoustic analogy. Our approach uses time-average 2-D or 3-D mean and turbulent statistics of the flow as input. The output is source distributions and spectral directivity. NASA has been investing in development of statistical jet noise prediction tools because these seem to fit the middle ground that allows enough flexibility and fidelity for jet noise source diagnostics while having reasonable computational requirements. These tools rely on Reynolds-averaged Navier-Stokes (RANS) computational fluid dynamics (CFD) solutions as input for computing far-field spectral directivity using an acoustic analogy. There are many ways acoustic analogies can be created, each with a series of assumptions and models, many often taken unknowingly. And the resulting prediction can be easily reverse-engineered by altering the models contained within. However, only an approach which is mathematically sound, with assumptions validated and modeled quantities checked against direct measurement will give consistently correct answers. Many quantities are modeled in acoustic analogies precisely because they have been impossible to measure or calculate, making this requirement a difficult task. The NASA team has spent considerable effort identifying all the assumptions and models used to take the Navier-Stokes equations to the point of a statistical calculation via an acoustic analogy very similar to that proposed by Lilley. Assumptions have been identified and experiments have been developed to test these assumptions. In some cases this has resulted in assumptions being changed. Beginning with the CFD used as input to the acoustic analogy, models for turbulence closure used in RANS CFD codes have been explored and compared against measurements of mean and rms velocity statistics over a range of jet speeds and temperatures. Models for flow parameters used in the acoustic analogy, most notably the space-time correlations of velocity, have been compared against direct measurements, and modified to better fit the observed data. These measurements have been extremely challenging for hot, high speed jets, and represent a sizeable investment in instrumentation development. As an intermediate check that the analysis is predicting the physics intended, phased arrays have been employed to measure source distributions for a wide range of jet cases. And finally, careful far-field spectral directivity measurements have been taken for final validation of the prediction code. Examples of each of these experimental efforts will be presented. The main result of these efforts is a noise prediction code, named JeNo, which is in middevelopment. JeNo is able to consistently predict spectral directivity, including aft angle directivity, for subsonic cold jets of most geometries. Current development on JeNo is focused on extending its capability to hot jets, requiring inclusion of a previously neglected second source associated with thermal fluctuations. A secondary result of the intensive experimentation is the archiving of various flow statistics applicable to other acoustic analogies and to development of time-resolved prediction methods. These will be of lasting value as we look ahead at future challenges to the aeroacoustic experimentalist.

Magnetospheric space plasma investigations

NASA Technical Reports Server (NTRS)

Comfort, Richard H.; Horwitz, James L.

1994-01-01

A time dependent semi-kinetic model that includes self collisions and ion-neutral collisions and chemistry was developed. Light ion outflow in the polar cap transition region was modeled and compared with data results. A model study of wave heating of O+ ions in the topside transition region was carried out using a code which does local calculations that include ion-neutral and Coulomb self collisions as well as production and loss of O+. Another project is a statistical study of hydrogen spin curve characteristics in the polar cap. A statistical study of the latitudinal distribution of core plasmas along the L=4.6 field line using DE-1/RIMS data was completed. A short paper on dual spacecraft estimates of ion temperature profiles and heat flows in the plasmasphere ionosphere system was prepared. An automated processing code was used to process RIMS data from 1981 to 1984.

Quantum error-correction failure distributions: Comparison of coherent and stochastic error models

NASA Astrophysics Data System (ADS)

Barnes, Jeff P.; Trout, Colin J.; Lucarelli, Dennis; Clader, B. D.

2017-06-01

We compare failure distributions of quantum error correction circuits for stochastic errors and coherent errors. We utilize a fully coherent simulation of a fault-tolerant quantum error correcting circuit for a d =3 Steane and surface code. We find that the output distributions are markedly different for the two error models, showing that no simple mapping between the two error models exists. Coherent errors create very broad and heavy-tailed failure distributions. This suggests that they are susceptible to outlier events and that mean statistics, such as pseudothreshold estimates, may not provide the key figure of merit. This provides further statistical insight into why coherent errors can be so harmful for quantum error correction. These output probability distributions may also provide a useful metric that can be utilized when optimizing quantum error correcting codes and decoding procedures for purely coherent errors.

Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons.

PubMed

Mensi, Skander; Hagens, Olivier; Gerstner, Wulfram; Pozzorini, Christian

2016-02-01

The way in which single neurons transform input into output spike trains has fundamental consequences for network coding. Theories and modeling studies based on standard Integrate-and-Fire models implicitly assume that, in response to increasingly strong inputs, neurons modify their coding strategy by progressively reducing their selective sensitivity to rapid input fluctuations. Combining mathematical modeling with in vitro experiments, we demonstrate that, in L5 pyramidal neurons, the firing threshold dynamics adaptively adjust the effective timescale of somatic integration in order to preserve sensitivity to rapid signals over a broad range of input statistics. For that, a new Generalized Integrate-and-Fire model featuring nonlinear firing threshold dynamics and conductance-based adaptation is introduced that outperforms state-of-the-art neuron models in predicting the spiking activity of neurons responding to a variety of in vivo-like fluctuating currents. Our model allows for efficient parameter extraction and can be analytically mapped to a Generalized Linear Model in which both the input filter--describing somatic integration--and the spike-history filter--accounting for spike-frequency adaptation--dynamically adapt to the input statistics, as experimentally observed. Overall, our results provide new insights on the computational role of different biophysical processes known to underlie adaptive coding in single neurons and support previous theoretical findings indicating that the nonlinear dynamics of the firing threshold due to Na+-channel inactivation regulate the sensitivity to rapid input fluctuations.

Influence of the plasma environment on atomic structure using an ion-sphere model

DOE PAGES

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

2015-09-03

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Influence of the plasma environment on atomic structure using an ion-sphere model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Incorporating Code-Based Software in an Introductory Statistics Course

ERIC Educational Resources Information Center

Doehler, Kirsten; Taylor, Laura

2015-01-01

This article is based on the experiences of two statistics professors who have taught students to write and effectively utilize code-based software in a college-level introductory statistics course. Advantages of using software and code-based software in this context are discussed. Suggestions are made on how to ease students into using code with…

Statistical and Biophysical Models for Predicting Total and Outdoor Water Use in Los Angeles

NASA Astrophysics Data System (ADS)

Mini, C.; Hogue, T. S.; Pincetl, S.

2012-04-01

Modeling water demand is a complex exercise in the choice of the functional form, techniques and variables to integrate in the model. The goal of the current research is to identify the determinants that control total and outdoor residential water use in semi-arid cities and to utilize that information in the development of statistical and biophysical models that can forecast spatial and temporal urban water use. The City of Los Angeles is unique in its highly diverse socio-demographic, economic and cultural characteristics across neighborhoods, which introduces significant challenges in modeling water use. Increasing climate variability also contributes to uncertainties in water use predictions in urban areas. Monthly individual water use records were acquired from the Los Angeles Department of Water and Power (LADWP) for the 2000 to 2010 period. Study predictors of residential water use include socio-demographic, economic, climate and landscaping variables at the zip code level collected from US Census database. Climate variables are estimated from ground-based observations and calculated at the centroid of each zip code by inverse-distance weighting method. Remotely-sensed products of vegetation biomass and landscape land cover are also utilized. Two linear regression models were developed based on the panel data and variables described: a pooled-OLS regression model and a linear mixed effects model. Both models show income per capita and the percentage of landscape areas in each zip code as being statistically significant predictors. The pooled-OLS model tends to over-estimate higher water use zip codes and both models provide similar RMSE values.Outdoor water use was estimated at the census tract level as the residual between total water use and indoor use. This residual is being compared with the output from a biophysical model including tree and grass cover areas, climate variables and estimates of evapotranspiration at very high spatial resolution. A genetic algorithm based model (Shuffled Complex Evolution-UA; SCE-UA) is also being developed to provide estimates of the predictions and parameters uncertainties and to compare against the linear regression models. Ultimately, models will be selected to undertake predictions for a range of climate change and landscape scenarios. Finally, project results will contribute to a better understanding of water demand to help predict future water use and implement targeted landscaping conservation programs to maintain sustainable water needs for a growing population under uncertain climate variability.

Performance and Architecture Lab Modeling Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-06-19

Analytical application performance models are critical for diagnosing performance-limiting resources, optimizing systems, and designing machines. Creating models, however, is difficult. Furthermore, models are frequently expressed in forms that are hard to distribute and validate. The Performance and Architecture Lab Modeling tool, or Palm, is a modeling tool designed to make application modeling easier. Palm provides a source code modeling annotation language. Not only does the modeling language divide the modeling task into sub problems, it formally links an application's source code with its model. This link is important because a model's purpose is to capture application behavior. Furthermore, this linkmore » makes it possible to define rules for generating models according to source code organization. Palm generates hierarchical models according to well-defined rules. Given an application, a set of annotations, and a representative execution environment, Palm will generate the same model. A generated model is a an executable program whose constituent parts directly correspond to the modeled application. Palm generates models by combining top-down (human-provided) semantic insight with bottom-up static and dynamic analysis. A model's hierarchy is defined by static and dynamic source code structure. Because Palm coordinates models and source code, Palm's models are 'first-class' and reproducible. Palm automates common modeling tasks. For instance, Palm incorporates measurements to focus attention, represent constant behavior, and validate models. Palm's workflow is as follows. The workflow's input is source code annotated with Palm modeling annotations. The most important annotation models an instance of a block of code. Given annotated source code, the Palm Compiler produces executables and the Palm Monitor collects a representative performance profile. The Palm Generator synthesizes a model based on the static and dynamic mapping of annotations to program behavior. The model -- an executable program -- is a hierarchical composition of annotation functions, synthesized functions, statistics for runtime values, and performance measurements.« less

Generalized background error covariance matrix model (GEN_BE v2.0)

NASA Astrophysics Data System (ADS)

Descombes, G.; Auligné, T.; Vandenberghe, F.; Barker, D. M.; Barré, J.

2015-03-01

The specification of state background error statistics is a key component of data assimilation since it affects the impact observations will have on the analysis. In the variational data assimilation approach, applied in geophysical sciences, the dimensions of the background error covariance matrix (B) are usually too large to be explicitly determined and B needs to be modeled. Recent efforts to include new variables in the analysis such as cloud parameters and chemical species have required the development of the code to GENerate the Background Errors (GEN_BE) version 2.0 for the Weather Research and Forecasting (WRF) community model. GEN_BE allows for a simpler, flexible, robust, and community-oriented framework that gathers methods used by some meteorological operational centers and researchers. We present the advantages of this new design for the data assimilation community by performing benchmarks of different modeling of B and showing some of the new features in data assimilation test cases. As data assimilation for clouds remains a challenge, we present a multivariate approach that includes hydrometeors in the control variables and new correlated errors. In addition, the GEN_BE v2.0 code is employed to diagnose error parameter statistics for chemical species, which shows that it is a tool flexible enough to implement new control variables. While the generation of the background errors statistics code was first developed for atmospheric research, the new version (GEN_BE v2.0) can be easily applied to other domains of science and chosen to diagnose and model B. Initially developed for variational data assimilation, the model of the B matrix may be useful for variational ensemble hybrid methods as well.

Statistical Methodologies to Integrate Experimental and Computational Research

NASA Technical Reports Server (NTRS)

Parker, P. A.; Johnson, R. T.; Montgomery, D. C.

2008-01-01

Development of advanced algorithms for simulating engine flow paths requires the integration of fundamental experiments with the validation of enhanced mathematical models. In this paper, we provide an overview of statistical methods to strategically and efficiently conduct experiments and computational model refinement. Moreover, the integration of experimental and computational research efforts is emphasized. With a statistical engineering perspective, scientific and engineering expertise is combined with statistical sciences to gain deeper insights into experimental phenomenon and code development performance; supporting the overall research objectives. The particular statistical methods discussed are design of experiments, response surface methodology, and uncertainty analysis and planning. Their application is illustrated with a coaxial free jet experiment and a turbulence model refinement investigation. Our goal is to provide an overview, focusing on concepts rather than practice, to demonstrate the benefits of using statistical methods in research and development, thereby encouraging their broader and more systematic application.

VAVUQ, Python and Matlab freeware for Verification and Validation, Uncertainty Quantification

NASA Astrophysics Data System (ADS)

Courtney, J. E.; Zamani, K.; Bombardelli, F. A.; Fleenor, W. E.

2015-12-01

A package of scripts is presented for automated Verification and Validation (V&V) and Uncertainty Quantification (UQ) for engineering codes that approximate Partial Differential Equations (PDFs). The code post-processes model results to produce V&V and UQ information. This information can be used to assess model performance. Automated information on code performance can allow for a systematic methodology to assess the quality of model approximations. The software implements common and accepted code verification schemes. The software uses the Method of Manufactured Solutions (MMS), the Method of Exact Solution (MES), Cross-Code Verification, and Richardson Extrapolation (RE) for solution (calculation) verification. It also includes common statistical measures that can be used for model skill assessment. Complete RE can be conducted for complex geometries by implementing high-order non-oscillating numerical interpolation schemes within the software. Model approximation uncertainty is quantified by calculating lower and upper bounds of numerical error from the RE results. The software is also able to calculate the Grid Convergence Index (GCI), and to handle adaptive meshes and models that implement mixed order schemes. Four examples are provided to demonstrate the use of the software for code and solution verification, model validation and uncertainty quantification. The software is used for code verification of a mixed-order compact difference heat transport solver; the solution verification of a 2D shallow-water-wave solver for tidal flow modeling in estuaries; the model validation of a two-phase flow computation in a hydraulic jump compared to experimental data; and numerical uncertainty quantification for 3D CFD modeling of the flow patterns in a Gust erosion chamber.

Quasi-experimental study designs series-paper 10: synthesizing evidence for effects collected from quasi-experimental studies presents surmountable challenges.

PubMed

Becker, Betsy Jane; Aloe, Ariel M; Duvendack, Maren; Stanley, T D; Valentine, Jeffrey C; Fretheim, Atle; Tugwell, Peter

2017-09-01

To outline issues of importance to analytic approaches to the synthesis of quasi-experiments (QEs) and to provide a statistical model for use in analysis. We drew on studies of statistics, epidemiology, and social-science methodology to outline methods for synthesis of QE studies. The design and conduct of QEs, effect sizes from QEs, and moderator variables for the analysis of those effect sizes were discussed. Biases, confounding, design complexities, and comparisons across designs offer serious challenges to syntheses of QEs. Key components of meta-analyses of QEs were identified, including the aspects of QE study design to be coded and analyzed. Of utmost importance are the design and statistical controls implemented in the QEs. Such controls and any potential sources of bias and confounding must be modeled in analyses, along with aspects of the interventions and populations studied. Because of such controls, effect sizes from QEs are more complex than those from randomized experiments. A statistical meta-regression model that incorporates important features of the QEs under review was presented. Meta-analyses of QEs provide particular challenges, but thorough coding of intervention characteristics and study methods, along with careful analysis, should allow for sound inferences. Copyright © 2017 Elsevier Inc. All rights reserved.

BACTERIAL MORTALITY DUE TO SOLAR RADIATION, COMPARING EXPERIMENTAL AND STATISTICAL EVIDENCE

EPA Science Inventory

Many researchers report that sunlight is a primary stressor of beach indicator bacteria. Some water quality models include code that quantifies the effect of radiation on bacterial decay. For example, the EPA Visual Plumes model includes two coliform and one enterococcus submodel...

Subband Image Coding with Jointly Optimized Quantizers

NASA Technical Reports Server (NTRS)

Kossentini, Faouzi; Chung, Wilson C.; Smith Mark J. T.

1995-01-01

An iterative design algorithm for the joint design of complexity- and entropy-constrained subband quantizers and associated entropy coders is proposed. Unlike conventional subband design algorithms, the proposed algorithm does not require the use of various bit allocation algorithms. Multistage residual quantizers are employed here because they provide greater control of the complexity-performance tradeoffs, and also because they allow efficient and effective high-order statistical modeling. The resulting subband coder exploits statistical dependencies within subbands, across subbands, and across stages, mainly through complexity-constrained high-order entropy coding. Experimental results demonstrate that the complexity-rate-distortion performance of the new subband coder is exceptional.

Assessment of uncertainties of the models used in thermal-hydraulic computer codes

NASA Astrophysics Data System (ADS)

Gricay, A. S.; Migrov, Yu. A.

2015-09-01

The article deals with matters concerned with the problem of determining the statistical characteristics of variable parameters (the variation range and distribution law) in analyzing the uncertainty and sensitivity of calculation results to uncertainty in input data. A comparative analysis of modern approaches to uncertainty in input data is presented. The need to develop an alternative method for estimating the uncertainty of model parameters used in thermal-hydraulic computer codes, in particular, in the closing correlations of the loop thermal hydraulics block, is shown. Such a method shall feature the minimal degree of subjectivism and must be based on objective quantitative assessment criteria. The method includes three sequential stages: selecting experimental data satisfying the specified criteria, identifying the key closing correlation using a sensitivity analysis, and carrying out case calculations followed by statistical processing of the results. By using the method, one can estimate the uncertainty range of a variable parameter and establish its distribution law in the above-mentioned range provided that the experimental information is sufficiently representative. Practical application of the method is demonstrated taking as an example the problem of estimating the uncertainty of a parameter appearing in the model describing transition to post-burnout heat transfer that is used in the thermal-hydraulic computer code KORSAR. The performed study revealed the need to narrow the previously established uncertainty range of this parameter and to replace the uniform distribution law in the above-mentioned range by the Gaussian distribution law. The proposed method can be applied to different thermal-hydraulic computer codes. In some cases, application of the method can make it possible to achieve a smaller degree of conservatism in the expert estimates of uncertainties pertinent to the model parameters used in computer codes.

The Evolution of Random Number Generation in MUVES

DTIC Science & Technology

2017-01-01

mathematical basis and statistical justification for algorithms used in the code. The working code provided produces results identical to the current...MUVES, includ- ing the mathematical basis and statistical justification for algorithms used in the code. The working code provided produces results...questionable numerical and statistical properties. The development of the modern system is traced through software change requests, resulting in a random number

Simulating the heterogeneity in braided channel belt deposits: 1. A geometric-based methodology and code

NASA Astrophysics Data System (ADS)

Ramanathan, Ramya; Guin, Arijit; Ritzi, Robert W.; Dominic, David F.; Freedman, Vicky L.; Scheibe, Timothy D.; Lunt, Ian A.

2010-04-01

A geometric-based simulation methodology was developed and incorporated into a computer code to model the hierarchical stratal architecture, and the corresponding spatial distribution of permeability, in braided channel belt deposits. The code creates digital models of these deposits as a three-dimensional cubic lattice, which can be used directly in numerical aquifer or reservoir models for fluid flow. The digital models have stratal units defined from the kilometer scale to the centimeter scale. These synthetic deposits are intended to be used as high-resolution base cases in various areas of computational research on multiscale flow and transport processes, including the testing of upscaling theories. The input parameters are primarily univariate statistics. These include the mean and variance for characteristic lengths of sedimentary unit types at each hierarchical level, and the mean and variance of log-permeability for unit types defined at only the lowest level (smallest scale) of the hierarchy. The code has been written for both serial and parallel execution. The methodology is described in part 1 of this paper. In part 2 (Guin et al., 2010), models generated by the code are presented and evaluated.

Simulating the Heterogeneity in Braided Channel Belt Deposits: Part 1. A Geometric-Based Methodology and Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramanathan, Ramya; Guin, Arijit; Ritzi, Robert W.

A geometric-based simulation methodology was developed and incorporated into a computer code to model the hierarchical stratal architecture, and the corresponding spatial distribution of permeability, in braided channel belt deposits. The code creates digital models of these deposits as a three-dimensional cubic lattice, which can be used directly in numerical aquifer or reservoir models for fluid flow. The digital models have stratal units defined from the km scale to the cm scale. These synthetic deposits are intended to be used as high-resolution base cases in various areas of computational research on multiscale flow and transport processes, including the testing ofmore » upscaling theories. The input parameters are primarily univariate statistics. These include the mean and variance for characteristic lengths of sedimentary unit types at each hierarchical level, and the mean and variance of log-permeability for unit types defined at only the lowest level (smallest scale) of the hierarchy. The code has been written for both serial and parallel execution. The methodology is described in Part 1 of this series. In Part 2, models generated by the code are presented and evaluated.« less

Data Needs and Modeling of the Upper Atmosphere

NASA Astrophysics Data System (ADS)

Brunger, M. J.; Campbell, L.

2007-04-01

We present results from our enhanced statistical equilibrium and time-step codes for atmospheric modeling. In particular we use these results to illustrate the role of electron-driven processes in atmospheric phenomena and the sensitivity of the model results to data inputs such as integral cross sections, dissociative recombination rates and chemical reaction rates.

A Statistical Analysis of IrisCode and Its Security Implications.

PubMed

Kong, Adams Wai-Kin

2015-03-01

IrisCode has been used to gather iris data for 430 million people. Because of the huge impact of IrisCode, it is vital that it is completely understood. This paper first studies the relationship between bit probabilities and a mean of iris images (The mean of iris images is defined as the average of independent iris images.) and then uses the Chi-square statistic, the correlation coefficient and a resampling algorithm to detect statistical dependence between bits. The results show that the statistical dependence forms a graph with a sparse and structural adjacency matrix. A comparison of this graph with a graph whose edges are defined by the inner product of the Gabor filters that produce IrisCodes shows that partial statistical dependence is induced by the filters and propagates through the graph. Using this statistical information, the security risk associated with two patented template protection schemes that have been deployed in commercial systems for producing application-specific IrisCodes is analyzed. To retain high identification speed, they use the same key to lock all IrisCodes in a database. The belief has been that if the key is not compromised, the IrisCodes are secure. This study shows that even without the key, application-specific IrisCodes can be unlocked and that the key can be obtained through the statistical dependence detected.

Statistical Surrogate Modeling of Atmospheric Dispersion Events Using Bayesian Adaptive Splines

NASA Astrophysics Data System (ADS)

Francom, D.; Sansó, B.; Bulaevskaya, V.; Lucas, D. D.

2016-12-01

Uncertainty in the inputs of complex computer models, including atmospheric dispersion and transport codes, is often assessed via statistical surrogate models. Surrogate models are computationally efficient statistical approximations of expensive computer models that enable uncertainty analysis. We introduce Bayesian adaptive spline methods for producing surrogate models that capture the major spatiotemporal patterns of the parent model, while satisfying all the necessities of flexibility, accuracy and computational feasibility. We present novel methodological and computational approaches motivated by a controlled atmospheric tracer release experiment conducted at the Diablo Canyon nuclear power plant in California. Traditional methods for building statistical surrogate models often do not scale well to experiments with large amounts of data. Our approach is well suited to experiments involving large numbers of model inputs, large numbers of simulations, and functional output for each simulation. Our approach allows us to perform global sensitivity analysis with ease. We also present an approach to calibration of simulators using field data.

Modeling and Simulation with INS.

ERIC Educational Resources Information Center

Roberts, Stephen D.; And Others

INS, the Integrated Network Simulation language, puts simulation modeling into a network framework and automatically performs such programming activities as placing the problem into a next event structure, coding events, collecting statistics, monitoring status, and formatting reports. To do this, INS provides a set of symbols (nodes and branches)…

Generalized Background Error covariance matrix model (GEN_BE v2.0)

NASA Astrophysics Data System (ADS)

Descombes, G.; Auligné, T.; Vandenberghe, F.; Barker, D. M.

2014-07-01

The specification of state background error statistics is a key component of data assimilation since it affects the impact observations will have on the analysis. In the variational data assimilation approach, applied in geophysical sciences, the dimensions of the background error covariance matrix (B) are usually too large to be explicitly determined and B needs to be modeled. Recent efforts to include new variables in the analysis such as cloud parameters and chemical species have required the development of the code to GENerate the Background Errors (GEN_BE) version 2.0 for the Weather Research and Forecasting (WRF) community model to allow for a simpler, flexible, robust, and community-oriented framework that gathers methods used by meteorological operational centers and researchers. We present the advantages of this new design for the data assimilation community by performing benchmarks and showing some of the new features on data assimilation test cases. As data assimilation for clouds remains a challenge, we present a multivariate approach that includes hydrometeors in the control variables and new correlated errors. In addition, the GEN_BE v2.0 code is employed to diagnose error parameter statistics for chemical species, which shows that it is a tool flexible enough to involve new control variables. While the generation of the background errors statistics code has been first developed for atmospheric research, the new version (GEN_BE v2.0) can be easily extended to other domains of science and be chosen as a testbed for diagnostic and new modeling of B. Initially developed for variational data assimilation, the model of the B matrix may be useful for variational ensemble hybrid methods as well.

49 CFR 1248.100 - Commodity classification designated.

Code of Federal Regulations, 2010 CFR

2010-10-01

... STATISTICS Commodity Code § 1248.100 Commodity classification designated. Commencing with reports for the..., reports of commodity statistics required to be made to the Board, shall be based on the commodity codes... Statistics, 1963, issued by the Bureau of the Budget, and on additional codes 411 through 462 shown in § 1248...

Learning Midlevel Auditory Codes from Natural Sound Statistics.

PubMed

Młynarski, Wiktor; McDermott, Josh H

2018-03-01

Interaction with the world requires an organism to transform sensory signals into representations in which behaviorally meaningful properties of the environment are made explicit. These representations are derived through cascades of neuronal processing stages in which neurons at each stage recode the output of preceding stages. Explanations of sensory coding may thus involve understanding how low-level patterns are combined into more complex structures. To gain insight into such midlevel representations for sound, we designed a hierarchical generative model of natural sounds that learns combinations of spectrotemporal features from natural stimulus statistics. In the first layer, the model forms a sparse convolutional code of spectrograms using a dictionary of learned spectrotemporal kernels. To generalize from specific kernel activation patterns, the second layer encodes patterns of time-varying magnitude of multiple first-layer coefficients. When trained on corpora of speech and environmental sounds, some second-layer units learned to group similar spectrotemporal features. Others instantiate opponency between distinct sets of features. Such groupings might be instantiated by neurons in the auditory cortex, providing a hypothesis for midlevel neuronal computation.

Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons

PubMed Central

Mensi, Skander; Hagens, Olivier; Gerstner, Wulfram; Pozzorini, Christian

2016-01-01

The way in which single neurons transform input into output spike trains has fundamental consequences for network coding. Theories and modeling studies based on standard Integrate-and-Fire models implicitly assume that, in response to increasingly strong inputs, neurons modify their coding strategy by progressively reducing their selective sensitivity to rapid input fluctuations. Combining mathematical modeling with in vitro experiments, we demonstrate that, in L5 pyramidal neurons, the firing threshold dynamics adaptively adjust the effective timescale of somatic integration in order to preserve sensitivity to rapid signals over a broad range of input statistics. For that, a new Generalized Integrate-and-Fire model featuring nonlinear firing threshold dynamics and conductance-based adaptation is introduced that outperforms state-of-the-art neuron models in predicting the spiking activity of neurons responding to a variety of in vivo-like fluctuating currents. Our model allows for efficient parameter extraction and can be analytically mapped to a Generalized Linear Model in which both the input filter—describing somatic integration—and the spike-history filter—accounting for spike-frequency adaptation—dynamically adapt to the input statistics, as experimentally observed. Overall, our results provide new insights on the computational role of different biophysical processes known to underlie adaptive coding in single neurons and support previous theoretical findings indicating that the nonlinear dynamics of the firing threshold due to Na+-channel inactivation regulate the sensitivity to rapid input fluctuations. PMID:26907675

Topological color codes on Union Jack lattices: a stable implementation of the whole Clifford group

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katzgraber, Helmut G.; Theoretische Physik, ETH Zurich, CH-8093 Zurich; Bombin, H.

We study the error threshold of topological color codes on Union Jack lattices that allow for the full implementation of the whole Clifford group of quantum gates. After mapping the error-correction process onto a statistical mechanical random three-body Ising model on a Union Jack lattice, we compute its phase diagram in the temperature-disorder plane using Monte Carlo simulations. Surprisingly, topological color codes on Union Jack lattices have a similar error stability to color codes on triangular lattices, as well as to the Kitaev toric code. The enhanced computational capabilities of the topological color codes on Union Jack lattices with respectmore » to triangular lattices and the toric code combined with the inherent robustness of this implementation show good prospects for future stable quantum computer implementations.« less

Influence of the plasma environment on atomic structure using an ion-sphere model

NASA Astrophysics Data System (ADS)

Belkhiri, Madeny; Fontes, Christopher J.; Poirier, Michel

2015-09-01

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22 +, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the multiconfiguration Dirac-Fock value of B. Saha and S. Fritzsche [J. Phys. B 40, 259 (2007), 10.1088/0953-4075/40/2/002]. Last, the present model is compared to experimental data in titanium measured on the terawatt Astra facility and provides values for electron temperature and density in agreement with the maria code.

Statistical properties of DNA sequences

NASA Technical Reports Server (NTRS)

Peng, C. K.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Simons, M.; Stanley, H. E.

1995-01-01

We review evidence supporting the idea that the DNA sequence in genes containing non-coding regions is correlated, and that the correlation is remarkably long range--indeed, nucleotides thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationarity" feature of the sequence of base pairs by applying a new algorithm called detrended fluctuation analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and non-coding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33301 coding and 29453 non-coding) in the entire GenBank database. Finally, we describe briefly some recent work showing that the non-coding sequences have certain statistical features in common with natural and artificial languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts. These statistical properties of non-coding sequences support the possibility that non-coding regions of DNA may carry biological information.

User's Manual for RESRAD-OFFSITE Version 2.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, C.; Gnanapragasam, E.; Biwer, B. M.

2007-09-05

The RESRAD-OFFSITE code is an extension of the RESRAD (onsite) code, which has been widely used for calculating doses and risks from exposure to radioactively contaminated soils. The development of RESRAD-OFFSITE started more than 10 years ago, but new models and methodologies have been developed, tested, and incorporated since then. Some of the new models have been benchmarked against other independently developed (international) models. The databases used have also expanded to include all the radionuclides (more than 830) contained in the International Commission on Radiological Protection (ICRP) 38 database. This manual provides detailed information on the design and application ofmore » the RESRAD-OFFSITE code. It describes in detail the new models used in the code, such as the three-dimensional dispersion groundwater flow and radionuclide transport model, the Gaussian plume model for atmospheric dispersion, and the deposition model used to estimate the accumulation of radionuclides in offsite locations and in foods. Potential exposure pathways and exposure scenarios that can be modeled by the RESRAD-OFFSITE code are also discussed. A user's guide is included in Appendix A of this manual. The default parameter values and parameter distributions are presented in Appendix B, along with a discussion on the statistical distributions for probabilistic analysis. A detailed discussion on how to reduce run time, especially when conducting probabilistic (uncertainty) analysis, is presented in Appendix C of this manual.« less

Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study

PubMed Central

Bornschein, Jörg; Henniges, Marc; Lücke, Jörg

2013-01-01

Simple cells in primary visual cortex were famously found to respond to low-level image components such as edges. Sparse coding and independent component analysis (ICA) emerged as the standard computational models for simple cell coding because they linked their receptive fields to the statistics of visual stimuli. However, a salient feature of image statistics, occlusions of image components, is not considered by these models. Here we ask if occlusions have an effect on the predicted shapes of simple cell receptive fields. We use a comparative approach to answer this question and investigate two models for simple cells: a standard linear model and an occlusive model. For both models we simultaneously estimate optimal receptive fields, sparsity and stimulus noise. The two models are identical except for their component superposition assumption. We find the image encoding and receptive fields predicted by the models to differ significantly. While both models predict many Gabor-like fields, the occlusive model predicts a much sparser encoding and high percentages of ‘globular’ receptive fields. This relatively new center-surround type of simple cell response is observed since reverse correlation is used in experimental studies. While high percentages of ‘globular’ fields can be obtained using specific choices of sparsity and overcompleteness in linear sparse coding, no or only low proportions are reported in the vast majority of studies on linear models (including all ICA models). Likewise, for the here investigated linear model and optimal sparsity, only low proportions of ‘globular’ fields are observed. In comparison, the occlusive model robustly infers high proportions and can match the experimentally observed high proportions of ‘globular’ fields well. Our computational study, therefore, suggests that ‘globular’ fields may be evidence for an optimal encoding of visual occlusions in primary visual cortex. PMID:23754938

Reproducible research in vadose zone sciences

USDA-ARS?s Scientific Manuscript database

A significant portion of present-day soil and Earth science research is computational, involving complex data analysis pipelines, advanced mathematical and statistical models, and sophisticated computer codes. Opportunities for scientific progress are greatly diminished if reproducing and building o...

Statistics on continuous IBD data: Exact distribution evaluation for a pair of full(half)-sibs and a pair of a (great-) grandchild with a (great-) grandparent

PubMed Central

Stefanov, Valeri T

2002-01-01

Background Pairs of related individuals are widely used in linkage analysis. Most of the tests for linkage analysis are based on statistics associated with identity by descent (IBD) data. The current biotechnology provides data on very densely packed loci, and therefore, it may provide almost continuous IBD data for pairs of closely related individuals. Therefore, the distribution theory for statistics on continuous IBD data is of interest. In particular, distributional results which allow the evaluation of p-values for relevant tests are of importance. Results A technology is provided for numerical evaluation, with any given accuracy, of the cumulative probabilities of some statistics on continuous genome data for pairs of closely related individuals. In the case of a pair of full-sibs, the following statistics are considered: (i) the proportion of genome with 2 (at least 1) haplotypes shared identical-by-descent (IBD) on a chromosomal segment, (ii) the number of distinct pieces (subsegments) of a chromosomal segment, on each of which exactly 2 (at least 1) haplotypes are shared IBD. The natural counterparts of these statistics for the other relationships are also considered. Relevant Maple codes are provided for a rapid evaluation of the cumulative probabilities of such statistics. The genomic continuum model, with Haldane's model for the crossover process, is assumed. Conclusions A technology, together with relevant software codes for its automated implementation, are provided for exact evaluation of the distributions of relevant statistics associated with continuous genome data on closely related individuals. PMID:11996673

The Two-Dimensional Gabor Function Adapted to Natural Image Statistics: A Model of Simple-Cell Receptive Fields and Sparse Structure in Images.

PubMed

Loxley, P N

2017-10-01

The two-dimensional Gabor function is adapted to natural image statistics, leading to a tractable probabilistic generative model that can be used to model simple cell receptive field profiles, or generate basis functions for sparse coding applications. Learning is found to be most pronounced in three Gabor function parameters representing the size and spatial frequency of the two-dimensional Gabor function and characterized by a nonuniform probability distribution with heavy tails. All three parameters are found to be strongly correlated, resulting in a basis of multiscale Gabor functions with similar aspect ratios and size-dependent spatial frequencies. A key finding is that the distribution of receptive-field sizes is scale invariant over a wide range of values, so there is no characteristic receptive field size selected by natural image statistics. The Gabor function aspect ratio is found to be approximately conserved by the learning rules and is therefore not well determined by natural image statistics. This allows for three distinct solutions: a basis of Gabor functions with sharp orientation resolution at the expense of spatial-frequency resolution, a basis of Gabor functions with sharp spatial-frequency resolution at the expense of orientation resolution, or a basis with unit aspect ratio. Arbitrary mixtures of all three cases are also possible. Two parameters controlling the shape of the marginal distributions in a probabilistic generative model fully account for all three solutions. The best-performing probabilistic generative model for sparse coding applications is found to be a gaussian copula with Pareto marginal probability density functions.

A Review of Structural Equation Modeling Applications in Turkish Educational Science Literature, 2010-2015

ERIC Educational Resources Information Center

Karakaya-Ozyer, Kubra; Aksu-Dunya, Beyza

2018-01-01

Structural equation modeling (SEM) is one of the most popular multivariate statistical techniques in Turkish educational research. This study elaborates the SEM procedures employed by 75 educational research articles which were published from 2010 to 2015 in Turkey. After documenting and coding 75 academic papers, categorical frequencies and…

Reduced Order Modeling Methods for Turbomachinery Design

DTIC Science & Technology

2009-03-01

and Ma- terials Conference, May 2006. [45] A. Gelman , J. B. Carlin, H. S. Stern, and D. B. Rubin, Bayesian Data Analysis. New York, NY: Chapman I& Hall...Macian- Juan , and R. Chawla, “A statistical methodology for quantif ca- tion of uncertainty in best estimate code physical models,” Annals of Nuclear En

The reliability of cause-of-death coding in The Netherlands.

PubMed

Harteloh, Peter; de Bruin, Kim; Kardaun, Jan

2010-08-01

Cause-of-death statistics are a major source of information for epidemiological research or policy decisions. Information on the reliability of these statistics is important for interpreting trends in time or differences between populations. Variations in coding the underlying cause of death could hinder the attribution of observed differences to determinants of health. Therefore we studied the reliability of cause-of-death statistics in The Netherlands. We performed a double coding study. Death certificates from the month of May 2005 were coded again in 2007. Each death certificate was coded manually by four coders. Reliability was measured by calculating agreement between coders (intercoder agreement) and by calculating the consistency of each individual coder in time (intracoder agreement). Our analysis covered an amount of 10,833 death certificates. The intercoder agreement of four coders on the underlying cause of death was 78%. In 2.2% of the cases coders agreed on a change of the code assigned in 2005. The (mean) intracoder agreement of four coders was 89%. Agreement was associated with the specificity of the ICD-10 code (chapter, three digits, four digits), the age of the deceased, the number of coders and the number of diseases reported on the death certificate. The reliability of cause-of-death statistics turned out to be high (>90%) for major causes of death such as cancers and acute myocardial infarction. For chronic diseases, such as diabetes and renal insufficiency, reliability was low (<70%). The reliability of cause-of-death statistics varies by ICD-10 code/chapter. A statistical office should provide coders with (additional) rules for coding diseases with a low reliability and evaluate these rules regularly. Users of cause-of-death statistics should exercise caution when interpreting causes of death with a low reliability. Studies of reliability should take into account the number of coders involved and the number of codes on a death certificate.

Study of statistical coding for digital TV

NASA Technical Reports Server (NTRS)

Gardenhire, L. W.

1972-01-01

The results are presented for a detailed study to determine a pseudo-optimum statistical code to be installed in a digital TV demonstration test set. Studies of source encoding were undertaken, using redundancy removal techniques in which the picture is reproduced within a preset tolerance. A method of source encoding, which preliminary studies show to be encouraging, is statistical encoding. A pseudo-optimum code was defined and the associated performance of the code was determined. The format was fixed at 525 lines per frame, 30 frames per second, as per commercial standards.

Estimating times of surgeries with two component procedures: comparison of the lognormal and normal models.

PubMed

Strum, David P; May, Jerrold H; Sampson, Allan R; Vargas, Luis G; Spangler, William E

2003-01-01

Variability inherent in the duration of surgical procedures complicates surgical scheduling. Modeling the duration and variability of surgeries might improve time estimates. Accurate time estimates are important operationally to improve utilization, reduce costs, and identify surgeries that might be considered outliers. Surgeries with multiple procedures are difficult to model because they are difficult to segment into homogenous groups and because they are performed less frequently than single-procedure surgeries. The authors studied, retrospectively, 10,740 surgeries each with exactly two CPTs and 46,322 surgical cases with only one CPT from a large teaching hospital to determine if the distribution of dual-procedure surgery times fit more closely a lognormal or a normal model. The authors tested model goodness of fit to their data using Shapiro-Wilk tests, studied factors affecting the variability of time estimates, and examined the impact of coding permutations (ordered combinations) on modeling. The Shapiro-Wilk tests indicated that the lognormal model is statistically superior to the normal model for modeling dual-procedure surgeries. Permutations of component codes did not appear to differ significantly with respect to total procedure time and surgical time. To improve individual models for infrequent dual-procedure surgeries, permutations may be reduced and estimates may be based on the longest component procedure and type of anesthesia. The authors recommend use of the lognormal model for estimating surgical times for surgeries with two component procedures. Their results help legitimize the use of log transforms to normalize surgical procedure times prior to hypothesis testing using linear statistical models. Multiple-procedure surgeries may be modeled using the longest (statistically most important) component procedure and type of anesthesia.

Implementation and Testing of Turbulence Models for the F18-HARV Simulation

NASA Technical Reports Server (NTRS)

Yeager, Jessie C.

1998-01-01

This report presents three methods of implementing the Dryden power spectral density model for atmospheric turbulence. Included are the equations which define the three methods and computer source code written in Advanced Continuous Simulation Language to implement the equations. Time-history plots and sample statistics of simulated turbulence results from executing the code in a test program are also presented. Power spectral densities were computed for sample sequences of turbulence and are plotted for comparison with the Dryden spectra. The three model implementations were installed in a nonlinear six-degree-of-freedom simulation of the High Alpha Research Vehicle airplane. Aircraft simulation responses to turbulence generated with the three implementations are presented as plots.

Statistical and linguistic features of DNA sequences

NASA Technical Reports Server (NTRS)

Havlin, S.; Buldyrev, S. V.; Goldberger, A. L.; Mantegna, R. N.; Peng, C. K.; Simons, M.; Stanley, H. E.

1995-01-01

We present evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range--indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationary" feature of the sequence of base pairs by applying a new algorithm called Detrended Fluctuation Analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and noncoding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to all eukaryotic DNA sequences (33 301 coding and 29 453 noncoding) in the entire GenBank database. We describe a simple model to account for the presence of long-range power-law correlations which is based upon a generalization of the classic Levy walk. Finally, we describe briefly some recent work showing that the noncoding sequences have certain statistical features in common with natural languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function. We suggest that noncoding regions in plants and invertebrates may display a smaller entropy and larger redundancy than coding regions, further supporting the possibility that noncoding regions of DNA may carry biological information.

Billing code algorithms to identify cases of peripheral artery disease from administrative data

PubMed Central

Fan, Jin; Arruda-Olson, Adelaide M; Leibson, Cynthia L; Smith, Carin; Liu, Guanghui; Bailey, Kent R; Kullo, Iftikhar J

2013-01-01

Objective To construct and validate billing code algorithms for identifying patients with peripheral arterial disease (PAD). Methods We extracted all encounters and line item details including PAD-related billing codes at Mayo Clinic Rochester, Minnesota, between July 1, 1997 and June 30, 2008; 22 712 patients evaluated in the vascular laboratory were divided into training and validation sets. Multiple logistic regression analysis was used to create an integer code score from the training dataset, and this was tested in the validation set. We applied a model-based code algorithm to patients evaluated in the vascular laboratory and compared this with a simpler algorithm (presence of at least one of the ICD-9 PAD codes 440.20–440.29). We also applied both algorithms to a community-based sample (n=4420), followed by a manual review. Results The logistic regression model performed well in both training and validation datasets (c statistic=0.91). In patients evaluated in the vascular laboratory, the model-based code algorithm provided better negative predictive value. The simpler algorithm was reasonably accurate for identification of PAD status, with lesser sensitivity and greater specificity. In the community-based sample, the sensitivity (38.7% vs 68.0%) of the simpler algorithm was much lower, whereas the specificity (92.0% vs 87.6%) was higher than the model-based algorithm. Conclusions A model-based billing code algorithm had reasonable accuracy in identifying PAD cases from the community, and in patients referred to the non-invasive vascular laboratory. The simpler algorithm had reasonable accuracy for identification of PAD in patients referred to the vascular laboratory but was significantly less sensitive in a community-based sample. PMID:24166724

Clinical study of the Erlanger silver catheter--data management and biometry.

PubMed

Martus, P; Geis, C; Lugauer, S; Böswald, M; Guggenbichler, J P

1999-01-01

The clinical evaluation of venous catheters for catheter-induced infections must conform to a strict biometric methodology. The statistical planning of the study (target population, design, degree of blinding), data management (database design, definition of variables, coding), quality assurance (data inspection at several levels) and the biometric evaluation of the Erlanger silver catheter project are described. The three-step data flow included: 1) primary data from the hospital, 2) relational database, 3) files accessible for statistical evaluation. Two different statistical models were compared: analyzing the first catheter only of a patient in the analysis (independent data) and analyzing several catheters from the same patient (dependent data) by means of the generalized estimating equations (GEE) method. The main result of the study was based on the comparison of both statistical models.

Personality assessment and model comparison with behavioral data: A statistical framework and empirical demonstration with bonobos (Pan paniscus).

PubMed

Martin, Jordan S; Suarez, Scott A

2017-08-01

Interest in quantifying consistent among-individual variation in primate behavior, also known as personality, has grown rapidly in recent decades. Although behavioral coding is the most frequently utilized method for assessing primate personality, limitations in current statistical practice prevent researchers' from utilizing the full potential of their coding datasets. These limitations include the use of extensive data aggregation, not modeling biologically relevant sources of individual variance during repeatability estimation, not partitioning between-individual (co)variance prior to modeling personality structure, the misuse of principal component analysis, and an over-reliance upon exploratory statistical techniques to compare personality models across populations, species, and data collection methods. In this paper, we propose a statistical framework for primate personality research designed to address these limitations. Our framework synthesizes recently developed mixed-effects modeling approaches for quantifying behavioral variation with an information-theoretic model selection paradigm for confirmatory personality research. After detailing a multi-step analytic procedure for personality assessment and model comparison, we employ this framework to evaluate seven models of personality structure in zoo-housed bonobos (Pan paniscus). We find that differences between sexes, ages, zoos, time of observation, and social group composition contributed to significant behavioral variance. Independently of these factors, however, personality nonetheless accounted for a moderate to high proportion of variance in average behavior across observational periods. A personality structure derived from past rating research receives the strongest support relative to our model set. This model suggests that personality variation across the measured behavioral traits is best described by two correlated but distinct dimensions reflecting individual differences in affiliation and sociability (Agreeableness) as well as activity level, social play, and neophilia toward non-threatening stimuli (Openness). These results underscore the utility of our framework for quantifying personality in primates and facilitating greater integration between the behavioral ecological and comparative psychological approaches to personality research. © 2017 Wiley Periodicals, Inc.

Statistics for laminar flamelet modeling

NASA Technical Reports Server (NTRS)

Cant, R. S.; Rutland, C. J.; Trouve, A.

1990-01-01

Statistical information required to support modeling of turbulent premixed combustion by laminar flamelet methods is extracted from a database of the results of Direct Numerical Simulation of turbulent flames. The simulations were carried out previously by Rutland (1989) using a pseudo-spectral code on a three dimensional mesh of 128 points in each direction. One-step Arrhenius chemistry was employed together with small heat release. A framework for the interpretation of the data is provided by the Bray-Moss-Libby model for the mean turbulent reaction rate. Probability density functions are obtained over surfaces of the constant reaction progress variable for the tangential strain rate and the principal curvature. New insights are gained which will greatly aid the development of modeling approaches.

A methodology for the rigorous verification of plasma simulation codes

NASA Astrophysics Data System (ADS)

Riva, Fabio

2016-10-01

The methodology used to assess the reliability of numerical simulation codes constitutes the Verification and Validation (V&V) procedure. V&V is composed by two separate tasks: the verification, which is a mathematical issue targeted to assess that the physical model is correctly solved, and the validation, which determines the consistency of the code results, and therefore of the physical model, with experimental data. In the present talk we focus our attention on the verification, which in turn is composed by the code verification, targeted to assess that a physical model is correctly implemented in a simulation code, and the solution verification, that quantifies the numerical error affecting a simulation. Bridging the gap between plasma physics and other scientific domains, we introduced for the first time in our domain a rigorous methodology for the code verification, based on the method of manufactured solutions, as well as a solution verification based on the Richardson extrapolation. This methodology was applied to GBS, a three-dimensional fluid code based on a finite difference scheme, used to investigate the plasma turbulence in basic plasma physics experiments and in the tokamak scrape-off layer. Overcoming the difficulty of dealing with a numerical method intrinsically affected by statistical noise, we have now generalized the rigorous verification methodology to simulation codes based on the particle-in-cell algorithm, which are employed to solve Vlasov equation in the investigation of a number of plasma physics phenomena.

Bayesian Atmospheric Radiative Transfer (BART): Model, Statistics Driver, and Application to HD 209458b

NASA Astrophysics Data System (ADS)

Cubillos, Patricio; Harrington, Joseph; Blecic, Jasmina; Stemm, Madison M.; Lust, Nate B.; Foster, Andrew S.; Rojo, Patricio M.; Loredo, Thomas J.

2014-11-01

Multi-wavelength secondary-eclipse and transit depths probe the thermo-chemical properties of exoplanets. In recent years, several research groups have developed retrieval codes to analyze the existing data and study the prospects of future facilities. However, the scientific community has limited access to these packages. Here we premiere the open-source Bayesian Atmospheric Radiative Transfer (BART) code. We discuss the key aspects of the radiative-transfer algorithm and the statistical package. The radiation code includes line databases for all HITRAN molecules, high-temperature H2O, TiO, and VO, and includes a preprocessor for adding additional line databases without recompiling the radiation code. Collision-induced absorption lines are available for H2-H2 and H2-He. The parameterized thermal and molecular abundance profiles can be modified arbitrarily without recompilation. The generated spectra are integrated over arbitrary bandpasses for comparison to data. BART's statistical package, Multi-core Markov-chain Monte Carlo (MC3), is a general-purpose MCMC module. MC3 implements the Differental-evolution Markov-chain Monte Carlo algorithm (ter Braak 2006, 2009). MC3 converges 20-400 times faster than the usual Metropolis-Hastings MCMC algorithm, and in addition uses the Message Passing Interface (MPI) to parallelize the MCMC chains. We apply the BART retrieval code to the HD 209458b data set to estimate the planet's temperature profile and molecular abundances. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

Derivation and Validation of the Surgical Site Infections Risk Model Using Health Administrative Data.

PubMed

van Walraven, Carl; Jackson, Timothy D; Daneman, Nick

2016-04-01

OBJECTIVE Surgical site infections (SSIs) are common hospital-acquired infections. Tracking SSIs is important to monitor their incidence, and this process requires primary data collection. In this study, we derived and validated a method using health administrative data to predict the probability that a person who had surgery would develop an SSI within 30 days. METHODS All patients enrolled in the National Surgical Quality Improvement Program (NSQIP) from 2 sites were linked to population-based administrative datasets in Ontario, Canada. We derived a multivariate model, stratified by surgical specialty, to determine the independent association of SSI status with patient and hospitalization covariates as well as physician claim codes. This SSI risk model was validated in 2 cohorts. RESULTS The derivation cohort included 5,359 patients with a 30-day SSI incidence of 6.0% (n=118). The SSI risk model predicted the probability that a person had an SSI based on 7 covariates: index hospitalization diagnostic score; physician claims score; emergency visit diagnostic score; operation duration; surgical service; and potential SSI codes. More than 90% of patients had predicted SSI risks lower than 10%. In the derivation group, model discrimination and calibration was excellent (C statistic, 0.912; Hosmer-Lemeshow [H-L] statistic, P=.47). In the 2 validation groups, performance decreased slightly (C statistics, 0.853 and 0.812; H-L statistics, 26.4 [P=.0009] and 8.0 [P=.42]), but low-risk patients were accurately identified. CONCLUSION Health administrative data can effectively identify postoperative patients with a very low risk of surgical site infection within 30 days of their procedure. Records of higher-risk patients can be reviewed to confirm SSI status.

Predicting trauma patient mortality: ICD [or ICD-10-AM] versus AIS based approaches.

PubMed

Willis, Cameron D; Gabbe, Belinda J; Jolley, Damien; Harrison, James E; Cameron, Peter A

2010-11-01

The International Classification of Diseases Injury Severity Score (ICISS) has been proposed as an International Classification of Diseases (ICD)-10-based alternative to mortality prediction tools that use Abbreviated Injury Scale (AIS) data, including the Trauma and Injury Severity Score (TRISS). To date, studies have not examined the performance of ICISS using Australian trauma registry data. This study aimed to compare the performance of ICISS with other mortality prediction tools in an Australian trauma registry. This was a retrospective review of prospectively collected data from the Victorian State Trauma Registry. A training dataset was created for model development and a validation dataset for evaluation. The multiplicative ICISS model was compared with a worst injury ICISS approach, Victorian TRISS (V-TRISS, using local coefficients), maximum AIS severity and a multivariable model including ICD-10-AM codes as predictors. Models were investigated for discrimination (C-statistic) and calibration (Hosmer-Lemeshow statistic). The multivariable approach had the highest level of discrimination (C-statistic 0.90) and calibration (H-L 7.65, P= 0.468). Worst injury ICISS, V-TRISS and maximum AIS had similar performance. The multiplicative ICISS produced the lowest level of discrimination (C-statistic 0.80) and poorest calibration (H-L 50.23, P < 0.001). The performance of ICISS may be affected by the data used to develop estimates, the ICD version employed, the methods for deriving estimates and the inclusion of covariates. In this analysis, a multivariable approach using ICD-10-AM codes was the best-performing method. A multivariable ICISS approach may therefore be a useful alternative to AIS-based methods and may have comparable predictive performance to locally derived TRISS models. © 2010 The Authors. ANZ Journal of Surgery © 2010 Royal Australasian College of Surgeons.

KEWPIE2: A cascade code for the study of dynamical decay of excited nuclei

NASA Astrophysics Data System (ADS)

Lü, Hongliang; Marchix, Anthony; Abe, Yasuhisa; Boilley, David

2016-03-01

KEWPIE-a cascade code devoted to investigating the dynamical decay of excited nuclei, specially designed for treating very low probability events related to the synthesis of super-heavy nuclei formed in fusion-evaporation reactions-has been improved and rewritten in C++ programming language to become KEWPIE2. The current version of the code comprises various nuclear models concerning the light-particle emission, fission process and statistical properties of excited nuclei. General features of the code, such as the numerical scheme and the main physical ingredients, are described in detail. Some typical calculations having been performed in the present paper clearly show that theoretical predictions are generally in accordance with experimental data. Furthermore, since the values of some input parameters cannot be determined neither theoretically nor experimentally, a sensibility analysis is presented. To this end, we systematically investigate the effects of using different parameter values and reaction models on the final results. As expected, in the case of heavy nuclei, the fission process has the most crucial role to play in theoretical predictions. This work would be essential for numerical modeling of fusion-evaporation reactions.

SPIDERMAN: an open-source code to model phase curves and secondary eclipses

NASA Astrophysics Data System (ADS)

Louden, Tom; Kreidberg, Laura

2018-06-01

We present SPIDERMAN (Secondary eclipse and Phase curve Integrator for 2D tempERature MAppiNg), a fast code for calculating exoplanet phase curves and secondary eclipses with arbitrary surface brightness distributions in two dimensions. Using a geometrical algorithm, the code solves exactly the area of sections of the disc of the planet that are occulted by the star. The code is written in C with a user-friendly Python interface, and is optimized to run quickly, with no loss in numerical precision. Approximately 1000 models can be generated per second in typical use, making Markov Chain Monte Carlo analyses practicable. The modular nature of the code allows easy comparison of the effect of multiple different brightness distributions for the data set. As a test case, we apply the code to archival data on the phase curve of WASP-43b using a physically motivated analytical model for the two-dimensional brightness map. The model provides a good fit to the data; however, it overpredicts the temperature of the nightside. We speculate that this could be due to the presence of clouds on the nightside of the planet, or additional reflected light from the dayside. When testing a simple cloud model, we find that the best-fitting model has a geometric albedo of 0.32 ± 0.02 and does not require a hot nightside. We also test for variation of the map parameters as a function of wavelength and find no statistically significant correlations. SPIDERMAN is available for download at https://github.com/tomlouden/spiderman.

Inference in the brain: Statistics flowing in redundant population codes

PubMed Central

Pitkow, Xaq; Angelaki, Dora E

2017-01-01

It is widely believed that the brain performs approximate probabilistic inference to estimate causal variables in the world from ambiguous sensory data. To understand these computations, we need to analyze how information is represented and transformed by the actions of nonlinear recurrent neural networks. We propose that these probabilistic computations function by a message-passing algorithm operating at the level of redundant neural populations. To explain this framework, we review its underlying concepts, including graphical models, sufficient statistics, and message-passing, and then describe how these concepts could be implemented by recurrently connected probabilistic population codes. The relevant information flow in these networks will be most interpretable at the population level, particularly for redundant neural codes. We therefore outline a general approach to identify the essential features of a neural message-passing algorithm. Finally, we argue that to reveal the most important aspects of these neural computations, we must study large-scale activity patterns during moderately complex, naturalistic behaviors. PMID:28595050

Response surface method in geotechnical/structural analysis, phase 1

NASA Astrophysics Data System (ADS)

Wong, F. S.

1981-02-01

In the response surface approach, an approximating function is fit to a long running computer code based on a limited number of code calculations. The approximating function, called the response surface, is then used to replace the code in subsequent repetitive computations required in a statistical analysis. The procedure of the response surface development and feasibility of the method are shown using a sample problem in slop stability which is based on data from centrifuge experiments of model soil slopes and involves five random soil parameters. It is shown that a response surface can be constructed based on as few as four code calculations and that the response surface is computationally extremely efficient compared to the code calculation. Potential applications of this research include probabilistic analysis of dynamic, complex, nonlinear soil/structure systems such as slope stability, liquefaction, and nuclear reactor safety.

Categorical data processing for real estate objects valuation using statistical analysis

NASA Astrophysics Data System (ADS)

Parygin, D. S.; Malikov, V. P.; Golubev, A. V.; Sadovnikova, N. P.; Petrova, T. M.; Finogeev, A. G.

2018-05-01

Theoretical and practical approaches to the use of statistical methods for studying various properties of infrastructure objects are analyzed in the paper. Methods of forecasting the value of objects are considered. A method for coding categorical variables describing properties of real estate objects is proposed. The analysis of the results of modeling the price of real estate objects using regression analysis and an algorithm based on a comparative approach is carried out.

Local statistics adaptive entropy coding method for the improvement of H.26L VLC coding

NASA Astrophysics Data System (ADS)

Yoo, Kook-yeol; Kim, Jong D.; Choi, Byung-Sun; Lee, Yung Lyul

2000-05-01

In this paper, we propose an adaptive entropy coding method to improve the VLC coding efficiency of H.26L TML-1 codec. First of all, we will show that the VLC coding presented in TML-1 does not satisfy the sibling property of entropy coding. Then, we will modify the coding method into the local statistics adaptive one to satisfy the property. The proposed method based on the local symbol statistics dynamically changes the mapping relationship between symbol and bit pattern in the VLC table according to sibling property. Note that the codewords in the VLC table of TML-1 codec is not changed. Since this changed mapping relationship also derived in the decoder side by using the decoded symbols, the proposed VLC coding method does not require any overhead information. The simulation results show that the proposed method gives about 30% and 37% reduction in average bit rate for MB type and CBP information, respectively.

Statistical Analysis of CFD Solutions from the Third AIAA Drag Prediction Workshop

NASA Technical Reports Server (NTRS)

Morrison, Joseph H.; Hemsch, Michael J.

2007-01-01

The first AIAA Drag Prediction Workshop, held in June 2001, evaluated the results from an extensive N-version test of a collection of Reynolds-Averaged Navier-Stokes CFD codes. The code-to-code scatter was more than an order of magnitude larger than desired for design and experimental validation of cruise conditions for a subsonic transport configuration. The second AIAA Drag Prediction Workshop, held in June 2003, emphasized the determination of installed pylon-nacelle drag increments and grid refinement studies. The code-to-code scatter was significantly reduced compared to the first DPW, but still larger than desired. However, grid refinement studies showed no significant improvement in code-to-code scatter with increasing grid refinement. The third Drag Prediction Workshop focused on the determination of installed side-of-body fairing drag increments and grid refinement studies for clean attached flow on wing alone configurations and for separated flow on the DLR-F6 subsonic transport model. This work evaluated the effect of grid refinement on the code-to-code scatter for the clean attached flow test cases and the separated flow test cases.

Constructing Noise-Invariant Representations of Sound in the Auditory Pathway

PubMed Central

Rabinowitz, Neil C.; Willmore, Ben D. B.; King, Andrew J.; Schnupp, Jan W. H.

2013-01-01

Identifying behaviorally relevant sounds in the presence of background noise is one of the most important and poorly understood challenges faced by the auditory system. An elegant solution to this problem would be for the auditory system to represent sounds in a noise-invariant fashion. Since a major effect of background noise is to alter the statistics of the sounds reaching the ear, noise-invariant representations could be promoted by neurons adapting to stimulus statistics. Here we investigated the extent of neuronal adaptation to the mean and contrast of auditory stimulation as one ascends the auditory pathway. We measured these forms of adaptation by presenting complex synthetic and natural sounds, recording neuronal responses in the inferior colliculus and primary fields of the auditory cortex of anaesthetized ferrets, and comparing these responses with a sophisticated model of the auditory nerve. We find that the strength of both forms of adaptation increases as one ascends the auditory pathway. To investigate whether this adaptation to stimulus statistics contributes to the construction of noise-invariant sound representations, we also presented complex, natural sounds embedded in stationary noise, and used a decoding approach to assess the noise tolerance of the neuronal population code. We find that the code for complex sounds in the periphery is affected more by the addition of noise than the cortical code. We also find that noise tolerance is correlated with adaptation to stimulus statistics, so that populations that show the strongest adaptation to stimulus statistics are also the most noise-tolerant. This suggests that the increase in adaptation to sound statistics from auditory nerve to midbrain to cortex is an important stage in the construction of noise-invariant sound representations in the higher auditory brain. PMID:24265596

Implications of Analytical Investigations about the Semiconductor Equations on Device Modeling Programs.

DTIC Science & Technology

1983-04-01

34.. .. . ...- "- -,-. SIGNIFICANCE AND EXPLANATION Many different codes for the simulation of semiconductor devices such as transitors , diodes, thyristors are already circulated...partially take into account the consequences introduced by degenerate semiconductors (e.g. invalidity of Boltzmann’s statistics , bandgap narrowing). These...ft - ni p nep /Ut(2.10) Sni *e p nie 2.11) .7. (2.10) can be physically interpreted as the application of Boltzmann statistics . However (2.10) a.,zo

Improving Our Ability to Evaluate Underlying Mechanisms of Behavioral Onset and Other Event Occurrence Outcomes: A Discrete-Time Survival Mediation Model

PubMed Central

Fairchild, Amanda J.; Abara, Winston E.; Gottschall, Amanda C.; Tein, Jenn-Yun; Prinz, Ronald J.

2015-01-01

The purpose of this article is to introduce and describe a statistical model that researchers can use to evaluate underlying mechanisms of behavioral onset and other event occurrence outcomes. Specifically, the article develops a framework for estimating mediation effects with outcomes measured in discrete-time epochs by integrating the statistical mediation model with discrete-time survival analysis. The methodology has the potential to help strengthen health research by targeting prevention and intervention work more effectively as well as by improving our understanding of discretized periods of risk. The model is applied to an existing longitudinal data set to demonstrate its use, and programming code is provided to facilitate its implementation. PMID:24296470

Structures of Neural Correlation and How They Favor Coding

PubMed Central

Franke, Felix; Fiscella, Michele; Sevelev, Maksim; Roska, Botond; Hierlemann, Andreas; da Silveira, Rava Azeredo

2017-01-01

Summary The neural representation of information suffers from “noise”—the trial-to-trial variability in the response of neurons. The impact of correlated noise upon population coding has been debated, but a direct connection between theory and experiment remains tenuous. Here, we substantiate this connection and propose a refined theoretical picture. Using simultaneous recordings from a population of direction-selective retinal ganglion cells, we demonstrate that coding benefits from noise correlations. The effect is appreciable already in small populations, yet it is a collective phenomenon. Furthermore, the stimulus-dependent structure of correlation is key. We develop simple functional models that capture the stimulus-dependent statistics. We then use them to quantify the performance of population coding, which depends upon interplays of feature sensitivities and noise correlations in the population. Because favorable structures of correlation emerge robustly in circuits with noisy, nonlinear elements, they will arise and benefit coding beyond the confines of retina. PMID:26796692

Metabolic Free Energy and Biological Codes: A 'Data Rate Theorem' Aging Model.

PubMed

Wallace, Rodrick

2015-06-01

A famous argument by Maturana and Varela (Autopoiesis and cognition. Reidel, Dordrecht, 1980) holds that the living state is cognitive at every scale and level of organization. Since it is possible to associate many cognitive processes with 'dual' information sources, pathologies can sometimes be addressed using statistical models based on the Shannon Coding, the Shannon-McMillan Source Coding, the Rate Distortion, and the Data Rate Theorems, which impose necessary conditions on information transmission and system control. Deterministic-but-for-error biological codes do not directly invoke cognition, but may be essential subcomponents within larger cognitive processes. A formal argument, however, places such codes within a similar framework, with metabolic free energy serving as a 'control signal' stabilizing biochemical code-and-translator dynamics in the presence of noise. Demand beyond available energy supply triggers punctuated destabilization of the coding channel, affecting essential biological functions. Aging, normal or prematurely driven by psychosocial or environmental stressors, must interfere with the routine operation of such mechanisms, initiating the chronic diseases associated with senescence. Amyloid fibril formation, intrinsically disordered protein logic gates, and cell surface glycan/lectin 'kelp bed' logic gates are reviewed from this perspective. The results generalize beyond coding machineries having easily recognizable symmetry modes, and strip a layer of mathematical complication from the study of phase transitions in nonequilibrium biological systems.

An open-access CMIP5 pattern library for temperature and precipitation: description and methodology

NASA Astrophysics Data System (ADS)

Lynch, Cary; Hartin, Corinne; Bond-Lamberty, Ben; Kravitz, Ben

2017-05-01

Pattern scaling is used to efficiently emulate general circulation models and explore uncertainty in climate projections under multiple forcing scenarios. Pattern scaling methods assume that local climate changes scale with a global mean temperature increase, allowing for spatial patterns to be generated for multiple models for any future emission scenario. For uncertainty quantification and probabilistic statistical analysis, a library of patterns with descriptive statistics for each file would be beneficial, but such a library does not presently exist. Of the possible techniques used to generate patterns, the two most prominent are the delta and least squares regression methods. We explore the differences and statistical significance between patterns generated by each method and assess performance of the generated patterns across methods and scenarios. Differences in patterns across seasons between methods and epochs were largest in high latitudes (60-90° N/S). Bias and mean errors between modeled and pattern-predicted output from the linear regression method were smaller than patterns generated by the delta method. Across scenarios, differences in the linear regression method patterns were more statistically significant, especially at high latitudes. We found that pattern generation methodologies were able to approximate the forced signal of change to within ≤ 0.5 °C, but the choice of pattern generation methodology for pattern scaling purposes should be informed by user goals and criteria. This paper describes our library of least squares regression patterns from all CMIP5 models for temperature and precipitation on an annual and sub-annual basis, along with the code used to generate these patterns. The dataset and netCDF data generation code are available at doi:10.5281/zenodo.495632.

Evaluation of Savannah River Plant emergency response models using standard and nonstandard meteorological data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoel, D.D.

1984-01-01

Two computer codes have been developed for operational use in performing real time evaluations of atmospheric releases from the Savannah River Plant (SRP) in South Carolina. These codes, based on mathematical models, are part of the SRP WIND (Weather Information and Display) automated emergency response system. Accuracy of ground level concentrations from a Gaussian puff-plume model and a two-dimensional sequential puff model are being evaluated with data from a series of short range diffusion experiments using sulfur hexafluoride as a tracer. The models use meteorological data collected from 7 towers on SRP and at the 300 m WJBF-TV tower aboutmore » 15 km northwest of SRP. The winds and the stability, which is based on turbulence measurements, are measured at the 60 m stack heights. These results are compared to downwind concentrations using only standard meteorological data, i.e., adjusted 10 m winds and stability determined by the Pasquill-Turner stability classification method. Scattergrams and simple statistics were used for model evaluations. Results indicate predictions within accepted limits for the puff-plume code and a bias in the sequential puff model predictions using the meteorologist-adjusted nonstandard data. 5 references, 4 figures, 2 tables.« less

A Categorization of Dynamic Analyzers

NASA Technical Reports Server (NTRS)

Lujan, Michelle R.

1997-01-01

Program analysis techniques and tools are essential to the development process because of the support they provide in detecting errors and deficiencies at different phases of development. The types of information rendered through analysis includes the following: statistical measurements of code, type checks, dataflow analysis, consistency checks, test data,verification of code, and debugging information. Analyzers can be broken into two major categories: dynamic and static. Static analyzers examine programs with respect to syntax errors and structural properties., This includes gathering statistical information on program content, such as the number of lines of executable code, source lines. and cyclomatic complexity. In addition, static analyzers provide the ability to check for the consistency of programs with respect to variables. Dynamic analyzers in contrast are dependent on input and the execution of a program providing the ability to find errors that cannot be detected through the use of static analysis alone. Dynamic analysis provides information on the behavior of a program rather than on the syntax. Both types of analysis detect errors in a program, but dynamic analyzers accomplish this through run-time behavior. This paper focuses on the following broad classification of dynamic analyzers: 1) Metrics; 2) Models; and 3) Monitors. Metrics are those analyzers that provide measurement. The next category, models, captures those analyzers that present the state of the program to the user at specified points in time. The last category, monitors, checks specified code based on some criteria. The paper discusses each classification and the techniques that are included under them. In addition, the role of each technique in the software life cycle is discussed. Familiarization with the tools that measure, model and monitor programs provides a framework for understanding the program's dynamic behavior from different, perspectives through analysis of the input/output data.

Structured Set Intra Prediction With Discriminative Learning in a Max-Margin Markov Network for High Efficiency Video Coding

PubMed Central

Dai, Wenrui; Xiong, Hongkai; Jiang, Xiaoqian; Chen, Chang Wen

2014-01-01

This paper proposes a novel model on intra coding for High Efficiency Video Coding (HEVC), which simultaneously predicts blocks of pixels with optimal rate distortion. It utilizes the spatial statistical correlation for the optimal prediction based on 2-D contexts, in addition to formulating the data-driven structural interdependences to make the prediction error coherent with the probability distribution, which is desirable for successful transform and coding. The structured set prediction model incorporates a max-margin Markov network (M3N) to regulate and optimize multiple block predictions. The model parameters are learned by discriminating the actual pixel value from other possible estimates to maximize the margin (i.e., decision boundary bandwidth). Compared to existing methods that focus on minimizing prediction error, the M3N-based model adaptively maintains the coherence for a set of predictions. Specifically, the proposed model concurrently optimizes a set of predictions by associating the loss for individual blocks to the joint distribution of succeeding discrete cosine transform coefficients. When the sample size grows, the prediction error is asymptotically upper bounded by the training error under the decomposable loss function. As an internal step, we optimize the underlying Markov network structure to find states that achieve the maximal energy using expectation propagation. For validation, we integrate the proposed model into HEVC for optimal mode selection on rate-distortion optimization. The proposed prediction model obtains up to 2.85% bit rate reduction and achieves better visual quality in comparison to the HEVC intra coding. PMID:25505829

The effects of nuclear data library processing on Geant4 and MCNP simulations of the thermal neutron scattering law

NASA Astrophysics Data System (ADS)

Hartling, K.; Ciungu, B.; Li, G.; Bentoumi, G.; Sur, B.

2018-05-01

Monte Carlo codes such as MCNP and Geant4 rely on a combination of physics models and evaluated nuclear data files (ENDF) to simulate the transport of neutrons through various materials and geometries. The grid representation used to represent the final-state scattering energies and angles associated with neutron scattering interactions can significantly affect the predictions of these codes. In particular, the default thermal scattering libraries used by MCNP6.1 and Geant4.10.3 do not accurately reproduce the ENDF/B-VII.1 model in simulations of the double-differential cross section for thermal neutrons interacting with hydrogen nuclei in a thin layer of water. However, agreement between model and simulation can be achieved within the statistical error by re-processing ENDF/B-VII.I thermal scattering libraries with the NJOY code. The structure of the thermal scattering libraries and sampling algorithms in MCNP and Geant4 are also reviewed.

Prior-to-Secondary School Course Classification System: School Codes for the Exchange of Data (SCED). NFES 2011-801

ERIC Educational Resources Information Center

National Forum on Education Statistics, 2011

2011-01-01

In this handbook, "Prior-to-Secondary School Course Classification System: School Codes for the Exchange of Data" (SCED), the National Center for Education Statistics (NCES) and the National Forum on Education Statistics have extended the existing secondary course classification system with codes and descriptions for courses offered at…

Certification of medical librarians, 1949--1977 statistical analysis.

PubMed

Schmidt, D

1979-01-01

The Medical Library Association's Code for Training and Certification of Medical Librarians was in effect from 1949 to August 1977, a period during which 3,216 individuals were certified. Statistics on each type of certificate granted each year are provided. Because 54.5% of those granted certification were awarded it in the last three-year, two-month period of the code's existence, these applications are reviewed in greater detail. Statistics on each type of certificate granted each year are provided. Because 54.5% of those granted certification were awarded it in the last three-year, two-month period of the code's existence, these applications are reviewed in greater detail. Statistics on MLA membership, sex, residence, library school, and method of meeting requirements are detailed. Questions relating to certification under the code now in existence are raised.

Certification of medical librarians, 1949--1977 statistical analysis.

PubMed Central

Schmidt, D

1979-01-01

The Medical Library Association's Code for Training and Certification of Medical Librarians was in effect from 1949 to August 1977, a period during which 3,216 individuals were certified. Statistics on each type of certificate granted each year are provided. Because 54.5% of those granted certification were awarded it in the last three-year, two-month period of the code's existence, these applications are reviewed in greater detail. Statistics on each type of certificate granted each year are provided. Because 54.5% of those granted certification were awarded it in the last three-year, two-month period of the code's existence, these applications are reviewed in greater detail. Statistics on MLA membership, sex, residence, library school, and method of meeting requirements are detailed. Questions relating to certification under the code now in existence are raised. PMID:427287

Study of helium emissions from active solar regions

NASA Technical Reports Server (NTRS)

Kulander, J. L.

1973-01-01

A theoretical study is made of the visible and UV line radiation of He I atoms and He II ions from a plane-parallel model flare layer. Codes were developed for the solution of the statistically steady state equation for a 30 level He I - II - III model, and the line and continuum transport equations. These codes are described and documented in the report along with sample solutions. Optical depths and some line intensities are presented for a 1000 km thick layer. Solutions of the steady state equations are presented for electron temperatures 10,000 to 50,000 K and electron densities 10 to the 10th power to 10 to the 14th power/cu cm.

Gamma-ray spectroscopy: The diffuse galactic glow

NASA Technical Reports Server (NTRS)

Hartmann, Dieter H.

1991-01-01

The goal of this project is the development of a numerical code that provides statistical models of the sky distribution of gamma-ray lines due to the production of radioactive isotopes by ongoing Galactic nucleosynthesis. We are particularly interested in quasi-steady emission from novae, supernovae, and stellar winds, but continuum radiation and transient sources must also be considered. We have made significant progress during the first half period of this project and expect the timely completion of a code that can be applied to Oriented Scintillation Spectrometer Experiment (OSSE) Galactic plane survey data.

Composite Load Spectra for Select Space Propulsion Structural Components

NASA Technical Reports Server (NTRS)

Ho, Hing W.; Newell, James F.

1994-01-01

Generic load models are described with multiple levels of progressive sophistication to simulate the composite (combined) load spectra (CLS) that are induced in space propulsion system components, representative of Space Shuttle Main Engines (SSME), such as transfer ducts, turbine blades and liquid oxygen (LOX) posts. These generic (coupled) models combine the deterministic models for composite load dynamic, acoustic, high-pressure and high rotational speed, etc., load simulation using statistically varying coefficients. These coefficients are then determined using advanced probabilistic simulation methods with and without strategically selected experimental data. The entire simulation process is included in a CLS computer code. Applications of the computer code to various components in conjunction with the PSAM (Probabilistic Structural Analysis Method) to perform probabilistic load evaluation and life prediction evaluations are also described to illustrate the effectiveness of the coupled model approach.

Liver segmentation from CT images using a sparse priori statistical shape model (SP-SSM).

PubMed

Wang, Xuehu; Zheng, Yongchang; Gan, Lan; Wang, Xuan; Sang, Xinting; Kong, Xiangfeng; Zhao, Jie

2017-01-01

This study proposes a new liver segmentation method based on a sparse a priori statistical shape model (SP-SSM). First, mark points are selected in the liver a priori model and the original image. Then, the a priori shape and its mark points are used to obtain a dictionary for the liver boundary information. Second, the sparse coefficient is calculated based on the correspondence between mark points in the original image and those in the a priori model, and then the sparse statistical model is established by combining the sparse coefficients and the dictionary. Finally, the intensity energy and boundary energy models are built based on the intensity information and the specific boundary information of the original image. Then, the sparse matching constraint model is established based on the sparse coding theory. These models jointly drive the iterative deformation of the sparse statistical model to approximate and accurately extract the liver boundaries. This method can solve the problems of deformation model initialization and a priori method accuracy using the sparse dictionary. The SP-SSM can achieve a mean overlap error of 4.8% and a mean volume difference of 1.8%, whereas the average symmetric surface distance and the root mean square symmetric surface distance can reach 0.8 mm and 1.4 mm, respectively.

Bayesian logistic regression approaches to predict incorrect DRG assignment.

PubMed

Suleiman, Mani; Demirhan, Haydar; Boyd, Leanne; Girosi, Federico; Aksakalli, Vural

2018-05-07

Episodes of care involving similar diagnoses and treatments and requiring similar levels of resource utilisation are grouped to the same Diagnosis-Related Group (DRG). In jurisdictions which implement DRG based payment systems, DRGs are a major determinant of funding for inpatient care. Hence, service providers often dedicate auditing staff to the task of checking that episodes have been coded to the correct DRG. The use of statistical models to estimate an episode's probability of DRG error can significantly improve the efficiency of clinical coding audits. This study implements Bayesian logistic regression models with weakly informative prior distributions to estimate the likelihood that episodes require a DRG revision, comparing these models with each other and to classical maximum likelihood estimates. All Bayesian approaches had more stable model parameters than maximum likelihood. The best performing Bayesian model improved overall classification per- formance by 6% compared to maximum likelihood, with a 34% gain compared to random classification, respectively. We found that the original DRG, coder and the day of coding all have a significant effect on the likelihood of DRG error. Use of Bayesian approaches has improved model parameter stability and classification accuracy. This method has already lead to improved audit efficiency in an operational capacity.

Maximum entropy models as a tool for building precise neural controls.

PubMed

Savin, Cristina; Tkačik, Gašper

2017-10-01

Neural responses are highly structured, with population activity restricted to a small subset of the astronomical range of possible activity patterns. Characterizing these statistical regularities is important for understanding circuit computation, but challenging in practice. Here we review recent approaches based on the maximum entropy principle used for quantifying collective behavior in neural activity. We highlight recent models that capture population-level statistics of neural data, yielding insights into the organization of the neural code and its biological substrate. Furthermore, the MaxEnt framework provides a general recipe for constructing surrogate ensembles that preserve aspects of the data, but are otherwise maximally unstructured. This idea can be used to generate a hierarchy of controls against which rigorous statistical tests are possible. Copyright © 2017 Elsevier Ltd. All rights reserved.

Parallel algorithm for solving Kepler’s equation on Graphics Processing Units: Application to analysis of Doppler exoplanet searches

NASA Astrophysics Data System (ADS)

Ford, Eric B.

2009-05-01

We present the results of a highly parallel Kepler equation solver using the Graphics Processing Unit (GPU) on a commercial nVidia GeForce 280GTX and the "Compute Unified Device Architecture" (CUDA) programming environment. We apply this to evaluate a goodness-of-fit statistic (e.g., χ2) for Doppler observations of stars potentially harboring multiple planetary companions (assuming negligible planet-planet interactions). Given the high-dimensionality of the model parameter space (at least five dimensions per planet), a global search is extremely computationally demanding. We expect that the underlying Kepler solver and model evaluator will be combined with a wide variety of more sophisticated algorithms to provide efficient global search, parameter estimation, model comparison, and adaptive experimental design for radial velocity and/or astrometric planet searches. We tested multiple implementations using single precision, double precision, pairs of single precision, and mixed precision arithmetic. We find that the vast majority of computations can be performed using single precision arithmetic, with selective use of compensated summation for increased precision. However, standard single precision is not adequate for calculating the mean anomaly from the time of observation and orbital period when evaluating the goodness-of-fit for real planetary systems and observational data sets. Using all double precision, our GPU code outperforms a similar code using a modern CPU by a factor of over 60. Using mixed precision, our GPU code provides a speed-up factor of over 600, when evaluating nsys > 1024 models planetary systems each containing npl = 4 planets and assuming nobs = 256 observations of each system. We conclude that modern GPUs also offer a powerful tool for repeatedly evaluating Kepler's equation and a goodness-of-fit statistic for orbital models when presented with a large parameter space.

Using DEWIS and R for Multi-Staged Statistics e-Assessments

ERIC Educational Resources Information Center

Gwynllyw, D. Rhys; Weir, Iain S.; Henderson, Karen L.

2016-01-01

We demonstrate how the DEWIS e-Assessment system may use embedded R code to facilitate the assessment of students' ability to perform involved statistical analyses. The R code has been written to emulate SPSS output and thus the statistical results for each bespoke data set can be generated efficiently and accurately using standard R routines.…

Hispanics/Latinos & Cardiovascular Disease: Statistical Fact Sheet

MedlinePlus

Statistical Fact Sheet 2013 Update Hispanics/Latinos & Cardiovascular Diseases Cardiovascular Disease (CVD) (ICD/10 codes I00-I99, Q20-Q28) (ICD/9 codes 390-459, 745-747)  Among Mexican-American adults age 20 ...

Wavelet-based compression of M-FISH images.

PubMed

Hua, Jianping; Xiong, Zixiang; Wu, Qiang; Castleman, Kenneth R

2005-05-01

Multiplex fluorescence in situ hybridization (M-FISH) is a recently developed technology that enables multi-color chromosome karyotyping for molecular cytogenetic analysis. Each M-FISH image set consists of a number of aligned images of the same chromosome specimen captured at different optical wavelength. This paper presents embedded M-FISH image coding (EMIC), where the foreground objects/chromosomes and the background objects/images are coded separately. We first apply critically sampled integer wavelet transforms to both the foreground and the background. We then use object-based bit-plane coding to compress each object and generate separate embedded bitstreams that allow continuous lossy-to-lossless compression of the foreground and the background. For efficient arithmetic coding of bit planes, we propose a method of designing an optimal context model that specifically exploits the statistical characteristics of M-FISH images in the wavelet domain. Our experiments show that EMIC achieves nearly twice as much compression as Lempel-Ziv-Welch coding. EMIC also performs much better than JPEG-LS and JPEG-2000 for lossless coding. The lossy performance of EMIC is significantly better than that of coding each M-FISH image with JPEG-2000.

Statistical Validation of a New Python-based Military Workforce Simulation Model

DTIC Science & Technology

2014-12-30

also having a straightforward syntax that is accessible to non-programmers. Furthermore, it is supported by an impressive variety of scientific... accessed by a given element of model logic or line of code. For example, in Arena, data arrays, queues and the simulation clock are part of the...global scope and are therefore accessible anywhere in the model. The disadvantage of scopes is that all names in a scope must be unique. If more than

Regional and temporal variations in coding of hospital diagnoses referring to upper gastrointestinal and oesophageal bleeding in Germany.

PubMed

Langner, Ingo; Mikolajczyk, Rafael; Garbe, Edeltraut

2011-08-17

Health insurance claims data are increasingly used for health services research in Germany. Hospital diagnoses in these data are coded according to the International Classification of Diseases, German modification (ICD-10-GM). Due to the historical division into West and East Germany, different coding practices might persist in both former parts. Additionally, the introduction of Diagnosis Related Groups (DRGs) in Germany in 2003/2004 might have changed the coding. The aim of this study was to investigate regional and temporal variations in coding of hospitalisation diagnoses in Germany. We analysed hospitalisation diagnoses for oesophageal bleeding (OB) and upper gastrointestinal bleeding (UGIB) from the official German Hospital Statistics provided by the Federal Statistical Office. Bleeding diagnoses were classified as "specific" (origin of bleeding provided) or "unspecific" (origin of bleeding not provided) coding. We studied regional (former East versus West Germany) differences in incidence of hospitalisations with specific or unspecific coding for OB and UGIB and temporal variations between 2000 and 2005. For each year, incidence ratios of hospitalisations for former East versus West Germany were estimated with log-linear regression models adjusting for age, gender and population density. Significant differences in specific and unspecific coding between East and West Germany and over time were found for both, OB and UGIB hospitalisation diagnoses, respectively. For example in 2002, incidence ratios of hospitalisations for East versus West Germany were 1.24 (95% CI 1.16-1.32) for specific and 0.67 (95% CI 0.60-0.74) for unspecific OB diagnoses and 1.43 (95% CI 1.36-1.51) for specific and 0.83 (95% CI 0.80-0.87) for unspecific UGIB. Regional differences nearly disappeared and time trends were less marked when using combined specific and unspecific diagnoses of OB or UGIB, respectively. During the study period, there were substantial regional and temporal variations in the coding of OB and UGIB diagnoses in hospitalised patients. Possible explanations for the observed regional variations are different coding preferences, further influenced by changes in coding and reimbursement rules. Analysing groups of diagnoses including specific and unspecific codes reduces the influence of varying coding practices.

Equations of state for explosive detonation products: The PANDA model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerley, G.I.

1994-05-01

This paper discusses a thermochemical model for calculating equations of state (EOS) for the detonation products of explosives. This model, which was first presented at the Eighth Detonation Symposium, is available in the PANDA code and is referred to here as ``the Panda model``. The basic features of the PANDA model are as follows. (1) Statistical-mechanical theories are used to construct EOS tables for each of the chemical species that are to be allowed in the detonation products. (2) The ideal mixing model is used to compute the thermodynamic functions for a mixture of these species, and the composition ofmore » the system is determined from assumption of chemical equilibrium. (3) For hydrocode calculations, the detonation product EOS are used in tabular form, together with a reactive burn model that allows description of shock-induced initiation and growth or failure as well as ideal detonation wave propagation. This model has been implemented in the three-dimensional Eulerian code, CTH.« less

Dynamic Alignment Models for Neural Coding

PubMed Central

Kollmorgen, Sepp; Hahnloser, Richard H. R.

2014-01-01

Recently, there have been remarkable advances in modeling the relationships between the sensory environment, neuronal responses, and behavior. However, most models cannot encompass variable stimulus-response relationships such as varying response latencies and state or context dependence of the neural code. Here, we consider response modeling as a dynamic alignment problem and model stimulus and response jointly by a mixed pair hidden Markov model (MPH). In MPHs, multiple stimulus-response relationships (e.g., receptive fields) are represented by different states or groups of states in a Markov chain. Each stimulus-response relationship features temporal flexibility, allowing modeling of variable response latencies, including noisy ones. We derive algorithms for learning of MPH parameters and for inference of spike response probabilities. We show that some linear-nonlinear Poisson cascade (LNP) models are a special case of MPHs. We demonstrate the efficiency and usefulness of MPHs in simulations of both jittered and switching spike responses to white noise and natural stimuli. Furthermore, we apply MPHs to extracellular single and multi-unit data recorded in cortical brain areas of singing birds to showcase a novel method for estimating response lag distributions. MPHs allow simultaneous estimation of receptive fields, latency statistics, and hidden state dynamics and so can help to uncover complex stimulus response relationships that are subject to variable timing and involve diverse neural codes. PMID:24625448

An Extensible NetLogo Model for Visualizing Message Routing Protocols

DTIC Science & Technology

2017-08-01

the hard sciences to the social sciences to computer-generated art. NetLogo represents the world as a set of...describe the model is shown here; for the supporting methods , refer to the source code. Approved for public release; distribution is unlimited. 4 iv...if ticks - last-inject > time-to-inject [inject] if run# > #runs [stop] end Next, we present some basic statistics collected for the

Population coding in sparsely connected networks of noisy neurons.

PubMed

Tripp, Bryan P; Orchard, Jeff

2012-01-01

This study examines the relationship between population coding and spatial connection statistics in networks of noisy neurons. Encoding of sensory information in the neocortex is thought to require coordinated neural populations, because individual cortical neurons respond to a wide range of stimuli, and exhibit highly variable spiking in response to repeated stimuli. Population coding is rooted in network structure, because cortical neurons receive information only from other neurons, and because the information they encode must be decoded by other neurons, if it is to affect behavior. However, population coding theory has often ignored network structure, or assumed discrete, fully connected populations (in contrast with the sparsely connected, continuous sheet of the cortex). In this study, we modeled a sheet of cortical neurons with sparse, primarily local connections, and found that a network with this structure could encode multiple internal state variables with high signal-to-noise ratio. However, we were unable to create high-fidelity networks by instantiating connections at random according to spatial connection probabilities. In our models, high-fidelity networks required additional structure, with higher cluster factors and correlations between the inputs to nearby neurons.

[Coding Causes of Death with IRIS Software. Impact in Navarre Mortality Statistic].

PubMed

Floristán Floristán, Yugo; Delfrade Osinaga, Josu; Carrillo Prieto, Jesus; Aguirre Perez, Jesus; Moreno-Iribas, Conchi

2016-08-02

There are few studies that analyze changes in mortality statistics derived from the use of IRIS software, an automatic system for coding multiple causes of death and for the selection of the underlying cause of death, compared to manual coding. This study evaluated the impact of the use of IRIS in the Navarre mortality statistic. We proceeded to double coding 5,060 death certificates corresponding to residents in Navarra in 2014. We calculated coincidence between the two encodings for ICD10 chapters and for the list of causes of the Spanish National Statistics Institute (INE-102) and we estimated the change on mortality rates. IRIS automatically coded 90% of death certificates. The coincidence to 4 characters and in the same chapter of the CIE10 was 79.1% and 92.0%, respectively. Furthermore, coincidence with the short INE-102 list was 88.3%. Higher matches were found in death certificate of people under 65 years. In comparison with manual coding there was an increase in deaths from endocrine diseases (31%), mental disorders (19%) and disease of nervous system (9%), while a decrease of genitourinary system diseases was observed (21%). The coincidence at level of ICD10 chapters coding by IRIS in comparison to manual coding was 9 out of 10 deaths, similar to what is observed in other studies. The implementation of IRIS has led to increased of endocrine diseases, especially diabetes and hyperlipidaemia, and mental disorders, especially dementias.

Multispectral Terrain Background Simulation Techniques For Use In Airborne Sensor Evaluation

NASA Astrophysics Data System (ADS)

Weinberg, Michael; Wohlers, Ronald; Conant, John; Powers, Edward

1988-08-01

A background simulation code developed at Aerodyne Research, Inc., called AERIE is designed to reflect the major sources of clutter that are of concern to staring and scanning sensors of the type being considered for various airborne threat warning (both aircraft and missiles) sensors. The code is a first principles model that could be used to produce a consistent image of the terrain for various spectral bands, i.e., provide the proper scene correlation both spectrally and spatially. The code utilizes both topographic and cultural features to model terrain, typically from DMA data, with a statistical overlay of the critical underlying surface properties (reflectance, emittance, and thermal factors) to simulate the resulting texture in the scene. Strong solar scattering from water surfaces is included with allowance for wind driven surface roughness. Clouds can be superimposed on the scene using physical cloud models and an analytical representation of the reflectivity obtained from scattering off spherical particles. The scene generator is augmented by collateral codes that allow for the generation of images at finer resolution. These codes provide interpolation of the basic DMA databases using fractal procedures that preserve the high frequency power spectral density behavior of the original scene. Scenes are presented illustrating variations in altitude, radiance, resolution, material, thermal factors, and emissivities. The basic models utilized for simulation of the various scene components and various "engineering level" approximations are incorporated to reduce the computational complexity of the simulation.

Rain rate duration statistics derived from the Mid-Atlantic coast rain gauge network

NASA Technical Reports Server (NTRS)

Goldhirsh, Julius

1993-01-01

A rain gauge network comprised of 10 tipping bucket rain gauges located in the Mid-Atlantic coast of the United States has been in continuous operation since June 1, 1986. Rain rate distributions and estimated slant path fade distributions at 20 GHz and 30 GHz covering the first five year period were derived from the gauge network measurements, and these results were described by Goldhirsh. In this effort, rain rate time duration statistics are presented. The rain duration statistics are of interest for better understanding the physical nature of precipitation and to present a data base which may be used by modelers to convert to slant path fade duration statistics. Such statistics are important for better assessing optimal coding procedures over defined bandwidths.

Test of the statistical model in {sup 96}Mo with the BaF{sub 2}{gamma} calorimeter DANCE array

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheets, S. A.; Mitchell, G. E.; Agvaanluvsan, U.

2009-02-15

The {gamma}-ray cascades following the {sup 95}Mo(n,{gamma}){sup 96}Mo reaction were studied with the {gamma} calorimeter DANCE (Detector for Advanced Neutron Capture Experiments) consisting of 160 BaF{sub 2} scintillation detectors at the Los Alamos Neutron Science Center. The {gamma}-ray energy spectra for different multiplicities were measured for s- and p-wave resonances below 2 keV. The shapes of these spectra were found to be in very good agreement with simulations using the DICEBOX statistical model code. The relevant model parameters used for the level density and photon strength functions were identical with those that provided the best fit of the data frommore » a recent measurement of the thermal {sup 95}Mo(n,{gamma}){sup 96}Mo reaction with the two-step-cascade method. The reported results strongly suggest that the extreme statistical model works very well in the mass region near A=100.« less

The importance of documenting code, and how you might make yourself do it

NASA Astrophysics Data System (ADS)

Tollerud, Erik Jon; Astropy Project

2016-01-01

Your science code is awesome. It reduces data, performs some statistical analysis, or models a physical process better than anyone has done before. You wisely decide that it is worth sharing with your student/advisor, research collaboration, or the whole world. But when you send it out, no one seems willing to use it. Why? Most of the time, it's your documentation. You wrote the code for yourself, so you know what every function, procedure, or class is supposed to do. Unfortunately, your users (sometimes including you 6 months later) do not. In this talk, I will describe some of the tools, both technical and psychological, to make that documentation happen (particularly for the Python ecosystem).

For the Love of Statistics: Appreciating and Learning to Apply Experimental Analysis and Statistics through Computer Programming Activities

ERIC Educational Resources Information Center

Mascaró, Maite; Sacristán, Ana Isabel; Rufino, Marta M.

2016-01-01

For the past 4 years, we have been involved in a project that aims to enhance the teaching and learning of experimental analysis and statistics, of environmental and biological sciences students, through computational programming activities (using R code). In this project, through an iterative design, we have developed sequences of R-code-based…

SAP- FORTRAN STATIC SOURCE CODE ANALYZER PROGRAM (IBM VERSION)

NASA Technical Reports Server (NTRS)

Manteufel, R.

1994-01-01

The FORTRAN Static Source Code Analyzer program, SAP, was developed to automatically gather statistics on the occurrences of statements and structures within a FORTRAN program and to provide for the reporting of those statistics. Provisions have been made for weighting each statistic and to provide an overall figure of complexity. Statistics, as well as figures of complexity, are gathered on a module by module basis. Overall summed statistics are also accumulated for the complete input source file. SAP accepts as input syntactically correct FORTRAN source code written in the FORTRAN 77 standard language. In addition, code written using features in the following languages is also accepted: VAX-11 FORTRAN, IBM S/360 FORTRAN IV Level H Extended; and Structured FORTRAN. The SAP program utilizes two external files in its analysis procedure. A keyword file allows flexibility in classifying statements and in marking a statement as either executable or non-executable. A statistical weight file allows the user to assign weights to all output statistics, thus allowing the user flexibility in defining the figure of complexity. The SAP program is written in FORTRAN IV for batch execution and has been implemented on a DEC VAX series computer under VMS and on an IBM 370 series computer under MVS. The SAP program was developed in 1978 and last updated in 1985.

SAP- FORTRAN STATIC SOURCE CODE ANALYZER PROGRAM (DEC VAX VERSION)

NASA Technical Reports Server (NTRS)

Merwarth, P. D.

1994-01-01

The FORTRAN Static Source Code Analyzer program, SAP, was developed to automatically gather statistics on the occurrences of statements and structures within a FORTRAN program and to provide for the reporting of those statistics. Provisions have been made for weighting each statistic and to provide an overall figure of complexity. Statistics, as well as figures of complexity, are gathered on a module by module basis. Overall summed statistics are also accumulated for the complete input source file. SAP accepts as input syntactically correct FORTRAN source code written in the FORTRAN 77 standard language. In addition, code written using features in the following languages is also accepted: VAX-11 FORTRAN, IBM S/360 FORTRAN IV Level H Extended; and Structured FORTRAN. The SAP program utilizes two external files in its analysis procedure. A keyword file allows flexibility in classifying statements and in marking a statement as either executable or non-executable. A statistical weight file allows the user to assign weights to all output statistics, thus allowing the user flexibility in defining the figure of complexity. The SAP program is written in FORTRAN IV for batch execution and has been implemented on a DEC VAX series computer under VMS and on an IBM 370 series computer under MVS. The SAP program was developed in 1978 and last updated in 1985.

Information-Theoretic Properties of Auditory Sequences Dynamically Influence Expectation and Memory

ERIC Educational Resources Information Center

Agres, Kat; Abdallah, Samer; Pearce, Marcus

2018-01-01

A basic function of cognition is to detect regularities in sensory input to facilitate the prediction and recognition of future events. It has been proposed that these implicit expectations arise from an internal predictive coding model, based on knowledge acquired through processes such as statistical learning, but it is unclear how different…

Measurement error and outcome distributions: Methodological issues in regression analyses of behavioral coding data.

PubMed

Holsclaw, Tracy; Hallgren, Kevin A; Steyvers, Mark; Smyth, Padhraic; Atkins, David C

2015-12-01

Behavioral coding is increasingly used for studying mechanisms of change in psychosocial treatments for substance use disorders (SUDs). However, behavioral coding data typically include features that can be problematic in regression analyses, including measurement error in independent variables, non normal distributions of count outcome variables, and conflation of predictor and outcome variables with third variables, such as session length. Methodological research in econometrics has shown that these issues can lead to biased parameter estimates, inaccurate standard errors, and increased Type I and Type II error rates, yet these statistical issues are not widely known within SUD treatment research, or more generally, within psychotherapy coding research. Using minimally technical language intended for a broad audience of SUD treatment researchers, the present paper illustrates the nature in which these data issues are problematic. We draw on real-world data and simulation-based examples to illustrate how these data features can bias estimation of parameters and interpretation of models. A weighted negative binomial regression is introduced as an alternative to ordinary linear regression that appropriately addresses the data characteristics common to SUD treatment behavioral coding data. We conclude by demonstrating how to use and interpret these models with data from a study of motivational interviewing. SPSS and R syntax for weighted negative binomial regression models is included in online supplemental materials. (c) 2016 APA, all rights reserved).

Measurement error and outcome distributions: Methodological issues in regression analyses of behavioral coding data

PubMed Central

Holsclaw, Tracy; Hallgren, Kevin A.; Steyvers, Mark; Smyth, Padhraic; Atkins, David C.

2015-01-01

Behavioral coding is increasingly used for studying mechanisms of change in psychosocial treatments for substance use disorders (SUDs). However, behavioral coding data typically include features that can be problematic in regression analyses, including measurement error in independent variables, non-normal distributions of count outcome variables, and conflation of predictor and outcome variables with third variables, such as session length. Methodological research in econometrics has shown that these issues can lead to biased parameter estimates, inaccurate standard errors, and increased type-I and type-II error rates, yet these statistical issues are not widely known within SUD treatment research, or more generally, within psychotherapy coding research. Using minimally-technical language intended for a broad audience of SUD treatment researchers, the present paper illustrates the nature in which these data issues are problematic. We draw on real-world data and simulation-based examples to illustrate how these data features can bias estimation of parameters and interpretation of models. A weighted negative binomial regression is introduced as an alternative to ordinary linear regression that appropriately addresses the data characteristics common to SUD treatment behavioral coding data. We conclude by demonstrating how to use and interpret these models with data from a study of motivational interviewing. SPSS and R syntax for weighted negative binomial regression models is included in supplementary materials. PMID:26098126

Computing Models of M-type Host Stars and their Panchromatic Spectral Output

NASA Astrophysics Data System (ADS)

Linsky, Jeffrey; Tilipman, Dennis; France, Kevin

2018-06-01

We have begun a program of computing state-of-the-art model atmospheres from the photospheres to the coronae of M stars that are the host stars of known exoplanets. For each model we are computing the emergent radiation at all wavelengths that are critical for assessingphotochemistry and mass-loss from exoplanet atmospheres. In particular, we are computing the stellar extreme ultraviolet radiation that drives hydrodynamic mass loss from exoplanet atmospheres and is essential for determing whether an exoplanet is habitable. The model atmospheres are computed with the SSRPM radiative transfer/statistical equilibrium code developed by Dr. Juan Fontenla. The code solves for the non-LTE statistical equilibrium populations of 18,538 levels of 52 atomic and ion species and computes the radiation from all species (435,986 spectral lines) and about 20,000,000 spectral lines of 20 diatomic species.The first model computed in this program was for the modestly active M1.5 V star GJ 832 by Fontenla et al. (ApJ 830, 152 (2016)). We will report on a preliminary model for the more active M5 V star GJ 876 and compare this model and its emergent spectrum with GJ 832. In the future, we will compute and intercompare semi-empirical models and spectra for all of the stars observed with the HST MUSCLES Treasury Survey, the Mega-MUSCLES Treasury Survey, and additional stars including Proxima Cen and Trappist-1.This multiyear theory program is supported by a grant from the Space Telescope Science Institute.

Statistical physics inspired energy-efficient coded-modulation for optical communications.

PubMed

Djordjevic, Ivan B; Xu, Lei; Wang, Ting

2012-04-15

Because Shannon's entropy can be obtained by Stirling's approximation of thermodynamics entropy, the statistical physics energy minimization methods are directly applicable to the signal constellation design. We demonstrate that statistical physics inspired energy-efficient (EE) signal constellation designs, in combination with large-girth low-density parity-check (LDPC) codes, significantly outperform conventional LDPC-coded polarization-division multiplexed quadrature amplitude modulation schemes. We also describe an EE signal constellation design algorithm. Finally, we propose the discrete-time implementation of D-dimensional transceiver and corresponding EE polarization-division multiplexed system. © 2012 Optical Society of America

Lungworm Infections in German Dairy Cattle Herds — Seroprevalence and GIS-Supported Risk Factor Analysis

PubMed Central

Schunn, Anne-Marie; Conraths, Franz J.; Staubach, Christoph; Fröhlich, Andreas; Forbes, Andrew; Strube, Christina

2013-01-01

In November 2008, a total of 19,910 bulk tank milk (BTM) samples were obtained from dairy farms from all over Germany, corresponding to about 20% of all German dairy herds, and analysed for antibodies against the bovine lungworm Dictyocaulus viviparus by use of the recombinant MSP-ELISA. A total number of 3,397 (17.1%; n = 19,910) BTM samples tested seropositive. The prevalences in individual German federal states varied between 0.0% and 31.2% positive herds. A geospatial map was drawn to show the distribution of seropositive and seronegative herds per postal code area. ELISA results were further analysed for associations with land-use and climate data. Bivariate statistical analysis was used to identify potential spatial risk factors for dictyocaulosis. Statistically significant positive associations were found between lungworm seropositive herds and the proportion of water bodies and grassed area per postal code area. Variables that showed a statistically significant association with a positive BTM test were included in a logistic regression model, which was further refined by controlled stepwise selection of variables. The low Pseudo R2 values (0.08 for the full model and 0.06 for the final model) and further evaluation of the model by ROC analysis indicate that additional, unrecorded factors (e.g. management factors) or random effects may substantially contribute to lungworm infections in dairy cows. Veterinarians should include lungworms in the differential diagnosis of respiratory disease in dairy cattle, particularly those at pasture. Monitoring of herds through BTM screening for antibodies can help farmers and veterinarians plan and implement appropriate control measures. PMID:24040243

Getting more from accuracy and response time data: methods for fitting the linear ballistic accumulator.

PubMed

Donkin, Chris; Averell, Lee; Brown, Scott; Heathcote, Andrew

2009-11-01

Cognitive models of the decision process provide greater insight into response time and accuracy than do standard ANOVA techniques. However, such models can be mathematically and computationally difficult to apply. We provide instructions and computer code for three methods for estimating the parameters of the linear ballistic accumulator (LBA), a new and computationally tractable model of decisions between two or more choices. These methods-a Microsoft Excel worksheet, scripts for the statistical program R, and code for implementation of the LBA into the Bayesian sampling software WinBUGS-vary in their flexibility and user accessibility. We also provide scripts in R that produce a graphical summary of the data and model predictions. In a simulation study, we explored the effect of sample size on parameter recovery for each method. The materials discussed in this article may be downloaded as a supplement from http://brm.psychonomic-journals.org/content/supplemental.

Musical Experience Influences Statistical Learning of a Novel Language

PubMed Central

Shook, Anthony; Marian, Viorica; Bartolotti, James; Schroeder, Scott R.

2014-01-01

Musical experience may benefit learning a new language by enhancing the fidelity with which the auditory system encodes sound. In the current study, participants with varying degrees of musical experience were exposed to two statistically-defined languages consisting of auditory Morse-code sequences which varied in difficulty. We found an advantage for highly-skilled musicians, relative to less-skilled musicians, in learning novel Morse-code based words. Furthermore, in the more difficult learning condition, performance of lower-skilled musicians was mediated by their general cognitive abilities. We suggest that musical experience may lead to enhanced processing of statistical information and that musicians’ enhanced ability to learn statistical probabilities in a novel Morse-code language may extend to natural language learning. PMID:23505962

Microsimulation Modeling for Health Decision Sciences Using R: A Tutorial.

PubMed

Krijkamp, Eline M; Alarid-Escudero, Fernando; Enns, Eva A; Jalal, Hawre J; Hunink, M G Myriam; Pechlivanoglou, Petros

2018-04-01

Microsimulation models are becoming increasingly common in the field of decision modeling for health. Because microsimulation models are computationally more demanding than traditional Markov cohort models, the use of computer programming languages in their development has become more common. R is a programming language that has gained recognition within the field of decision modeling. It has the capacity to perform microsimulation models more efficiently than software commonly used for decision modeling, incorporate statistical analyses within decision models, and produce more transparent models and reproducible results. However, no clear guidance for the implementation of microsimulation models in R exists. In this tutorial, we provide a step-by-step guide to build microsimulation models in R and illustrate the use of this guide on a simple, but transferable, hypothetical decision problem. We guide the reader through the necessary steps and provide generic R code that is flexible and can be adapted for other models. We also show how this code can be extended to address more complex model structures and provide an efficient microsimulation approach that relies on vectorization solutions.

High-Speed, Low-Cost Workstation for Computation-Intensive Statistics. Phase 1

DTIC Science & Technology

1990-06-20

routine implementation and performance. 5 The two compiled versions given in the table were coded in an attempt to obtain an optimized compiled version...level statistics and linear algebra routines (BSAS and BLAS) that have been prototyped in this study. For each routine, both the C code ( Turbo C...OISTRIBUTION /AVAILABILITY STATEMENT 12b. DISTRIBUTION CODE Unlimited distribution 13. ABSTRACT (Maximum 200 words) High-performance and low-cost

Round Robin Study: Molecular Simulation of Thermodynamic Properties from Models with Internal Degrees of Freedom.

PubMed

Schappals, Michael; Mecklenfeld, Andreas; Kröger, Leif; Botan, Vitalie; Köster, Andreas; Stephan, Simon; García, Edder J; Rutkai, Gabor; Raabe, Gabriele; Klein, Peter; Leonhard, Kai; Glass, Colin W; Lenhard, Johannes; Vrabec, Jadran; Hasse, Hans

2017-09-12

Thermodynamic properties are often modeled by classical force fields which describe the interactions on the atomistic scale. Molecular simulations are used for retrieving thermodynamic data from such models, and many simulation techniques and computer codes are available for that purpose. In the present round robin study, the following fundamental question is addressed: Will different user groups working with different simulation codes obtain coinciding results within the statistical uncertainty of their data? A set of 24 simple simulation tasks is defined and solved by five user groups working with eight molecular simulation codes: DL_POLY, GROMACS, IMC, LAMMPS, ms2, NAMD, Tinker, and TOWHEE. Each task consists of the definition of (1) a pure fluid that is described by a force field and (2) the conditions under which that property is to be determined. The fluids are four simple alkanes: ethane, propane, n-butane, and iso-butane. All force fields consider internal degrees of freedom: OPLS, TraPPE, and a modified OPLS version with bond stretching vibrations. Density and potential energy are determined as a function of temperature and pressure on a grid which is specified such that all states are liquid. The user groups worked independently and reported their results to a central instance. The full set of results was disclosed to all user groups only at the end of the study. During the study, the central instance gave only qualitative feedback. The results reveal the challenges of carrying out molecular simulations. Several iterations were needed to eliminate gross errors. For most simulation tasks, the remaining deviations between the results of the different groups are acceptable from a practical standpoint, but they are often outside of the statistical errors of the individual simulation data. However, there are also cases where the deviations are unacceptable. This study highlights similarities between computer experiments and laboratory experiments, which are both subject not only to statistical error but also to systematic error.

Genetic Programming as Alternative for Predicting Development Effort of Individual Software Projects

PubMed Central

Chavoya, Arturo; Lopez-Martin, Cuauhtemoc; Andalon-Garcia, Irma R.; Meda-Campaña, M. E.

2012-01-01

Statistical and genetic programming techniques have been used to predict the software development effort of large software projects. In this paper, a genetic programming model was used for predicting the effort required in individually developed projects. Accuracy obtained from a genetic programming model was compared against one generated from the application of a statistical regression model. A sample of 219 projects developed by 71 practitioners was used for generating the two models, whereas another sample of 130 projects developed by 38 practitioners was used for validating them. The models used two kinds of lines of code as well as programming language experience as independent variables. Accuracy results from the model obtained with genetic programming suggest that it could be used to predict the software development effort of individual projects when these projects have been developed in a disciplined manner within a development-controlled environment. PMID:23226305

SurfKin: an ab initio kinetic code for modeling surface reactions.

PubMed

Le, Thong Nguyen-Minh; Liu, Bin; Huynh, Lam K

2014-10-05

In this article, we describe a C/C++ program called SurfKin (Surface Kinetics) to construct microkinetic mechanisms for modeling gas-surface reactions. Thermodynamic properties of reaction species are estimated based on density functional theory calculations and statistical mechanics. Rate constants for elementary steps (including adsorption, desorption, and chemical reactions on surfaces) are calculated using the classical collision theory and transition state theory. Methane decomposition and water-gas shift reaction on Ni(111) surface were chosen as test cases to validate the code implementations. The good agreement with literature data suggests this is a powerful tool to facilitate the analysis of complex reactions on surfaces, and thus it helps to effectively construct detailed microkinetic mechanisms for such surface reactions. SurfKin also opens a possibility for designing nanoscale model catalysts. Copyright © 2014 Wiley Periodicals, Inc.

The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods.

PubMed

Nagy, László G; Urban, Alexander; Orstadius, Leif; Papp, Tamás; Larsson, Ellen; Vágvölgyi, Csaba

2010-12-01

Recently developed comparative phylogenetic methods offer a wide spectrum of applications in evolutionary biology, although it is generally accepted that their statistical properties are incompletely known. Here, we examine and compare the statistical power of the ML and Bayesian methods with regard to selection of best-fit models of fruiting-body evolution and hypothesis testing of ancestral states on a real-life data set of a physiological trait (autodigestion) in the family Psathyrellaceae. Our phylogenies are based on the first multigene data set generated for the family. Two different coding regimes (binary and multistate) and two data sets differing in taxon sampling density are examined. The Bayesian method outperformed Maximum Likelihood with regard to statistical power in all analyses. This is particularly evident if the signal in the data is weak, i.e. in cases when the ML approach does not provide support to choose among competing hypotheses. Results based on binary and multistate coding differed only modestly, although it was evident that multistate analyses were less conclusive in all cases. It seems that increased taxon sampling density has favourable effects on inference of ancestral states, while model parameters are influenced to a smaller extent. The model best fitting our data implies that the rate of losses of deliquescence equals zero, although model selection in ML does not provide proper support to reject three of the four candidate models. The results also support the hypothesis that non-deliquescence (lack of autodigestion) has been ancestral in Psathyrellaceae, and that deliquescent fruiting bodies represent the preferred state, having evolved independently several times during evolution. Copyright © 2010 Elsevier Inc. All rights reserved.

Faunus: An object oriented framework for molecular simulation

PubMed Central

Lund, Mikael; Trulsson, Martin; Persson, Björn

2008-01-01

Background We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that – subsequently – are collected to automatically build a web-based manual. Results We show how an object oriented design can be used to create an intuitively appealing coding framework for molecular simulation. This is exemplified in a minimalistic C++ program that can calculate protein protonation states. We further discuss performance issues related to high level coding abstraction. Conclusion C++ and the Standard Template Library (STL) provide a high-performance platform for generic molecular modeling. Automatic generation of code documentation from inline comments has proven particularly useful in that no separate manual needs to be maintained. PMID:18241331

Progressive Failure And Life Prediction of Ceramic and Textile Composites

NASA Technical Reports Server (NTRS)

Xue, David Y.; Shi, Yucheng; Katikala, Madhu; Johnston, William M., Jr.; Card, Michael F.

1998-01-01

An engineering approach to predict the fatigue life and progressive failure of multilayered composite and textile laminates is presented. Analytical models which account for matrix cracking, statistical fiber failures and nonlinear stress-strain behavior have been developed for both composites and textiles. The analysis method is based on a combined micromechanics, fracture mechanics and failure statistics analysis. Experimentally derived empirical coefficients are used to account for the interface of fiber and matrix, fiber strength, and fiber-matrix stiffness reductions. Similar approaches were applied to textiles using Repeating Unit Cells. In composite fatigue analysis, Walker's equation is applied for matrix fatigue cracking and Heywood's formulation is used for fiber strength fatigue degradation. The analysis has been compared with experiment with good agreement. Comparisons were made with Graphite-Epoxy, C/SiC and Nicalon/CAS composite materials. For textile materials, comparisons were made with triaxial braided and plain weave materials under biaxial or uniaxial tension. Fatigue predictions were compared with test data obtained from plain weave C/SiC materials tested at AS&M. Computer codes were developed to perform the analysis. Composite Progressive Failure Analysis for Laminates is contained in the code CPFail. Micromechanics Analysis for Textile Composites is contained in the code MicroTex. Both codes were adapted to run as subroutines for the finite element code ABAQUS and CPFail-ABAQUS and MicroTex-ABAQUS. Graphic user interface (GUI) was developed to connect CPFail and MicroTex with ABAQUS.

Binary recursive partitioning: background, methods, and application to psychology.

PubMed

Merkle, Edgar C; Shaffer, Victoria A

2011-02-01

Binary recursive partitioning (BRP) is a computationally intensive statistical method that can be used in situations where linear models are often used. Instead of imposing many assumptions to arrive at a tractable statistical model, BRP simply seeks to accurately predict a response variable based on values of predictor variables. The method outputs a decision tree depicting the predictor variables that were related to the response variable, along with the nature of the variables' relationships. No significance tests are involved, and the tree's 'goodness' is judged based on its predictive accuracy. In this paper, we describe BRP methods in a detailed manner and illustrate their use in psychological research. We also provide R code for carrying out the methods.

GPU-computing in econophysics and statistical physics

NASA Astrophysics Data System (ADS)

Preis, T.

2011-03-01

A recent trend in computer science and related fields is general purpose computing on graphics processing units (GPUs), which can yield impressive performance. With multiple cores connected by high memory bandwidth, today's GPUs offer resources for non-graphics parallel processing. This article provides a brief introduction into the field of GPU computing and includes examples. In particular computationally expensive analyses employed in financial market context are coded on a graphics card architecture which leads to a significant reduction of computing time. In order to demonstrate the wide range of possible applications, a standard model in statistical physics - the Ising model - is ported to a graphics card architecture as well, resulting in large speedup values.

Predictions of the residue cross-sections for the elements Z = 113 and Z = 114

NASA Astrophysics Data System (ADS)

Bouriquet, B.; Abe, Y.; Kosenko, G.

2004-10-01

A good reproduction of experimental excitation functions is obtained for the 1 n reactions producing the elements with Z = 108, 110, 111 and 112 by the combined usage of the two-step model for fusion and the statistical decay code KEWPIE. Furthermore, the model provides reliable predictions of productions of the elements with Z = 113 and Z = 114 which will be a useful guide for plannings of experiments.

The Lake Tahoe Basin Land Use Simulation Model

USGS Publications Warehouse

Forney, William M.; Oldham, I. Benson

2011-01-01

This U.S. Geological Survey Open-File Report describes the final modeling product for the Tahoe Decision Support System project for the Lake Tahoe Basin funded by the Southern Nevada Public Land Management Act and the U.S. Geological Survey's Geographic Analysis and Monitoring Program. This research was conducted by the U.S. Geological Survey Western Geographic Science Center. The purpose of this report is to describe the basic elements of the novel Lake Tahoe Basin Land Use Simulation Model, publish samples of the data inputs, basic outputs of the model, and the details of the Python code. The results of this report include a basic description of the Land Use Simulation Model, descriptions and summary statistics of model inputs, two figures showing the graphical user interface from the web-based tool, samples of the two input files, seven tables of basic output results from the web-based tool and descriptions of their parameters, and the fully functional Python code.

On the Way to Appropriate Model Complexity

NASA Astrophysics Data System (ADS)

Höge, M.

2016-12-01

When statistical models are used to represent natural phenomena they are often too simple or too complex - this is known. But what exactly is model complexity? Among many other definitions, the complexity of a model can be conceptualized as a measure of statistical dependence between observations and parameters (Van der Linde, 2014). However, several issues remain when working with model complexity: A unique definition for model complexity is missing. Assuming a definition is accepted, how can model complexity be quantified? How can we use a quantified complexity to the better of modeling? Generally defined, "complexity is a measure of the information needed to specify the relationships between the elements of organized systems" (Bawden & Robinson, 2015). The complexity of a system changes as the knowledge about the system changes. For models this means that complexity is not a static concept: With more data or higher spatio-temporal resolution of parameters, the complexity of a model changes. There are essentially three categories into which all commonly used complexity measures can be classified: (1) An explicit representation of model complexity as "Degrees of freedom" of a model, e.g. effective number of parameters. (2) Model complexity as code length, a.k.a. "Kolmogorov complexity": The longer the shortest model code, the higher its complexity (e.g. in bits). (3) Complexity defined via information entropy of parametric or predictive uncertainty. Preliminary results show that Bayes theorem allows for incorporating all parts of the non-static concept of model complexity like data quality and quantity or parametric uncertainty. Therefore, we test how different approaches for measuring model complexity perform in comparison to a fully Bayesian model selection procedure. Ultimately, we want to find a measure that helps to assess the most appropriate model.

Use of FEC coding to improve statistical multiplexing performance for video transport over ATM networks

NASA Astrophysics Data System (ADS)

Kurceren, Ragip; Modestino, James W.

1998-12-01

The use of forward error-control (FEC) coding, possibly in conjunction with ARQ techniques, has emerged as a promising approach for video transport over ATM networks for cell-loss recovery and/or bit error correction, such as might be required for wireless links. Although FEC provides cell-loss recovery capabilities it also introduces transmission overhead which can possibly cause additional cell losses. A methodology is described to maximize the number of video sources multiplexed at a given quality of service (QoS), measured in terms of decoded cell loss probability, using interlaced FEC codes. The transport channel is modelled as a block interference channel (BIC) and the multiplexer as single server, deterministic service, finite buffer supporting N users. Based upon an information-theoretic characterization of the BIC and large deviation bounds on the buffer overflow probability, the described methodology provides theoretically achievable upper limits on the number of sources multiplexed. Performance of specific coding techniques using interlaced nonbinary Reed-Solomon (RS) codes and binary rate-compatible punctured convolutional (RCPC) codes is illustrated.

Multilevel modelling: Beyond the basic applications.

PubMed

Wright, Daniel B; London, Kamala

2009-05-01

Over the last 30 years statistical algorithms have been developed to analyse datasets that have a hierarchical/multilevel structure. Particularly within developmental and educational psychology these techniques have become common where the sample has an obvious hierarchical structure, like pupils nested within a classroom. We describe two areas beyond the basic applications of multilevel modelling that are important to psychology: modelling the covariance structure in longitudinal designs and using generalized linear multilevel modelling as an alternative to methods from signal detection theory (SDT). Detailed code for all analyses is described using packages for the freeware R.

Study on Standard Fatigue Vehicle Load Model

NASA Astrophysics Data System (ADS)

Huang, H. Y.; Zhang, J. P.; Li, Y. H.

2018-02-01

Based on the measured data of truck from three artery expressways in Guangdong Province, the statistical analysis of truck weight was conducted according to axle number. The standard fatigue vehicle model applied to industrial areas in the middle and late was obtained, which adopted equivalence damage principle, Miner linear accumulation law, water discharge method and damage ratio theory. Compared with the fatigue vehicle model Specified by the current bridge design code, the proposed model has better applicability. It is of certain reference value for the fatigue design of bridge in China.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Argo, P.E.; DeLapp, D.; Sutherland, C.D.

TRACKER is an extension of a three-dimensional Hamiltonian raytrace code developed some thirty years ago by R. Michael Jones. Subsequent modifications to this code, which is commonly called the {open_quotes}Jones Code,{close_quotes} were documented by Jones and Stephensen (1975). TRACKER incorporates an interactive user`s interface, modern differential equation integrators, graphical outputs, homing algorithms, and the Ionospheric Conductivity and Electron Density (ICED) ionosphere. TRACKER predicts the three-dimensional paths of radio waves through model ionospheres by numerically integrating Hamilton`s equations, which are a differential expression of Fermat`s principle of least time. By using continuous models, the Hamiltonian method avoids false caustics and discontinuousmore » raypath properties often encountered in other raytracing methods. In addition to computing the raypath, TRACKER also calculates the group path (or pulse travel time), the phase path, the geometrical (or {open_quotes}real{close_quotes}) pathlength, and the Doppler shift (if the time variation of the ionosphere is explicitly included). Computational speed can be traded for accuracy by specifying the maximum allowable integration error per step in the integration. Only geometrical optics are included in the main raytrace code; no partial reflections or diffraction effects are taken into account. In addition, TRACKER does not lend itself to statistical descriptions of propagation -- it requires a deterministic model of the ionosphere.« less

Side-information-dependent correlation channel estimation in hash-based distributed video coding.

PubMed

Deligiannis, Nikos; Barbarien, Joeri; Jacobs, Marc; Munteanu, Adrian; Skodras, Athanassios; Schelkens, Peter

2012-04-01

In the context of low-cost video encoding, distributed video coding (DVC) has recently emerged as a potential candidate for uplink-oriented applications. This paper builds on a concept of correlation channel (CC) modeling, which expresses the correlation noise as being statistically dependent on the side information (SI). Compared with classical side-information-independent (SII) noise modeling adopted in current DVC solutions, it is theoretically proven that side-information-dependent (SID) modeling improves the Wyner-Ziv coding performance. Anchored in this finding, this paper proposes a novel algorithm for online estimation of the SID CC parameters based on already decoded information. The proposed algorithm enables bit-plane-by-bit-plane successive refinement of the channel estimation leading to progressively improved accuracy. Additionally, the proposed algorithm is included in a novel DVC architecture that employs a competitive hash-based motion estimation technique to generate high-quality SI at the decoder. Experimental results corroborate our theoretical gains and validate the accuracy of the channel estimation algorithm. The performance assessment of the proposed architecture shows remarkable and consistent coding gains over a germane group of state-of-the-art distributed and standard video codecs, even under strenuous conditions, i.e., large groups of pictures and highly irregular motion content.

Adaptation in Coding by Large Populations of Neurons in the Retina

NASA Astrophysics Data System (ADS)

Ioffe, Mark L.

A comprehensive theory of neural computation requires an understanding of the statistical properties of the neural population code. The focus of this work is the experimental study and theoretical analysis of the statistical properties of neural activity in the tiger salamander retina. This is an accessible yet complex system, for which we control the visual input and record from a substantial portion--greater than a half--of the ganglion cell population generating the spiking output. Our experiments probe adaptation of the retina to visual statistics: a central feature of sensory systems which have to adjust their limited dynamic range to a far larger space of possible inputs. In Chapter 1 we place our work in context with a brief overview of the relevant background. In Chapter 2 we describe the experimental methodology of recording from 100+ ganglion cells in the tiger salamander retina. In Chapter 3 we first present the measurements of adaptation of individual cells to changes in stimulation statistics and then investigate whether pairwise correlations in fluctuations of ganglion cell activity change across different stimulation conditions. We then transition to a study of the population-level probability distribution of the retinal response captured with maximum-entropy models. Convergence of the model inference is presented in Chapter 4. In Chapter 5 we first test the empirical presence of a phase transition in such models fitting the retinal response to different experimental conditions, and then proceed to develop other characterizations which are sensitive to complexity in the interaction matrix. This includes an analysis of the dynamics of sampling at finite temperature, which demonstrates a range of subtle attractor-like properties in the energy landscape. These are largely conserved when ambient illumination is varied 1000-fold, a result not necessarily apparent from the measured low-order statistics of the distribution. Our results form a consistent picture which is discussed at the end of Chapter 5. We conclude with a few future directions related to this thesis.

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.

PubMed

Lopes, J S; Arenas, M; Posada, D; Beaumont, M A

2014-03-01

The estimation of parameters in molecular evolution may be biased when some processes are not considered. For example, the estimation of selection at the molecular level using codon-substitution models can have an upward bias when recombination is ignored. Here we address the joint estimation of recombination, molecular adaptation and substitution rates from coding sequences using approximate Bayesian computation (ABC). We describe the implementation of a regression-based strategy for choosing subsets of summary statistics for coding data, and show that this approach can accurately infer recombination allowing for intracodon recombination breakpoints, molecular adaptation and codon substitution rates. We demonstrate that our ABC approach can outperform other analytical methods under a variety of evolutionary scenarios. We also show that although the choice of the codon-substitution model is important, our inferences are robust to a moderate degree of model misspecification. In addition, we demonstrate that our approach can accurately choose the evolutionary model that best fits the data, providing an alternative for when the use of full-likelihood methods is impracticable. Finally, we applied our ABC method to co-estimate recombination, substitution and molecular adaptation rates from 24 published human immunodeficiency virus 1 coding data sets.

Impact of documentation errors on accuracy of cause of death coding in an educational hospital in Southern Iran.

PubMed

Haghighi, Mohammad Hosein Hayavi; Dehghani, Mohammad; Teshnizi, Saeid Hoseini; Mahmoodi, Hamid

2014-01-01

Accurate cause of death coding leads to organised and usable death information but there are some factors that influence documentation on death certificates and therefore affect the coding. We reviewed the role of documentation errors on the accuracy of death coding at Shahid Mohammadi Hospital (SMH), Bandar Abbas, Iran. We studied the death certificates of all deceased patients in SMH from October 2010 to March 2011. Researchers determined and coded the underlying cause of death on the death certificates according to the guidelines issued by the World Health Organization in Volume 2 of the International Statistical Classification of Diseases and Health Related Problems-10th revision (ICD-10). Necessary ICD coding rules (such as the General Principle, Rules 1-3, the modification rules and other instructions about death coding) were applied to select the underlying cause of death on each certificate. Demographic details and documentation errors were then extracted. Data were analysed with descriptive statistics and chi square tests. The accuracy rate of causes of death coding was 51.7%, demonstrating a statistically significant relationship (p=.001) with major errors but not such a relationship with minor errors. Factors that result in poor quality of Cause of Death coding in SMH are lack of coder training, documentation errors and the undesirable structure of death certificates.

An efficient system for reliably transmitting image and video data over low bit rate noisy channels

NASA Technical Reports Server (NTRS)

Costello, Daniel J., Jr.; Huang, Y. F.; Stevenson, Robert L.

1994-01-01

This research project is intended to develop an efficient system for reliably transmitting image and video data over low bit rate noisy channels. The basic ideas behind the proposed approach are the following: employ statistical-based image modeling to facilitate pre- and post-processing and error detection, use spare redundancy that the source compression did not remove to add robustness, and implement coded modulation to improve bandwidth efficiency and noise rejection. Over the last six months, progress has been made on various aspects of the project. Through our studies of the integrated system, a list-based iterative Trellis decoder has been developed. The decoder accepts feedback from a post-processor which can detect channel errors in the reconstructed image. The error detection is based on the Huber Markov random field image model for the compressed image. The compression scheme used here is that of JPEG (Joint Photographic Experts Group). Experiments were performed and the results are quite encouraging. The principal ideas here are extendable to other compression techniques. In addition, research was also performed on unequal error protection channel coding, subband vector quantization as a means of source coding, and post processing for reducing coding artifacts. Our studies on unequal error protection (UEP) coding for image transmission focused on examining the properties of the UEP capabilities of convolutional codes. The investigation of subband vector quantization employed a wavelet transform with special emphasis on exploiting interband redundancy. The outcome of this investigation included the development of three algorithms for subband vector quantization. The reduction of transform coding artifacts was studied with the aid of a non-Gaussian Markov random field model. This results in improved image decompression. These studies are summarized and the technical papers included in the appendices.

Evaluation of neutron total and capture cross sections on 99Tc in the unresolved resonance region

NASA Astrophysics Data System (ADS)

Iwamoto, Nobuyuki; Katabuchi, Tatsuya

2017-09-01

Long-lived fission product Technetium-99 is one of the most important radioisotopes for nuclear transmutation. The reliable nuclear data are indispensable for a wide energy range up to a few MeV, in order to develop environmental load reducing technology. The statistical analyses of resolved resonances were performed by using the truncated Porter-Thomas distribution, coupled-channels optical model, nuclear level density model and Bayes' theorem on conditional probability. The total and capture cross sections were calculated by a nuclear reaction model code CCONE. The resulting cross sections have statistical consistency between the resolved and unresolved resonance regions. The evaluated capture data reproduce those recently measured at ANNRI of J-PARC/MLF above resolved resonance region up to 800 keV.

Case-crossover design and its implementation in R

PubMed Central

2016-01-01

Case-crossover design is a variation of case-control design that it employs persons’ history periods as controls. Case-crossover design can be viewed as the hybrid of case-control study and crossover design. Characteristic confounding that is constant within one person can be well controlled with this method. The relative risk and odds ratio, as well as their 95% confidence intervals (CIs), can be estimated using Cochran-Mantel-Haenszel method. R codes for the calculation are provided in the main text. Readers may adapt these codes to their own task. Conditional logistic regression model is another way to estimate odds ratio of the exposure. Furthermore, it allows for incorporation of other time-varying covariates that are not constant within subjects. The model fitting per se is not technically difficult because there is well developed statistical package. However, it is challenging to convert original dataset obtained from case report form to that suitable to be passed to clogit() function. R code for this task is provided and explained in the text. PMID:27761445

49 CFR 1248.100 - Commodity classification designated.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 9 2011-10-01 2011-10-01 false Commodity classification designated. 1248.100... STATISTICS Commodity Code § 1248.100 Commodity classification designated. Commencing with reports for the..., reports of commodity statistics required to be made to the Board, shall be based on the commodity codes...

Visual–Motor Transformations Within Frontal Eye Fields During Head-Unrestrained Gaze Shifts in the Monkey

PubMed Central

Sajad, Amirsaman; Sadeh, Morteza; Keith, Gerald P.; Yan, Xiaogang; Wang, Hongying; Crawford, John Douglas

2015-01-01

A fundamental question in sensorimotor control concerns the transformation of spatial signals from the retina into eye and head motor commands required for accurate gaze shifts. Here, we investigated these transformations by identifying the spatial codes embedded in visually evoked and movement-related responses in the frontal eye fields (FEFs) during head-unrestrained gaze shifts. Monkeys made delayed gaze shifts to the remembered location of briefly presented visual stimuli, with delay serving to dissociate visual and movement responses. A statistical analysis of nonparametric model fits to response field data from 57 neurons (38 with visual and 49 with movement activities) eliminated most effector-specific, head-fixed, and space-fixed models, but confirmed the dominance of eye-centered codes observed in head-restrained studies. More importantly, the visual response encoded target location, whereas the movement response mainly encoded the final position of the imminent gaze shift (including gaze errors). This spatiotemporal distinction between target and gaze coding was present not only at the population level, but even at the single-cell level. We propose that an imperfect visual–motor transformation occurs during the brief memory interval between perception and action, and further transformations from the FEF's eye-centered gaze motor code to effector-specific codes in motor frames occur downstream in the subcortical areas. PMID:25491118

Code-division multiple-access multiuser demodulator by using quantum fluctuations.

PubMed

Otsubo, Yosuke; Inoue, Jun-Ichi; Nagata, Kenji; Okada, Masato

2014-07-01

We examine the average-case performance of a code-division multiple-access (CDMA) multiuser demodulator in which quantum fluctuations are utilized to demodulate the original message within the context of Bayesian inference. The quantum fluctuations are built into the system as a transverse field in the infinite-range Ising spin glass model. We evaluate the performance measurements by using statistical mechanics. We confirm that the CDMA multiuser modulator using quantum fluctuations achieve roughly the same performance as the conventional CDMA multiuser modulator through thermal fluctuations on average. We also find that the relationship between the quality of the original information retrieval and the amplitude of the transverse field is somehow a "universal feature" in typical probabilistic information processing, viz., in image restoration, error-correcting codes, and CDMA multiuser demodulation.

Code-division multiple-access multiuser demodulator by using quantum fluctuations

NASA Astrophysics Data System (ADS)

Otsubo, Yosuke; Inoue, Jun-ichi; Nagata, Kenji; Okada, Masato

2014-07-01

We examine the average-case performance of a code-division multiple-access (CDMA) multiuser demodulator in which quantum fluctuations are utilized to demodulate the original message within the context of Bayesian inference. The quantum fluctuations are built into the system as a transverse field in the infinite-range Ising spin glass model. We evaluate the performance measurements by using statistical mechanics. We confirm that the CDMA multiuser modulator using quantum fluctuations achieve roughly the same performance as the conventional CDMA multiuser modulator through thermal fluctuations on average. We also find that the relationship between the quality of the original information retrieval and the amplitude of the transverse field is somehow a "universal feature" in typical probabilistic information processing, viz., in image restoration, error-correcting codes, and CDMA multiuser demodulation.

CTF (Subchannel) Calculations and Validation L3:VVI.H2L.P15.01

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gordon, Natalie

The goal of the Verification and Validation Implementation (VVI) High to Low (Hi2Lo) process is utilizing a validated model in a high resolution code to generate synthetic data for improvement of the same model in a lower resolution code. This process is useful in circumstances where experimental data does not exist or it is not sufficient in quantity or resolution. Data from the high-fidelity code is treated as calibration data (with appropriate uncertainties and error bounds) which can be used to train parameters that affect solution accuracy in the lower-fidelity code model, thereby reducing uncertainty. This milestone presents a demonstrationmore » of the Hi2Lo process derived in the VVI focus area. The majority of the work performed herein describes the steps of the low-fidelity code used in the process with references to the work detailed in the companion high-fidelity code milestone (Reference 1). The CASL low-fidelity code used to perform this work was Cobra Thermal Fluid (CTF) and the high-fidelity code was STAR-CCM+ (STAR). The master branch version of CTF (pulled May 5, 2017 – Reference 2) was utilized for all CTF analyses performed as part of this milestone. The statistical and VVUQ components of the Hi2Lo framework were performed using Dakota version 6.6 (release date May 15, 2017 – Reference 3). Experimental data from Westinghouse Electric Company (WEC – Reference 4) was used throughout the demonstrated process to compare with the high-fidelity STAR results. A CTF parameter called Beta was chosen as the calibration parameter for this work. By default, Beta is defined as a constant mixing coefficient in CTF and is essentially a tuning parameter for mixing between subchannels. Since CTF does not have turbulence models like STAR, Beta is the parameter that performs the most similar function to the turbulence models in STAR. The purpose of the work performed in this milestone is to tune Beta to an optimal value that brings the CTF results closer to those measured in the WEC experiments.« less

DRG coding practice: a nationwide hospital survey in Thailand.

PubMed

Pongpirul, Krit; Walker, Damian G; Rahman, Hafizur; Robinson, Courtland

2011-10-31

Diagnosis Related Group (DRG) payment is preferred by healthcare reform in various countries but its implementation in resource-limited countries has not been fully explored. This study was aimed (1) to compare the characteristics of hospitals in Thailand that were audited with those that were not and (2) to develop a simplified scale to measure hospital coding practice. A questionnaire survey was conducted of 920 hospitals in the Summary and Coding Audit Database (SCAD hospitals, all of which were audited in 2008 because of suspicious reports of possible DRG miscoding); the questionnaire also included 390 non-SCAD hospitals. The questionnaire asked about general demographics of the hospitals, hospital coding structure and process, and also included a set of 63 opinion-oriented items on the current hospital coding practice. Descriptive statistics and exploratory factor analysis (EFA) were used for data analysis. SCAD and Non-SCAD hospitals were different in many aspects, especially the number of medical statisticians, experience of medical statisticians and physicians, as well as number of certified coders. Factor analysis revealed a simplified 3-factor, 20-item model to assess hospital coding practice and classify hospital intention. Hospital providers should not be assumed capable of producing high quality DRG codes, especially in resource-limited settings.

Specification and Prediction of the Radiation Environment Using Data Assimilative VERB code

NASA Astrophysics Data System (ADS)

Shprits, Yuri; Kellerman, Adam

2016-07-01

We discuss how data assimilation can be used for the reconstruction of long-term evolution, bench-marking of the physics based codes and used to improve the now-casting and focusing of the radiation belts and ring current. We also discuss advanced data assimilation methods such as parameter estimation and smoothing. We present a number of data assimilation applications using the VERB 3D code. The 3D data assimilative VERB allows us to blend together data from GOES, RBSP A and RBSP B. 1) Model with data assimilation allows us to propagate data to different pitch angles, energies, and L-shells and blends them together with the physics-based VERB code in an optimal way. We illustrate how to use this capability for the analysis of the previous events and for obtaining a global and statistical view of the system. 2) The model predictions strongly depend on initial conditions that are set up for the model. Therefore, the model is as good as the initial conditions that it uses. To produce the best possible initial conditions, data from different sources (GOES, RBSP A, B, our empirical model predictions based on ACE) are all blended together in an optimal way by means of data assimilation, as described above. The resulting initial conditions do not have gaps. This allows us to make more accurate predictions. Real-time prediction framework operating on our website, based on GOES, RBSP A, B and ACE data, and 3D VERB, is presented and discussed.

Statistics of single unit responses in the human medial temporal lobe: A sparse and overdispersed code

NASA Astrophysics Data System (ADS)

Magyar, Andrew

The recent discovery of cells that respond to purely conceptual features of the environment (particular people, landmarks, objects, etc) in the human medial temporal lobe (MTL), has raised many questions about the nature of the neural code in humans. The goal of this dissertation is to develop a novel statistical method based upon maximum likelihood regression which will then be applied to these experiments in order to produce a quantitative description of the coding properties of the human MTL. In general, the method is applicable to any experiments in which a sequence of stimuli are presented to an organism while the binary responses of a large number of cells are recorded in parallel. The central concept underlying the approach is the total probability that a neuron responds to a random stimulus, called the neuronal sparsity. The model then estimates the distribution of response probabilities across the population of cells. Applying the method to single-unit recordings from the human medial temporal lobe, estimates of the sparsity distributions are acquired in four regions: the hippocampus, the entorhinal cortex, the amygdala, and the parahippocampal cortex. The resulting distributions are found to be sparse (large fraction of cells with a low response probability) and highly non-uniform, with a large proportion of ultra-sparse neurons that possess a very low response probability, and a smaller population of cells which respond much more frequently. Rammifications of the results are discussed in relation to the sparse coding hypothesis, and comparisons are made between the statistics of the human medial temporal lobe cells and place cells observed in the rodent hippocampus.

It's Only a Phase: Applying the 5 Phases of Clinical Trials to the NSCR Model Improvement Process

NASA Technical Reports Server (NTRS)

Elgart, S. R.; Milder, C. M.; Chappell, L. J.; Semones, E. J.

2017-01-01

NASA limits astronaut radiation exposures to a 3% risk of exposure-induced death from cancer (REID) at the upper 95% confidence level. Since astronauts approach this limit, it is important that the estimate of REID be as accurate as possible. The NASA Space Cancer Risk 2012 (NSCR-2012) model has been the standard for NASA's space radiation protection guidelines since its publication in 2013. The model incorporates elements from U.S. baseline statistics, Japanese atomic bomb survivor research, animal models, cellular studies, and radiation transport to calculate astronaut baseline risk of cancer and REID. The NSCR model is under constant revision to ensure emerging research is incorporated into radiation protection standards. It is important to develop guidelines, however, to determine what new research is appropriate for integration. Certain standards of transparency are necessary in order to assess data quality, statistical quality, and analytical quality. To this effect, all original source code and any raw data used to develop the code are required to confirm there are no errors which significantly change reported outcomes. It is possible to apply a clinical trials approach to select and assess the improvement concepts that will be incorporated into future iterations of NSCR. This poster describes the five phases of clinical trials research, pre-clinical research, and clinical research phases I-IV, explaining how each step can be translated into an appropriate NSCR model selection guideline.

Injury Severity Score coding: Data analyst v. emerging m-health technology.

PubMed

Spence, R T; Zargaran, E; Hameed, M; Fong, D; Shangguan, E; Martinez, R; Navsaria, P; Nicol, A

2016-09-08

The cost of Abbreviated Injury Scale (AIS) coding has limited its utility in areas of the world with the highest incidence of trauma. We hypothesised that emerging mobile health (m-health) technology could offer a cost-effective alternative to the current gold-standard AIS mechanism in a high-volume trauma centre in South Africa. A prospectively collected sample of consecutive patients admitted following a traumatic injury that required an operation during a 1-month period was selected for the study. AISs and Injury Severity Scores (ISSs) were generated by clinician-entered data using an m-health application (ISS eTHR) as well as by a team of AIS coders at Vancouver General Hospital, Canada (ISS VGH). Rater agreements for ISSs were analysed using Bland-Altman plots with 95% limits of agreement (LoA) and kappa statistics of the ISSs grouped into ordinal categories. Reliability was analysed using a two-way mixed-model intraclass correlation coefficient (ICC). Calibration and discrimination of univariate logistic regression models built to predict in-hospital complications using ISSs coded by the two methods were also compared. Fifty-seven patients were managed operatively during the study period. The mean age of the cohort was 27.2 years (range 14 - 62), and 96.3% were male. The mechanism of injury was penetrating in 93.4% of cases, of which 52.8% were gunshot injuries. The LoA fell within -8.6 - 9.4. The mean ISS difference was 0.4 (95% CI -0.8 - 1.6). The kappa statistic was 0.53. The ICC of the individual ISS was 0.88 (95% CI 0.81 - 0.93) and the categorical ISS was 0.81 (95% CI 0.68 - 0.87). Model performance to predict in-hospital complications using either the ISS eTHR or the ISS VGH was equivalent. ISSs calculated by the eTHR and gold-standard coding were comparable. Emerging m-health technology provides a cost-effective alternative for injury severity scoring.

A Nonlinear Model for Fuel Atomization in Spray Combustion

NASA Technical Reports Server (NTRS)

Liu, Nan-Suey (Technical Monitor); Ibrahim, Essam A.; Sree, Dave

2003-01-01

Most gas turbine combustion codes rely on ad-hoc statistical assumptions regarding the outcome of fuel atomization processes. The modeling effort proposed in this project is aimed at developing a realistic model to produce accurate predictions of fuel atomization parameters. The model involves application of the nonlinear stability theory to analyze the instability and subsequent disintegration of the liquid fuel sheet that is produced by fuel injection nozzles in gas turbine combustors. The fuel sheet is atomized into a multiplicity of small drops of large surface area to volume ratio to enhance the evaporation rate and combustion performance. The proposed model will effect predictions of fuel sheet atomization parameters such as drop size, velocity, and orientation as well as sheet penetration depth, breakup time and thickness. These parameters are essential for combustion simulation codes to perform a controlled and optimized design of gas turbine fuel injectors. Optimizing fuel injection processes is crucial to improving combustion efficiency and hence reducing fuel consumption and pollutants emissions.

Reversibility in Quantum Models of Stochastic Processes

NASA Astrophysics Data System (ADS)

Gier, David; Crutchfield, James; Mahoney, John; James, Ryan

Natural phenomena such as time series of neural firing, orientation of layers in crystal stacking and successive measurements in spin-systems are inherently probabilistic. The provably minimal classical models of such stochastic processes are ɛ-machines, which consist of internal states, transition probabilities between states and output values. The topological properties of the ɛ-machine for a given process characterize the structure, memory and patterns of that process. However ɛ-machines are often not ideal because their statistical complexity (Cμ) is demonstrably greater than the excess entropy (E) of the processes they represent. Quantum models (q-machines) of the same processes can do better in that their statistical complexity (Cq) obeys the relation Cμ >= Cq >= E. q-machines can be constructed to consider longer lengths of strings, resulting in greater compression. With code-words of sufficiently long length, the statistical complexity becomes time-symmetric - a feature apparently novel to this quantum representation. This result has ramifications for compression of classical information in quantum computing and quantum communication technology.

Case studies in Bayesian microbial risk assessments.

PubMed

Kennedy, Marc C; Clough, Helen E; Turner, Joanne

2009-12-21

The quantification of uncertainty and variability is a key component of quantitative risk analysis. Recent advances in Bayesian statistics make it ideal for integrating multiple sources of information, of different types and quality, and providing a realistic estimate of the combined uncertainty in the final risk estimates. We present two case studies related to foodborne microbial risks. In the first, we combine models to describe the sequence of events resulting in illness from consumption of milk contaminated with VTEC O157. We used Monte Carlo simulation to propagate uncertainty in some of the inputs to computer models describing the farm and pasteurisation process. Resulting simulated contamination levels were then assigned to consumption events from a dietary survey. Finally we accounted for uncertainty in the dose-response relationship and uncertainty due to limited incidence data to derive uncertainty about yearly incidences of illness in young children. Options for altering the risk were considered by running the model with different hypothetical policy-driven exposure scenarios. In the second case study we illustrate an efficient Bayesian sensitivity analysis for identifying the most important parameters of a complex computer code that simulated VTEC O157 prevalence within a managed dairy herd. This was carried out in 2 stages, first to screen out the unimportant inputs, then to perform a more detailed analysis on the remaining inputs. The method works by building a Bayesian statistical approximation to the computer code using a number of known code input/output pairs (training runs). We estimated that the expected total number of children aged 1.5-4.5 who become ill due to VTEC O157 in milk is 8.6 per year, with 95% uncertainty interval (0,11.5). The most extreme policy we considered was banning on-farm pasteurisation of milk, which reduced the estimate to 6.4 with 95% interval (0,11). In the second case study the effective number of inputs was reduced from 30 to 7 in the screening stage, and just 2 inputs were found to explain 82.8% of the output variance. A combined total of 500 runs of the computer code were used. These case studies illustrate the use of Bayesian statistics to perform detailed uncertainty and sensitivity analyses, integrating multiple information sources in a way that is both rigorous and efficient.

Spin distributions and cross sections of evaporation residues in the 28Si+176Yb reaction

NASA Astrophysics Data System (ADS)

Sudarshan, K.; Tripathi, R.; Sodaye, S.; Sharma, S. K.; Pujari, P. K.; Gehlot, J.; Madhavan, N.; Nath, S.; Mohanto, G.; Mukul, I.; Jhingan, A.; Mazumdar, I.

2017-02-01

Background: Non-compound-nucleus fission in the preactinide region has been an active area of investigation in the recent past. Based on the measurements of fission-fragment mass distributions in the fission of 202Po, populated by reactions with varying entrance channel mass asymmetry, the onset of non-compound-nucleus fission was proposed to be around ZpZt˜1000 [Phys. Rev. C 77, 024606 (2008), 10.1103/PhysRevC.77.024606], where Zp and Zt are the projectile and target proton numbers, respectively. Purpose: The present paper is aimed at the measurement of cross sections and spin distributions of evaporation residues in the 28Si+176Yb reaction (ZpZt=980 ) to investigate the fusion hindrance which, in turn, would give information about the contribution from non-compound-nucleus fission in this reaction. Method: Evaporation-residue cross sections were measured in the beam energy range of 129-166 MeV using the hybrid recoil mass analyzer (HYRA) operated in the gas-filled mode. Evaporation-residue cross sections were also measured by the recoil catcher technique followed by off-line γ -ray spectrometry at few intermediate energies. γ -ray multiplicities of evaporation residues were measured to infer about their spin distribution. The measurements were carried out using NaI(Tl) detector-based 4π-spin spectrometer from the Tata Institute of Fundamental Research, Mumbai, coupled to the HYRA. Results: Evaporation-residue cross sections were significantly lower compared to those calculated using the statistical model code pace2 [Phys. Rev. C 21, 230 (1980), 10.1103/PhysRevC.21.230] with the coupled-channel fusion model code ccfus [Comput. Phys. Commun. 46, 187 (1987), 10.1016/0010-4655(87)90045-2] at beam energies close to the entrance channel Coulomb barrier. At higher beam energies, experimental cross sections were close to those predicted by the model. Average γ -ray multiplicities or angular momentum values of evaporation residues were in agreement with the calculations of the code ccfus + pace2 within the experimental uncertainties at all the beam energies. Conclusions: Deviation of evaporation-residue cross sections from the "fusion + statistical model" predictions at beam energies close to the entrance channel Coulomb barrier indicates fusion hindrance at these beam energies which would lead to non-compound-nucleus fission. However, reasonable agreement of average angular momentum values of evaporation residues at these beam energies with those calculated using the coupled-channel fusion model with the statistical model codes ccfus + pace2 suggests that fusion suppression at beam energies close to the entrance channel Coulomb barrier where populated l waves are low is not l dependent.

Rfam: Wikipedia, clans and the “decimal” release

PubMed Central

Gardner, Paul P.; Daub, Jennifer; Tate, John; Moore, Benjamin L.; Osuch, Isabelle H.; Griffiths-Jones, Sam; Finn, Robert D.; Nawrocki, Eric P.; Kolbe, Diana L.; Eddy, Sean R.; Bateman, Alex

2011-01-01

The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community-derived annotation. We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk. PMID:21062808

Imaging Analysis of the Hard X-Ray Telescope ProtoEXIST2 and New Techniques for High-Resolution Coded-Aperture Telescopes

NASA Technical Reports Server (NTRS)

Hong, Jaesub; Allen, Branden; Grindlay, Jonathan; Barthelmy, Scott D.

2016-01-01

Wide-field (greater than or approximately equal to 100 degrees squared) hard X-ray coded-aperture telescopes with high angular resolution (greater than or approximately equal to 2 minutes) will enable a wide range of time domain astrophysics. For instance, transient sources such as gamma-ray bursts can be precisely localized without the assistance of secondary focusing X-ray telescopes to enable rapid followup studies. On the other hand, high angular resolution in coded-aperture imaging introduces a new challenge in handling the systematic uncertainty: the average photon count per pixel is often too small to establish a proper background pattern or model the systematic uncertainty in a timescale where the model remains invariant. We introduce two new techniques to improve detection sensitivity, which are designed for, but not limited to, a high-resolution coded-aperture system: a self-background modeling scheme which utilizes continuous scan or dithering operations, and a Poisson-statistics based probabilistic approach to evaluate the significance of source detection without subtraction in handling the background. We illustrate these new imaging analysis techniques in high resolution coded-aperture telescope using the data acquired by the wide-field hard X-ray telescope ProtoEXIST2 during a high-altitude balloon flight in fall 2012. We review the imaging sensitivity of ProtoEXIST2 during the flight, and demonstrate the performance of the new techniques using our balloon flight data in comparison with a simulated ideal Poisson background.

Synchrony and motor mimicking in chimpanzee observational learning

PubMed Central

Fuhrmann, Delia; Ravignani, Andrea; Marshall-Pescini, Sarah; Whiten, Andrew

2014-01-01

Cumulative tool-based culture underwrote our species' evolutionary success, and tool-based nut-cracking is one of the strongest candidates for cultural transmission in our closest relatives, chimpanzees. However the social learning processes that may explain both the similarities and differences between the species remain unclear. A previous study of nut-cracking by initially naïve chimpanzees suggested that a learning chimpanzee holding no hammer nevertheless replicated hammering actions it witnessed. This observation has potentially important implications for the nature of the social learning processes and underlying motor coding involved. In the present study, model and observer actions were quantified frame-by-frame and analysed with stringent statistical methods, demonstrating synchrony between the observer's and model's movements, cross-correlation of these movements above chance level and a unidirectional transmission process from model to observer. These results provide the first quantitative evidence for motor mimicking underlain by motor coding in apes, with implications for mirror neuron function. PMID:24923651

Synchrony and motor mimicking in chimpanzee observational learning.

PubMed

Fuhrmann, Delia; Ravignani, Andrea; Marshall-Pescini, Sarah; Whiten, Andrew

2014-06-13

Cumulative tool-based culture underwrote our species' evolutionary success, and tool-based nut-cracking is one of the strongest candidates for cultural transmission in our closest relatives, chimpanzees. However the social learning processes that may explain both the similarities and differences between the species remain unclear. A previous study of nut-cracking by initially naïve chimpanzees suggested that a learning chimpanzee holding no hammer nevertheless replicated hammering actions it witnessed. This observation has potentially important implications for the nature of the social learning processes and underlying motor coding involved. In the present study, model and observer actions were quantified frame-by-frame and analysed with stringent statistical methods, demonstrating synchrony between the observer's and model's movements, cross-correlation of these movements above chance level and a unidirectional transmission process from model to observer. These results provide the first quantitative evidence for motor mimicking underlain by motor coding in apes, with implications for mirror neuron function.

TRIPOLI-4® - MCNP5 ITER A-lite neutronic model benchmarking

NASA Astrophysics Data System (ADS)

Jaboulay, J.-C.; Cayla, P.-Y.; Fausser, C.; Lee, Y.-K.; Trama, J.-C.; Li-Puma, A.

2014-06-01

The aim of this paper is to present the capability of TRIPOLI-4®, the CEA Monte Carlo code, to model a large-scale fusion reactor with complex neutron source and geometry. In the past, numerous benchmarks were conducted for TRIPOLI-4® assessment on fusion applications. Experiments (KANT, OKTAVIAN, FNG) analysis and numerical benchmarks (between TRIPOLI-4® and MCNP5) on the HCLL DEMO2007 and ITER models were carried out successively. In this previous ITER benchmark, nevertheless, only the neutron wall loading was analyzed, its main purpose was to present MCAM (the FDS Team CAD import tool) extension for TRIPOLI-4®. Starting from this work a more extended benchmark has been performed about the estimation of neutron flux, nuclear heating in the shielding blankets and tritium production rate in the European TBMs (HCLL and HCPB) and it is presented in this paper. The methodology to build the TRIPOLI-4® A-lite model is based on MCAM and the MCNP A-lite model (version 4.1). Simplified TBMs (from KIT) have been integrated in the equatorial-port. Comparisons of neutron wall loading, flux, nuclear heating and tritium production rate show a good agreement between the two codes. Discrepancies are mainly included in the Monte Carlo codes statistical error.

Portal of medical data models: information infrastructure for medical research and healthcare.

PubMed

Dugas, Martin; Neuhaus, Philipp; Meidt, Alexandra; Doods, Justin; Storck, Michael; Bruland, Philipp; Varghese, Julian

2016-01-01

Information systems are a key success factor for medical research and healthcare. Currently, most of these systems apply heterogeneous and proprietary data models, which impede data exchange and integrated data analysis for scientific purposes. Due to the complexity of medical terminology, the overall number of medical data models is very high. At present, the vast majority of these models are not available to the scientific community. The objective of the Portal of Medical Data Models (MDM, https://medical-data-models.org) is to foster sharing of medical data models. MDM is a registered European information infrastructure. It provides a multilingual platform for exchange and discussion of data models in medicine, both for medical research and healthcare. The system is developed in collaboration with the University Library of Münster to ensure sustainability. A web front-end enables users to search, view, download and discuss data models. Eleven different export formats are available (ODM, PDF, CDA, CSV, MACRO-XML, REDCap, SQL, SPSS, ADL, R, XLSX). MDM contents were analysed with descriptive statistics. MDM contains 4387 current versions of data models (in total 10,963 versions). 2475 of these models belong to oncology trials. The most common keyword (n = 3826) is 'Clinical Trial'; most frequent diseases are breast cancer, leukemia, lung and colorectal neoplasms. Most common languages of data elements are English (n = 328,557) and German (n = 68,738). Semantic annotations (UMLS codes) are available for 108,412 data items, 2453 item groups and 35,361 code list items. Overall 335,087 UMLS codes are assigned with 21,847 unique codes. Few UMLS codes are used several thousand times, but there is a long tail of rarely used codes in the frequency distribution. Expected benefits of the MDM portal are improved and accelerated design of medical data models by sharing best practice, more standardised data models with semantic annotation and better information exchange between information systems, in particular Electronic Data Capture (EDC) and Electronic Health Records (EHR) systems. Contents of the MDM portal need to be further expanded to reach broad coverage of all relevant medical domains. Database URL: https://medical-data-models.org. © The Author(s) 2016. Published by Oxford University Press.

Making COD statistics useful for public health at local level in the city of Cape Town: utilidad para la salud pública a nivel local en Ciudad del Cabo.

PubMed Central

Bradshaw, Debbie; Groenewald, Pamela; Bourne, David E.; Mahomed, Hassan; Nojilana, Beatrice; Daniels, Johan; Nixon, Jo

2006-01-01

OBJECTIVE: To review the quality of the coding of the cause of death (COD) statistics and assess the mortality information needs of the City of Cape Town. METHODS: Using an action research approach, a study was set up to investigate the quality of COD information, the accuracy of COD coding and consistency of coding practices in the larger health subdistricts. Mortality information needs and the best way of presenting the statistics to assist health managers were explored. FINDINGS: Useful information was contained in 75% of death certificates, but nearly 60% had only a single cause certified; 55% of forms were coded accurately. Disagreement was mainly because routine coders coded the immediate instead of the underlying COD. An abridged classification of COD, based on causes of public health importance, prevalent causes and selected combinations of diseases was implemented with training on underlying cause. Analysis of the 2001 data identified the leading causes of death and premature mortality and illustrated striking differences in the disease burden and profile between health subdistricts. CONCLUSION: Action research is particularly useful for improving information systems and revealed the need to standardize the coding practice to identify underlying cause. The specificity of the full ICD classification is beyond the level of detail on the death certificates currently available. An abridged classification for coding provides a practical tool appropriate for local level public health surveillance. Attention to the presentation of COD statistics is important to enable the data to inform decision-makers. PMID:16583080

Making COD statistics useful for public health at local level in the city of Cape Town: utilidad para la salud pública a nivel local en Ciudad del Cabo.

PubMed

Bradshaw, Debbie; Groenewald, Pamela; Bourne, David E; Mahomed, Hassan; Nojilana, Beatrice; Daniels, Johan; Nixon, Jo

2006-03-01

To review the quality of the coding of the cause of death (COD) statistics and assess the mortality information needs of the City of Cape Town. Using an action research approach, a study was set up to investigate the quality of COD information, the accuracy of COD coding and consistency of coding practices in the larger health subdistricts. Mortality information needs and the best way of presenting the statistics to assist health managers were explored. Useful information was contained in 75% of death certificates, but nearly 60% had only a single cause certified; 55% of forms were coded accurately. Disagreement was mainly because routine coders coded the immediate instead of the underlying COD. An abridged classification of COD, based on causes of public health importance, prevalent causes and selected combinations of diseases was implemented with training on underlying cause. Analysis of the 2001 data identified the leading causes of death and premature mortality and illustrated striking differences in the disease burden and profile between health subdistricts. Action research is particularly useful for improving information systems and revealed the need to standardize the coding practice to identify underlying cause. The specificity of the full ICD classification is beyond the level of detail on the death certificates currently available. An abridged classification for coding provides a practical tool appropriate for local level public health surveillance. Attention to the presentation of COD statistics is important to enable the data to inform decision-makers.

Establishing Consensus Turbulence Statistics for Hot Subsonic Jets

NASA Technical Reports Server (NTRS)

Bridges, James; Werner, Mark P.

2010-01-01

Many tasks in fluids engineering require knowledge of the turbulence in jets. There is a strong, although fragmented, literature base for low order statistics, such as jet spread and other meanvelocity field characteristics. Some sources, particularly for low speed cold jets, also provide turbulence intensities that are required for validating Reynolds-averaged Navier-Stokes (RANS) Computational Fluid Dynamics (CFD) codes. There are far fewer sources for jet spectra and for space-time correlations of turbulent velocity required for aeroacoustics applications, although there have been many singular publications with various unique statistics, such as Proper Orthogonal Decomposition, designed to uncover an underlying low-order dynamical description of turbulent jet flow. As the complexity of the statistic increases, the number of flows for which the data has been categorized and assembled decreases, making it difficult to systematically validate prediction codes that require high-level statistics over a broad range of jet flow conditions. For several years, researchers at NASA have worked on developing and validating jet noise prediction codes. One such class of codes, loosely called CFD-based or statistical methods, uses RANS CFD to predict jet mean and turbulent intensities in velocity and temperature. These flow quantities serve as the input to the acoustic source models and flow-sound interaction calculations that yield predictions of far-field jet noise. To develop this capability, a catalog of turbulent jet flows has been created with statistics ranging from mean velocity to space-time correlations of Reynolds stresses. The present document aims to document this catalog and to assess the accuracies of the data, e.g. establish uncertainties for the data. This paper covers the following five tasks: Document acquisition and processing procedures used to create the particle image velocimetry (PIV) datasets. Compare PIV data with hotwire and laser Doppler velocimetry (LDV) data published in the open literature. Compare different datasets acquired at roughly the same flow conditions to establish uncertainties. Create a consensus dataset for a range of hot jet flows, including uncertainty bands. Analyze this consensus dataset for self-consistency and compare jet characteristics to those of the open literature. One final objective fulfilled by this work was the demonstration of a universal scaling for the jet flow fields, at least within the region of interest to aeroacoustics. The potential core length and the spread rate of the half-velocity radius were used to collapse of the mean and turbulent velocity fields over the first 20 jet diameters in a highly satisfying manner.

DSN telemetry system performance using a maximum likelihood convolutional decoder

NASA Technical Reports Server (NTRS)

Benjauthrit, B.; Kemp, R. P.

1977-01-01

Results are described of telemetry system performance testing using DSN equipment and a Maximum Likelihood Convolutional Decoder (MCD) for code rates 1/2 and 1/3, constraint length 7 and special test software. The test results confirm the superiority of the rate 1/3 over that of the rate 1/2. The overall system performance losses determined at the output of the Symbol Synchronizer Assembly are less than 0.5 db for both code rates. Comparison of the performance is also made with existing mathematical models. Error statistics of the decoded data are examined. The MCD operational threshold is found to be about 1.96 db.

Spontaneous action potentials and neural coding in unmyelinated axons.

PubMed

O'Donnell, Cian; van Rossum, Mark C W

2015-04-01

The voltage-gated Na and K channels in neurons are responsible for action potential generation. Because ion channels open and close in a stochastic fashion, spontaneous (ectopic) action potentials can result even in the absence of stimulation. While spontaneous action potentials have been studied in detail in single-compartment models, studies on spatially extended processes have been limited. The simulations and analysis presented here show that spontaneous rate in unmyelinated axon depends nonmonotonically on the length of the axon, that the spontaneous activity has sub-Poisson statistics, and that neural coding can be hampered by the spontaneous spikes by reducing the probability of transmitting the first spike in a train.

Incorporation of the statistical multi-fragmentation model in PHITS and its application for simulation of fragmentation by heavy ions and protons

NASA Astrophysics Data System (ADS)

Ogawa, Tatsuhiko; Sato, Tatsuhiko; Hashimoto, Shintaro; Niita, Koji

2014-06-01

The fragmentation reactions of relativistic-energy nucleus-nucleus and proton-nucleus collisions were simulated using the Statistical Multi-fragmentation Model (SMM) incorporated with the Particle and Heavy Ion Transport code System (PHITS). The comparisons of calculated cross-sections with literature data showed that PHITS-SMM predicts the fragmentation cross-sections of heavy nuclei up to two orders of magnitude more accurately than PHITS for heavy-ion-induced reactions. For proton-induced reactions, noticeable improvements are observed for interactions of the heavy target with protons at an energy greater than 1 GeV. Therefore, consideration for multi-fragmentation reactions is necessary for the accurate simulation of energetic fragmentation reactions of heavy nuclei.

Four types of ensemble coding in data visualizations.

PubMed

Szafir, Danielle Albers; Haroz, Steve; Gleicher, Michael; Franconeri, Steven

2016-01-01

Ensemble coding supports rapid extraction of visual statistics about distributed visual information. Researchers typically study this ability with the goal of drawing conclusions about how such coding extracts information from natural scenes. Here we argue that a second domain can serve as another strong inspiration for understanding ensemble coding: graphs, maps, and other visual presentations of data. Data visualizations allow observers to leverage their ability to perform visual ensemble statistics on distributions of spatial or featural visual information to estimate actual statistics on data. We survey the types of visual statistical tasks that occur within data visualizations across everyday examples, such as scatterplots, and more specialized images, such as weather maps or depictions of patterns in text. We divide these tasks into four categories: identification of sets of values, summarization across those values, segmentation of collections, and estimation of structure. We point to unanswered questions for each category and give examples of such cross-pollination in the current literature. Increased collaboration between the data visualization and perceptual psychology research communities can inspire new solutions to challenges in visualization while simultaneously exposing unsolved problems in perception research.

Ordered phase and non-equilibrium fluctuation in stock market

NASA Astrophysics Data System (ADS)

Maskawa, Jun-ichi

2002-08-01

We analyze the statistics of daily price change of stock market in the framework of a statistical physics model for the collective fluctuation of stock portfolio. In this model the time series of price changes are coded into the sequences of up and down spins, and the Hamiltonian of the system is expressed by spin-spin interactions as in spin glass models of disordered magnetic systems. Through the analysis of Dow-Jones industrial portfolio consisting of 30 stock issues by this model, we find a non-equilibrium fluctuation mode on the point slightly below the boundary between ordered and disordered phases. The remaining 29 modes are still in disordered phase and well described by Gibbs distribution. The variance of the fluctuation is outlined by the theoretical curve and peculiarly large in the non-equilibrium mode compared with those in the other modes remaining in ordinary phase.

Analysis Code - Data Analysis in 'Leveraging Multiple Statistical Methods for Inverse Prediction in Nuclear Forensics Applications' (LMSMIPNFA) v. 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewis, John R

R code that performs the analysis of a data set presented in the paper ‘Leveraging Multiple Statistical Methods for Inverse Prediction in Nuclear Forensics Applications’ by Lewis, J., Zhang, A., Anderson-Cook, C. It provides functions for doing inverse predictions in this setting using several different statistical methods. The data set is a publicly available data set from a historical Plutonium production experiment.

Development of computer-assisted instruction application for statistical data analysis android platform as learning resource

NASA Astrophysics Data System (ADS)

Hendikawati, P.; Arifudin, R.; Zahid, M. Z.

2018-03-01

This study aims to design an android Statistics Data Analysis application that can be accessed through mobile devices to making it easier for users to access. The Statistics Data Analysis application includes various topics of basic statistical along with a parametric statistics data analysis application. The output of this application system is parametric statistics data analysis that can be used for students, lecturers, and users who need the results of statistical calculations quickly and easily understood. Android application development is created using Java programming language. The server programming language uses PHP with the Code Igniter framework, and the database used MySQL. The system development methodology used is the Waterfall methodology with the stages of analysis, design, coding, testing, and implementation and system maintenance. This statistical data analysis application is expected to support statistical lecturing activities and make students easier to understand the statistical analysis of mobile devices.

Hidden Markov models and other machine learning approaches in computational molecular biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baldi, P.

1995-12-31

This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Computational tools are increasingly needed to process the massive amounts of data, to organize and classify sequences, to detect weak similarities, to separate coding from non-coding regions, and reconstruct the underlying evolutionary history. The fundamental problem in machine learning is the same as in scientific reasoning in general, as well as statistical modeling: to come up with a good model for the data. In thismore » tutorial four classes of models are reviewed. They are: Hidden Markov models; artificial Neural Networks; Belief Networks; and Stochastic Grammars. When dealing with DNA and protein primary sequences, Hidden Markov models are one of the most flexible and powerful alignments and data base searches. In this tutorial, attention is focused on the theory of Hidden Markov Models, and how to apply them to problems in molecular biology.« less

Collision Models for Particle Orbit Code on SSX

NASA Astrophysics Data System (ADS)

Fisher, M. W.; Dandurand, D.; Gray, T.; Brown, M. R.; Lukin, V. S.

2011-10-01

Coulomb collision models are being developed and incorporated into the Hamiltonian particle pushing code (PPC) for applications to the Swarthmore Spheromak eXperiment (SSX). A Monte Carlo model based on that of Takizuka and Abe [JCP 25, 205 (1977)] performs binary collisions between test particles and thermal plasma field particles randomly drawn from a stationary Maxwellian distribution. A field-based electrostatic fluctuation model scatters particles from a spatially uniform random distribution of positive and negative spherical potentials generated throughout the plasma volume. The number, radii, and amplitude of these potentials are chosen to mimic the correct particle diffusion statistics without the use of random particle draws or collision frequencies. An electromagnetic fluctuating field model will be presented, if available. These numerical collision models will be benchmarked against known analytical solutions, including beam diffusion rates and Spitzer resistivity, as well as each other. The resulting collisional particle orbit models will be used to simulate particle collection with electrostatic probes in the SSX wind tunnel, as well as particle confinement in typical SSX fields. This work has been supported by US DOE, NSF and ONR.

Identifying Pediatric Severe Sepsis and Septic Shock: Accuracy of Diagnosis Codes.

PubMed

Balamuth, Fran; Weiss, Scott L; Hall, Matt; Neuman, Mark I; Scott, Halden; Brady, Patrick W; Paul, Raina; Farris, Reid W D; McClead, Richard; Centkowski, Sierra; Baumer-Mouradian, Shannon; Weiser, Jason; Hayes, Katie; Shah, Samir S; Alpern, Elizabeth R

2015-12-01

To evaluate accuracy of 2 established administrative methods of identifying children with sepsis using a medical record review reference standard. Multicenter retrospective study at 6 US children's hospitals. Subjects were children >60 days to <19 years of age and identified in 4 groups based on International Classification of Diseases, Ninth Revision, Clinical Modification codes: (1) severe sepsis/septic shock (sepsis codes); (2) infection plus organ dysfunction (combination codes); (3) subjects without codes for infection, organ dysfunction, or severe sepsis; and (4) infection but not severe sepsis or organ dysfunction. Combination codes were allowed, but not required within the sepsis codes group. We determined the presence of reference standard severe sepsis according to consensus criteria. Logistic regression was performed to determine whether addition of codes for sepsis therapies improved case identification. A total of 130 out of 432 subjects met reference SD of severe sepsis. Sepsis codes had sensitivity 73% (95% CI 70-86), specificity 92% (95% CI 87-95), and positive predictive value 79% (95% CI 70-86). Combination codes had sensitivity 15% (95% CI 9-22), specificity 71% (95% CI 65-76), and positive predictive value 18% (95% CI 11-27). Slight improvements in model characteristics were observed when codes for vasoactive medications and endotracheal intubation were added to sepsis codes (c-statistic 0.83 vs 0.87, P = .008). Sepsis specific International Classification of Diseases, Ninth Revision, Clinical Modification codes identify pediatric patients with severe sepsis in administrative data more accurately than a combination of codes for infection plus organ dysfunction. Copyright © 2015 Elsevier Inc. All rights reserved.

Statistical and temporal irradiance fluctuations modeling for a ground-to-geostationary satellite optical link.

PubMed

Camboulives, A-R; Velluet, M-T; Poulenard, S; Saint-Antonin, L; Michau, V

2018-02-01

An optical communication link performance between the ground and a geostationary satellite can be impaired by scintillation, beam wandering, and beam spreading due to its propagation through atmospheric turbulence. These effects on the link performance can be mitigated by tracking and error correction codes coupled with interleaving. Precise numerical tools capable of describing the irradiance fluctuations statistically and of creating an irradiance time series are needed to characterize the benefits of these techniques and optimize them. The wave optics propagation methods have proven their capability of modeling the effects of atmospheric turbulence on a beam, but these are known to be computationally intensive. We present an analytical-numerical model which provides good results on the probability density functions of irradiance fluctuations as well as a time series with an important saving of time and computational resources.

A new software for deformation source optimization, the Bayesian Earthquake Analysis Tool (BEAT)

NASA Astrophysics Data System (ADS)

Vasyura-Bathke, H.; Dutta, R.; Jonsson, S.; Mai, P. M.

2017-12-01

Modern studies of crustal deformation and the related source estimation, including magmatic and tectonic sources, increasingly use non-linear optimization strategies to estimate geometric and/or kinematic source parameters and often consider both jointly, geodetic and seismic data. Bayesian inference is increasingly being used for estimating posterior distributions of deformation source model parameters, given measured/estimated/assumed data and model uncertainties. For instance, some studies consider uncertainties of a layered medium and propagate these into source parameter uncertainties, while others use informative priors to reduce the model parameter space. In addition, innovative sampling algorithms have been developed to efficiently explore the high-dimensional parameter spaces. Compared to earlier studies, these improvements have resulted in overall more robust source model parameter estimates that include uncertainties. However, the computational burden of these methods is high and estimation codes are rarely made available along with the published results. Even if the codes are accessible, it is usually challenging to assemble them into a single optimization framework as they are typically coded in different programing languages. Therefore, further progress and future applications of these methods/codes are hampered, while reproducibility and validation of results has become essentially impossible. In the spirit of providing open-access and modular codes to facilitate progress and reproducible research in deformation source estimations, we undertook the effort of developing BEAT, a python package that comprises all the above-mentioned features in one single programing environment. The package builds on the pyrocko seismological toolbox (www.pyrocko.org), and uses the pymc3 module for Bayesian statistical model fitting. BEAT is an open-source package (https://github.com/hvasbath/beat), and we encourage and solicit contributions to the project. Here, we present our strategy for developing BEAT and show application examples; especially the effect of including the model prediction uncertainty of the velocity model in following source optimizations: full moment tensor, Mogi source, moderate strike-slip earth-quake.

hybrid\\scriptsize{{MANTIS}}: a CPU-GPU Monte Carlo method for modeling indirect x-ray detectors with columnar scintillators

NASA Astrophysics Data System (ADS)

Sharma, Diksha; Badal, Andreu; Badano, Aldo

2012-04-01

The computational modeling of medical imaging systems often requires obtaining a large number of simulated images with low statistical uncertainty which translates into prohibitive computing times. We describe a novel hybrid approach for Monte Carlo simulations that maximizes utilization of CPUs and GPUs in modern workstations. We apply the method to the modeling of indirect x-ray detectors using a new and improved version of the code \\scriptsize{{MANTIS}}, an open source software tool used for the Monte Carlo simulations of indirect x-ray imagers. We first describe a GPU implementation of the physics and geometry models in fast\\scriptsize{{DETECT}}2 (the optical transport model) and a serial CPU version of the same code. We discuss its new features like on-the-fly column geometry and columnar crosstalk in relation to the \\scriptsize{{MANTIS}} code, and point out areas where our model provides more flexibility for the modeling of realistic columnar structures in large area detectors. Second, we modify \\scriptsize{{PENELOPE}} (the open source software package that handles the x-ray and electron transport in \\scriptsize{{MANTIS}}) to allow direct output of location and energy deposited during x-ray and electron interactions occurring within the scintillator. This information is then handled by optical transport routines in fast\\scriptsize{{DETECT}}2. A load balancer dynamically allocates optical transport showers to the GPU and CPU computing cores. Our hybrid\\scriptsize{{MANTIS}} approach achieves a significant speed-up factor of 627 when compared to \\scriptsize{{MANTIS}} and of 35 when compared to the same code running only in a CPU instead of a GPU. Using hybrid\\scriptsize{{MANTIS}}, we successfully hide hours of optical transport time by running it in parallel with the x-ray and electron transport, thus shifting the computational bottleneck from optical to x-ray transport. The new code requires much less memory than \\scriptsize{{MANTIS}} and, as a result, allows us to efficiently simulate large area detectors.

The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins.

PubMed

Ponce de Leon, Miguel; de Miranda, Antonio Basilio; Alvarez-Valin, Fernando; Carels, Nicolas

2014-01-01

For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a regularity (the codon structure) resulting from physicochemical constraints on proteins and thermodynamic constraints on ribosomal machinery. The physicochemical constraints on proteins mainly come from the hydropathy and molecular weight (MW) of secondary structures as well as the energy cost of amino acid synthesis. These constraints appear through a network of statistical correlations, such as (i) the cost of amino acid synthesis, which is in favor of a higher level of guanine in the first codon position, (ii) the constructive contribution of hydropathy alternation in proteins, (iii) the spatial organization of secondary structure in proteins according to solvent accessibility, (iv) the spatial organization of secondary structure according to amino acid hydropathy, (v) the statistical correlation of MW with protein secondary structures and their overall hydropathy, (vi) the statistical correlation of thymine in the second codon position with hydropathy and the energy cost of amino acid synthesis, and (vii) the statistical correlation of adenine in the second codon position with amino acid complexity and the MW of secondary protein structures. Amino acid physicochemical properties and functional constraints on proteins constitute a code that is translated into a purine bias within the coding DNA via tRNAs. In that sense, the Rrr pattern within coding DNA is the effect of information transfer on nucleotide composition from protein to DNA by selection according to the codon positions. Thus, coding DNA structure and ribosomal machinery co-evolved to minimize the energy cost of protein coding given the functional constraints on proteins.

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

PubMed Central

Washietl, Stefan; Findeiß, Sven; Müller, Stephan A.; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L.; Stadler, Peter F.; Goldman, Nick

2011-01-01

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied “out of the box,” without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as “noncoding.” RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode. PMID:21357752

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

PubMed

Washietl, Stefan; Findeiss, Sven; Müller, Stephan A; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L; Stadler, Peter F; Goldman, Nick

2011-04-01

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied "out of the box," without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as "noncoding." RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode.

Coupled Kinetic-MHD Simulations of Divertor Heat Load with ELM Perturbations

NASA Astrophysics Data System (ADS)

Cummings, Julian; Chang, C. S.; Park, Gunyoung; Sugiyama, Linda; Pankin, Alexei; Klasky, Scott; Podhorszki, Norbert; Docan, Ciprian; Parashar, Manish

2010-11-01

The effect of Type-I ELM activity on divertor plate heat load is a key component of the DOE OFES Joint Research Target milestones for this year. In this talk, we present simulations of kinetic edge physics, ELM activity, and the associated divertor heat loads in which we couple the discrete guiding-center neoclassical transport code XGC0 with the nonlinear extended MHD code M3D using the End-to-end Framework for Fusion Integrated Simulations, or EFFIS. In these coupled simulations, the kinetic code and the MHD code run concurrently on the same massively parallel platform and periodic data exchanges are performed using a memory-to-memory coupling technology provided by EFFIS. The M3D code models the fast ELM event and sends frequent updates of the magnetic field perturbations and electrostatic potential to XGC0, which in turn tracks particle dynamics under the influence of these perturbations and collects divertor particle and energy flux statistics. We describe here how EFFIS technologies facilitate these coupled simulations and discuss results for DIII-D, NSTX and Alcator C-Mod tokamak discharges.

A Validation and Code-to-Code Verification of FAST for a Megawatt-Scale Wind Turbine with Aeroelastically Tailored Blades

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guntur, Srinivas; Jonkman, Jason; Sievers, Ryan

This paper presents validation and code-to-code verification of the latest version of the U.S. Department of Energy, National Renewable Energy Laboratory wind turbine aeroelastic engineering simulation tool, FAST v8. A set of 1,141 test cases, for which experimental data from a Siemens 2.3 MW machine have been made available and were in accordance with the International Electrotechnical Commission 61400-13 guidelines, were identified. These conditions were simulated using FAST as well as the Siemens in-house aeroelastic code, BHawC. This paper presents a detailed analysis comparing results from FAST with those from BHawC as well as experimental measurements, using statistics including themore » means and the standard deviations along with the power spectral densities of select turbine parameters and loads. Results indicate a good agreement among the predictions using FAST, BHawC, and experimental measurements. Here, these agreements are discussed in detail in this paper, along with some comments regarding the differences seen in these comparisons relative to the inherent uncertainties in such a model-based analysis.« less

A Validation and Code-to-Code Verification of FAST for a Megawatt-Scale Wind Turbine with Aeroelastically Tailored Blades

DOE PAGES

Guntur, Srinivas; Jonkman, Jason; Sievers, Ryan; ...

2017-08-29

This paper presents validation and code-to-code verification of the latest version of the U.S. Department of Energy, National Renewable Energy Laboratory wind turbine aeroelastic engineering simulation tool, FAST v8. A set of 1,141 test cases, for which experimental data from a Siemens 2.3 MW machine have been made available and were in accordance with the International Electrotechnical Commission 61400-13 guidelines, were identified. These conditions were simulated using FAST as well as the Siemens in-house aeroelastic code, BHawC. This paper presents a detailed analysis comparing results from FAST with those from BHawC as well as experimental measurements, using statistics including themore » means and the standard deviations along with the power spectral densities of select turbine parameters and loads. Results indicate a good agreement among the predictions using FAST, BHawC, and experimental measurements. Here, these agreements are discussed in detail in this paper, along with some comments regarding the differences seen in these comparisons relative to the inherent uncertainties in such a model-based analysis.« less

Received response based heuristic LDPC code for short-range non-line-of-sight ultraviolet communication.

PubMed

Qin, Heng; Zuo, Yong; Zhang, Dong; Li, Yinghui; Wu, Jian

2017-03-06

Through slight modification on typical photon multiplier tube (PMT) receiver output statistics, a generalized received response model considering both scattered propagation and random detection is presented to investigate the impact of inter-symbol interference (ISI) on link data rate of short-range non-line-of-sight (NLOS) ultraviolet communication. Good agreement with the experimental results by numerical simulation is shown. Based on the received response characteristics, a heuristic check matrix construction algorithm of low-density-parity-check (LDPC) code is further proposed to approach the data rate bound derived in a delayed sampling (DS) binary pulse position modulation (PPM) system. Compared to conventional LDPC coding methods, better bit error ratio (BER) below 1E-05 is achieved for short-range NLOS UVC systems operating at data rate of 2Mbps.

A combined Fuzzy and Naive Bayesian strategy can be used to assign event codes to injury narratives.

PubMed

Marucci-Wellman, H; Lehto, M; Corns, H

2011-12-01

Bayesian methods show promise for classifying injury narratives from large administrative datasets into cause groups. This study examined a combined approach where two Bayesian models (Fuzzy and Naïve) were used to either classify a narrative or select it for manual review. Injury narratives were extracted from claims filed with a worker's compensation insurance provider between January 2002 and December 2004. Narratives were separated into a training set (n=11,000) and prediction set (n=3,000). Expert coders assigned two-digit Bureau of Labor Statistics Occupational Injury and Illness Classification event codes to each narrative. Fuzzy and Naïve Bayesian models were developed using manually classified cases in the training set. Two semi-automatic machine coding strategies were evaluated. The first strategy assigned cases for manual review if the Fuzzy and Naïve models disagreed on the classification. The second strategy selected additional cases for manual review from the Agree dataset using prediction strength to reach a level of 50% computer coding and 50% manual coding. When agreement alone was used as the filtering strategy, the majority were coded by the computer (n=1,928, 64%) leaving 36% for manual review. The overall combined (human plus computer) sensitivity was 0.90 and positive predictive value (PPV) was >0.90 for 11 of 18 2-digit event categories. Implementing the 2nd strategy improved results with an overall sensitivity of 0.95 and PPV >0.90 for 17 of 18 categories. A combined Naïve-Fuzzy Bayesian approach can classify some narratives with high accuracy and identify others most beneficial for manual review, reducing the burden on human coders.

BayeSED: A General Approach to Fitting the Spectral Energy Distribution of Galaxies

NASA Astrophysics Data System (ADS)

Han, Yunkun; Han, Zhanwen

2014-11-01

We present a newly developed version of BayeSED, a general Bayesian approach to the spectral energy distribution (SED) fitting of galaxies. The new BayeSED code has been systematically tested on a mock sample of galaxies. The comparison between the estimated and input values of the parameters shows that BayeSED can recover the physical parameters of galaxies reasonably well. We then applied BayeSED to interpret the SEDs of a large Ks -selected sample of galaxies in the COSMOS/UltraVISTA field with stellar population synthesis models. Using the new BayeSED code, a Bayesian model comparison of stellar population synthesis models has been performed for the first time. We found that the 2003 model by Bruzual & Charlot, statistically speaking, has greater Bayesian evidence than the 2005 model by Maraston for the Ks -selected sample. In addition, while setting the stellar metallicity as a free parameter obviously increases the Bayesian evidence of both models, varying the initial mass function has a notable effect only on the Maraston model. Meanwhile, the physical parameters estimated with BayeSED are found to be generally consistent with those obtained using the popular grid-based FAST code, while the former parameters exhibit more natural distributions. Based on the estimated physical parameters of the galaxies in the sample, we qualitatively classified the galaxies in the sample into five populations that may represent galaxies at different evolution stages or in different environments. We conclude that BayeSED could be a reliable and powerful tool for investigating the formation and evolution of galaxies from the rich multi-wavelength observations currently available. A binary version of the BayeSED code parallelized with Message Passing Interface is publicly available at https://bitbucket.org/hanyk/bayesed.

An object-based visual attention model for robotic applications.

PubMed

Yu, Yuanlong; Mann, George K I; Gosine, Raymond G

2010-10-01

By extending integrated competition hypothesis, this paper presents an object-based visual attention model, which selects one object of interest using low-dimensional features, resulting that visual perception starts from a fast attentional selection procedure. The proposed attention model involves seven modules: learning of object representations stored in a long-term memory (LTM), preattentive processing, top-down biasing, bottom-up competition, mediation between top-down and bottom-up ways, generation of saliency maps, and perceptual completion processing. It works in two phases: learning phase and attending phase. In the learning phase, the corresponding object representation is trained statistically when one object is attended. A dual-coding object representation consisting of local and global codings is proposed. Intensity, color, and orientation features are used to build the local coding, and a contour feature is employed to constitute the global coding. In the attending phase, the model preattentively segments the visual field into discrete proto-objects using Gestalt rules at first. If a task-specific object is given, the model recalls the corresponding representation from LTM and deduces the task-relevant feature(s) to evaluate top-down biases. The mediation between automatic bottom-up competition and conscious top-down biasing is then performed to yield a location-based saliency map. By combination of location-based saliency within each proto-object, the proto-object-based saliency is evaluated. The most salient proto-object is selected for attention, and it is finally put into the perceptual completion processing module to yield a complete object region. This model has been applied into distinct tasks of robots: detection of task-specific stationary and moving objects. Experimental results under different conditions are shown to validate this model.

BayeSED: A GENERAL APPROACH TO FITTING THE SPECTRAL ENERGY DISTRIBUTION OF GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Yunkun; Han, Zhanwen, E-mail: hanyk@ynao.ac.cn, E-mail: zhanwenhan@ynao.ac.cn

2014-11-01

We present a newly developed version of BayeSED, a general Bayesian approach to the spectral energy distribution (SED) fitting of galaxies. The new BayeSED code has been systematically tested on a mock sample of galaxies. The comparison between the estimated and input values of the parameters shows that BayeSED can recover the physical parameters of galaxies reasonably well. We then applied BayeSED to interpret the SEDs of a large K{sub s} -selected sample of galaxies in the COSMOS/UltraVISTA field with stellar population synthesis models. Using the new BayeSED code, a Bayesian model comparison of stellar population synthesis models has beenmore » performed for the first time. We found that the 2003 model by Bruzual and Charlot, statistically speaking, has greater Bayesian evidence than the 2005 model by Maraston for the K{sub s} -selected sample. In addition, while setting the stellar metallicity as a free parameter obviously increases the Bayesian evidence of both models, varying the initial mass function has a notable effect only on the Maraston model. Meanwhile, the physical parameters estimated with BayeSED are found to be generally consistent with those obtained using the popular grid-based FAST code, while the former parameters exhibit more natural distributions. Based on the estimated physical parameters of the galaxies in the sample, we qualitatively classified the galaxies in the sample into five populations that may represent galaxies at different evolution stages or in different environments. We conclude that BayeSED could be a reliable and powerful tool for investigating the formation and evolution of galaxies from the rich multi-wavelength observations currently available. A binary version of the BayeSED code parallelized with Message Passing Interface is publicly available at https://bitbucket.org/hanyk/bayesed.« less

SETI in vivo: testing the we-are-them hypothesis

NASA Astrophysics Data System (ADS)

Makukov, Maxim A.; Shcherbak, Vladimir I.

2018-04-01

After it was proposed that life on Earth might descend from seeding by an earlier extraterrestrial civilization motivated to secure and spread life, some authors noted that this alternative offers a testable implication: microbial seeds could be intentionally supplied with a durable signature that might be found in extant organisms. In particular, it was suggested that the optimal location for such an artefact is the genetic code, as the least evolving part of cells. However, as the mainstream view goes, this scenario is too speculative and cannot be meaningfully tested because encoding/decoding a signature within the genetic code is something ill-defined, so any retrieval attempt is doomed to guesswork. Here we refresh the seeded-Earth hypothesis in light of recent observations, and discuss the motivation for inserting a signature. We then show that `biological SETI' involves even weaker assumptions than traditional SETI and admits a well-defined methodological framework. After assessing the possibility in terms of molecular and evolutionary biology, we formalize the approach and, adopting the standard guideline of SETI that encoding/decoding should follow from first principles and be convention-free, develop a universal retrieval strategy. Applied to the canonical genetic code, it reveals a non-trivial precision structure of interlocked logical and numerical attributes of systematic character (previously we found these heuristically). To assess this result in view of the initial assumption, we perform statistical, comparison, interdependence and semiotic analyses. Statistical analysis reveals no causal connection of the result to evolutionary models of the genetic code, interdependence analysis precludes overinterpretation, and comparison analysis shows that known variations of the code lack any precision-logic structures, in agreement with these variations being post-LUCA (i.e. post-seeding) evolutionary deviations from the canonical code. Finally, semiotic analysis shows that not only the found attributes are consistent with the initial assumption, but that they make perfect sense from SETI perspective, as they ultimately maintain some of the most universal codes of culture.

Simulation of parametric model towards the fixed covariate of right censored lung cancer data

NASA Astrophysics Data System (ADS)

Afiqah Muhamad Jamil, Siti; Asrul Affendi Abdullah, M.; Kek, Sie Long; Ridwan Olaniran, Oyebayo; Enera Amran, Syahila

2017-09-01

In this study, simulation procedure was applied to measure the fixed covariate of right censored data by using parametric survival model. The scale and shape parameter were modified to differentiate the analysis of parametric regression survival model. Statistically, the biases, mean biases and the coverage probability were used in this analysis. Consequently, different sample sizes were employed to distinguish the impact of parametric regression model towards right censored data with 50, 100, 150 and 200 number of sample. R-statistical software was utilised to develop the coding simulation with right censored data. Besides, the final model of right censored simulation was compared with the right censored lung cancer data in Malaysia. It was found that different values of shape and scale parameter with different sample size, help to improve the simulation strategy for right censored data and Weibull regression survival model is suitable fit towards the simulation of survival of lung cancer patients data in Malaysia.

A Plastic Temporal Brain Code for Conscious State Generation

PubMed Central

Dresp-Langley, Birgitta; Durup, Jean

2009-01-01

Consciousness is known to be limited in processing capacity and often described in terms of a unique processing stream across a single dimension: time. In this paper, we discuss a purely temporal pattern code, functionally decoupled from spatial signals, for conscious state generation in the brain. Arguments in favour of such a code include Dehaene et al.'s long-distance reverberation postulate, Ramachandran's remapping hypothesis, evidence for a temporal coherence index and coincidence detectors, and Grossberg's Adaptive Resonance Theory. A time-bin resonance model is developed, where temporal signatures of conscious states are generated on the basis of signal reverberation across large distances in highly plastic neural circuits. The temporal signatures are delivered by neural activity patterns which, beyond a certain statistical threshold, activate, maintain, and terminate a conscious brain state like a bar code would activate, maintain, or inactivate the electronic locks of a safe. Such temporal resonance would reflect a higher level of neural processing, independent from sensorial or perceptual brain mechanisms. PMID:19644552

Error control techniques for satellite and space communications

NASA Technical Reports Server (NTRS)

Costello, Daniel J., Jr.

1994-01-01

Brief summaries of research in the following areas are presented: (1) construction of optimum geometrically uniform trellis codes; (2) a statistical approach to constructing convolutional code generators; and (3) calculating the exact performance of a convolutional code.

75 FR 94 - Amendments to the Section 7216 Regulations-Disclosure or Use of Information by Preparers of Returns

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-04

... use of statistical compilations of data under section 7216 of the Internal Revenue Code (Code) by a... preparation business, including identification of additional limited circumstances when a tax return preparer... tax return business under Sec. 301.7216-2(n); disclose and use statistical compilations of data...

MAI statistics estimation and analysis in a DS-CDMA system

NASA Astrophysics Data System (ADS)

Alami Hassani, A.; Zouak, M.; Mrabti, M.; Abdi, F.

2018-05-01

A primary limitation of Direct Sequence Code Division Multiple Access DS-CDMA link performance and system capacity is multiple access interference (MAI). To examine the performance of CDMA systems in the presence of MAI, i.e., in a multiuser environment, several works assumed that the interference can be approximated by a Gaussian random variable. In this paper, we first develop a new and simple approach to characterize the MAI in a multiuser system. In addition to statistically quantifying the MAI power, the paper also proposes a statistical model for both variance and mean of the MAI for synchronous and asynchronous CDMA transmission. We show that the MAI probability density function (PDF) is Gaussian for the equal-received-energy case and validate it by computer simulations.

Anyonic self-induced disorder in a stabilizer code: Quasi many-body localization in a translational invariant model

NASA Astrophysics Data System (ADS)

Yarloo, H.; Langari, A.; Vaezi, A.

2018-02-01

We enquire into the quasi many-body localization in topologically ordered states of matter, revolving around the case of Kitaev toric code on the ladder geometry, where different types of anyonic defects carry different masses induced by environmental errors. Our study verifies that the presence of anyons generates a complex energy landscape solely through braiding statistics, which suffices to suppress the diffusion of defects in such clean, multicomponent anyonic liquid. This nonergodic dynamics suggests a promising scenario for investigation of quasi many-body localization. Computing standard diagnostics evidences that a typical initial inhomogeneity of anyons gives birth to a glassy dynamics with an exponentially diverging time scale of the full relaxation. Our results unveil how self-generated disorder ameliorates the vulnerability of topological order away from equilibrium. This setting provides a new platform which paves the way toward impeding logical errors by self-localization of anyons in a generic, high energy state, originated exclusively in their exotic statistics.

A Vignette (User's Guide) for “An R Package for Statistical ...

EPA Pesticide Factsheets

StatCharrms is a graphical user front-end for ease of use in analyzing data generated from OCSPP 890.2200, Medaka Extended One Generation Reproduction Test (MEOGRT) and OCSPP 890.2300, Larval Amphibian Gonad Development Assay (LAGDA). The analyses StatCharrms is capable of performing are: Rao-Scott adjusted Cochran-Armitage test for trend By Slices (RSCABS), a Standard Cochran-Armitage test for trend By Slices (SCABS), mixed effects Cox proportional model, Jonckheere-Terpstra step down trend test, Dunn test, one way ANOVA, weighted ANOVA, mixed effects ANOVA, repeated measures ANOVA, and Dunnett test. This document provides a User’s Manual (termed a Vignette by the Comprehensive R Archive Network (CRAN)) for the previously created R-code tool called StatCharrms (Statistical analysis of Chemistry, Histopathology, and Reproduction endpoints using Repeated measures and Multi-generation Studies). The StatCharrms R-code has been publically available directly from EPA staff since the approval of OCSPP 890.2200 and 890.2300, and now is available publically available at the CRAN.

Neutron Capture Gamma-Ray Libraries for Nuclear Applications

NASA Astrophysics Data System (ADS)

Sleaford, B. W.; Firestone, R. B.; Summers, N.; Escher, J.; Hurst, A.; Krticka, M.; Basunia, S.; Molnar, G.; Belgya, T.; Revay, Z.; Choi, H. D.

2011-06-01

The neutron capture reaction is useful in identifying and analyzing the gamma-ray spectrum from an unknown assembly as it gives unambiguous information on its composition. This can be done passively or actively where an external neutron source is used to probe an unknown assembly. There are known capture gamma-ray data gaps in the ENDF libraries used by transport codes for various nuclear applications. The Evaluated Gamma-ray Activation file (EGAF) is a new thermal neutron capture database of discrete line spectra and cross sections for over 260 isotopes that was developed as part of an IAEA Coordinated Research Project. EGAF is being used to improve the capture gamma production in ENDF libraries. For medium to heavy nuclei the quasi continuum contribution to the gamma cascades is not experimentally resolved. The continuum contains up to 90% of all the decay energy and is modeled here with the statistical nuclear structure code DICEBOX. This code also provides a consistency check of the level scheme nuclear structure evaluation. The calculated continuum is of sufficient accuracy to include in the ENDF libraries. This analysis also determines new total thermal capture cross sections and provides an improved RIPL database. For higher energy neutron capture there is less experimental data available making benchmarking of the modeling codes more difficult. We are investigating the capture spectra from higher energy neutrons experimentally using surrogate reactions and modeling this with Hauser-Feshbach codes. This can then be used to benchmark CASINO, a version of DICEBOX modified for neutron capture at higher energy. This can be used to simulate spectra from neutron capture at incident neutron energies up to 20 MeV to improve the gamma-ray spectrum in neutron data libraries used for transport modeling of unknown assemblies.

Visual-Motor Transformations Within Frontal Eye Fields During Head-Unrestrained Gaze Shifts in the Monkey.

PubMed

Sajad, Amirsaman; Sadeh, Morteza; Keith, Gerald P; Yan, Xiaogang; Wang, Hongying; Crawford, John Douglas

2015-10-01

A fundamental question in sensorimotor control concerns the transformation of spatial signals from the retina into eye and head motor commands required for accurate gaze shifts. Here, we investigated these transformations by identifying the spatial codes embedded in visually evoked and movement-related responses in the frontal eye fields (FEFs) during head-unrestrained gaze shifts. Monkeys made delayed gaze shifts to the remembered location of briefly presented visual stimuli, with delay serving to dissociate visual and movement responses. A statistical analysis of nonparametric model fits to response field data from 57 neurons (38 with visual and 49 with movement activities) eliminated most effector-specific, head-fixed, and space-fixed models, but confirmed the dominance of eye-centered codes observed in head-restrained studies. More importantly, the visual response encoded target location, whereas the movement response mainly encoded the final position of the imminent gaze shift (including gaze errors). This spatiotemporal distinction between target and gaze coding was present not only at the population level, but even at the single-cell level. We propose that an imperfect visual-motor transformation occurs during the brief memory interval between perception and action, and further transformations from the FEF's eye-centered gaze motor code to effector-specific codes in motor frames occur downstream in the subcortical areas. © The Author 2014. Published by Oxford University Press.

The impact of rare variation on gene expression across tissues.

PubMed

Li, Xin; Kim, Yungil; Tsang, Emily K; Davis, Joe R; Damani, Farhan N; Chiang, Colby; Hess, Gaelen T; Zappala, Zachary; Strober, Benjamin J; Scott, Alexandra J; Li, Amy; Ganna, Andrea; Bassik, Michael C; Merker, Jason D; Hall, Ira M; Battle, Alexis; Montgomery, Stephen B

2017-10-11

Rare genetic variants are abundant in humans and are expected to contribute to individual disease risk. While genetic association studies have successfully identified common genetic variants associated with susceptibility, these studies are not practical for identifying rare variants. Efforts to distinguish pathogenic variants from benign rare variants have leveraged the genetic code to identify deleterious protein-coding alleles, but no analogous code exists for non-coding variants. Therefore, ascertaining which rare variants have phenotypic effects remains a major challenge. Rare non-coding variants have been associated with extreme gene expression in studies using single tissues, but their effects across tissues are unknown. Here we identify gene expression outliers, or individuals showing extreme expression levels for a particular gene, across 44 human tissues by using combined analyses of whole genomes and multi-tissue RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project v6p release. We find that 58% of underexpression and 28% of overexpression outliers have nearby conserved rare variants compared to 8% of non-outliers. Additionally, we developed RIVER (RNA-informed variant effect on regulation), a Bayesian statistical model that incorporates expression data to predict a regulatory effect for rare variants with higher accuracy than models using genomic annotations alone. Overall, we demonstrate that rare variants contribute to large gene expression changes across tissues and provide an integrative method for interpretation of rare variants in individual genomes.

Mixed models, linear dependency, and identification in age-period-cohort models.

PubMed

O'Brien, Robert M

2017-07-20

This paper examines the identification problem in age-period-cohort models that use either linear or categorically coded ages, periods, and cohorts or combinations of these parameterizations. These models are not identified using the traditional fixed effect regression model approach because of a linear dependency between the ages, periods, and cohorts. However, these models can be identified if the researcher introduces a single just identifying constraint on the model coefficients. The problem with such constraints is that the results can differ substantially depending on the constraint chosen. Somewhat surprisingly, age-period-cohort models that specify one or more of ages and/or periods and/or cohorts as random effects are identified. This is the case without introducing an additional constraint. I label this identification as statistical model identification and show how statistical model identification comes about in mixed models and why which effects are treated as fixed and which are treated as random can substantially change the estimates of the age, period, and cohort effects. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Performance Analysis, Modeling and Scaling of HPC Applications and Tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhatele, Abhinav

2016-01-13

E cient use of supercomputers at DOE centers is vital for maximizing system throughput, mini- mizing energy costs and enabling science breakthroughs faster. This requires complementary e orts along several directions to optimize the performance of scienti c simulation codes and the under- lying runtimes and software stacks. This in turn requires providing scalable performance analysis tools and modeling techniques that can provide feedback to physicists and computer scientists developing the simulation codes and runtimes respectively. The PAMS project is using time allocations on supercomputers at ALCF, NERSC and OLCF to further the goals described above by performing research alongmore » the following fronts: 1. Scaling Study of HPC applications; 2. Evaluation of Programming Models; 3. Hardening of Performance Tools; 4. Performance Modeling of Irregular Codes; and 5. Statistical Analysis of Historical Performance Data. We are a team of computer and computational scientists funded by both DOE/NNSA and DOE/ ASCR programs such as ECRP, XStack (Traleika Glacier, PIPER), ExaOSR (ARGO), SDMAV II (MONA) and PSAAP II (XPACC). This allocation will enable us to study big data issues when analyzing performance on leadership computing class systems and to assist the HPC community in making the most e ective use of these resources.« less

Administrative data measured surgical site infection probability within 30 days of surgery in elderly patients.

PubMed

van Walraven, Carl; Jackson, Timothy D; Daneman, Nick

2016-09-01

Elderly patients are inordinately affected by surgical site infections (SSIs). This study derived and internally validated a model that used routinely collected health administrative data to measure the probability of SSI in elderly patients within 30 days of surgery. All people exceeding 65 years undergoing surgery from two hospitals with known SSI status were linked to population-based administrative data sets in Ontario, Canada. We used bootstrap methods to create a multivariate model that used health administrative data to predict the probability of SSI. Of 3,436 patients, 177 (5.1%) had an SSI. The Elderly SSI Risk Model included six covariates: number of distinct physician fee codes within 30 days of surgery; presence or absence of a postdischarge prescription for an antibiotic; presence or absence of three diagnostic codes; and a previously derived score that gauged SSI risk based on procedure codes. The model was highly explanatory (Nagelkerke's R 2 , 0.458), strongly discriminative (C statistic, 0.918), and well calibrated (calibration slope, 1). Health administrative data can effectively determine 30-day risk of SSI risk in elderly patients undergoing a broad assortment of surgeries. External validation is necessary before this can be routinely used to monitor SSIs in the elderly. Copyright © 2016 Elsevier Inc. All rights reserved.

Encoding Dissimilarity Data for Statistical Model Building.

PubMed

Wahba, Grace

2010-12-01

We summarize, review and comment upon three papers which discuss the use of discrete, noisy, incomplete, scattered pairwise dissimilarity data in statistical model building. Convex cone optimization codes are used to embed the objects into a Euclidean space which respects the dissimilarity information while controlling the dimension of the space. A "newbie" algorithm is provided for embedding new objects into this space. This allows the dissimilarity information to be incorporated into a Smoothing Spline ANOVA penalized likelihood model, a Support Vector Machine, or any model that will admit Reproducing Kernel Hilbert Space components, for nonparametric regression, supervised learning, or semi-supervised learning. Future work and open questions are discussed. The papers are: F. Lu, S. Keles, S. Wright and G. Wahba 2005. A framework for kernel regularization with application to protein clustering. Proceedings of the National Academy of Sciences 102, 12332-1233.G. Corrada Bravo, G. Wahba, K. Lee, B. Klein, R. Klein and S. Iyengar 2009. Examining the relative influence of familial, genetic and environmental covariate information in flexible risk models. Proceedings of the National Academy of Sciences 106, 8128-8133F. Lu, Y. Lin and G. Wahba. Robust manifold unfolding with kernel regularization. TR 1008, Department of Statistics, University of Wisconsin-Madison.

Adaptive variable-length coding for efficient compression of spacecraft television data.

NASA Technical Reports Server (NTRS)

Rice, R. F.; Plaunt, J. R.

1971-01-01

An adaptive variable length coding system is presented. Although developed primarily for the proposed Grand Tour missions, many features of this system clearly indicate a much wider applicability. Using sample to sample prediction, the coding system produces output rates within 0.25 bit/picture element (pixel) of the one-dimensional difference entropy for entropy values ranging from 0 to 8 bit/pixel. This is accomplished without the necessity of storing any code words. Performance improvements of 0.5 bit/pixel can be simply achieved by utilizing previous line correlation. A Basic Compressor, using concatenated codes, adapts to rapid changes in source statistics by automatically selecting one of three codes to use for each block of 21 pixels. The system adapts to less frequent, but more dramatic, changes in source statistics by adjusting the mode in which the Basic Compressor operates on a line-to-line basis. Furthermore, the compression system is independent of the quantization requirements of the pulse-code modulation system.

DRG coding practice: a nationwide hospital survey in Thailand

PubMed Central

2011-01-01

Background Diagnosis Related Group (DRG) payment is preferred by healthcare reform in various countries but its implementation in resource-limited countries has not been fully explored. Objectives This study was aimed (1) to compare the characteristics of hospitals in Thailand that were audited with those that were not and (2) to develop a simplified scale to measure hospital coding practice. Methods A questionnaire survey was conducted of 920 hospitals in the Summary and Coding Audit Database (SCAD hospitals, all of which were audited in 2008 because of suspicious reports of possible DRG miscoding); the questionnaire also included 390 non-SCAD hospitals. The questionnaire asked about general demographics of the hospitals, hospital coding structure and process, and also included a set of 63 opinion-oriented items on the current hospital coding practice. Descriptive statistics and exploratory factor analysis (EFA) were used for data analysis. Results SCAD and Non-SCAD hospitals were different in many aspects, especially the number of medical statisticians, experience of medical statisticians and physicians, as well as number of certified coders. Factor analysis revealed a simplified 3-factor, 20-item model to assess hospital coding practice and classify hospital intention. Conclusion Hospital providers should not be assumed capable of producing high quality DRG codes, especially in resource-limited settings. PMID:22040256

Circular codes revisited: a statistical approach.

PubMed

Gonzalez, D L; Giannerini, S; Rosa, R

2011-04-21

In 1996 Arquès and Michel [1996. A complementary circular code in the protein coding genes. J. Theor. Biol. 182, 45-58] discovered the existence of a common circular code in eukaryote and prokaryote genomes. Since then, circular code theory has provoked great interest and underwent a rapid development. In this paper we discuss some theoretical issues related to the synchronization properties of coding sequences and circular codes with particular emphasis on the problem of retrieval and maintenance of the reading frame. Motivated by the theoretical discussion, we adopt a rigorous statistical approach in order to try to answer different questions. First, we investigate the covering capability of the whole class of 216 self-complementary, C(3) maximal codes with respect to a large set of coding sequences. The results indicate that, on average, the code proposed by Arquès and Michel has the best covering capability but, still, there exists a great variability among sequences. Second, we focus on such code and explore the role played by the proportion of the bases by means of a hierarchy of permutation tests. The results show the existence of a sort of optimization mechanism such that coding sequences are tailored as to maximize or minimize the coverage of circular codes on specific reading frames. Such optimization clearly relates the function of circular codes with reading frame synchronization. Copyright © 2011 Elsevier Ltd. All rights reserved.

Statistical Field Estimation for Complex Coastal Regions and Archipelagos (PREPRINT)

DTIC Science & Technology

2011-04-09

and study the computational properties of these schemes. Specifically, we extend a multiscale Objective Analysis (OA) approach to complex coastal...computational properties of these schemes. Specifically, we extend a multiscale Objective Analysis (OA) approach to complex coastal regions and... multiscale free-surface code builds on the primitive-equation model of the Harvard Ocean Predic- tion System (HOPS, Haley et al. (2009)). Additionally

Process and metaphors in the evolutionary paradigm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, M.; Fox, S

1988-01-01

Presents thinking on the processes and interpretation of biological evolution, emphasizing the study of biological processes as they occur in living organisms and their communities, rather than through mechanical or statistical models. Contributors explore processes and metaphors in evolution, the origin of the genetic code, new genetic mechanisms and their implications for the formation of new species, panbiogeography, the active role of behavior in evolution, sociobiology, and more.

The Population Tracking Model: A Simple, Scalable Statistical Model for Neural Population Data

PubMed Central

O'Donnell, Cian; alves, J. Tiago Gonç; Whiteley, Nick; Portera-Cailliau, Carlos; Sejnowski, Terrence J.

2017-01-01

Our understanding of neural population coding has been limited by a lack of analysis methods to characterize spiking data from large populations. The biggest challenge comes from the fact that the number of possible network activity patterns scales exponentially with the number of neurons recorded (∼2Neurons). Here we introduce a new statistical method for characterizing neural population activity that requires semi-independent fitting of only as many parameters as the square of the number of neurons, requiring drastically smaller data sets and minimal computation time. The model works by matching the population rate (the number of neurons synchronously active) and the probability that each individual neuron fires given the population rate. We found that this model can accurately fit synthetic data from up to 1000 neurons. We also found that the model could rapidly decode visual stimuli from neural population data from macaque primary visual cortex about 65 ms after stimulus onset. Finally, we used the model to estimate the entropy of neural population activity in developing mouse somatosensory cortex and, surprisingly, found that it first increases, and then decreases during development. This statistical model opens new options for interrogating neural population data and can bolster the use of modern large-scale in vivo Ca2+ and voltage imaging tools. PMID:27870612

Uranium resource assessment through statistical analysis of exploration geochemical and other data. Final report. [Codes EVAL, SURE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koch, G.S. Jr.; Howarth, R.J.; Schuenemeyer, J.H.

1981-02-01

We have developed a procedure that can help quadrangle evaluators to systematically summarize and use hydrogeochemical and stream sediment reconnaissance (HSSR) and occurrence data. Although we have not provided an independent estimate of uranium endowment, we have devised a methodology that will provide this independent estimate when additional calibration is done by enlarging the study area. Our statistical model for evaluation (system EVAL) ranks uranium endowment for each quadrangle. Because using this model requires experience in geology, statistics, and data analysis, we have also devised a simplified model, presented in the package SURE, a System for Uranium Resource Evaluation. Wemore » have developed and tested these models for the four quadrangles in southern Colorado that comprise the study area; to investigate their generality, the models should be applied to other quandrangles. Once they are calibrated with accepted uranium endowments for several well-known quadrangles, the models can be used to give independent estimates for less-known quadrangles. The point-oriented models structure the objective comparison of the quandrangles on the bases of: (1) Anomalies (a) derived from stream sediments, (b) derived from waters (stream, well, pond, etc.), (2) Geology (a) source rocks, as defined by the evaluator, (b) host rocks, as defined by the evaluator, and (3) Aerial radiometric anomalies.« less

Dark Energy Survey Year 1 Results: Multi-Probe Methodology and Simulated Likelihood Analyses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krause, E.; et al.

We present the methodology for and detail the implementation of the Dark Energy Survey (DES) 3x2pt DES Year 1 (Y1) analysis, which combines configuration-space two-point statistics from three different cosmological probes: cosmic shear, galaxy-galaxy lensing, and galaxy clustering, using data from the first year of DES observations. We have developed two independent modeling pipelines and describe the code validation process. We derive expressions for analytical real-space multi-probe covariances, and describe their validation with numerical simulations. We stress-test the inference pipelines in simulated likelihood analyses that vary 6-7 cosmology parameters plus 20 nuisance parameters and precisely resemble the analysis to be presented in the DES 3x2pt analysis paper, using a variety of simulated input data vectors with varying assumptions. We find that any disagreement between pipelines leads to changes in assigned likelihoodmore » $$\\Delta \\chi^2 \\le 0.045$$ with respect to the statistical error of the DES Y1 data vector. We also find that angular binning and survey mask do not impact our analytic covariance at a significant level. We determine lower bounds on scales used for analysis of galaxy clustering (8 Mpc$$~h^{-1}$$) and galaxy-galaxy lensing (12 Mpc$$~h^{-1}$$) such that the impact of modeling uncertainties in the non-linear regime is well below statistical errors, and show that our analysis choices are robust against a variety of systematics. These tests demonstrate that we have a robust analysis pipeline that yields unbiased cosmological parameter inferences for the flagship 3x2pt DES Y1 analysis. We emphasize that the level of independent code development and subsequent code comparison as demonstrated in this paper is necessary to produce credible constraints from increasingly complex multi-probe analyses of current data.« less

Causes of Death Data in the Global Burden of Disease Estimates for Ischemic and Hemorrhagic Stroke.

PubMed

Truelsen, Thomas; Krarup, Lars-Henrik; Iversen, Helle K; Mensah, George A; Feigin, Valery L; Sposato, Luciano A; Naghavi, Mohsen

2015-01-01

Stroke mortality estimates in the Global Burden of Disease (GBD) study are based on routine mortality statistics and redistribution of ill-defined codes that cannot be a cause of death, the so-called 'garbage codes' (GCs). This study describes the contribution of these codes to stroke mortality estimates. All available mortality data were compiled and non-specific cause codes were redistributed based on literature review and statistical methods. Ill-defined codes were redistributed to their specific cause of disease by age, sex, country and year. The reassignment was done based on the International Classification of Diseases and the pathology behind each code by checking multiple causes of death and literature review. Unspecified stroke and primary and secondary hypertension are leading contributing 'GCs' to stroke mortality estimates for hemorrhagic stroke (HS) and ischemic stroke (IS). There were marked differences in the fraction of death assigned to IS and HS for unspecified stroke and hypertension between GBD regions and between age groups. A large proportion of stroke fatalities are derived from the redistribution of 'unspecified stroke' and 'hypertension' with marked regional differences. Future advancements in stroke certification, data collections and statistical analyses may improve the estimation of the global stroke burden. © 2015 S. Karger AG, Basel.

The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory.

PubMed

Di Giulio, Massimo

2017-11-07

The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been. Indeed, if the biosynthetic transformations between amino acids occurred on tRNA-like molecules, then there was no need to link amino acids to these molecules because amino acids were already charged on tRNA-like molecules, as the coevolution theory suggests. In spite of the fact that ARSs make the genetic code responsible for the first interaction between a component of nucleic acids and that of proteins, for the coevolution theory the role of ARSs should have been entirely marginal in the genetic code origin. Therefore, I have conducted a further analysis of the distribution of the two classes of ARSs and of their subclasses-in the genetic code table-in order to perform a falsification test of the coevolution theory. Indeed, in the case in which the distribution of ARSs within the genetic code would have been highly significant, then the coevolution theory would be falsified since the mechanism on which it is based would not predict a fundamental role of ARSs in the origin of the genetic code. I found that the statistical significance of the distribution of the two classes of ARSs in the table of the genetic code is low or marginal, whereas that of the subclasses of ARSs statistically significant. However, this is in perfect agreement with the postulates of the coevolution theory. Indeed, the only case of statistical significance-regarding the classes of ARSs-is appreciable for the CAG code, whereas for its complement-the UNN/NUN code-only a marginal significance is measurable. These two codes codify roughly for the two ARS classes, in particular, the CAG code for the class II while the UNN/NUN code for the class I. Furthermore, the subclasses of ARSs show a statistical significance of their distribution in the genetic code table. Nevertheless, the more sensible explanation for these observations would be the following. The observation that would link the two classes of ARSs to the CAG and UNN/NUN codes, and the statistical significance of the distribution of the subclasses of ARSs in the genetic code table, would be only a secondary effect due to the highly significant distribution of the polarity of amino acids and their biosynthetic relationships in the genetic code. That is to say, the polarity of amino acids and their biosynthetic relationships would have conditioned the evolution of ARSs so that their presence in the genetic code would have been detectable. Even if the ARSs would not have-on their own-influenced directly the evolutionary organization of the genetic code. In other words, the role that ARSs had in the origin of the genetic code would have been entirely marginal. This conclusion would be in perfect accord with the predictions of the coevolution theory. Conversely, this conclusion would be in contrast-at least partially-with the physicochemical theories of the origin of the genetic code because they would foresee an absolutely more active role of ARSs in the origin of the organization of the genetic code. Copyright © 2017 Elsevier Ltd. All rights reserved.

Python package for model STructure ANalysis (pySTAN)

NASA Astrophysics Data System (ADS)

Van Hoey, Stijn; van der Kwast, Johannes; Nopens, Ingmar; Seuntjens, Piet

2013-04-01

The selection and identification of a suitable hydrological model structure is more than fitting parameters of a model structure to reproduce a measured hydrograph. The procedure is highly dependent on various criteria, i.e. the modelling objective, the characteristics and the scale of the system under investigation as well as the available data. Rigorous analysis of the candidate model structures is needed to support and objectify the selection of the most appropriate structure for a specific case (or eventually justify the use of a proposed ensemble of structures). This holds both in the situation of choosing between a limited set of different structures as well as in the framework of flexible model structures with interchangeable components. Many different methods to evaluate and analyse model structures exist. This leads to a sprawl of available methods, all characterized by different assumptions, changing conditions of application and various code implementations. Methods typically focus on optimization, sensitivity analysis or uncertainty analysis, with backgrounds from optimization, machine-learning or statistics amongst others. These methods also need an evaluation metric (objective function) to compare the model outcome with some observed data. However, for current methods described in literature, implementations are not always transparent and reproducible (if available at all). No standard procedures exist to share code and the popularity (and amount of applications) of the methods is sometimes more dependent on the availability than the merits of the method. Moreover, new implementations of existing methods are difficult to verify and the different theoretical backgrounds make it difficult for environmental scientists to decide about the usefulness of a specific method. A common and open framework with a large set of methods can support users in deciding about the most appropriate method. Hence, it enables to simultaneously apply and compare different methods on a fair basis. We developed and present pySTAN (python framework for STructure Analysis), a python package containing a set of functions for model structure evaluation to provide the analysis of (hydrological) model structures. A selected set of algorithms for optimization, uncertainty and sensitivity analysis is currently available, together with a set of evaluation (objective) functions and input distributions to sample from. The methods are implemented model-independent and the python language provides the wrapper functions to apply administer external model codes. Different objective functions can be considered simultaneously with both statistical metrics and more hydrology specific metrics. By using so-called reStructuredText (sphinx documentation generator) and Python documentation strings (docstrings), the generation of manual pages is semi-automated and a specific environment is available to enhance both the readability and transparency of the code. It thereby enables a larger group of users to apply and compare these methods and to extend the functionalities.

Reliability analysis of single crystal NiAl turbine blades

NASA Technical Reports Server (NTRS)

Salem, Jonathan; Noebe, Ronald; Wheeler, Donald R.; Holland, Fred; Palko, Joseph; Duffy, Stephen; Wright, P. Kennard

1995-01-01

As part of a co-operative agreement with General Electric Aircraft Engines (GEAE), NASA LeRC is modifying and validating the Ceramic Analysis and Reliability Evaluation of Structures algorithm for use in design of components made of high strength NiAl based intermetallic materials. NiAl single crystal alloys are being actively investigated by GEAE as a replacement for Ni-based single crystal superalloys for use in high pressure turbine blades and vanes. The driving force for this research lies in the numerous property advantages offered by NiAl alloys over their superalloy counterparts. These include a reduction of density by as much as a third without significantly sacrificing strength, higher melting point, greater thermal conductivity, better oxidation resistance, and a better response to thermal barrier coatings. The current drawback to high strength NiAl single crystals is their limited ductility. Consequently, significant efforts including the work agreement with GEAE are underway to develop testing and design methodologies for these materials. The approach to validation and component analysis involves the following steps: determination of the statistical nature and source of fracture in a high strength, NiAl single crystal turbine blade material; measurement of the failure strength envelope of the material; coding of statistically based reliability models; verification of the code and model; and modeling of turbine blades and vanes for rig testing.

Learning optimal features for visual pattern recognition

NASA Astrophysics Data System (ADS)

Labusch, Kai; Siewert, Udo; Martinetz, Thomas; Barth, Erhardt

2007-02-01

The optimal coding hypothesis proposes that the human visual system has adapted to the statistical properties of the environment by the use of relatively simple optimality criteria. We here (i) discuss how the properties of different models of image coding, i.e. sparseness, decorrelation, and statistical independence are related to each other (ii) propose to evaluate the different models by verifiable performance measures (iii) analyse the classification performance on images of handwritten digits (MNIST data base). We first employ the SPARSENET algorithm (Olshausen, 1998) to derive a local filter basis (on 13 × 13 pixels windows). We then filter the images in the database (28 × 28 pixels images of digits) and reduce the dimensionality of the resulting feature space by selecting the locally maximal filter responses. We then train a support vector machine on a training set to classify the digits and report results obtained on a separate test set. Currently, the best state-of-the-art result on the MNIST data base has an error rate of 0,4%. This result, however, has been obtained by using explicit knowledge that is specific to the data (elastic distortion model for digits). We here obtain an error rate of 0,55% which is second best but does not use explicit data specific knowledge. In particular it outperforms by far all methods that do not use data-specific knowledge.

Nonlinear Hebbian Learning as a Unifying Principle in Receptive Field Formation.

PubMed

Brito, Carlos S N; Gerstner, Wulfram

2016-09-01

The development of sensory receptive fields has been modeled in the past by a variety of models including normative models such as sparse coding or independent component analysis and bottom-up models such as spike-timing dependent plasticity or the Bienenstock-Cooper-Munro model of synaptic plasticity. Here we show that the above variety of approaches can all be unified into a single common principle, namely nonlinear Hebbian learning. When nonlinear Hebbian learning is applied to natural images, receptive field shapes were strongly constrained by the input statistics and preprocessing, but exhibited only modest variation across different choices of nonlinearities in neuron models or synaptic plasticity rules. Neither overcompleteness nor sparse network activity are necessary for the development of localized receptive fields. The analysis of alternative sensory modalities such as auditory models or V2 development lead to the same conclusions. In all examples, receptive fields can be predicted a priori by reformulating an abstract model as nonlinear Hebbian learning. Thus nonlinear Hebbian learning and natural statistics can account for many aspects of receptive field formation across models and sensory modalities.

Nonlinear Hebbian Learning as a Unifying Principle in Receptive Field Formation

PubMed Central

Gerstner, Wulfram

2016-01-01

The development of sensory receptive fields has been modeled in the past by a variety of models including normative models such as sparse coding or independent component analysis and bottom-up models such as spike-timing dependent plasticity or the Bienenstock-Cooper-Munro model of synaptic plasticity. Here we show that the above variety of approaches can all be unified into a single common principle, namely nonlinear Hebbian learning. When nonlinear Hebbian learning is applied to natural images, receptive field shapes were strongly constrained by the input statistics and preprocessing, but exhibited only modest variation across different choices of nonlinearities in neuron models or synaptic plasticity rules. Neither overcompleteness nor sparse network activity are necessary for the development of localized receptive fields. The analysis of alternative sensory modalities such as auditory models or V2 development lead to the same conclusions. In all examples, receptive fields can be predicted a priori by reformulating an abstract model as nonlinear Hebbian learning. Thus nonlinear Hebbian learning and natural statistics can account for many aspects of receptive field formation across models and sensory modalities. PMID:27690349

The Use of a Bayesian Hierarchy to Develop and Validate a Co-Morbidity Score to Predict Mortality for Linked Primary and Secondary Care Data from the NHS in England

PubMed Central

Card, Tim R.; West, Joe

2016-01-01

Background We have assessed whether the linkage between routine primary and secondary care records provided an opportunity to develop an improved population based co-morbidity score with the combined information on co-morbidities from both health care settings. Methods We extracted all people older than 20 years at the start of 2005 within the linkage between the Hospital Episodes Statistics, Clinical Practice Research Datalink, and Office for National Statistics death register in England. A random 50% sample was used to identify relevant diagnostic codes using a Bayesian hierarchy to share information between similar Read and ICD 10 code groupings. Internal validation of the score was performed in the remaining 50% and discrimination was assessed using Harrell’s C statistic. Comparisons were made over time, age, and consultation rate with the Charlson and Elixhauser indexes. Results 657,264 people were followed up from the 1st January 2005. 98 groupings of codes were derived from the Bayesian hierarchy, and 37 had an adjusted weighting of greater than zero in the Cox proportional hazards model. 11 of these groupings had a different weighting dependent on whether they were coded from hospital or primary care. The C statistic reduced from 0.88 (95% confidence interval 0.88–0.88) in the first year of follow up, to 0.85 (0.85–0.85) including all 5 years. When we stratified the linked score by consultation rate the association with mortality remained consistent, but there was a significant interaction with age, with improved discrimination and fit in those under 50 years old (C = 0.85, 0.83–0.87) compared to the Charlson (C = 0.79, 0.77–0.82) or Elixhauser index (C = 0.81, 0.79–0.83). Conclusions The use of linked population based primary and secondary care data developed a co-morbidity score that had improved discrimination, particularly in younger age groups, and had a greater effect when adjusting for co-morbidity than existing scores. PMID:27788230

Faster Mass Spectrometry-based Protein Inference: Junction Trees are More Efficient than Sampling and Marginalization by Enumeration

PubMed Central

Serang, Oliver; Noble, William Stafford

2012-01-01

The problem of identifying the proteins in a complex mixture using tandem mass spectrometry can be framed as an inference problem on a graph that connects peptides to proteins. Several existing protein identification methods make use of statistical inference methods for graphical models, including expectation maximization, Markov chain Monte Carlo, and full marginalization coupled with approximation heuristics. We show that, for this problem, the majority of the cost of inference usually comes from a few highly connected subgraphs. Furthermore, we evaluate three different statistical inference methods using a common graphical model, and we demonstrate that junction tree inference substantially improves rates of convergence compared to existing methods. The python code used for this paper is available at http://noble.gs.washington.edu/proj/fido. PMID:22331862

Metamodels for Computer-Based Engineering Design: Survey and Recommendations

NASA Technical Reports Server (NTRS)

Simpson, Timothy W.; Peplinski, Jesse; Koch, Patrick N.; Allen, Janet K.

1997-01-01

The use of statistical techniques to build approximations of expensive computer analysis codes pervades much of todays engineering design. These statistical approximations, or metamodels, are used to replace the actual expensive computer analyses, facilitating multidisciplinary, multiobjective optimization and concept exploration. In this paper we review several of these techniques including design of experiments, response surface methodology, Taguchi methods, neural networks, inductive learning, and kriging. We survey their existing application in engineering design and then address the dangers of applying traditional statistical techniques to approximate deterministic computer analysis codes. We conclude with recommendations for the appropriate use of statistical approximation techniques in given situations and how common pitfalls can be avoided.

Statistical Analysis of CFD Solutions from the Drag Prediction Workshop

NASA Technical Reports Server (NTRS)

Hemsch, Michael J.

2002-01-01

A simple, graphical framework is presented for robust statistical evaluation of results obtained from N-Version testing of a series of RANS CFD codes. The solutions were obtained by a variety of code developers and users for the June 2001 Drag Prediction Workshop sponsored by the AIAA Applied Aerodynamics Technical Committee. The aerodynamic configuration used for the computational tests is the DLR-F4 wing-body combination previously tested in several European wind tunnels and for which a previous N-Version test had been conducted. The statistical framework is used to evaluate code results for (1) a single cruise design point, (2) drag polars and (3) drag rise. The paper concludes with a discussion of the meaning of the results, especially with respect to predictability, Validation, and reporting of solutions.

Video transmission on ATM networks. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Chen, Yun-Chung

1993-01-01

The broadband integrated services digital network (B-ISDN) is expected to provide high-speed and flexible multimedia applications. Multimedia includes data, graphics, image, voice, and video. Asynchronous transfer mode (ATM) is the adopted transport techniques for B-ISDN and has the potential for providing a more efficient and integrated environment for multimedia. It is believed that most broadband applications will make heavy use of visual information. The prospect of wide spread use of image and video communication has led to interest in coding algorithms for reducing bandwidth requirements and improving image quality. The major results of a study on the bridging of network transmission performance and video coding are: Using two representative video sequences, several video source models are developed. The fitness of these models are validated through the use of statistical tests and network queuing performance. A dual leaky bucket algorithm is proposed as an effective network policing function. The concept of the dual leaky bucket algorithm can be applied to a prioritized coding approach to achieve transmission efficiency. A mapping of the performance/control parameters at the network level into equivalent parameters at the video coding level is developed. Based on that, a complete set of principles for the design of video codecs for network transmission is proposed.

Human performance across decision making, selective attention, and working memory tasks: Experimental data and computer simulations.

PubMed

Stocco, Andrea; Yamasaki, Brianna L; Prat, Chantel S

2018-04-01

This article describes the data analyzed in the paper "Individual differences in the Simon effect are underpinned by differences in the competitive dynamics in the basal ganglia: An experimental verification and a computational model" (Stocco et al., 2017) [1]. The data includes behavioral results from participants performing three cognitive tasks (Probabilistic Stimulus Selection (Frank et al., 2004) [2], Simon task (Craft and Simon, 1970) [3], and Automated Operation Span (Unsworth et al., 2005) [4]), as well as simulationed traces generated by a computational neurocognitive model that accounts for individual variations in human performance across the tasks. The experimental data encompasses individual data files (in both preprocessed and native output format) as well as group-level summary files. The simulation data includes the entire model code, the results of a full-grid search of the model's parameter space, and the code used to partition the model space and parallelize the simulations. Finally, the repository includes the R scripts used to carry out the statistical analyses reported in the original paper.

Uncertainty evaluation of nuclear reaction model parameters using integral and microscopic measurements. Covariances evaluation with CONRAD code

NASA Astrophysics Data System (ADS)

de Saint Jean, C.; Habert, B.; Archier, P.; Noguere, G.; Bernard, D.; Tommasi, J.; Blaise, P.

2010-10-01

In the [eV;MeV] energy range, modelling of the neutron induced reactions are based on nuclear reaction models having parameters. Estimation of co-variances on cross sections or on nuclear reaction model parameters is a recurrent puzzle in nuclear data evaluation. Major breakthroughs were asked by nuclear reactor physicists to assess proper uncertainties to be used in applications. In this paper, mathematical methods developped in the CONRAD code[2] will be presented to explain the treatment of all type of uncertainties, including experimental ones (statistical and systematic) and propagate them to nuclear reaction model parameters or cross sections. Marginalization procedure will thus be exposed using analytical or Monte-Carlo solutions. Furthermore, one major drawback found by reactor physicist is the fact that integral or analytical experiments (reactor mock-up or simple integral experiment, e.g. ICSBEP, …) were not taken into account sufficiently soon in the evaluation process to remove discrepancies. In this paper, we will describe a mathematical framework to take into account properly this kind of information.

A New Methodology for Open Pit Slope Design in Karst-Prone Ground Conditions Based on Integrated Stochastic-Limit Equilibrium Analysis

NASA Astrophysics Data System (ADS)

Zhang, Ke; Cao, Ping; Ma, Guowei; Fan, Wenchen; Meng, Jingjing; Li, Kaihui

2016-07-01

Using the Chengmenshan Copper Mine as a case study, a new methodology for open pit slope design in karst-prone ground conditions is presented based on integrated stochastic-limit equilibrium analysis. The numerical modeling and optimization design procedure contain a collection of drill core data, karst cave stochastic model generation, SLIDE simulation and bisection method optimization. Borehole investigations are performed, and the statistical result shows that the length of the karst cave fits a negative exponential distribution model, but the length of carbonatite does not exactly follow any standard distribution. The inverse transform method and acceptance-rejection method are used to reproduce the length of the karst cave and carbonatite, respectively. A code for karst cave stochastic model generation, named KCSMG, is developed. The stability of the rock slope with the karst cave stochastic model is analyzed by combining the KCSMG code and the SLIDE program. This approach is then applied to study the effect of the karst cave on the stability of the open pit slope, and a procedure to optimize the open pit slope angle is presented.

Development of Computer Models for the Assessment of Foreign Body Impact Events on Composite Structures

NASA Technical Reports Server (NTRS)

Bucinell, Ronald B.

1997-01-01

The objective of this project was to model the 5-3/4 inch pressure vessels used on the NASA RTOP program in an attempt to learn more about how impact damage forms and what are the residual effects of the resulting damage. A global-local finite element model was developed for the bottle and the states of stress in the bottles were determined down to the constituent level. The experimental data that was generated on the NASA RTOP program was not in a form that enabled the model developed under this grant to be correlated with the experimental data. As a result of this exercise it is recommended that an experimental program be designed using statistical design of experiment techniques to generate data that can be used to isolate the phenomenon that control the formation of impact damage. This data should include residual property determinations so that models for post impact structural integrity can be developed. It is also recommended that the global-local methodology be integrated directly into the finite element code. This will require considerable code development.

Braiding by Majorana tracking and long-range CNOT gates with color codes

NASA Astrophysics Data System (ADS)

Litinski, Daniel; von Oppen, Felix

2017-11-01

Color-code quantum computation seamlessly combines Majorana-based hardware with topological error correction. Specifically, as Clifford gates are transversal in two-dimensional color codes, they enable the use of the Majoranas' non-Abelian statistics for gate operations at the code level. Here, we discuss the implementation of color codes in arrays of Majorana nanowires that avoid branched networks such as T junctions, thereby simplifying their realization. We show that, in such implementations, non-Abelian statistics can be exploited without ever performing physical braiding operations. Physical braiding operations are replaced by Majorana tracking, an entirely software-based protocol which appropriately updates the Majoranas involved in the color-code stabilizer measurements. This approach minimizes the required hardware operations for single-qubit Clifford gates. For Clifford completeness, we combine color codes with surface codes, and use color-to-surface-code lattice surgery for long-range multitarget CNOT gates which have a time overhead that grows only logarithmically with the physical distance separating control and target qubits. With the addition of magic state distillation, our architecture describes a fault-tolerant universal quantum computer in systems such as networks of tetrons, hexons, or Majorana box qubits, but can also be applied to nontopological qubit platforms.

Moments of inclination error distribution computer program

NASA Technical Reports Server (NTRS)

Myler, T. R.

1981-01-01

A FORTRAN coded computer program is described which calculates orbital inclination error statistics using a closed-form solution. This solution uses a data base of trajectory errors from actual flights to predict the orbital inclination error statistics. The Scott flight history data base consists of orbit insertion errors in the trajectory parameters - altitude, velocity, flight path angle, flight azimuth, latitude and longitude. The methods used to generate the error statistics are of general interest since they have other applications. Program theory, user instructions, output definitions, subroutine descriptions and detailed FORTRAN coding information are included.

A Severe Sepsis Mortality Prediction Model and Score for Use with Administrative Data

PubMed Central

Ford, Dee W.; Goodwin, Andrew J.; Simpson, Annie N.; Johnson, Emily; Nadig, Nandita; Simpson, Kit N.

2016-01-01

Objective Administrative data is used for research, quality improvement, and health policy in severe sepsis. However, there is not a sepsis-specific tool applicable to administrative data with which to adjust for illness severity. Our objective was to develop, internally validate, and externally validate a severe sepsis mortality prediction model and associated mortality prediction score. Design Retrospective cohort study using 2012 administrative data from five US states. Three cohorts of patients with severe sepsis were created: 1) ICD-9-CM codes for severe sepsis/septic shock, 2) ‘Martin’ approach, and 3) ‘Angus’ approach. The model was developed and internally validated in ICD-9-CM cohort and externally validated in other cohorts. Integer point values for each predictor variable were generated to create a sepsis severity score. Setting Acute care, non-federal hospitals in NY, MD, FL, MI, and WA Subjects Patients in one of three severe sepsis cohorts: 1) explicitly coded (n=108,448), 2) Martin cohort (n=139,094), and 3) Angus cohort (n=523,637) Interventions None Measurements and Main Results Maximum likelihood estimation logistic regression to develop a predictive model for in-hospital mortality. Model calibration and discrimination assessed via Hosmer-Lemeshow goodness-of-fit (GOF) and C-statistics respectively. Primary cohort subset into risk deciles and observed versus predicted mortality plotted. GOF demonstrated p>0.05 for each cohort demonstrating sound calibration. C-statistic ranged from low of 0.709 (sepsis severity score) to high of 0.838 (Angus cohort) suggesting good to excellent model discrimination. Comparison of observed versus expected mortality was robust although accuracy decreased in highest risk decile. Conclusions Our sepsis severity model and score is a tool that provides reliable risk adjustment for administrative data. PMID:26496452

The Dutch Hospital Standardised Mortality Ratio (HSMR) method and cardiac surgery: benchmarking in a national cohort using hospital administration data versus a clinical database

PubMed Central

Siregar, S; Pouw, M E; Moons, K G M; Versteegh, M I M; Bots, M L; van der Graaf, Y; Kalkman, C J; van Herwerden, L A; Groenwold, R H H

2014-01-01

Objective To compare the accuracy of data from hospital administration databases and a national clinical cardiac surgery database and to compare the performance of the Dutch hospital standardised mortality ratio (HSMR) method and the logistic European System for Cardiac Operative Risk Evaluation, for the purpose of benchmarking of mortality across hospitals. Methods Information on all patients undergoing cardiac surgery between 1 January 2007 and 31 December 2010 in 10 centres was extracted from The Netherlands Association for Cardio-Thoracic Surgery database and the Hospital Discharge Registry. The number of cardiac surgery interventions was compared between both databases. The European System for Cardiac Operative Risk Evaluation and hospital standardised mortality ratio models were updated in the study population and compared using the C-statistic, calibration plots and the Brier-score. Results The number of cardiac surgery interventions performed could not be assessed using the administrative database as the intervention code was incorrect in 1.4–26.3%, depending on the type of intervention. In 7.3% no intervention code was registered. The updated administrative model was inferior to the updated clinical model with respect to discrimination (c-statistic of 0.77 vs 0.85, p<0.001) and calibration (Brier Score of 2.8% vs 2.6%, p<0.001, maximum score 3.0%). Two average performing hospitals according to the clinical model became outliers when benchmarking was performed using the administrative model. Conclusions In cardiac surgery, administrative data are less suitable than clinical data for the purpose of benchmarking. The use of either administrative or clinical risk-adjustment models can affect the outlier status of hospitals. Risk-adjustment models including procedure-specific clinical risk factors are recommended. PMID:24334377

Investigating the use of quick response codes in the gross anatomy laboratory.

PubMed

Traser, Courtney J; Hoffman, Leslie A; Seifert, Mark F; Wilson, Adam B

2015-01-01

The use of quick response (QR) codes within undergraduate university courses is on the rise, yet literature concerning their use in medical education is scant. This study examined student perceptions on the usefulness of QR codes as learning aids in a medical gross anatomy course, statistically analyzed whether this learning aid impacted student performance, and evaluated whether performance could be explained by the frequency of QR code usage. Question prompts and QR codes tagged on cadaveric specimens and models were available for four weeks as learning aids to medical (n = 155) and doctor of physical therapy (n = 39) students. Each QR code provided answers to posed questions in the form of embedded text or hyperlinked web pages. Students' perceptions were gathered using a formative questionnaire and practical examination scores were used to assess potential gains in student achievement. Overall, students responded positively to the use of QR codes in the gross anatomy laboratory as 89% (57/64) agreed the codes augmented their learning of anatomy. The users' most noticeable objection to using QR codes was the reluctance to bring their smartphones into the gross anatomy laboratory. A comparison between the performance of QR code users and non-users was found to be nonsignificant (P = 0.113), and no significant gains in performance (P = 0.302) were observed after the intervention. Learners welcomed the implementation of QR code technology in the gross anatomy laboratory, yet this intervention had no apparent effect on practical examination performance. © 2014 American Association of Anatomists.

A Multiscale Progressive Failure Modeling Methodology for Composites that Includes Fiber Strength Stochastics

NASA Technical Reports Server (NTRS)

Ricks, Trenton M.; Lacy, Thomas E., Jr.; Bednarcyk, Brett A.; Arnold, Steven M.; Hutchins, John W.

2014-01-01

A multiscale modeling methodology was developed for continuous fiber composites that incorporates a statistical distribution of fiber strengths into coupled multiscale micromechanics/finite element (FE) analyses. A modified two-parameter Weibull cumulative distribution function, which accounts for the effect of fiber length on the probability of failure, was used to characterize the statistical distribution of fiber strengths. A parametric study using the NASA Micromechanics Analysis Code with the Generalized Method of Cells (MAC/GMC) was performed to assess the effect of variable fiber strengths on local composite failure within a repeating unit cell (RUC) and subsequent global failure. The NASA code FEAMAC and the ABAQUS finite element solver were used to analyze the progressive failure of a unidirectional SCS-6/TIMETAL 21S metal matrix composite tensile dogbone specimen at 650 degC. Multiscale progressive failure analyses were performed to quantify the effect of spatially varying fiber strengths on the RUC-averaged and global stress-strain responses and failure. The ultimate composite strengths and distribution of failure locations (predominately within the gage section) reasonably matched the experimentally observed failure behavior. The predicted composite failure behavior suggests that use of macroscale models that exploit global geometric symmetries are inappropriate for cases where the actual distribution of local fiber strengths displays no such symmetries. This issue has not received much attention in the literature. Moreover, the model discretization at a specific length scale can have a profound effect on the computational costs associated with multiscale simulations.models that yield accurate yet tractable results.

Statistical correlation analysis for comparing vibration data from test and analysis

NASA Technical Reports Server (NTRS)

Butler, T. G.; Strang, R. F.; Purves, L. R.; Hershfeld, D. J.

1986-01-01

A theory was developed to compare vibration modes obtained by NASTRAN analysis with those obtained experimentally. Because many more analytical modes can be obtained than experimental modes, the analytical set was treated as expansion functions for putting both sources in comparative form. The dimensional symmetry was developed for three general cases: nonsymmetric whole model compared with a nonsymmetric whole structural test, symmetric analytical portion compared with a symmetric experimental portion, and analytical symmetric portion with a whole experimental test. The theory was coded and a statistical correlation program was installed as a utility. The theory is established with small classical structures.

A new computer code for discrete fracture network modelling

NASA Astrophysics Data System (ADS)

Xu, Chaoshui; Dowd, Peter

2010-03-01

The authors describe a comprehensive software package for two- and three-dimensional stochastic rock fracture simulation using marked point processes. Fracture locations can be modelled by a Poisson, a non-homogeneous, a cluster or a Cox point process; fracture geometries and properties are modelled by their respective probability distributions. Virtual sampling tools such as plane, window and scanline sampling are included in the software together with a comprehensive set of statistical tools including histogram analysis, probability plots, rose diagrams and hemispherical projections. The paper describes in detail the theoretical basis of the implementation and provides a case study in rock fracture modelling to demonstrate the application of the software.

IUTAM Symposium on Statistical Energy Analysis, 8-11 July 1997, Programme

DTIC Science & Technology

1997-01-01

distribution is unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (Maximum200 words) This was the first international scientific gathering devoted...energy flow, continuum dynamics, vibrational energy, statistical energy analysis (SEA) 15. NUMBER OF PAGES 16. PRICE CODE INSECURITY... correlation v=V(ɘ ’• • determination of the correlation n^, =11^, (<?). When harmonic motion and time-average are considered, the following I

Development and Implementation of Dynamic Scripts to Execute Cycled GSI/WRF Forecasts

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley; Srikishen, Jayanthi; Berndt, Emily; Li, Xuanli; Watson, Leela

2014-01-01

The Weather Research and Forecasting (WRF) numerical weather prediction (NWP) model and Gridpoint Statistical Interpolation (GSI) data assimilation (DA) are the operational systems that make up the North American Mesoscale (NAM) model and the NAM Data Assimilation System (NDAS) analysis used by National Weather Service forecasters. The Developmental Testbed Center (DTC) manages and distributes the code for the WRF and GSI, but it is up to individual researchers to link the systems together and write scripts to run the systems, which can take considerable time for those not familiar with the code. The objective of this project is to develop and disseminate a set of dynamic scripts that mimic the unique cycling configuration of the operational NAM to enable researchers to develop new modeling and data assimilation techniques that can be easily transferred to operations. The current version of the SPoRT GSI/WRF Scripts (v3.0.1) is compatible with WRF v3.3 and GSI v3.0.

A Framework for Performing Multiscale Stochastic Progressive Failure Analysis of Composite Structures

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2006-01-01

A framework is presented that enables coupled multiscale analysis of composite structures. The recently developed, free, Finite Element Analysis - Micromechanics Analysis Code (FEAMAC) software couples the Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) with ABAQUS to perform micromechanics based FEA such that the nonlinear composite material response at each integration point is modeled at each increment by MAC/GMC. As a result, the stochastic nature of fiber breakage in composites can be simulated through incorporation of an appropriate damage and failure model that operates within MAC/GMC on the level of the fiber. Results are presented for the progressive failure analysis of a titanium matrix composite tensile specimen that illustrate the power and utility of the framework and address the techniques needed to model the statistical nature of the problem properly. In particular, it is shown that incorporating fiber strength randomness on multiple scales improves the quality of the simulation by enabling failure at locations other than those associated with structural level stress risers.

A Framework for Performing Multiscale Stochastic Progressive Failure Analysis of Composite Structures

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2007-01-01

A framework is presented that enables coupled multiscale analysis of composite structures. The recently developed, free, Finite Element Analysis-Micromechanics Analysis Code (FEAMAC) software couples the Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) with ABAQUS to perform micromechanics based FEA such that the nonlinear composite material response at each integration point is modeled at each increment by MAC/GMC. As a result, the stochastic nature of fiber breakage in composites can be simulated through incorporation of an appropriate damage and failure model that operates within MAC/GMC on the level of the fiber. Results are presented for the progressive failure analysis of a titanium matrix composite tensile specimen that illustrate the power and utility of the framework and address the techniques needed to model the statistical nature of the problem properly. In particular, it is shown that incorporating fiber strength randomness on multiple scales improves the quality of the simulation by enabling failure at locations other than those associated with structural level stress risers.

One-dimensional statistical parametric mapping in Python.

PubMed

Pataky, Todd C

2012-01-01

Statistical parametric mapping (SPM) is a topological methodology for detecting field changes in smooth n-dimensional continua. Many classes of biomechanical data are smooth and contained within discrete bounds and as such are well suited to SPM analyses. The current paper accompanies release of 'SPM1D', a free and open-source Python package for conducting SPM analyses on a set of registered 1D curves. Three example applications are presented: (i) kinematics, (ii) ground reaction forces and (iii) contact pressure distribution in probabilistic finite element modelling. In addition to offering a high-level interface to a variety of common statistical tests like t tests, regression and ANOVA, SPM1D also emphasises fundamental concepts of SPM theory through stand-alone example scripts. Source code and documentation are available at: www.tpataky.net/spm1d/.

Computational Analysis for Rocket-Based Combined-Cycle Systems During Rocket-Only Operation

NASA Technical Reports Server (NTRS)

Steffen, C. J., Jr.; Smith, T. D.; Yungster, S.; Keller, D. J.

2000-01-01

A series of Reynolds-averaged Navier-Stokes calculations were employed to study the performance of rocket-based combined-cycle systems operating in an all-rocket mode. This parametric series of calculations were executed within a statistical framework, commonly known as design of experiments. The parametric design space included four geometric and two flowfield variables set at three levels each, for a total of 729 possible combinations. A D-optimal design strategy was selected. It required that only 36 separate computational fluid dynamics (CFD) solutions be performed to develop a full response surface model, which quantified the linear, bilinear, and curvilinear effects of the six experimental variables. The axisymmetric, Reynolds-averaged Navier-Stokes simulations were executed with the NPARC v3.0 code. The response used in the statistical analysis was created from Isp efficiency data integrated from the 36 CFD simulations. The influence of turbulence modeling was analyzed by using both one- and two-equation models. Careful attention was also given to quantify the influence of mesh dependence, iterative convergence, and artificial viscosity upon the resulting statistical model. Thirteen statistically significant effects were observed to have an influence on rocket-based combined-cycle nozzle performance. It was apparent that the free-expansion process, directly downstream of the rocket nozzle, can influence the Isp efficiency. Numerical schlieren images and particle traces have been used to further understand the physical phenomena behind several of the statistically significant results.

Binary logistic regression modelling: Measuring the probability of relapse cases among drug addict

NASA Astrophysics Data System (ADS)

Ismail, Mohd Tahir; Alias, Siti Nor Shadila

2014-07-01

For many years Malaysia faced the drug addiction issues. The most serious case is relapse phenomenon among treated drug addict (drug addict who have under gone the rehabilitation programme at Narcotic Addiction Rehabilitation Centre, PUSPEN). Thus, the main objective of this study is to find the most significant factor that contributes to relapse to happen. The binary logistic regression analysis was employed to model the relationship between independent variables (predictors) and dependent variable. The dependent variable is the status of the drug addict either relapse, (Yes coded as 1) or not, (No coded as 0). Meanwhile the predictors involved are age, age at first taking drug, family history, education level, family crisis, community support and self motivation. The total of the sample is 200 which the data are provided by AADK (National Antidrug Agency). The finding of the study revealed that age and self motivation are statistically significant towards the relapse cases..

Active Duty - U.S. Army Noise Induced Hearing Injury Surveillance Calendar Years 2009-2013

DTIC Science & Technology

2014-06-01

rates for sensorineural hearing loss, significant threshold shift, tinnitus , and Noise-Induced Hearing Loss. The intention is to monitor the morbidity...surveillance. These code groups include sensorineural hearing loss (SNHL), significant threshold shift (STS), noise-induced hearing loss (NIHL) and tinnitus ... Tinnitus ) was analyzed using a regression model to determine the trend of incidence rates from 2007 to the current year. Statistical significance of a

Models for Scoring Missing Responses to Multiple-Choice Items. Program Statistics Research Technical Report No. 94-1.

ERIC Educational Resources Information Center

Longford, Nicholas T.

This study is a critical evaluation of the roles for coding and scoring of missing responses to multiple-choice items in educational tests. The focus is on tests in which the test-takers have little or no motivation; in such tests omitting and not reaching (as classified by the currently adopted operational rules) is quite frequent. Data from the…

Ozone data and mission sampling analysis

NASA Technical Reports Server (NTRS)

Robbins, J. L.

1980-01-01

A methodology was developed to analyze discrete data obtained from the global distribution of ozone. Statistical analysis techniques were applied to describe the distribution of data variance in terms of empirical orthogonal functions and components of spherical harmonic models. The effects of uneven data distribution and missing data were considered. Data fill based on the autocorrelation structure of the data is described. Computer coding of the analysis techniques is included.

Universal biology and the statistical mechanics of early life.

PubMed

Goldenfeld, Nigel; Biancalani, Tommaso; Jafarpour, Farshid

2017-12-28

All known life on the Earth exhibits at least two non-trivial common features: the canonical genetic code and biological homochirality, both of which emerged prior to the Last Universal Common Ancestor state. This article describes recent efforts to provide a narrative of this epoch using tools from statistical mechanics. During the emergence of self-replicating life far from equilibrium in a period of chemical evolution, minimal models of autocatalysis show that homochirality would have necessarily co-evolved along with the efficiency of early-life self-replicators. Dynamical system models of the evolution of the genetic code must explain its universality and its highly refined error-minimization properties. These have both been accounted for in a scenario where life arose from a collective, networked phase where there was no notion of species and perhaps even individuality itself. We show how this phase ultimately terminated during an event sometimes known as the Darwinian transition, leading to the present epoch of tree-like vertical descent of organismal lineages. These examples illustrate concrete examples of universal biology: the quest for a fundamental understanding of the basic properties of living systems, independent of precise instantiation in chemistry or other media.This article is part of the themed issue 'Reconceptualizing the origins of life'. © 2017 The Author(s).

Universal biology and the statistical mechanics of early life

NASA Astrophysics Data System (ADS)

Goldenfeld, Nigel; Biancalani, Tommaso; Jafarpour, Farshid

2017-11-01

All known life on the Earth exhibits at least two non-trivial common features: the canonical genetic code and biological homochirality, both of which emerged prior to the Last Universal Common Ancestor state. This article describes recent efforts to provide a narrative of this epoch using tools from statistical mechanics. During the emergence of self-replicating life far from equilibrium in a period of chemical evolution, minimal models of autocatalysis show that homochirality would have necessarily co-evolved along with the efficiency of early-life self-replicators. Dynamical system models of the evolution of the genetic code must explain its universality and its highly refined error-minimization properties. These have both been accounted for in a scenario where life arose from a collective, networked phase where there was no notion of species and perhaps even individuality itself. We show how this phase ultimately terminated during an event sometimes known as the Darwinian transition, leading to the present epoch of tree-like vertical descent of organismal lineages. These examples illustrate concrete examples of universal biology: the quest for a fundamental understanding of the basic properties of living systems, independent of precise instantiation in chemistry or other media. This article is part of the themed issue 'Reconceptualizing the origins of life'.

A Probabilistic Model of Meter Perception: Simulating Enculturation.

PubMed

van der Weij, Bastiaan; Pearce, Marcus T; Honing, Henkjan

2017-01-01

Enculturation is known to shape the perception of meter in music but this is not explicitly accounted for by current cognitive models of meter perception. We hypothesize that the induction of meter is a result of predictive coding: interpreting onsets in a rhythm relative to a periodic meter facilitates prediction of future onsets. Such prediction, we hypothesize, is based on previous exposure to rhythms. As such, predictive coding provides a possible explanation for the way meter perception is shaped by the cultural environment. Based on this hypothesis, we present a probabilistic model of meter perception that uses statistical properties of the relation between rhythm and meter to infer meter from quantized rhythms. We show that our model can successfully predict annotated time signatures from quantized rhythmic patterns derived from folk melodies. Furthermore, we show that by inferring meter, our model improves prediction of the onsets of future events compared to a similar probabilistic model that does not infer meter. Finally, as a proof of concept, we demonstrate how our model can be used in a simulation of enculturation. From the results of this simulation, we derive a class of rhythms that are likely to be interpreted differently by enculturated listeners with different histories of exposure to rhythms.

Modelling explicit fracture of nuclear fuel pellets using peridynamics

NASA Astrophysics Data System (ADS)

Mella, R.; Wenman, M. R.

2015-12-01

Three dimensional models of explicit cracking of nuclear fuel pellets for a variety of power ratings have been explored with peridynamics, a non-local, mesh free, fracture mechanics method. These models were implemented in the explicitly integrated molecular dynamics code LAMMPS, which was modified to include thermal strains in solid bodies. The models of fuel fracture, during initial power transients, are shown to correlate with the mean number of cracks observed on the inner and outer edges of the pellet, by experimental post irradiation examination of fuel, for power ratings of 10 and 15 W g-1 UO2. The models of the pellet show the ability to predict expected features such as the mid-height pellet crack, the correct number of radial cracks and initiation and coalescence of radial cracks. This work presents a modelling alternative to empirical fracture data found in many fuel performance codes and requires just one parameter of fracture strain. Weibull distributions of crack numbers were fitted to both numerical and experimental data using maximum likelihood estimation so that statistical comparison could be made. The findings show P-values of less than 0.5% suggesting an excellent agreement between model and experimental distributions.

Development and Implementation of Dynamic Scripts to Execute Cycled WRF/GSI Forecasts

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley; Srikishen, Jayanthi; Berndt, Emily; Li, Quanli; Watson, Leela

2014-01-01

Automating the coupling of data assimilation (DA) and modeling systems is a unique challenge in the numerical weather prediction (NWP) research community. In recent years, the Development Testbed Center (DTC) has released well-documented tools such as the Weather Research and Forecasting (WRF) model and the Gridpoint Statistical Interpolation (GSI) DA system that can be easily downloaded, installed, and run by researchers on their local systems. However, developing a coupled system in which the various preprocessing, DA, model, and postprocessing capabilities are all integrated can be labor-intensive if one has little experience with any of these individual systems. Additionally, operational modeling entities generally have specific coupling methodologies that can take time to understand and develop code to implement properly. To better enable collaborating researchers to perform modeling and DA experiments with GSI, the Short-term Prediction Research and Transition (SPoRT) Center has developed a set of Perl scripts that couple GSI and WRF in a cycling methodology consistent with the use of real-time, regional observation data from the National Centers for Environmental Prediction (NCEP)/Environmental Modeling Center (EMC). Because Perl is open source, the code can be easily downloaded and executed regardless of the user's native shell environment. This paper will provide a description of this open-source code and descriptions of a number of the use cases that have been performed by SPoRT collaborators using the scripts on different computing systems.

R2 effect-size measures for mediation analysis

PubMed Central

Fairchild, Amanda J.; MacKinnon, David P.; Taborga, Marcia P.; Taylor, Aaron B.

2010-01-01

R2 effect-size measures are presented to assess variance accounted for in mediation models. The measures offer a means to evaluate both component paths and the overall mediated effect in mediation models. Statistical simulation results indicate acceptable bias across varying parameter and sample-size combinations. The measures are applied to a real-world example using data from a team-based health promotion program to improve the nutrition and exercise habits of firefighters. SAS and SPSS computer code are also provided for researchers to compute the measures in their own data. PMID:19363189

R2 effect-size measures for mediation analysis.

PubMed

Fairchild, Amanda J; Mackinnon, David P; Taborga, Marcia P; Taylor, Aaron B

2009-05-01

R(2) effect-size measures are presented to assess variance accounted for in mediation models. The measures offer a means to evaluate both component paths and the overall mediated effect in mediation models. Statistical simulation results indicate acceptable bias across varying parameter and sample-size combinations. The measures are applied to a real-world example using data from a team-based health promotion program to improve the nutrition and exercise habits of firefighters. SAS and SPSS computer code are also provided for researchers to compute the measures in their own data.

Molecular Dynamics of Hot Dense Plasmas: New Horizons

NASA Astrophysics Data System (ADS)

Graziani, Frank

2011-10-01

We describe the status of a new time-dependent simulation capability for hot dense plasmas. The backbone of this multi-institutional computational and experimental effort--the Cimarron Project--is the massively parallel molecular dynamics (MD) code ``ddcMD''. The project's focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low- Zelements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This talk summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision and highlights some significant results obtained to date. We describe the status of a new time-dependent simulation capability for hot dense plasmas. The backbone of this multi-institutional computational and experimental effort--the Cimarron Project--is the massively parallel molecular dynamics (MD) code ``ddcMD''. The project's focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low- Zelements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This talk summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision and highlights some significant results obtained to date. This work is performed under the auspices of the U. S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Ethics, culture and nursing practice in Ghana.

PubMed

Donkor, N T; Andrews, L D

2011-03-01

This paper describes how nurses in Ghana approach ethical problems. The International Council of Nurses' (ICN) Code for Nurses (2006) that serves as the model for professional code of ethics worldwide also acknowledges respect for healthy cultural values. Using the ICN's Code and universal ethical principles as a benchmark, a survey was conducted in 2009 to ascertain how nurses in Ghana respond to ethical and cultural issues in their practice. The study was qualitative with 200 participant nurses. Data were obtained through anonymous self-administered questionnaires. Descriptive statistics were used to analyze the data. Nurses' approaches to ethical problems in Ghana do not always meet expectations of the ICN Code for Nurses. They are also informed by local ethical practices related to the institutional setting and cultural environment in the country. While some cultural values complemented the ICN's Code and universal ethical principles, others conflicted with them. These data can assist nurses to provide culturally competent solutions to ethical dilemmas in their practice. Dynamic communication between nurses and patients/clients, intentional study of local cultural beliefs, and the development of ethics education will improve the conformity between universal ethical standards and local cultural values. © 2011 The Authors. International Nursing Review © 2011 International Council of Nurses.

Social media messaging in pregnancy: comparing content of Text4baby to content of free smart phone applications of pregnancy.

PubMed

Lewkowitz, Adam K; O'Donnell, Betsy E; Nakagawa, Sanae; Vargas, Juan E; Zlatnik, Marya G

2016-03-01

Text4baby is the only free text-message program for pregnancy available. Our objective was to determine whether content differed between Text4baby and popular pregnancy smart phone applications (apps). Researchers enrolled in Text4baby in 2012 and downloaded the four most-popular free pregnancy smart phone apps in July 2013; content was re-extracted in February 2014. Messages were assigned thematic codes. Two researchers coded messages independently before reviewing all the codes jointly to ensure consistency. Logistic regression modeling determined statistical differences between Text4baby and smart phone apps. About 1399 messages were delivered. Of these, 333 messages had content related to more than one theme and were coded as such, resulting in 1820 codes analyzed. Compared to smart phone apps, Text4baby was significantly more likely to have content regarding Postpartum Planning, Seeking Care, Recruitment and Prevention and significantly less likely to mention Normal Pregnancy Symptoms. No messaging program included content regarding postpartum contraception. To improve content without increasing text message number, Text4baby could replace messages on recruitment with messages regarding normal pregnancy symptoms, fetal development and postpartum contraception.

pyblocxs: Bayesian Low-Counts X-ray Spectral Analysis in Sherpa

NASA Astrophysics Data System (ADS)

Siemiginowska, A.; Kashyap, V.; Refsdal, B.; van Dyk, D.; Connors, A.; Park, T.

2011-07-01

Typical X-ray spectra have low counts and should be modeled using the Poisson distribution. However, χ2 statistic is often applied as an alternative and the data are assumed to follow the Gaussian distribution. A variety of weights to the statistic or a binning of the data is performed to overcome the low counts issues. However, such modifications introduce biases or/and a loss of information. Standard modeling packages such as XSPEC and Sherpa provide the Poisson likelihood and allow computation of rudimentary MCMC chains, but so far do not allow for setting a full Bayesian model. We have implemented a sophisticated Bayesian MCMC-based algorithm to carry out spectral fitting of low counts sources in the Sherpa environment. The code is a Python extension to Sherpa and allows to fit a predefined Sherpa model to high-energy X-ray spectral data and other generic data. We present the algorithm and discuss several issues related to the implementation, including flexible definition of priors and allowing for variations in the calibration information.

Coding pulmonary sepsis and mortality statistics in Rio de Janeiro, RJ.

PubMed

Cardoso, Bruno Baptista; Kale, Pauline Lorena

2016-01-01

This study aimed to describe "pulmonary sepsis" reported as a cause of death, measure its association to pneumonia, and the significance of the coding rules in mortality statistics, including the diagnosis of pneumonia on death certificates (DC) with the mention of pulmonary sepsis in Rio de Janeiro, Brazil, in 2011. DC with mention of pulmonary sepsis was identified, regardless of the underlying cause of death. Medical records related to the certificates with reference to "pulmonary sepsis" were reviewed and physicians were interviewed to measure the association between pulmonary sepsis and pneumonia. A simulation was performed in the mortality data by inserting the International Classification of Diseases (ICD-10) code for pneumonia in the certificates with pulmonary sepsis. "Pulmonary sepsis" constituted 30.9% of reported sepsis and pneumonia was not reported in 51.3% of these DC. Pneumonia was registered in 82.8% of the sample of the medical records. Among physicians interviewed, 93.3% declared pneumonia as the most common cause of "pulmonary sepsis." The simulation of the coding process resulted in a different underlying cause of death for 7.8% of the deaths with sepsis reported and 2.4% of all deaths, regardless the original cause. The conclusion is that "pulmonary sepsis" is frequently associated to pneumonia and that the addition of the ICD-10 code for pneumonia in DC could affect the mortality statistics, highlighting the need to improve mortality coding rules.

Recent advances in lossless coding techniques

NASA Astrophysics Data System (ADS)

Yovanof, Gregory S.

Current lossless techniques are reviewed with reference to both sequential data files and still images. Two major groups of sequential algorithms, dictionary and statistical techniques, are discussed. In particular, attention is given to Lempel-Ziv coding, Huffman coding, and arithmewtic coding. The subject of lossless compression of imagery is briefly discussed. Finally, examples of practical implementations of lossless algorithms and some simulation results are given.

Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: the role of mixing statistics and frame shift of neighboring genes.

PubMed

Cocho, Germinal; Miramontes, Pedro; Mansilla, Ricardo; Li, Wentian

2014-12-01

We examine the relationship between exponential correlation functions and Markov models in a bacterial genome in detail. Despite the well known fact that Markov models generate sequences with correlation function that decays exponentially, simply constructed Markov models based on nearest-neighbor dimer (first-order), trimer (second-order), up to hexamer (fifth-order), and treating the DNA sequence as being homogeneous all fail to predict the value of exponential decay rate. Even reading-frame-specific Markov models (both first- and fifth-order) could not explain the fact that the exponential decay is very slow. Starting with the in-phase coding-DNA-sequence (CDS), we investigated correlation within a fixed-codon-position subsequence, and in artificially constructed sequences by packing CDSs with out-of-phase spacers, as well as altering CDS length distribution by imposing an upper limit. From these targeted analyses, we conclude that the correlation in the bacterial genomic sequence is mainly due to a mixing of heterogeneous statistics at different codon positions, and the decay of correlation is due to the possible out-of-phase between neighboring CDSs. There are also small contributions to the correlation from bases at the same codon position, as well as by non-coding sequences. These show that the seemingly simple exponential correlation functions in bacterial genome hide a complexity in correlation structure which is not suitable for a modeling by Markov chain in a homogeneous sequence. Other results include: use of the (absolute value) second largest eigenvalue to represent the 16 correlation functions and the prediction of a 10-11 base periodicity from the hexamer frequencies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Potential Projective Material on the Rorschach: Comparing Comprehensive System Protocols to Their Modeled R-Optimized Administration Counterparts.

PubMed

Pianowski, Giselle; Meyer, Gregory J; Villemor-Amaral, Anna Elisa de

2016-01-01

Exner ( 1989 ) and Weiner ( 2003 ) identified 3 types of Rorschach codes that are most likely to contain personally relevant projective material: Distortions, Movement, and Embellishments. We examine how often these types of codes occur in normative data and whether their frequency changes for the 1st, 2nd, 3rd, 4th, or last response to a card. We also examine the impact on these variables of the Rorschach Performance Assessment System's (R-PAS) statistical modeling procedures that convert the distribution of responses (R) from Comprehensive System (CS) administered protocols to match the distribution of R found in protocols obtained using R-optimized administration guidelines. In 2 normative reference databases, the results indicated that about 40% of responses (M = 39.25) have 1 type of code, 15% have 2 types, and 1.5% have all 3 types, with frequencies not changing by response number. In addition, there were no mean differences in the original CS and R-optimized modeled records (M Cohen's d = -0.04 in both databases). When considered alongside findings showing minimal differences between the protocols of people randomly assigned to CS or R-optimized administration, the data suggest R-optimized administration should not alter the extent to which potential projective material is present in a Rorschach protocol.

egs_brachy: a versatile and fast Monte Carlo code for brachytherapy

NASA Astrophysics Data System (ADS)

Chamberland, Marc J. P.; Taylor, Randle E. P.; Rogers, D. W. O.; Thomson, Rowan M.

2016-12-01

egs_brachy is a versatile and fast Monte Carlo (MC) code for brachytherapy applications. It is based on the EGSnrc code system, enabling simulation of photons and electrons. Complex geometries are modelled using the EGSnrc C++ class library and egs_brachy includes a library of geometry models for many brachytherapy sources, in addition to eye plaques and applicators. Several simulation efficiency enhancing features are implemented in the code. egs_brachy is benchmarked by comparing TG-43 source parameters of three source models to previously published values. 3D dose distributions calculated with egs_brachy are also compared to ones obtained with the BrachyDose code. Well-defined simulations are used to characterize the effectiveness of many efficiency improving techniques, both as an indication of the usefulness of each technique and to find optimal strategies. Efficiencies and calculation times are characterized through single source simulations and simulations of idealized and typical treatments using various efficiency improving techniques. In general, egs_brachy shows agreement within uncertainties with previously published TG-43 source parameter values. 3D dose distributions from egs_brachy and BrachyDose agree at the sub-percent level. Efficiencies vary with radionuclide and source type, number of sources, phantom media, and voxel size. The combined effects of efficiency-improving techniques in egs_brachy lead to short calculation times: simulations approximating prostate and breast permanent implant (both with (2 mm)3 voxels) and eye plaque (with (1 mm)3 voxels) treatments take between 13 and 39 s, on a single 2.5 GHz Intel Xeon E5-2680 v3 processor core, to achieve 2% average statistical uncertainty on doses within the PTV. egs_brachy will be released as free and open source software to the research community.

egs_brachy: a versatile and fast Monte Carlo code for brachytherapy.

PubMed

Chamberland, Marc J P; Taylor, Randle E P; Rogers, D W O; Thomson, Rowan M

2016-12-07

egs_brachy is a versatile and fast Monte Carlo (MC) code for brachytherapy applications. It is based on the EGSnrc code system, enabling simulation of photons and electrons. Complex geometries are modelled using the EGSnrc C++ class library and egs_brachy includes a library of geometry models for many brachytherapy sources, in addition to eye plaques and applicators. Several simulation efficiency enhancing features are implemented in the code. egs_brachy is benchmarked by comparing TG-43 source parameters of three source models to previously published values. 3D dose distributions calculated with egs_brachy are also compared to ones obtained with the BrachyDose code. Well-defined simulations are used to characterize the effectiveness of many efficiency improving techniques, both as an indication of the usefulness of each technique and to find optimal strategies. Efficiencies and calculation times are characterized through single source simulations and simulations of idealized and typical treatments using various efficiency improving techniques. In general, egs_brachy shows agreement within uncertainties with previously published TG-43 source parameter values. 3D dose distributions from egs_brachy and BrachyDose agree at the sub-percent level. Efficiencies vary with radionuclide and source type, number of sources, phantom media, and voxel size. The combined effects of efficiency-improving techniques in egs_brachy lead to short calculation times: simulations approximating prostate and breast permanent implant (both with (2 mm) 3 voxels) and eye plaque (with (1 mm) 3 voxels) treatments take between 13 and 39 s, on a single 2.5 GHz Intel Xeon E5-2680 v3 processor core, to achieve 2% average statistical uncertainty on doses within the PTV. egs_brachy will be released as free and open source software to the research community.

Parallel tempering simulation of the three-dimensional Edwards-Anderson model with compact asynchronous multispin coding on GPU

NASA Astrophysics Data System (ADS)

Fang, Ye; Feng, Sheng; Tam, Ka-Ming; Yun, Zhifeng; Moreno, Juana; Ramanujam, J.; Jarrell, Mark

2014-10-01

Monte Carlo simulations of the Ising model play an important role in the field of computational statistical physics, and they have revealed many properties of the model over the past few decades. However, the effect of frustration due to random disorder, in particular the possible spin glass phase, remains a crucial but poorly understood problem. One of the obstacles in the Monte Carlo simulation of random frustrated systems is their long relaxation time making an efficient parallel implementation on state-of-the-art computation platforms highly desirable. The Graphics Processing Unit (GPU) is such a platform that provides an opportunity to significantly enhance the computational performance and thus gain new insight into this problem. In this paper, we present optimization and tuning approaches for the CUDA implementation of the spin glass simulation on GPUs. We discuss the integration of various design alternatives, such as GPU kernel construction with minimal communication, memory tiling, and look-up tables. We present a binary data format, Compact Asynchronous Multispin Coding (CAMSC), which provides an additional 28.4% speedup compared with the traditionally used Asynchronous Multispin Coding (AMSC). Our overall design sustains a performance of 33.5 ps per spin flip attempt for simulating the three-dimensional Edwards-Anderson model with parallel tempering, which significantly improves the performance over existing GPU implementations.

Investigation of the ellipsoidal-statistical Bhatnagar-Gross-Krook kinetic model applied to gas-phase transport of heat and tangential momentum between parallel walls

NASA Astrophysics Data System (ADS)

Gallis, M. A.; Torczynski, J. R.

2011-03-01

The ellipsoidal-statistical Bhatnagar-Gross-Krook (ES-BGK) kinetic model is investigated for steady gas-phase transport of heat, tangential momentum, and mass between parallel walls (i.e., Fourier, Couette, and Fickian flows). This investigation extends the original study of Cercignani and Tironi, who first applied the ES-BGK model to heat transport (i.e., Fourier flow) shortly after this model was proposed by Holway. The ES-BGK model is implemented in a molecular-gas-dynamics code so that results from this model can be compared directly to results from the full Boltzmann collision term, as computed by the same code with the direct simulation Monte Carlo (DSMC) algorithm of Bird. A gas of monatomic molecules is considered. These molecules collide in a pairwise fashion according to either the Maxwell or the hard-sphere interaction and reflect from the walls according to the Cercignani-Lampis-Lord model with unity accommodation coefficients. Simulations are performed at pressures from near-free-molecular to near-continuum. Unlike the BGK model, the ES-BGK model produces heat-flux and shear-stress values that both agree closely with the DSMC values at all pressures. However, for both interactions, the ES-BGK model produces molecular-velocity-distribution functions that are qualitatively similar to those determined for the Maxwell interaction from Chapman-Enskog theory for small wall temperature differences and moment-hierarchy theory for large wall temperature differences. Moreover, the ES-BGK model does not produce accurate values of the mass self-diffusion coefficient for either interaction. Nevertheless, given its reasonable accuracy for heat and tangential-momentum transport, its sound theoretical foundation (it obeys the H-theorem), and its available extension to polyatomic molecules, the ES-BGK model may be a useful method for simulating certain classes of single-species noncontinuum gas flows, as Cercignani suggested.

Error floor behavior study of LDPC codes for concatenated codes design

NASA Astrophysics Data System (ADS)

Chen, Weigang; Yin, Liuguo; Lu, Jianhua

2007-11-01

Error floor behavior of low-density parity-check (LDPC) codes using quantized decoding algorithms is statistically studied with experimental results on a hardware evaluation platform. The results present the distribution of the residual errors after decoding failure and reveal that the number of residual error bits in a codeword is usually very small using quantized sum-product (SP) algorithm. Therefore, LDPC code may serve as the inner code in a concatenated coding system with a high code rate outer code and thus an ultra low error floor can be achieved. This conclusion is also verified by the experimental results.

PEBBED Uncertainty and Sensitivity Analysis of the CRP-5 PBMR DLOFC Transient Benchmark with the SUSA Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerhard Strydom

2011-01-01

The need for a defendable and systematic uncertainty and sensitivity approach that conforms to the Code Scaling, Applicability, and Uncertainty (CSAU) process, and that could be used for a wide variety of software codes, was defined in 2008. The GRS (Gesellschaft für Anlagen und Reaktorsicherheit) company of Germany has developed one type of CSAU approach that is particularly well suited for legacy coupled core analysis codes, and a trial version of their commercial software product SUSA (Software for Uncertainty and Sensitivity Analyses) was acquired on May 12, 2010. This report summarized the results of the initial investigations performed with SUSA,more » utilizing a typical High Temperature Reactor benchmark (the IAEA CRP-5 PBMR 400MW Exercise 2) and the PEBBED-THERMIX suite of codes. The following steps were performed as part of the uncertainty and sensitivity analysis: 1. Eight PEBBED-THERMIX model input parameters were selected for inclusion in the uncertainty study: the total reactor power, inlet gas temperature, decay heat, and the specific heat capability and thermal conductivity of the fuel, pebble bed and reflector graphite. 2. The input parameters variations and probability density functions were specified, and a total of 800 PEBBED-THERMIX model calculations were performed, divided into 4 sets of 100 and 2 sets of 200 Steady State and Depressurized Loss of Forced Cooling (DLOFC) transient calculations each. 3. The steady state and DLOFC maximum fuel temperature, as well as the daily pebble fuel load rate data, were supplied to SUSA as model output parameters of interest. The 6 data sets were statistically analyzed to determine the 5% and 95% percentile values for each of the 3 output parameters with a 95% confidence level, and typical statistical indictors were also generated (e.g. Kendall, Pearson and Spearman coefficients). 4. A SUSA sensitivity study was performed to obtain correlation data between the input and output parameters, and to identify the primary contributors to the output data uncertainties. It was found that the uncertainties in the decay heat, pebble bed and reflector thermal conductivities were responsible for the bulk of the propagated uncertainty in the DLOFC maximum fuel temperature. It was also determined that the two standard deviation (2s) uncertainty on the maximum fuel temperature was between ±58oC (3.6%) and ±76oC (4.7%) on a mean value of 1604 oC. These values mostly depended on the selection of the distributions types, and not on the number of model calculations above the required Wilks criteria (a (95%,95%) statement would usually require 93 model runs).« less

Sequence-based heuristics for faster annotation of non-coding RNA families.

PubMed

Weinberg, Zasha; Ruzzo, Walter L

2006-01-01

Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM's accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be. In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that--unlike family-specific solutions--can scale to hundreds of ncRNA families. The source code is available under GNU Public License at the supplementary web site.

Seeing the mean: ensemble coding for sets of faces.

PubMed

Haberman, Jason; Whitney, David

2009-06-01

We frequently encounter groups of similar objects in our visual environment: a bed of flowers, a basket of oranges, a crowd of people. How does the visual system process such redundancy? Research shows that rather than code every element in a texture, the visual system favors a summary statistical representation of all the elements. The authors demonstrate that although it may facilitate texture perception, ensemble coding also occurs for faces-a level of processing well beyond that of textures. Observers viewed sets of faces varying in emotionality (e.g., happy to sad) and assessed the mean emotion of each set. Although observers retained little information about the individual set members, they had a remarkably precise representation of the mean emotion. Observers continued to discriminate the mean emotion accurately even when they viewed sets of 16 faces for 500 ms or less. Modeling revealed that perceiving the average facial expression in groups of faces was not due to noisy representation or noisy discrimination. These findings support the hypothesis that ensemble coding occurs extremely fast at multiple levels of visual analysis. (c) 2009 APA, all rights reserved.

FIRETEC: A transport description of wildfire behavior

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linn, R.R.; Harlow, F.H.

1997-12-01

Wildfires are a threat to human life and property, yet they are an unavoidable part of nature and in some instances they are necessary for the natural maintenance and evolution of forests. Investigators have attempted to describe the behavior (speed, direction, modes of spread) of wildfires for over fifty years. Current models for numerical description are mainly algebraic and based on statistical or empirical ideas. The authors describe, in contrast, a transport model called FIRETEC, which is a self-determining fire behavior model. The use of transport formulations connects the propagation rates to the full conservation equations for energy, momentum, speciesmore » concentrations, mass, and turbulence. In this text, highlights of the model formulation and results are described. The goal of the FIRETEC model is to describe average behavior of the gases and fuels. It represents the essence of the combination of many small-scale processes without resolving each process in complete detail. The FIRETEC model is implemented into a computer code that examines line-fire propagation in a vertical spatial cut parallel to the direction of advancement. With this code the authors are able to examine wind effects, slope effects, and the effects of nonhomogeneous fuel distribution.« less

Leveraging Code Comments to Improve Software Reliability

ERIC Educational Resources Information Center

Tan, Lin

2009-01-01

Commenting source code has long been a common practice in software development. This thesis, consisting of three pieces of work, made novel use of the code comments written in natural language to improve software reliability. Our solution combines Natural Language Processing (NLP), Machine Learning, Statistics, and Program Analysis techniques to…

49 CFR 1248.1 - Freight commodity statistics.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 9 2011-10-01 2011-10-01 false Freight commodity statistics. 1248.1 Section 1248... STATISTICS § 1248.1 Freight commodity statistics. All class I railroads, as described in § 1240.1 of this... statistics on the basis of the commodity codes named in § 1248.101. Carriers shall report quarterly on the...

49 CFR 1248.1 - Freight commodity statistics.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 9 2010-10-01 2010-10-01 false Freight commodity statistics. 1248.1 Section 1248... STATISTICS § 1248.1 Freight commodity statistics. All class I railroads, as described in § 1240.1 of this... statistics on the basis of the commodity codes named in § 1248.101. Carriers shall report quarterly on the...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simonen, F.A.; Khaleel, M.A.

This paper describes a statistical evaluation of the through-thickness copper variation for welds in reactor pressure vessels, and reviews the historical basis for the static and arrest fracture toughness (K{sub Ic} and K{sub Ia}) equations used in the VISA-II code. Copper variability in welds is due to fabrication procedures with copper contents being randomly distributed, variable from one location to another through the thickness of the vessel. The VISA-II procedure of sampling the copper content from a statistical distribution for every 6.35- to 12.7-mm (1/4- to 1/2-in.) layer through the thickness was found to be consistent with the statistical observations.more » However, the parameters of the VISA-II distribution and statistical limits required further investigation. Copper contents at few locations through the thickness were found to exceed the 0.4% upper limit of the VISA-II code. The data also suggest that the mean copper content varies systematically through the thickness. While, the assumption of normality is not clearly supported by the available data, a statistical evaluation based on all the available data results in mean and standard deviations within the VISA-II code limits.« less

Model documentation report: Transportation sector model of the National Energy Modeling System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1994-03-01

This report documents the objectives, analytical approach and development of the National Energy Modeling System (NEMS) Transportation Model (TRAN). The report catalogues and describes the model assumptions, computational methodology, parameter estimation techniques, model source code, and forecast results generated by the model. This document serves three purposes. First, it is a reference document providing a detailed description of TRAN for model analysts, users, and the public. Second, this report meets the legal requirements of the Energy Information Administration (EIA) to provide adequate documentation in support of its statistical and forecast reports (Public Law 93-275, 57(b)(1)). Third, it permits continuity inmore » model development by providing documentation from which energy analysts can undertake model enhancements, data updates, and parameter refinements.« less

Self-Organization: Complex Dynamical Systems in the Evolution of Speech

NASA Astrophysics Data System (ADS)

Oudeyer, Pierre-Yves

Human vocalization systems are characterized by complex structural properties. They are combinatorial, based on the systematic reuse of phonemes, and the set of repertoires in human languages is characterized by both strong statistical regularities—universals—and a great diversity. Besides, they are conventional codes culturally shared in each community of speakers. What are the origins of the forms of speech? What are the mechanisms that permitted their evolution in the course of phylogenesis and cultural evolution? How can a shared speech code be formed in a community of individuals? This chapter focuses on the way the concept of self-organization, and its interaction with natural selection, can throw light on these three questions. In particular, a computational model is presented which shows that a basic neural equipment for adaptive holistic vocal imitation, coupling directly motor and perceptual representations in the brain, can generate spontaneously shared combinatorial systems of vocalizations in a society of babbling individuals. Furthermore, we show how morphological and physiological innate constraints can interact with these self-organized mechanisms to account for both the formation of statistical regularities and diversity in vocalization systems.

System statistical reliability model and analysis

NASA Technical Reports Server (NTRS)

Lekach, V. S.; Rood, H.

1973-01-01

A digital computer code was developed to simulate the time-dependent behavior of the 5-kwe reactor thermoelectric system. The code was used to determine lifetime sensitivity coefficients for a number of system design parameters, such as thermoelectric module efficiency and degradation rate, radiator absorptivity and emissivity, fuel element barrier defect constant, beginning-of-life reactivity, etc. A probability distribution (mean and standard deviation) was estimated for each of these design parameters. Then, error analysis was used to obtain a probability distribution for the system lifetime (mean = 7.7 years, standard deviation = 1.1 years). From this, the probability that the system will achieve the design goal of 5 years lifetime is 0.993. This value represents an estimate of the degradation reliability of the system.

Visual feature extraction from voxel-weighted averaging of stimulus images in 2 fMRI studies.

PubMed

Hart, Corey B; Rose, William J

2013-11-01

Multiple studies have provided evidence for distributed object representation in the brain, with several recent experiments leveraging basis function estimates for partial image reconstruction from fMRI data. Using a novel combination of statistical decomposition, generalized linear models, and stimulus averaging on previously examined image sets and Bayesian regression of recorded fMRI activity during presentation of these data sets, we identify a subset of relevant voxels that appear to code for covarying object features. Using a technique we term "voxel-weighted averaging," we isolate image filters that these voxels appear to implement. The results, though very cursory, appear to have significant implications for hierarchical and deep-learning-type approaches toward the understanding of neural coding and representation.

Causes of Death Data in the Global Burden of Disease Estimates for Ischemic and Hemorrhagic Stroke

PubMed Central

Truelsen, Thomas; Krarup, Lars-Henrik; Iversen, Helle; Mensah, George A.; Feigin, Valery; Sposato, Luciano; Naghavi, Mohsen

2015-01-01

Background Stroke mortality estimates in the Global Burden of Disease (GBD) study are based on routine mortality statistics and redistribution of ill-defined codes that cannot be a cause of death, the so-called “garbage codes”. This study describes the contribution of these codes to stroke mortality estimates. Methods All available mortality data were compiled and non-specific cause codes were redistributed based on literature review and statistical methods. Ill-defined codes were redistributed to their specific cause of disease by age, sex, country, and year. The reassignment was done based on the international classification of diseases and the pathology behind each code by checking multiple causes of death and literature review. Results Unspecified stroke, and primary and secondary hypertension are leading contributing “garbage codes” to stroke mortality estimates for intracranial hemorrhagic stroke and ischemic stroke. There were marked differences in the fraction of death assigned to ischemic stroke and hemorrhagic stroke for unspecified stroke and hypertension between GBD regions and between age groups. Conclusions A large proportion of stroke fatalities is derived from the redistribution of “unspecified stroke” and “hypertension” with marked regional differences. Future advancements in stroke certification, data collections, and statistical analyses may improve the estimation of the global stroke burden. PMID:26505189

Statistical Calibration and Validation of a Homogeneous Ventilated Wall-Interference Correction Method for the National Transonic Facility

NASA Technical Reports Server (NTRS)

Walker, Eric L.

2005-01-01

Wind tunnel experiments will continue to be a primary source of validation data for many types of mathematical and computational models in the aerospace industry. The increased emphasis on accuracy of data acquired from these facilities requires understanding of the uncertainty of not only the measurement data but also any correction applied to the data. One of the largest and most critical corrections made to these data is due to wall interference. In an effort to understand the accuracy and suitability of these corrections, a statistical validation process for wall interference correction methods has been developed. This process is based on the use of independent cases which, after correction, are expected to produce the same result. Comparison of these independent cases with respect to the uncertainty in the correction process establishes a domain of applicability based on the capability of the method to provide reasonable corrections with respect to customer accuracy requirements. The statistical validation method was applied to the version of the Transonic Wall Interference Correction System (TWICS) recently implemented in the National Transonic Facility at NASA Langley Research Center. The TWICS code generates corrections for solid and slotted wall interference in the model pitch plane based on boundary pressure measurements. Before validation could be performed on this method, it was necessary to calibrate the ventilated wall boundary condition parameters. Discrimination comparisons are used to determine the most representative of three linear boundary condition models which have historically been used to represent longitudinally slotted test section walls. Of the three linear boundary condition models implemented for ventilated walls, the general slotted wall model was the most representative of the data. The TWICS code using the calibrated general slotted wall model was found to be valid to within the process uncertainty for test section Mach numbers less than or equal to 0.60. The scatter among the mean corrected results of the bodies of revolution validation cases was within one count of drag on a typical transport aircraft configuration for Mach numbers at or below 0.80 and two counts of drag for Mach numbers at or below 0.90.

Recurrence time statistics: versatile tools for genomic DNA sequence analysis.

PubMed

Cao, Yinhe; Tung, Wen-Wen; Gao, J B

2004-01-01

With the completion of the human and a few model organisms' genomes, and the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop faster computational tools which are capable of easily identifying the structures and extracting features from DNA sequences. One of the more important structures in a DNA sequence is repeat-related. Often they have to be masked before protein coding regions along a DNA sequence are to be identified or redundant expressed sequence tags (ESTs) are to be sequenced. Here we report a novel recurrence time based method for sequence analysis. The method can conveniently study all kinds of periodicity and exhaustively find all repeat-related features from a genomic DNA sequence. An efficient codon index is also derived from the recurrence time statistics, which has the salient features of being largely species-independent and working well on very short sequences. Efficient codon indices are key elements of successful gene finding algorithms, and are particularly useful for determining whether a suspected EST belongs to a coding or non-coding region. We illustrate the power of the method by studying the genomes of E. coli, the yeast S. cervisivae, the nematode worm C. elegans, and the human, Homo sapiens. Computationally, our method is very efficient. It allows us to carry out analysis of genomes on the whole genomic scale by a PC.

Joint Services Electronics Program Annual Progress Report.

DTIC Science & Technology

1985-11-01

one symbol memory) adaptive lHuffman codes were performed, and the compression achieved was compared with that of Ziv - Lempel coding. As was expected...MATERIALS 8 4. Information Systems 9 4.1 REAL TIME STATISTICAL DATA PROCESSING 9 -. 4.2 DATA COMPRESSION for COMPUTER DATA STRUCTURES 9 5. PhD...a. Real Time Statistical Data Processing (T. Kailatb) b. Data Compression for Computer Data Structures (J. Gill) Acces Fo NTIS CRA&I I " DTIC TAB

Jet Measurements for Development of Jet Noise Prediction Tools

NASA Technical Reports Server (NTRS)

Bridges, James E.

2006-01-01

The primary focus of my presentation is the development of the jet noise prediction code JeNo with most examples coming from the experimental work that drove the theoretical development and validation. JeNo is a statistical jet noise prediction code, based upon the Lilley acoustic analogy. Our approach uses time-average 2-D or 3-D mean and turbulent statistics of the flow as input. The output is source distributions and spectral directivity.

TOWARD THE DEVELOPMENT OF A CONSENSUS MATERIALS DATABASE FOR PRESSURE TECHNOLGY APPLICATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swindeman, Robert W; Ren, Weiju

The ASME construction code books specify materials and fabrication procedures that are acceptable for pressure technology applications. However, with few exceptions, the materials properties provided in the ASME code books provide no statistics or other information pertaining to material variability. Such information is central to the prediction and prevention of failure events. Many sources of materials data exist that provide variability information but such sources do not necessarily represent a consensus of experts with respect to the reported trends that are represented. Such a need has been identified by the ASME Standards Technology, LLC and initial steps have been takenmore » to address these needs: however, these steps are limited to project-specific applications only, such as the joint DOE-ASME project on materials for Generation IV nuclear reactors. In contrast to light-water reactor technology, the experience base for the Generation IV nuclear reactors is somewhat lacking and heavy reliance must be placed on model development and predictive capability. The database for model development is being assembled and includes existing code alloys such as alloy 800H and 9Cr-1Mo-V steel. Ownership and use rights are potential barriers that must be addressed.« less

Fourier and Wavelet Analysis of Coronal Time Series

NASA Astrophysics Data System (ADS)

Auchère, F.; Froment, C.; Bocchialini, K.; Buchlin, E.; Solomon, J.

2016-10-01

Using Fourier and wavelet analysis, we critically re-assess the significance of our detection of periodic pulsations in coronal loops. We show that the proper identification of the frequency dependence and statistical properties of the different components of the power spectra provies a strong argument against the common practice of data detrending, which tends to produce spurious detections around the cut-off frequency of the filter. In addition, the white and red noise models built into the widely used wavelet code of Torrence & Compo cannot, in most cases, adequately represent the power spectra of coronal time series, thus also possibly causing false positives. Both effects suggest that several reports of periodic phenomena should be re-examined. The Torrence & Compo code nonetheless effectively computes rigorous confidence levels if provided with pertinent models of mean power spectra, and we describe the appropriate manner in which to call its core routines. We recall the meaning of the default confidence levels output from the code, and we propose new Monte-Carlo-derived levels that take into account the total number of degrees of freedom in the wavelet spectra. These improvements allow us to confirm that the power peaks that we detected have a very low probability of being caused by noise.

The ALI-ARMS Code for Modeling Atmospheric non-LTE Molecular Band Emissions: Current Status and Applications

NASA Technical Reports Server (NTRS)

Kutepov, A. A.; Feofilov, A. G.; Manuilova, R. O.; Yankovsky, V. A.; Rezac, L.; Pesnell, W. D.; Goldberg, R. A.

2008-01-01

The Accelerated Lambda Iteration (ALI) technique was developed in stellar astrophysics at the beginning of 1990s for solving the non-LTE radiative transfer problem in atomic lines and multiplets in stellar atmospheres. It was later successfully applied to modeling the non-LTE emissions and radiative cooling/heating in the vibrational-rotational bands of molecules in planetary atmospheres. Similar to the standard lambda iterations ALI operates with the matrices of minimal dimension. However, it provides higher convergence rate and stability due to removing from the iterating process the photons trapped in the optically thick line cores. In the current ALI-ARMS (ALI for Atmospheric Radiation and Molecular Spectra) code version additional acceleration of calculations is provided by utilizing the opacity distribution function (ODF) approach and "decoupling". The former allows replacing the band branches by single lines of special shape, whereas the latter treats non-linearity caused by strong near-resonant vibration-vibrational level coupling without additional linearizing the statistical equilibrium equations. Latest code application for the non-LTE diagnostics of the molecular band emissions of Earth's and Martian atmospheres as well as for the non-LTE IR cooling/heating calculations are discussed.

Mitigating the impact of the DESI fiber assignment on galaxy clustering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burden, Angela; Padmanabhan, Nikhil; Cahn, Robert N.

2017-03-01

We present a simple strategy to mitigate the impact of an incomplete spectroscopic redshift galaxy sample as a result of fiber assignment and survey tiling. The method has been designed for the Dark Energy Spectroscopic Instrument (DESI) galaxy survey but may have applications beyond this. We propose a modification to the usual correlation function that nulls the almost purely angular modes affected by survey incompleteness due to fiber assignment. Predictions of this modified statistic can be calculated given a model of the two point correlation function. The new statistic can be computed with a slight modification to the data cataloguesmore » input to the standard correlation function code and does not incur any additional computational time. Finally we show that the spherically averaged baryon acoustic oscillation signal is not biased by the new statistic.« less

FIREFLY (Fitting IteRativEly For Likelihood analYsis): a full spectral fitting code

NASA Astrophysics Data System (ADS)

Wilkinson, David M.; Maraston, Claudia; Goddard, Daniel; Thomas, Daniel; Parikh, Taniya

2017-12-01

We present a new spectral fitting code, FIREFLY, for deriving the stellar population properties of stellar systems. FIREFLY is a chi-squared minimization fitting code that fits combinations of single-burst stellar population models to spectroscopic data, following an iterative best-fitting process controlled by the Bayesian information criterion. No priors are applied, rather all solutions within a statistical cut are retained with their weight. Moreover, no additive or multiplicative polynomials are employed to adjust the spectral shape. This fitting freedom is envisaged in order to map out the effect of intrinsic spectral energy distribution degeneracies, such as age, metallicity, dust reddening on galaxy properties, and to quantify the effect of varying input model components on such properties. Dust attenuation is included using a new procedure, which was tested on Integral Field Spectroscopic data in a previous paper. The fitting method is extensively tested with a comprehensive suite of mock galaxies, real galaxies from the Sloan Digital Sky Survey and Milky Way globular clusters. We also assess the robustness of the derived properties as a function of signal-to-noise ratio (S/N) and adopted wavelength range. We show that FIREFLY is able to recover age, metallicity, stellar mass, and even the star formation history remarkably well down to an S/N ∼ 5, for moderately dusty systems. Code and results are publicly available.1

Putting Priors in Mixture Density Mercer Kernels

NASA Technical Reports Server (NTRS)

Srivastava, Ashok N.; Schumann, Johann; Fischer, Bernd

2004-01-01

This paper presents a new methodology for automatic knowledge driven data mining based on the theory of Mercer Kernels, which are highly nonlinear symmetric positive definite mappings from the original image space to a very high, possibly infinite dimensional feature space. We describe a new method called Mixture Density Mercer Kernels to learn kernel function directly from data, rather than using predefined kernels. These data adaptive kernels can en- code prior knowledge in the kernel using a Bayesian formulation, thus allowing for physical information to be encoded in the model. We compare the results with existing algorithms on data from the Sloan Digital Sky Survey (SDSS). The code for these experiments has been generated with the AUTOBAYES tool, which automatically generates efficient and documented C/C++ code from abstract statistical model specifications. The core of the system is a schema library which contains template for learning and knowledge discovery algorithms like different versions of EM, or numeric optimization methods like conjugate gradient methods. The template instantiation is supported by symbolic- algebraic computations, which allows AUTOBAYES to find closed-form solutions and, where possible, to integrate them into the code. The results show that the Mixture Density Mercer-Kernel described here outperforms tree-based classification in distinguishing high-redshift galaxies from low- redshift galaxies by approximately 16% on test data, bagged trees by approximately 7%, and bagged trees built on a much larger sample of data by approximately 2%.

Improving accuracy of clinical coding in surgery: collaboration is key.

PubMed

Heywood, Nick A; Gill, Michael D; Charlwood, Natasha; Brindle, Rachel; Kirwan, Cliona C

2016-08-01

Clinical coding data provide the basis for Hospital Episode Statistics and Healthcare Resource Group codes. High accuracy of this information is required for payment by results, allocation of health and research resources, and public health data and planning. We sought to identify the level of accuracy of clinical coding in general surgical admissions across hospitals in the Northwest of England. Clinical coding departments identified a total of 208 emergency general surgical patients discharged between 1st March and 15th August 2013 from seven hospital trusts (median = 20, range = 16-60). Blinded re-coding was performed by a senior clinical coder and clinician, with results compared with the original coding outcome. Recorded codes were generated from OPCS-4 & ICD-10. Of all cases, 194 of 208 (93.3%) had at least one coding error and 9 of 208 (4.3%) had errors in both primary diagnosis and primary procedure. Errors were found in 64 of 208 (30.8%) of primary diagnoses and 30 of 137 (21.9%) of primary procedure codes. Median tariff using original codes was £1411.50 (range, £409-9138). Re-calculation using updated clinical codes showed a median tariff of £1387.50, P = 0.997 (range, £406-10,102). The most frequent reasons for incorrect coding were "coder error" and a requirement for "clinical interpretation of notes". Errors in clinical coding are multifactorial and have significant impact on primary diagnosis, potentially affecting the accuracy of Hospital Episode Statistics data and in turn the allocation of health care resources and public health planning. As we move toward surgeon specific outcomes, surgeons should increase collaboration with coding departments to ensure the system is robust. Copyright © 2016 Elsevier Inc. All rights reserved.

Dependency graph for code analysis on emerging architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shashkov, Mikhail Jurievich; Lipnikov, Konstantin

Direct acyclic dependency (DAG) graph is becoming the standard for modern multi-physics codes.The ideal DAG is the true block-scheme of a multi-physics code. Therefore, it is the convenient object for insitu analysis of the cost of computations and algorithmic bottlenecks related to statistical frequent data motion and dymanical machine state.

Video traffic characteristics of modern encoding standards: H.264/AVC with SVC and MVC extensions and H.265/HEVC.

PubMed

Seeling, Patrick; Reisslein, Martin

2014-01-01

Video encoding for multimedia services over communication networks has significantly advanced in recent years with the development of the highly efficient and flexible H.264/AVC video coding standard and its SVC extension. The emerging H.265/HEVC video coding standard as well as 3D video coding further advance video coding for multimedia communications. This paper first gives an overview of these new video coding standards and then examines their implications for multimedia communications by studying the traffic characteristics of long videos encoded with the new coding standards. We review video coding advances from MPEG-2 and MPEG-4 Part 2 to H.264/AVC and its SVC and MVC extensions as well as H.265/HEVC. For single-layer (nonscalable) video, we compare H.265/HEVC and H.264/AVC in terms of video traffic and statistical multiplexing characteristics. Our study is the first to examine the H.265/HEVC traffic variability for long videos. We also illustrate the video traffic characteristics and statistical multiplexing of scalable video encoded with the SVC extension of H.264/AVC as well as 3D video encoded with the MVC extension of H.264/AVC.

Video Traffic Characteristics of Modern Encoding Standards: H.264/AVC with SVC and MVC Extensions and H.265/HEVC

PubMed Central

2014-01-01

Video encoding for multimedia services over communication networks has significantly advanced in recent years with the development of the highly efficient and flexible H.264/AVC video coding standard and its SVC extension. The emerging H.265/HEVC video coding standard as well as 3D video coding further advance video coding for multimedia communications. This paper first gives an overview of these new video coding standards and then examines their implications for multimedia communications by studying the traffic characteristics of long videos encoded with the new coding standards. We review video coding advances from MPEG-2 and MPEG-4 Part 2 to H.264/AVC and its SVC and MVC extensions as well as H.265/HEVC. For single-layer (nonscalable) video, we compare H.265/HEVC and H.264/AVC in terms of video traffic and statistical multiplexing characteristics. Our study is the first to examine the H.265/HEVC traffic variability for long videos. We also illustrate the video traffic characteristics and statistical multiplexing of scalable video encoded with the SVC extension of H.264/AVC as well as 3D video encoded with the MVC extension of H.264/AVC. PMID:24701145

The challenge of mapping between two medical coding systems.

PubMed

Wojcik, Barbara E; Stein, Catherine R; Devore, Raymond B; Hassell, L Harrison

2006-11-01

Deployable medical systems patient conditions (PCs) designate groups of patients with similar medical conditions and, therefore, similar treatment requirements. PCs are used by the U.S. military to estimate field medical resources needed in combat operations. Information associated with each of the 389 PCs is based on subject matter expert opinion, instead of direct derivation from standard medical codes. Currently, no mechanisms exist to tie current or historical medical data to PCs. Our study objective was to determine whether reliable conversion between PC codes and International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM) diagnosis codes is possible. Data were analyzed for three professional coders assigning all applicable ICD-9-CM diagnosis codes to each PC code. Inter-rater reliability was measured by using Cohen's K statistic and percent agreement. Methods were developed to calculate kappa statistics when multiple responses could be selected from many possible categories. Overall, we found moderate support for the possibility of reliable conversion between PCs and ICD-9-CM diagnoses (mean kappa = 0.61). Current PCs should be modified into a system that is verifiable with real data.

A discriminative test among the different theories proposed to explain the origin of the genetic code: the coevolution theory finds additional support.

PubMed

Giulio, Massimo Di

2018-05-19

A discriminative statistical test among the different theories proposed to explain the origin of the genetic code is presented. Gathering the amino acids into polarity and biosynthetic classes that are the first expression of the physicochemical theory of the origin of the genetic code and the second expression of the coevolution theory, these classes are utilized in the Fisher's exact test to establish their significance within the genetic code table. Linking to the rows and columns of the genetic code of probabilities that express the statistical significance of these classes, I have finally been in the condition to be able to calculate a χ value to link to both the physicochemical theory and to the coevolution theory that would express the corroboration level referred to these theories. The comparison between these two χ values showed that the coevolution theory is able to explain - in this strictly empirical analysis - the origin of the genetic code better than that of the physicochemical theory. Copyright © 2018 Elsevier B.V. All rights reserved.

Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences.

PubMed

Schbath, S; Prum, B; de Turckheim, E

1995-01-01

Identifying exceptional motifs is often used for extracting information from long DNA sequences. The two difficulties of the method are the choice of the model that defines the expected frequencies of words and the approximation of the variance of the difference T(W) between the number of occurrences of a word W and its estimation. We consider here different Markov chain models, either with stationary or periodic transition probabilities. We estimate the variance of the difference T(W) by the conditional variance of the number of occurrences of W given the oligonucleotides counts that define the model. Two applications show how to use asymptotically standard normal statistics associated with the counts to describe a given sequence in terms of its outlying words. Sequences of Escherichia coli and of Bacillus subtilis are compared with respect to their exceptional tri- and tetranucleotides. For both bacteria, exceptional 3-words are mainly found in the coding frame. E. coli palindrome counts are analyzed in different models, showing that many overabundant words are one-letter mutations of avoided palindromes.

A new Bayesian Earthquake Analysis Tool (BEAT)

NASA Astrophysics Data System (ADS)

Vasyura-Bathke, Hannes; Dutta, Rishabh; Jónsson, Sigurjón; Mai, Martin

2017-04-01

Modern earthquake source estimation studies increasingly use non-linear optimization strategies to estimate kinematic rupture parameters, often considering geodetic and seismic data jointly. However, the optimization process is complex and consists of several steps that need to be followed in the earthquake parameter estimation procedure. These include pre-describing or modeling the fault geometry, calculating the Green's Functions (often assuming a layered elastic half-space), and estimating the distributed final slip and possibly other kinematic source parameters. Recently, Bayesian inference has become popular for estimating posterior distributions of earthquake source model parameters given measured/estimated/assumed data and model uncertainties. For instance, some research groups consider uncertainties of the layered medium and propagate these to the source parameter uncertainties. Other groups make use of informative priors to reduce the model parameter space. In addition, innovative sampling algorithms have been developed that efficiently explore the often high-dimensional parameter spaces. Compared to earlier studies, these improvements have resulted in overall more robust source model parameter estimates that include uncertainties. However, the computational demands of these methods are high and estimation codes are rarely distributed along with the published results. Even if codes are made available, it is often difficult to assemble them into a single optimization framework as they are typically coded in different programing languages. Therefore, further progress and future applications of these methods/codes are hampered, while reproducibility and validation of results has become essentially impossible. In the spirit of providing open-access and modular codes to facilitate progress and reproducible research in earthquake source estimations, we undertook the effort of producing BEAT, a python package that comprises all the above-mentioned features in one single programing environment. The package is build on top of the pyrocko seismological toolbox (www.pyrocko.org) and makes use of the pymc3 module for Bayesian statistical model fitting. BEAT is an open-source package (https://github.com/hvasbath/beat) and we encourage and solicit contributions to the project. In this contribution, we present our strategy for developing BEAT, show application examples, and discuss future developments.

Cognitive problem solving patterns of medical students correlate with success in diagnostic case solutions.

PubMed

Kiesewetter, Jan; Ebersbach, René; Görlitz, Anja; Holzer, Matthias; Fischer, Martin R; Schmidmaier, Ralf

2013-01-01

Problem-solving in terms of clinical reasoning is regarded as a key competence of medical doctors. Little is known about the general cognitive actions underlying the strategies of problem-solving among medical students. In this study, a theory-based model was used and adapted in order to investigate the cognitive actions in which medical students are engaged when dealing with a case and how patterns of these actions are related to the correct solution. Twenty-three medical students worked on three cases on clinical nephrology using the think-aloud method. The transcribed recordings were coded using a theory-based model consisting of eight different cognitive actions. The coded data was analysed using time sequences in a graphical representation software. Furthermore the relationship between the coded data and accuracy of diagnosis was investigated with inferential statistical methods. The observation of all main actions in a case elaboration, including evaluation, representation and integration, was considered a complete model and was found in the majority of cases (56%). This pattern significantly related to the accuracy of the case solution (φ = 0.55; p<.001). Extent of prior knowledge was neither related to the complete model nor to the correct solution. The proposed model is suitable to empirically verify the cognitive actions of problem-solving of medical students. The cognitive actions evaluation, representation and integration are crucial for the complete model and therefore for the accuracy of the solution. The educational implication which may be drawn from this study is to foster students reasoning by focusing on higher level reasoning.

Free Energy Gap and Statistical Thermodynamic Fidelity of DNA Codes

DTIC Science & Technology

2007-10-01

reverse-complement unless otherwise stated. For strand x, let Nx denote its complement. A (perfect) Watson - Crick duplex is the joining of complement...is possible for complementary sequences to form a non-perfectly aligned duplex, we will call any x W Nx duplex a Watson - Crick (WC) duplex. Two...DATES COVERED (From - To) 4. TITLE AND SUBTITLE FREE ENERGY GAP AND STATISTICAL THERMODYNAMIC FIDELITY OF DNA CODES 5a. CONTRACT NUMBER FA8750-07

Free Energy Gap and Statistical Thermodynamic Fidelity of DNA Codes (Postprint)

DTIC Science & Technology

2007-01-01

reverse-complement unless otherwise stated. For strand x, let Nx denote its complement. A (perfect) Watson - Crick duplex is the joining of complement...is possible for complementary sequences to form a non-perfectly aligned duplex, we will call any x W Nx duplex a Watson - Crick (WC) duplex. Two...DATES COVERED (From - To) 4. TITLE AND SUBTITLE FREE ENERGY GAP AND STATISTICAL THERMODYNAMIC FIDELITY OF DNA CODES 5a. CONTRACT NUMBER FA8750-07

Gene Identification Algorithms Using Exploratory Statistical Analysis of Periodicity

NASA Astrophysics Data System (ADS)

Mukherjee, Shashi Bajaj; Sen, Pradip Kumar

2010-10-01

Studying periodic pattern is expected as a standard line of attack for recognizing DNA sequence in identification of gene and similar problems. But peculiarly very little significant work is done in this direction. This paper studies statistical properties of DNA sequences of complete genome using a new technique. A DNA sequence is converted to a numeric sequence using various types of mappings and standard Fourier technique is applied to study the periodicity. Distinct statistical behaviour of periodicity parameters is found in coding and non-coding sequences, which can be used to distinguish between these parts. Here DNA sequences of Drosophila melanogaster were analyzed with significant accuracy.

The Statistical Consulting Center for Astronomy (SCCA)

NASA Technical Reports Server (NTRS)

Akritas, Michael

2001-01-01

The process by which raw astronomical data acquisition is transformed into scientifically meaningful results and interpretation typically involves many statistical steps. Traditional astronomy limits itself to a narrow range of old and familiar statistical methods: means and standard deviations; least-squares methods like chi(sup 2) minimization; and simple nonparametric procedures such as the Kolmogorov-Smirnov tests. These tools are often inadequate for the complex problems and datasets under investigations, and recent years have witnessed an increased usage of maximum-likelihood, survival analysis, multivariate analysis, wavelet and advanced time-series methods. The Statistical Consulting Center for Astronomy (SCCA) assisted astronomers with the use of sophisticated tools, and to match these tools with specific problems. The SCCA operated with two professors of statistics and a professor of astronomy working together. Questions were received by e-mail, and were discussed in detail with the questioner. Summaries of those questions and answers leading to new approaches were posted on the Web (www.state.psu.edu/ mga/SCCA). In addition to serving individual astronomers, the SCCA established a Web site for general use that provides hypertext links to selected on-line public-domain statistical software and services. The StatCodes site (www.astro.psu.edu/statcodes) provides over 200 links in the areas of: Bayesian statistics; censored and truncated data; correlation and regression, density estimation and smoothing, general statistics packages and information; image analysis; interactive Web tools; multivariate analysis; multivariate clustering and classification; nonparametric analysis; software written by astronomers; spatial statistics; statistical distributions; time series analysis; and visualization tools. StatCodes has received a remarkable high and constant hit rate of 250 hits/week (over 10,000/year) since its inception in mid-1997. It is of interest to scientists both within and outside of astronomy. The most popular sections are multivariate techniques, image analysis, and time series analysis. Hundreds of copies of the ASURV, SLOPES and CENS-TAU codes developed by SCCA scientists were also downloaded from the StatCodes site. In addition to formal SCCA duties, SCCA scientists continued a variety of related activities in astrostatistics, including refereeing of statistically oriented papers submitted to the Astrophysical Journal, talks in meetings including Feigelson's talk to science journalists entitled "The reemergence of astrostatistics" at the American Association for the Advancement of Science meeting, and published papers of astrostatistical content.

Are procedures codes in claims data a reliable indicator of intraoperative splenic injury compared with clinical registry data?

PubMed

Stey, Anne M; Ko, Clifford Y; Hall, Bruce Lee; Louie, Rachel; Lawson, Elise H; Gibbons, Melinda M; Zingmond, David S; Russell, Marcia M

2014-08-01

Identifying iatrogenic injuries using existing data sources is important for improved transparency in the occurrence of intraoperative events. There is evidence that procedure codes are reliably recorded in claims data. The objective of this study was to assess whether concurrent splenic procedure codes in patients undergoing colectomy procedures are reliably coded in claims data as compared with clinical registry data. Patients who underwent colectomy procedures in the absence of neoplastic diagnosis codes were identified from American College of Surgeons (ACS) NSQIP data linked with Medicare inpatient claims data file (2005 to 2008). A κ statistic was used to assess coding concordance between ACS NSQIP and Medicare inpatient claims, with ACS NSQIP serving as the reference standard. A total of 11,367 colectomy patients were identified from 212 hospitals. There were 114 patients (1%) who had a concurrent splenic procedure code recorded in either ACS NSQIP or Medicare inpatient claims. There were 7 patients who had a splenic injury diagnosis code recorded in either data source. Agreement of splenic procedure codes between the data sources was substantial (κ statistic 0.72; 95% CI, 0.64-0.79). Medicare inpatient claims identified 81% of the splenic procedure codes recorded in ACS NSQIP, and 99% of the patients without a splenic procedure code. It is feasible to use Medicare claims data to identify splenic injuries occurring during colectomy procedures, as claims data have moderate sensitivity and excellent specificity for capturing concurrent splenic procedure codes compared with ACS NSQIP. Copyright © 2014 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

An overview of data acquisition, signal coding and data analysis techniques for MST radars

NASA Technical Reports Server (NTRS)

Rastogi, P. K.

1986-01-01

An overview is given of the data acquisition, signal processing, and data analysis techniques that are currently in use with high power MST/ST (mesosphere stratosphere troposphere/stratosphere troposphere) radars. This review supplements the works of Rastogi (1983) and Farley (1984) presented at previous MAP workshops. A general description is given of data acquisition and signal processing operations and they are characterized on the basis of their disparate time scales. Then signal coding, a brief description of frequently used codes, and their limitations are discussed, and finally, several aspects of statistical data processing such as signal statistics, power spectrum and autocovariance analysis, outlier removal techniques are discussed.

Methods for evaluating the predictive accuracy of structural dynamic models

NASA Technical Reports Server (NTRS)

Hasselman, Timothy K.; Chrostowski, Jon D.

1991-01-01

Modeling uncertainty is defined in terms of the difference between predicted and measured eigenvalues and eigenvectors. Data compiled from 22 sets of analysis/test results was used to create statistical databases for large truss-type space structures and both pretest and posttest models of conventional satellite-type space structures. Modeling uncertainty is propagated through the model to produce intervals of uncertainty on frequency response functions, both amplitude and phase. This methodology was used successfully to evaluate the predictive accuracy of several structures, including the NASA CSI Evolutionary Structure tested at Langley Research Center. Test measurements for this structure were within + one-sigma intervals of predicted accuracy for the most part, demonstrating the validity of the methodology and computer code.

The Impact of Measurement Noise in GPA Diagnostic Analysis of a Gas Turbine Engine

NASA Astrophysics Data System (ADS)

Ntantis, Efstratios L.; Li, Y. G.

2013-12-01

The performance diagnostic analysis of a gas turbine is accomplished by estimating a set of internal engine health parameters from available sensor measurements. No physical measuring instruments however can ever completely eliminate the presence of measurement uncertainties. Sensor measurements are often distorted by noise and bias leading to inaccurate estimation results. This paper explores the impact of measurement noise on Gas Turbine GPA analysis. The analysis is demonstrated with a test case where gas turbine performance simulation and diagnostics code TURBOMATCH is used to build a performance model of a model engine similar to Rolls-Royce Trent 500 turbofan engine, and carry out the diagnostic analysis with the presence of different levels of measurement noise. Conclusively, to improve the reliability of the diagnostic results, a statistical analysis of the data scattering caused by sensor uncertainties is made. The diagnostic tool used to deal with the statistical analysis of measurement noise impact is a model-based method utilizing a non-linear GPA.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaurov, Alexander A., E-mail: kaurov@uchicago.edu

The methods for studying the epoch of cosmic reionization vary from full radiative transfer simulations to purely analytical models. While numerical approaches are computationally expensive and are not suitable for generating many mock catalogs, analytical methods are based on assumptions and approximations. We explore the interconnection between both methods. First, we ask how the analytical framework of excursion set formalism can be used for statistical analysis of numerical simulations and visual representation of the morphology of ionization fronts. Second, we explore the methods of training the analytical model on a given numerical simulation. We present a new code which emergedmore » from this study. Its main application is to match the analytical model with a numerical simulation. Then, it allows one to generate mock reionization catalogs with volumes exceeding the original simulation quickly and computationally inexpensively, meanwhile reproducing large-scale statistical properties. These mock catalogs are particularly useful for cosmic microwave background polarization and 21 cm experiments, where large volumes are required to simulate the observed signal.« less

The opponent channel population code of sound location is an efficient representation of natural binaural sounds.

PubMed

Młynarski, Wiktor

2015-05-01

In mammalian auditory cortex, sound source position is represented by a population of broadly tuned neurons whose firing is modulated by sounds located at all positions surrounding the animal. Peaks of their tuning curves are concentrated at lateral position, while their slopes are steepest at the interaural midline, allowing for the maximum localization accuracy in that area. These experimental observations contradict initial assumptions that the auditory space is represented as a topographic cortical map. It has been suggested that a "panoramic" code has evolved to match specific demands of the sound localization task. This work provides evidence suggesting that properties of spatial auditory neurons identified experimentally follow from a general design principle- learning a sparse, efficient representation of natural stimuli. Natural binaural sounds were recorded and served as input to a hierarchical sparse-coding model. In the first layer, left and right ear sounds were separately encoded by a population of complex-valued basis functions which separated phase and amplitude. Both parameters are known to carry information relevant for spatial hearing. Monaural input converged in the second layer, which learned a joint representation of amplitude and interaural phase difference. Spatial selectivity of each second-layer unit was measured by exposing the model to natural sound sources recorded at different positions. Obtained tuning curves match well tuning characteristics of neurons in the mammalian auditory cortex. This study connects neuronal coding of the auditory space with natural stimulus statistics and generates new experimental predictions. Moreover, results presented here suggest that cortical regions with seemingly different functions may implement the same computational strategy-efficient coding.

The fast non-LTE code DEDALE

NASA Astrophysics Data System (ADS)

Gilleron, Franck; Piron, Robin

2015-12-01

We present Dédale, a fast code implementing a simplified non-local-thermodynamic-equilibrium (NLTE) plasma model. In this approach, the stationary collisional-radiative rates equations are solved for a set of well-chosen Layzer complexes in order to determine the ion state populations. The electronic structure is approximated using the screened hydrogenic model (SHM) of More with relativistic corrections. The radiative and collisional cross-sections are based on Kramers and Van Regemorter formula, respectively, which are extrapolated to derive analytical expressions for all the rates. The latter are improved thereafter using Gaunt factors or more accurate tabulated data. Special care is taken for dielectronic rates which are compared and rescaled with quantum calculations from the Averroès code. The emissivity and opacity spectra are calculated under the same assumptions as for the radiative rates, either in a detailed manner by summing the transitions between each pair of complexes, or in a coarser statistical way by summing the one-electron transitions averaged over the complexes. Optionally, nℓ-splitting can be accounted for using a WKB approach in an approximate potential reconstructed analytically from the screened charges. It is also possible to improve the spectra by replacing some transition arrays with more accurate data tabulated using the SCO-RCG or FAC codes. This latter option is particularly useful for K-shell emission spectroscopy. The Dédale code was used to submit neon and tungsten cases in the last NLTE-8 workshop (Santa Fe, November 4-8, 2013). Some of these results are presented, as well as comparisons with Averroès calculations.

TU-AB-BRC-10: Modeling of Radiotherapy Linac Source Terms Using ARCHER Monte Carlo Code: Performance Comparison of GPU and MIC Computing Accelerators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, T; Lin, H; Xu, X

Purpose: (1) To perform phase space (PS) based source modeling for Tomotherapy and Varian TrueBeam 6 MV Linacs, (2) to examine the accuracy and performance of the ARCHER Monte Carlo code on a heterogeneous computing platform with Many Integrated Core coprocessors (MIC, aka Xeon Phi) and GPUs, and (3) to explore the software micro-optimization methods. Methods: The patient-specific source of Tomotherapy and Varian TrueBeam Linacs was modeled using the PS approach. For the helical Tomotherapy case, the PS data were calculated in our previous study (Su et al. 2014 41(7) Medical Physics). For the single-view Varian TrueBeam case, we analyticallymore » derived them from the raw patient-independent PS data in IAEA’s database, partial geometry information of the jaw and MLC as well as the fluence map. The phantom was generated from DICOM images. The Monte Carlo simulation was performed by ARCHER-MIC and GPU codes, which were benchmarked against a modified parallel DPM code. Software micro-optimization was systematically conducted, and was focused on SIMD vectorization of tight for-loops and data prefetch, with the ultimate goal of increasing 512-bit register utilization and reducing memory access latency. Results: Dose calculation was performed for two clinical cases, a Tomotherapy-based prostate cancer treatment and a TrueBeam-based left breast treatment. ARCHER was verified against the DPM code. The statistical uncertainty of the dose to the PTV was less than 1%. Using double-precision, the total wall time of the multithreaded CPU code on a X5650 CPU was 339 seconds for the Tomotherapy case and 131 seconds for the TrueBeam, while on 3 5110P MICs it was reduced to 79 and 59 seconds, respectively. The single-precision GPU code on a K40 GPU took 45 seconds for the Tomotherapy dose calculation. Conclusion: We have extended ARCHER, the MIC and GPU-based Monte Carlo dose engine to Tomotherapy and Truebeam dose calculations.« less

General RMP Guidance - Appendix B: Selected NAICS Codes

EPA Pesticide Factsheets

This appendix contains a list of selected 2002 North American Industry Classification System (NAICS) codes used by Federal statistical agencies, in designating business types or functions in categories such as farming, manufacturing, and waste management.

Comparison and correlation of Simple Sequence Repeats distribution in genomes of Brucella species

PubMed Central

Kiran, Jangampalli Adi Pradeep; Chakravarthi, Veeraraghavulu Praveen; Kumar, Yellapu Nanda; Rekha, Somesula Swapna; Kruti, Srinivasan Shanthi; Bhaskar, Matcha

2011-01-01

Computational genomics is one of the important tools to understand the distribution of closely related genomes including simple sequence repeats (SSRs) in an organism, which gives valuable information regarding genetic variations. The central objective of the present study was to screen the SSRs distributed in coding and non-coding regions among different human Brucella species which are involved in a range of pathological disorders. Computational analysis of the SSRs in the Brucella indicates few deviations from expected random models. Statistical analysis also reveals that tri-nucleotide SSRs are overrepresented and tetranucleotide SSRs underrepresented in Brucella genomes. From the data, it can be suggested that over expressed tri-nucleotide SSRs in genomic and coding regions might be responsible in the generation of functional variation of proteins expressed which in turn may lead to different pathogenicity, virulence determinants, stress response genes, transcription regulators and host adaptation proteins of Brucella genomes. Abbreviations SSRs - Simple Sequence Repeats, ORFs - Open Reading Frames. PMID:21738309

Code System for Performance Assessment Ground-water Analysis for Low-level Nuclear Waste.

DOE Office of Scientific and Technical Information (OSTI.GOV)

MATTHEW,; KOZAK, W.

1994-02-09

Version 00 The PAGAN code system is a part of the performance assessment methodology developed for use by the U. S. Nuclear Regulatory Commission in evaluating license applications for low-level waste disposal facilities. In this methodology, PAGAN is used as one candidate approach for analysis of the ground-water pathway. PAGAN, Version 1.1 has the capability to model the source term, vadose-zone transport, and aquifer transport of radionuclides from a waste disposal unit. It combines the two codes SURFACE and DISPERSE which are used as semi-analytical solutions to the convective-dispersion equation. This system uses menu driven input/out for implementing a simplemore » ground-water transport analysis and incorporates statistical uncertainty functions for handling data uncertainties. The output from PAGAN includes a time- and location-dependent radionuclide concentration at a well in the aquifer, or a time- and location-dependent radionuclide flux into a surface-water body.« less

Development code for sensitivity and uncertainty analysis of input on the MCNPX for neutronic calculation in PWR core

NASA Astrophysics Data System (ADS)

Hartini, Entin; Andiwijayakusuma, Dinan

2014-09-01

This research was carried out on the development of code for uncertainty analysis is based on a statistical approach for assessing the uncertainty input parameters. In the butn-up calculation of fuel, uncertainty analysis performed for input parameters fuel density, coolant density and fuel temperature. This calculation is performed during irradiation using Monte Carlo N-Particle Transport. The Uncertainty method based on the probabilities density function. Development code is made in python script to do coupling with MCNPX for criticality and burn-up calculations. Simulation is done by modeling the geometry of PWR terrace, with MCNPX on the power 54 MW with fuel type UO2 pellets. The calculation is done by using the data library continuous energy cross-sections ENDF / B-VI. MCNPX requires nuclear data in ACE format. Development of interfaces for obtaining nuclear data in the form of ACE format of ENDF through special process NJOY calculation to temperature changes in a certain range.

Development code for sensitivity and uncertainty analysis of input on the MCNPX for neutronic calculation in PWR core

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hartini, Entin, E-mail: entin@batan.go.id; Andiwijayakusuma, Dinan, E-mail: entin@batan.go.id

2014-09-30

This research was carried out on the development of code for uncertainty analysis is based on a statistical approach for assessing the uncertainty input parameters. In the butn-up calculation of fuel, uncertainty analysis performed for input parameters fuel density, coolant density and fuel temperature. This calculation is performed during irradiation using Monte Carlo N-Particle Transport. The Uncertainty method based on the probabilities density function. Development code is made in python script to do coupling with MCNPX for criticality and burn-up calculations. Simulation is done by modeling the geometry of PWR terrace, with MCNPX on the power 54 MW with fuelmore » type UO2 pellets. The calculation is done by using the data library continuous energy cross-sections ENDF / B-VI. MCNPX requires nuclear data in ACE format. Development of interfaces for obtaining nuclear data in the form of ACE format of ENDF through special process NJOY calculation to temperature changes in a certain range.« less

Acoustic Prediction State of the Art Assessment

NASA Technical Reports Server (NTRS)

Dahl, Milo D.

2007-01-01

The acoustic assessment task for both the Subsonic Fixed Wing and the Supersonic projects under NASA s Fundamental Aeronautics Program was designed to assess the current state-of-the-art in noise prediction capability and to establish baselines for gauging future progress. The documentation of our current capabilities included quantifying the differences between predictions of noise from computer codes and measurements of noise from experimental tests. Quantifying the accuracy of both the computed and experimental results further enhanced the credibility of the assessment. This presentation gives sample results from codes representative of NASA s capabilities in aircraft noise prediction both for systems and components. These include semi-empirical, statistical, analytical, and numerical codes. System level results are shown for both aircraft and engines. Component level results are shown for a landing gear prototype, for fan broadband noise, for jet noise from a subsonic round nozzle, and for propulsion airframe aeroacoustic interactions. Additional results are shown for modeling of the acoustic behavior of duct acoustic lining and the attenuation of sound in lined ducts with flow.

Percolation technique for galaxy clustering

NASA Technical Reports Server (NTRS)

Klypin, Anatoly; Shandarin, Sergei F.

1993-01-01

We study percolation in mass and galaxy distributions obtained in 3D simulations of the CDM, C + HDM, and the power law (n = -1) models in the Omega = 1 universe. Percolation statistics is used here as a quantitative measure of the degree to which a mass or galaxy distribution is of a filamentary or cellular type. The very fast code used calculates the statistics of clusters along with the direct detection of percolation. We found that the two parameters mu(infinity), characterizing the size of the largest cluster, and mu-squared, characterizing the weighted mean size of all clusters excluding the largest one, are extremely useful for evaluating the percolation threshold. An advantage of using these parameters is their low sensitivity to boundary effects. We show that both the CDM and the C + HDM models are extremely filamentary both in mass and galaxy distribution. The percolation thresholds for the mass distributions are determined.

Anomalous Brownian motion discloses viscoelasticity in the ear's mechanoelectrical-transduction apparatus.

PubMed

Kozlov, Andrei S; Andor-Ardó, Daniel; Hudspeth, A J

2012-02-21

The ear detects sounds so faint that they produce only atomic-scale displacements in the mechanoelectrical transducer, yet thermal noise causes fluctuations larger by an order of magnitude. Explaining how hearing can operate when the magnitude of the noise greatly exceeds that of the signal requires an understanding both of the transducer's micromechanics and of the associated noise. Using microrheology, we characterize the statistics of this noise; exploiting the fluctuation-dissipation theorem, we determine the associated micromechanics. The statistics reveal unusual Brownian motion in which the mean square displacement increases as a fractional power of time, indicating that the mechanisms governing energy dissipation are related to those of energy storage. This anomalous scaling contradicts the canonical model of mechanoelectrical transduction, but the results can be explained if the micromechanics incorporates viscoelasticity, a salient characteristic of biopolymers. We amend the canonical model and demonstrate several consequences of viscoelasticity for sensory coding.

Anomalous Brownian motion discloses viscoelasticity in the ear’s mechanoelectrical-transduction apparatus

PubMed Central

Kozlov, Andrei S.; Andor-Ardó, Daniel; Hudspeth, A. J.

2012-01-01

The ear detects sounds so faint that they produce only atomic-scale displacements in the mechanoelectrical transducer, yet thermal noise causes fluctuations larger by an order of magnitude. Explaining how hearing can operate when the magnitude of the noise greatly exceeds that of the signal requires an understanding both of the transducer’s micromechanics and of the associated noise. Using microrheology, we characterize the statistics of this noise; exploiting the fluctuation-dissipation theorem, we determine the associated micromechanics. The statistics reveal unusual Brownian motion in which the mean square displacement increases as a fractional power of time, indicating that the mechanisms governing energy dissipation are related to those of energy storage. This anomalous scaling contradicts the canonical model of mechanoelectrical transduction, but the results can be explained if the micromechanics incorporates viscoelasticity, a salient characteristic of biopolymers. We amend the canonical model and demonstrate several consequences of viscoelasticity for sensory coding. PMID:22328158

UCODE_2005 and six other computer codes for universal sensitivity analysis, calibration, and uncertainty evaluation constructed using the JUPITER API

USGS Publications Warehouse

Poeter, Eileen E.; Hill, Mary C.; Banta, Edward R.; Mehl, Steffen; Christensen, Steen

2006-01-01

This report documents the computer codes UCODE_2005 and six post-processors. Together the codes can be used with existing process models to perform sensitivity analysis, data needs assessment, calibration, prediction, and uncertainty analysis. Any process model or set of models can be used; the only requirements are that models have numerical (ASCII or text only) input and output files, that the numbers in these files have sufficient significant digits, that all required models can be run from a single batch file or script, and that simulated values are continuous functions of the parameter values. Process models can include pre-processors and post-processors as well as one or more models related to the processes of interest (physical, chemical, and so on), making UCODE_2005 extremely powerful. An estimated parameter can be a quantity that appears in the input files of the process model(s), or a quantity used in an equation that produces a value that appears in the input files. In the latter situation, the equation is user-defined. UCODE_2005 can compare observations and simulated equivalents. The simulated equivalents can be any simulated value written in the process-model output files or can be calculated from simulated values with user-defined equations. The quantities can be model results, or dependent variables. For example, for ground-water models they can be heads, flows, concentrations, and so on. Prior, or direct, information on estimated parameters also can be considered. Statistics are calculated to quantify the comparison of observations and simulated equivalents, including a weighted least-squares objective function. In addition, data-exchange files are produced that facilitate graphical analysis. UCODE_2005 can be used fruitfully in model calibration through its sensitivity analysis capabilities and its ability to estimate parameter values that result in the best possible fit to the observations. Parameters are estimated using nonlinear regression: a weighted least-squares objective function is minimized with respect to the parameter values using a modified Gauss-Newton method or a double-dogleg technique. Sensitivities needed for the method can be read from files produced by process models that can calculate sensitivities, such as MODFLOW-2000, or can be calculated by UCODE_2005 using a more general, but less accurate, forward- or central-difference perturbation technique. Problems resulting from inaccurate sensitivities and solutions related to the perturbation techniques are discussed in the report. Statistics are calculated and printed for use in (1) diagnosing inadequate data and identifying parameters that probably cannot be estimated; (2) evaluating estimated parameter values; and (3) evaluating how well the model represents the simulated processes. Results from UCODE_2005 and codes RESIDUAL_ANALYSIS and RESIDUAL_ANALYSIS_ADV can be used to evaluate how accurately the model represents the processes it simulates. Results from LINEAR_UNCERTAINTY can be used to quantify the uncertainty of model simulated values if the model is sufficiently linear. Results from MODEL_LINEARITY and MODEL_LINEARITY_ADV can be used to evaluate model linearity and, thereby, the accuracy of the LINEAR_UNCERTAINTY results. UCODE_2005 can also be used to calculate nonlinear confidence and predictions intervals, which quantify the uncertainty of model simulated values when the model is not linear. CORFAC_PLUS can be used to produce factors that allow intervals to account for model intrinsic nonlinearity and small-scale variations in system characteristics that are not explicitly accounted for in the model or the observation weighting. The six post-processing programs are independent of UCODE_2005 and can use the results of other programs that produce the required data-exchange files. UCODE_2005 and the other six codes are intended for use on any computer operating system. The programs con

Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models.

PubMed

Mereghetti, Paolo; Maccari, Giuseppe; Spampinato, Giulia Lia Beatrice; Tozzini, Valentina

2016-08-25

The increasing trend in the recent literature on coarse grained (CG) models testifies their impact in the study of complex systems. However, the CG model landscape is variegated: even considering a given resolution level, the force fields are very heterogeneous and optimized with very different parametrization procedures. Along the road for standardization of CG models for biopolymers, here we describe a strategy to aid building and optimization of statistics based analytical force fields and its implementation in the software package AsParaGS (Assisted Parameterization platform for coarse Grained modelS). Our method is based on the use and optimization of analytical potentials, optimized by targeting internal variables statistical distributions by means of the combination of different algorithms (i.e., relative entropy driven stochastic exploration of the parameter space and iterative Boltzmann inversion). This allows designing a custom model that endows the force field terms with a physically sound meaning. Furthermore, the level of transferability and accuracy can be tuned through the choice of statistical data set composition. The method-illustrated by means of applications to helical polypeptides-also involves the analysis of two and three variable distributions, and allows handling issues related to the FF term correlations. AsParaGS is interfaced with general-purpose molecular dynamics codes and currently implements the "minimalist" subclass of CG models (i.e., one bead per amino acid, Cα based). Extensions to nucleic acids and different levels of coarse graining are in the course.

Performance Comparison of NAMI DANCE and FLOW-3D® Models in Tsunami Propagation, Inundation and Currents using NTHMP Benchmark Problems

NASA Astrophysics Data System (ADS)

Velioglu Sogut, Deniz; Yalciner, Ahmet Cevdet

2018-06-01

Field observations provide valuable data regarding nearshore tsunami impact, yet only in inundation areas where tsunami waves have already flooded. Therefore, tsunami modeling is essential to understand tsunami behavior and prepare for tsunami inundation. It is necessary that all numerical models used in tsunami emergency planning be subject to benchmark tests for validation and verification. This study focuses on two numerical codes, NAMI DANCE and FLOW-3D®, for validation and performance comparison. NAMI DANCE is an in-house tsunami numerical model developed by the Ocean Engineering Research Center of Middle East Technical University, Turkey and Laboratory of Special Research Bureau for Automation of Marine Research, Russia. FLOW-3D® is a general purpose computational fluid dynamics software, which was developed by scientists who pioneered in the design of the Volume-of-Fluid technique. The codes are validated and their performances are compared via analytical, experimental and field benchmark problems, which are documented in the ``Proceedings and Results of the 2011 National Tsunami Hazard Mitigation Program (NTHMP) Model Benchmarking Workshop'' and the ``Proceedings and Results of the NTHMP 2015 Tsunami Current Modeling Workshop". The variations between the numerical solutions of these two models are evaluated through statistical error analysis.

A data compression technique for synthetic aperture radar images

NASA Technical Reports Server (NTRS)

Frost, V. S.; Minden, G. J.

1986-01-01

A data compression technique is developed for synthetic aperture radar (SAR) imagery. The technique is based on an SAR image model and is designed to preserve the local statistics in the image by an adaptive variable rate modification of block truncation coding (BTC). A data rate of approximately 1.6 bit/pixel is achieved with the technique while maintaining the image quality and cultural (pointlike) targets. The algorithm requires no large data storage and is computationally simple.

Population Synthesis of Radio and Gamma-ray Pulsars using the Maximum Likelihood Approach

NASA Astrophysics Data System (ADS)

Billman, Caleb; Gonthier, P. L.; Harding, A. K.

2012-01-01

We present the results of a pulsar population synthesis of normal pulsars from the Galactic disk using a maximum likelihood method. We seek to maximize the likelihood of a set of parameters in a Monte Carlo population statistics code to better understand their uncertainties and the confidence region of the model's parameter space. The maximum likelihood method allows for the use of more applicable Poisson statistics in the comparison of distributions of small numbers of detected gamma-ray and radio pulsars. Our code simulates pulsars at birth using Monte Carlo techniques and evolves them to the present assuming initial spatial, kick velocity, magnetic field, and period distributions. Pulsars are spun down to the present and given radio and gamma-ray emission characteristics. We select measured distributions of radio pulsars from the Parkes Multibeam survey and Fermi gamma-ray pulsars to perform a likelihood analysis of the assumed model parameters such as initial period and magnetic field, and radio luminosity. We present the results of a grid search of the parameter space as well as a search for the maximum likelihood using a Markov Chain Monte Carlo method. We express our gratitude for the generous support of the Michigan Space Grant Consortium, of the National Science Foundation (REU and RUI), the NASA Astrophysics Theory and Fundamental Program and the NASA Fermi Guest Investigator Program.

Committee Representation and Medicare Reimbursements-An Examination of the Resource-Based Relative Value Scale.

PubMed

Gao, Y Nina

2018-04-06

The Resource-Based Relative Value Scale Update Committee (RUC) submits recommended reimbursement values for physician work (wRVUs) under Medicare Part B. The RUC includes rotating representatives from medical specialties. To identify changes in physician reimbursements associated with RUC rotating seat representation. Relative Value Scale Update Committee members 1994-2013; Medicare Part B Relative Value Scale 1994-2013; Physician/Supplier Procedure Summary Master File 2007; Part B National Summary Data File 2000-2011. I match service and procedure codes to specialties using 2007 Medicare billing data. Subsequently, I model wRVUs as a function of RUC rotating committee representation and level of code specialization. An annual RUC rotating seat membership is associated with a statistically significant 3-5 percent increase in Medicare expenditures for codes billed to that specialty. For codes that are performed by a small number of physicians, the association between reimbursement and rotating subspecialty representation is positive, 0.177 (SE = 0.024). For codes that are performed by a large number of physicians, the association is negative, -0.183 (SE = 0.026). Rotating representation on the RUC is correlated with overall reimbursement rates. The resulting differential changes may exacerbate existing reimbursement discrepancies between generalist and specialist practitioners. © Health Research and Educational Trust.

Investigating the Use of Quick Response Codes in the Gross Anatomy Laboratory

ERIC Educational Resources Information Center

Traser, Courtney J.; Hoffman, Leslie A.; Seifert, Mark F.; Wilson, Adam B.

2015-01-01

The use of quick response (QR) codes within undergraduate university courses is on the rise, yet literature concerning their use in medical education is scant. This study examined student perceptions on the usefulness of QR codes as learning aids in a medical gross anatomy course, statistically analyzed whether this learning aid impacted student…

Deciphering the Diagnostic Codes: A Guide for School Counselors. Practical Skills for Counselors.

ERIC Educational Resources Information Center

Jones, W. Paul

Although school counselors have more contact with children and adolescents than most other human service professionals, they are frequently left out of discussions on diagnostic coding. Ways in which school counselors can use the codes in the Diagnostic and Statistical Manual of Mental Disorders IV (DSM-IV) are explored in this text. The book…

Physical and Hydrological Meaning of the Spectral Information from Hydrodynamic Signals at Karst Springs

NASA Astrophysics Data System (ADS)

Dufoyer, A.; Lecoq, N.; Massei, N.; Marechal, J. C.

2017-12-01

Physics-based modeling of karst systems remains almost impossible without enough accurate information about the inner physical characteristics. Usually, the only available hydrodynamic information is the flow rate at the karst outlet. Numerous works in the past decades have used and proven the usefulness of time-series analysis and spectral techniques applied to spring flow, precipitations or even physico-chemical parameters, for interpreting karst hydrological functioning. However, identifying or interpreting the karst systems physical features that control statistical or spectral characteristics of spring flow variations is still challenging, not to say sometimes controversial. The main objective of this work is to determine how the statistical and spectral characteristics of the hydrodynamic signal at karst springs can be related to inner physical and hydraulic properties. In order to address this issue, we undertake an empirical approach based on the use of both distributed and physics-based models, and on synthetic systems responses. The first step of the research is to conduct a sensitivity analysis of time-series/spectral methods to karst hydraulic and physical properties. For this purpose, forward modeling of flow through several simple, constrained and synthetic cases in response to precipitations is undertaken. It allows us to quantify how the statistical and spectral characteristics of flow at the outlet are sensitive to changes (i) in conduit geometries, and (ii) in hydraulic parameters of the system (matrix/conduit exchange rate, matrix hydraulic conductivity and storativity). The flow differential equations resolved by MARTHE, a computer code developed by the BRGM, allows karst conduits modeling. From signal processing on simulated spring responses, we hope to determine if specific frequencies are always modified, thanks to Fourier series and multi-resolution analysis. We also hope to quantify which parameters are the most variable with auto-correlation analysis: first results seem to show higher variations due to conduit conductivity than the ones due to matrix/conduit exchange rate. Future steps will be using another computer code, based on double-continuum approach and allowing turbulent conduit flow, and modeling a natural system.

Applied Mathematics in EM Studies with Special Emphasis on an Uncertainty Quantification and 3-D Integral Equation Modelling

NASA Astrophysics Data System (ADS)

Pankratov, Oleg; Kuvshinov, Alexey

2016-01-01

Despite impressive progress in the development and application of electromagnetic (EM) deterministic inverse schemes to map the 3-D distribution of electrical conductivity within the Earth, there is one question which remains poorly addressed—uncertainty quantification of the recovered conductivity models. Apparently, only an inversion based on a statistical approach provides a systematic framework to quantify such uncertainties. The Metropolis-Hastings (M-H) algorithm is the most popular technique for sampling the posterior probability distribution that describes the solution of the statistical inverse problem. However, all statistical inverse schemes require an enormous amount of forward simulations and thus appear to be extremely demanding computationally, if not prohibitive, if a 3-D set up is invoked. This urges development of fast and scalable 3-D modelling codes which can run large-scale 3-D models of practical interest for fractions of a second on high-performance multi-core platforms. But, even with these codes, the challenge for M-H methods is to construct proposal functions that simultaneously provide a good approximation of the target density function while being inexpensive to be sampled. In this paper we address both of these issues. First we introduce a variant of the M-H method which uses information about the local gradient and Hessian of the penalty function. This, in particular, allows us to exploit adjoint-based machinery that has been instrumental for the fast solution of deterministic inverse problems. We explain why this modification of M-H significantly accelerates sampling of the posterior probability distribution. In addition we show how Hessian handling (inverse, square root) can be made practicable by a low-rank approximation using the Lanczos algorithm. Ultimately we discuss uncertainty analysis based on stochastic inversion results. In addition, we demonstrate how this analysis can be performed within a deterministic approach. In the second part, we summarize modern trends in the development of efficient 3-D EM forward modelling schemes with special emphasis on recent advances in the integral equation approach.

Death Certification Errors and the Effect on Mortality Statistics.

PubMed

McGivern, Lauri; Shulman, Leanne; Carney, Jan K; Shapiro, Steven; Bundock, Elizabeth

Errors in cause and manner of death on death certificates are common and affect families, mortality statistics, and public health research. The primary objective of this study was to characterize errors in the cause and manner of death on death certificates completed by non-Medical Examiners. A secondary objective was to determine the effects of errors on national mortality statistics. We retrospectively compared 601 death certificates completed between July 1, 2015, and January 31, 2016, from the Vermont Electronic Death Registration System with clinical summaries from medical records. Medical Examiners, blinded to original certificates, reviewed summaries, generated mock certificates, and compared mock certificates with original certificates. They then graded errors using a scale from 1 to 4 (higher numbers indicated increased impact on interpretation of the cause) to determine the prevalence of minor and major errors. They also compared International Classification of Diseases, 10th Revision (ICD-10) codes on original certificates with those on mock certificates. Of 601 original death certificates, 319 (53%) had errors; 305 (51%) had major errors; and 59 (10%) had minor errors. We found no significant differences by certifier type (physician vs nonphysician). We did find significant differences in major errors in place of death ( P < .001). Certificates for deaths occurring in hospitals were more likely to have major errors than certificates for deaths occurring at a private residence (59% vs 39%, P < .001). A total of 580 (93%) death certificates had a change in ICD-10 codes between the original and mock certificates, of which 348 (60%) had a change in the underlying cause-of-death code. Error rates on death certificates in Vermont are high and extend to ICD-10 coding, thereby affecting national mortality statistics. Surveillance and certifier education must expand beyond local and state efforts. Simplifying and standardizing underlying literal text for cause of death may improve accuracy, decrease coding errors, and improve national mortality statistics.

Application of survival analysis methodology to the quantitative analysis of LC-MS proteomics data.

PubMed

Tekwe, Carmen D; Carroll, Raymond J; Dabney, Alan R

2012-08-01

Protein abundance in quantitative proteomics is often based on observed spectral features derived from liquid chromatography mass spectrometry (LC-MS) or LC-MS/MS experiments. Peak intensities are largely non-normal in distribution. Furthermore, LC-MS-based proteomics data frequently have large proportions of missing peak intensities due to censoring mechanisms on low-abundance spectral features. Recognizing that the observed peak intensities detected with the LC-MS method are all positive, skewed and often left-censored, we propose using survival methodology to carry out differential expression analysis of proteins. Various standard statistical techniques including non-parametric tests such as the Kolmogorov-Smirnov and Wilcoxon-Mann-Whitney rank sum tests, and the parametric survival model and accelerated failure time-model with log-normal, log-logistic and Weibull distributions were used to detect any differentially expressed proteins. The statistical operating characteristics of each method are explored using both real and simulated datasets. Survival methods generally have greater statistical power than standard differential expression methods when the proportion of missing protein level data is 5% or more. In particular, the AFT models we consider consistently achieve greater statistical power than standard testing procedures, with the discrepancy widening with increasing missingness in the proportions. The testing procedures discussed in this article can all be performed using readily available software such as R. The R codes are provided as supplemental materials. ctekwe@stat.tamu.edu.

Radiation shielding quality assurance

NASA Astrophysics Data System (ADS)

Um, Dallsun

For the radiation shielding quality assurance, the validity and reliability of the neutron transport code MCNP, which is now one of the most widely used radiation shielding analysis codes, were checked with lot of benchmark experiments. And also as a practical example, follows were performed in this thesis. One integral neutron transport experiment to measure the effect of neutron streaming in iron and void was performed with Dog-Legged Void Assembly in Knolls Atomic Power Laboratory in 1991. Neutron flux was measured six different places with the methane detectors and a BF-3 detector. The main purpose of the measurements was to provide benchmark against which various neutron transport calculation tools could be compared. Those data were used in verification of Monte Carlo Neutron & Photon Transport Code, MCNP, with the modeling for that. Experimental results and calculation results were compared in both ways, as the total integrated value of neutron fluxes along neutron energy range from 10 KeV to 2 MeV and as the neutron spectrum along with neutron energy range. Both results are well matched with the statistical error +/-20%. MCNP results were also compared with those of TORT, a three dimensional discrete ordinates code which was developed by Oak Ridge National Laboratory. MCNP results are superior to the TORT results at all detector places except one. This means that MCNP is proved as a very powerful tool for the analysis of neutron transport through iron & air and further it could be used as a powerful tool for the radiation shielding analysis. For one application of the analysis of variance (ANOVA) to neutron and gamma transport problems, uncertainties for the calculated values of critical K were evaluated as in the ANOVA on statistical data.

National Variation in Costs and Mortality for Leukodystrophy Patients in U.S. Children’s Hospitals

PubMed Central

Brimley, Cameron J; Lopez, Jonathan; van Haren, Keith; Wilkes, Jacob; Sheng, Xiaoming; Nelson, Clint; Korgenski, E. Kent; Srivastava, Rajendu; Bonkowsky, Joshua L.

2013-01-01

Background Inherited leukodystrophies are progressive, debilitating neurological disorders with few treatment options and high mortality rates. Our objective was to determine national variation in the costs for leukodystrophy patients, and to evaluate differences in their care. Methods We developed an algorithm to identify inherited leukodystrophy patients in de-identified data sets using a recursive tree model based on ICD-9 CM diagnosis and procedure charge codes. Validation of the algorithm was performed independently at two institutions, and with data from the Pediatric Health Information System (PHIS) of 43 U.S. children’s hospitals, for a seven year time period, 2004–2010. Results A recursive algorithm was developed and validated, based on six ICD-9 codes and one procedure code, that had a sensitivity up to 90% (range 61–90%) and a specificity up to 99% (range 53–99%) for identifying inherited leukodystrophy patients. Inherited leukodystrophy patients comprise 0.4% of admissions to children’s hospitals and 0.7% of costs. Over seven years these patients required $411 million of hospital care, or $131,000/patient. Hospital costs for leukodystrophy patients varied at different institutions, ranging from 2 to 15 times more than the average pediatric patient. There was a statistically significant correlation between higher volume and increased cost efficiency. Increased mortality rates had an inverse relationship with increased patient volume that was not statistically significant. Conclusions We developed and validated a code-based algorithm for identifying leukodystrophy patients in deidentified national datasets. Leukodystrophy patients account for $59 million of costs yearly at children’s hospitals. Our data highlight potential to reduce unwarranted variability and improve patient care. PMID:23953952

Natural image sequences constrain dynamic receptive fields and imply a sparse code.

PubMed

Häusler, Chris; Susemihl, Alex; Nawrot, Martin P

2013-11-06

In their natural environment, animals experience a complex and dynamic visual scenery. Under such natural stimulus conditions, neurons in the visual cortex employ a spatially and temporally sparse code. For the input scenario of natural still images, previous work demonstrated that unsupervised feature learning combined with the constraint of sparse coding can predict physiologically measured receptive fields of simple cells in the primary visual cortex. This convincingly indicated that the mammalian visual system is adapted to the natural spatial input statistics. Here, we extend this approach to the time domain in order to predict dynamic receptive fields that can account for both spatial and temporal sparse activation in biological neurons. We rely on temporal restricted Boltzmann machines and suggest a novel temporal autoencoding training procedure. When tested on a dynamic multi-variate benchmark dataset this method outperformed existing models of this class. Learning features on a large dataset of natural movies allowed us to model spatio-temporal receptive fields for single neurons. They resemble temporally smooth transformations of previously obtained static receptive fields and are thus consistent with existing theories. A neuronal spike response model demonstrates how the dynamic receptive field facilitates temporal and population sparseness. We discuss the potential mechanisms and benefits of a spatially and temporally sparse representation of natural visual input. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

HydroApps: An R package for statistical simulation to use in regional analysis

NASA Astrophysics Data System (ADS)

Ganora, D.

2013-12-01

The HydroApps package is a newborn R extension initially developed to support the use of a recent model for flood frequency estimation developed for applications in Northwestern Italy; it also contains some general tools for regional analyses and can be easily extended to include other statistical models. The package is currently at an experimental level of development. The HydroApps is a corollary of the SSEM project for regional flood frequency analysis, although it was developed independently to support various instances of regional analyses. Its aim is to provide a basis for interplay between statistical simulation and practical operational use. In particular, the main module of the package deals with the building of the confidence bands of flood frequency curves expressed by means of their L-moments. Other functions include pre-processing and visualization of hydrologic time series, analysis of the optimal design-flood under uncertainty, but also tools useful in water resources management for the estimation of flow duration curves and their sensitivity to water withdrawals. Particular attention is devoted to the code granularity, i.e. the level of detail and aggregation of the code: a greater detail means more low-level functions, which entails more flexibility but reduces the ease of use for practical use. A balance between detail and simplicity is necessary and can be resolved with appropriate wrapping functions and specific help pages for each working block. From a more general viewpoint, the package has not really and user-friendly interface, but runs on multiple operating systems and it's easy to update, as many other open-source projects., The HydroApps functions and their features are reported in order to share ideas and materials to improve the ';technological' and information transfer between scientist communities and final users like policy makers.

MIRACAL: A mission radiation calculation program for analysis of lunar and interplanetary missions

NASA Technical Reports Server (NTRS)

Nealy, John E.; Striepe, Scott A.; Simonsen, Lisa C.

1992-01-01

A computational procedure and data base are developed for manned space exploration missions for which estimates are made for the energetic particle fluences encountered and the resulting dose equivalent incurred. The data base includes the following options: statistical or continuum model for ordinary solar proton events, selection of up to six large proton flare spectra, and galactic cosmic ray fluxes for elemental nuclei of charge numbers 1 through 92. The program requires an input trajectory definition information and specifications of optional parameters, which include desired spectral data and nominal shield thickness. The procedure may be implemented as an independent program or as a subroutine in trajectory codes. This code should be most useful in mission optimization and selection studies for which radiation exposure is of special importance.

Online Tools for Astronomy and Cosmochemistry

NASA Technical Reports Server (NTRS)

Meyer, B. S.

2005-01-01

Over the past year, the Webnucleo Group at Clemson University has been developing a web site with a number of interactive online tools for astronomy and cosmochemistry applications. The site uses SHP (Simplified Hypertext Preprocessor), which, because of its flexibility, allows us to embed almost any computer language into our web pages. For a description of SHP, please see http://www.joeldenny.com/ At our web site, an internet user may mine large and complex data sets, such as our stellar evolution models, and make graphs or tables of the results. The user may also run some of our detailed nuclear physics and astrophysics codes, such as our nuclear statistical equilibrium code, which is written in fortran and C. Again, the user may make graphs and tables and download the results.

GPU acceleration of the Locally Selfconsistent Multiple Scattering code for first principles calculation of the ground state and statistical physics of materials

NASA Astrophysics Data System (ADS)

Eisenbach, Markus; Larkin, Jeff; Lutjens, Justin; Rennich, Steven; Rogers, James H.

2017-02-01

The Locally Self-consistent Multiple Scattering (LSMS) code solves the first principles Density Functional theory Kohn-Sham equation for a wide range of materials with a special focus on metals, alloys and metallic nano-structures. It has traditionally exhibited near perfect scalability on massively parallel high performance computer architectures. We present our efforts to exploit GPUs to accelerate the LSMS code to enable first principles calculations of O(100,000) atoms and statistical physics sampling of finite temperature properties. We reimplement the scattering matrix calculation for GPUs with a block matrix inversion algorithm that only uses accelerator memory. Using the Cray XK7 system Titan at the Oak Ridge Leadership Computing Facility we achieve a sustained performance of 14.5PFlop/s and a speedup of 8.6 compared to the CPU only code.

GPU acceleration of the Locally Selfconsistent Multiple Scattering code for first principles calculation of the ground state and statistical physics of materials

DOE PAGES

Eisenbach, Markus; Larkin, Jeff; Lutjens, Justin; ...

2016-07-12

The Locally Self-consistent Multiple Scattering (LSMS) code solves the first principles Density Functional theory Kohn–Sham equation for a wide range of materials with a special focus on metals, alloys and metallic nano-structures. It has traditionally exhibited near perfect scalability on massively parallel high performance computer architectures. In this paper, we present our efforts to exploit GPUs to accelerate the LSMS code to enable first principles calculations of O(100,000) atoms and statistical physics sampling of finite temperature properties. We reimplement the scattering matrix calculation for GPUs with a block matrix inversion algorithm that only uses accelerator memory. Finally, using the Craymore » XK7 system Titan at the Oak Ridge Leadership Computing Facility we achieve a sustained performance of 14.5PFlop/s and a speedup of 8.6 compared to the CPU only code.« less

14 CFR Sec. 19-7 - Passenger origin-destination survey.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Transportation Statistics' Director of Airline Information. (c) A statistically valid sample of light coupons... LAX Salt Lake City NorthwestOperating Carrier NorthwestTicketed Carrier Fare Code Phoenix American...

Wave Propagation in Non-Stationary Statistical Mantle Models at the Global Scale

NASA Astrophysics Data System (ADS)

Meschede, M.; Romanowicz, B. A.

2014-12-01

We study the effect of statistically distributed heterogeneities that are smaller than the resolution of current tomographic models on seismic waves that propagate through the Earth's mantle at teleseismic distances. Current global tomographic models are missing small-scale structure as evidenced by the failure of even accurate numerical synthetics to explain enhanced coda in observed body and surface waveforms. One way to characterize small scale heterogeneity is to construct random models and confront observed coda waveforms with predictions from these models. Statistical studies of the coda typically rely on models with simplified isotropic and stationary correlation functions in Cartesian geometries. We show how to construct more complex random models for the mantle that can account for arbitrary non-stationary and anisotropic correlation functions as well as for complex geometries. Although this method is computationally heavy, model characteristics such as translational, cylindrical or spherical symmetries can be used to greatly reduce the complexity such that this method becomes practical. With this approach, we can create 3D models of the full spherical Earth that can be radially anisotropic, i.e. with different horizontal and radial correlation functions, and radially non-stationary, i.e. with radially varying model power and correlation functions. Both of these features are crucial for a statistical description of the mantle in which structure depends to first order on the spherical geometry of the Earth. We combine different random model realizations of S velocity with current global tomographic models that are robust at long wavelengths (e.g. Meschede and Romanowicz, 2014, GJI submitted), and compute the effects of these hybrid models on the wavefield with a spectral element code (SPECFEM3D_GLOBE). We finally analyze the resulting coda waves for our model selection and compare our computations with observations. Based on these observations, we make predictions about the strength of unresolved small-scale structure and extrinsic attenuation.

Using clinical data to predict high-cost performance coding issues associated with pressure ulcers: a multilevel cohort model.

PubMed

Padula, William V; Gibbons, Robert D; Pronovost, Peter J; Hedeker, Donald; Mishra, Manish K; Makic, Mary Beth F; Bridges, John Fp; Wald, Heidi L; Valuck, Robert J; Ginensky, Adam J; Ursitti, Anthony; Venable, Laura Ruth; Epstein, Ziv; Meltzer, David O

2017-04-01

Hospital-acquired pressure ulcers (HAPUs) have a mortality rate of 11.6%, are costly to treat, and result in Medicare reimbursement penalties. Medicare codes HAPUs according to Agency for Healthcare Research and Quality Patient-Safety Indicator 3 (PSI-03), but they are sometimes inappropriately coded. The objective is to use electronic health records to predict pressure ulcers and to identify coding issues leading to penalties. We evaluated all hospitalized patient electronic medical records at an academic medical center data repository between 2011 and 2014. These data contained patient encounter level demographic variables, diagnoses, prescription drugs, and provider orders. HAPUs were defined by PSI-03: stages III, IV, or unstageable pressure ulcers not present on admission as a secondary diagnosis, excluding cases of paralysis. Random forests reduced data dimensionality. Multilevel logistic regression of patient encounters evaluated associations between covariates and HAPU incidence. The approach produced a sample population of 21 153 patients with 1549 PSI-03 cases. The greatest odds ratio (OR) of HAPU incidence was among patients diagnosed with spinal cord injury (ICD-9 907.2: OR = 14.3; P  < .001), and 71% of spinal cord injuries were not properly coded for paralysis, leading to a PSI-03 flag. Other high ORs included bed confinement (ICD-9 V49.84: OR = 3.1, P  < .001) and provider-ordered pre-albumin lab (OR = 2.5, P  < .001). This analysis identifies spinal cord injuries as high risk for HAPUs and as being often inappropriately coded without paralysis, leading to PSI-03 flags. The resulting statistical model can be tested to predict HAPUs during hospitalization. Inappropriate coding of conditions leads to poor hospital performance measures and Medicare reimbursement penalties. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Genetics of PCOS: A systematic bioinformatics approach to unveil the proteins responsible for PCOS.

PubMed

Panda, Pritam Kumar; Rane, Riya; Ravichandran, Rahul; Singh, Shrinkhla; Panchal, Hetalkumar

2016-06-01

Polycystic ovary syndrome (PCOS) is a hormonal imbalance in women, which causes problems during menstrual cycle and in pregnancy that sometimes results in fatality. Though the genetics of PCOS is not fully understood, early diagnosis and treatment can prevent long-term effects. In this study, we have studied the proteins involved in PCOS and the structural aspects of the proteins that are taken into consideration using computational tools. The proteins involved are modeled using Modeller 9v14 and Ab-initio programs. All the 43 proteins responsible for PCOS were subjected to phylogenetic analysis to identify the relatedness of the proteins. Further, microarray data analysis of PCOS datasets was analyzed that was downloaded from GEO datasets to find the significant protein-coding genes responsible for PCOS, which is an addition to the reported protein-coding genes. Various statistical analyses were done using R programming to get an insight into the structural aspects of PCOS that can be used as drug targets to treat PCOS and other related reproductive diseases.

Probabilistically modeling lava flows with MOLASSES

NASA Astrophysics Data System (ADS)

Richardson, J. A.; Connor, L.; Connor, C.; Gallant, E.

2017-12-01

Modeling lava flows through Cellular Automata methods enables a computationally inexpensive means to quickly forecast lava flow paths and ultimate areal extents. We have developed a lava flow simulator, MOLASSES, that forecasts lava flow inundation over an elevation model from a point source eruption. This modular code can be implemented in a deterministic fashion with given user inputs that will produce a single lava flow simulation. MOLASSES can also be implemented in a probabilistic fashion where given user inputs define parameter distributions that are randomly sampled to create many lava flow simulations. This probabilistic approach enables uncertainty in input data to be expressed in the model results and MOLASSES outputs a probability map of inundation instead of a determined lava flow extent. Since the code is comparatively fast, we use it probabilistically to investigate where potential vents are located that may impact specific sites and areas, as well as the unconditional probability of lava flow inundation of sites or areas from any vent. We have validated the MOLASSES code to community-defined benchmark tests and to the real world lava flows at Tolbachik (2012-2013) and Pico do Fogo (2014-2015). To determine the efficacy of the MOLASSES simulator at accurately and precisely mimicking the inundation area of real flows, we report goodness of fit using both model sensitivity and the Positive Predictive Value, the latter of which is a Bayesian posterior statistic. Model sensitivity is often used in evaluating lava flow simulators, as it describes how much of the lava flow was successfully modeled by the simulation. We argue that the positive predictive value is equally important in determining how good a simulator is, as it describes the percentage of the simulation space that was actually inundated by lava.

The Statistical Analysis Techniques to Support the NGNP Fuel Performance Experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bihn T. Pham; Jeffrey J. Einerson

2010-06-01

This paper describes the development and application of statistical analysis techniques to support the AGR experimental program on NGNP fuel performance. The experiments conducted in the Idaho National Laboratory’s Advanced Test Reactor employ fuel compacts placed in a graphite cylinder shrouded by a steel capsule. The tests are instrumented with thermocouples embedded in graphite blocks and the target quantity (fuel/graphite temperature) is regulated by the He-Ne gas mixture that fills the gap volume. Three techniques for statistical analysis, namely control charting, correlation analysis, and regression analysis, are implemented in the SAS-based NGNP Data Management and Analysis System (NDMAS) for automatedmore » processing and qualification of the AGR measured data. The NDMAS also stores daily neutronic (power) and thermal (heat transfer) code simulation results along with the measurement data, allowing for their combined use and comparative scrutiny. The ultimate objective of this work includes (a) a multi-faceted system for data monitoring and data accuracy testing, (b) identification of possible modes of diagnostics deterioration and changes in experimental conditions, (c) qualification of data for use in code validation, and (d) identification and use of data trends to support effective control of test conditions with respect to the test target. Analysis results and examples given in the paper show the three statistical analysis techniques providing a complementary capability to warn of thermocouple failures. It also suggests that the regression analysis models relating calculated fuel temperatures and thermocouple readings can enable online regulation of experimental parameters (i.e. gas mixture content), to effectively maintain the target quantity (fuel temperature) within a given range.« less

Testing the Porcelli Sawtooth Trigger Module

NASA Astrophysics Data System (ADS)

Bateman, G.; Nave, M. F. F.; Parail, V.

2005-10-01

The Porcelli sawtooth trigger model [1] is implemented as a module for the National Transport Code Collaboration Module Library [2] and is tested using BALDUR and JETTO integrated modeling simulations of JET and other tokamak discharges. Statistical techniques are used to compute the average sawtooth period and the random scatter in sawtooth periods obtained during selected time intervals in the simulations compared with the corresponding statistical measures obtained from experimental data. It is found that the results are affected systematically by the fraction of magnetic reconnection during each sawtooth crash and by the model that is used for transport within the sawtooth mixing region. The physical processes that affect the sawtooth cycle in the simulations are found to involve an interaction among magnetic diffusion, reheating within the sawtooth mixing region, the instabilities that trigger a sawtooth crash in the Porcelli model, and the magnetic reconnection produced by each sawtooth crash. [1] F. Porcelli, et al., Plasma Phys. Contol. Fusion 38 (1996) 2163. [2] A.H. Kritz, et al., Comput. Phys. Commun. 164 (2004) 108; http://w3.pppl.gov/NTCC. Supported by DOE DE-FG02-92-ER-54141.

Rates of profit as correlated sums of random variables

NASA Astrophysics Data System (ADS)

Greenblatt, R. E.

2013-10-01

Profit realization is the dominant feature of market-based economic systems, determining their dynamics to a large extent. Rather than attaining an equilibrium, profit rates vary widely across firms, and the variation persists over time. Differing definitions of profit result in differing empirical distributions. To study the statistical properties of profit rates, I used data from a publicly available database for the US Economy for 2009-2010 (Risk Management Association). For each of three profit rate measures, the sample space consists of 771 points. Each point represents aggregate data from a small number of US manufacturing firms of similar size and type (NAICS code of principal product). When comparing the empirical distributions of profit rates, significant ‘heavy tails’ were observed, corresponding principally to a number of firms with larger profit rates than would be expected from simple models. An apparently novel correlated sum of random variables statistical model was used to model the data. In the case of operating and net profit rates, a number of firms show negative profits (losses), ruling out simple gamma or lognormal distributions as complete models for these data.

Extraction and development of inset models in support of groundwater age calculations for glacial aquifers

USGS Publications Warehouse

Feinstein, Daniel T.; Kauffman, Leon J.; Haserodt, Megan J.; Clark, Brian R.; Juckem, Paul F.

2018-06-22

The U.S. Geological Survey developed a regional model of Lake Michigan Basin (LMB). This report describes the construction of five MODFLOW inset models extracted from the LMB regional model and their application using the particle-tracking code MODPATH to simulate the groundwater age distribution of discharge to wells pumping from glacial deposits. The five study areas of the inset model correspond to 8-digit hydrologic unit code (HUC8) basins. Two of the basins are tributary to Lake Michigan from the east, two are tributary to the lake from the west, and one is just west of the western boundary of the Lake Michigan topographic basin. The inset models inherited many of the inputs to the parent LMB model, including the hydrostratigraphy and layering scheme, the hydraulic conductivity assigned to bedrock layers, recharge distribution, and water use in the form of pumping rates from glacial and bedrock wells. The construction of the inset models entailed modifying some inputs, most notably the grid spacing (reduced from cells 5,000 feet on a side in the parent LMB model to 500 feet on a side in the inset models). The refined grid spacing allowed for more precise location of pumped wells and more detailed simulation of groundwater/surface-water interactions. The glacial hydraulic conductivity values, the top bedrock surface elevation, and the surface-water network input to the inset models also were modified. The inset models are solved using the MODFLOW–NWT code, which allows for more robust handling of conditions in unconfined aquifers than previous versions of MODFLOW. Comparison of the MODFLOW inset models reveals that they incorporate a range of hydrogeologic conditions relative to the glacial part of the flow system, demonstrated by visualization and analysis of model inputs and outputs and reflected in the range of ages generated by MODPATH for existing and hypothetical glacial wells. Certain inputs and outputs are judged to be candidate predictors that, if treated statistically, may be capable of explaining much of the variance in the simulated age metrics. One example of a predictor that model results indicate strongly affects simulated age is the depth of the well open interval below the simulated water table. The strength of this example variable as an overall predictor of groundwater age and its relation to other predictors can be statistically tested through the metamodeling process. In this way the inset models are designed to serve as a training area for metamodels that estimate groundwater age in glacial wells, which in turn will contribute to ongoing studies, under the direction of the U.S. Geological Survey National Water Quality Assessment, of contaminant susceptibility of shallow groundwater across the glacial aquifer system.

Combined proportional and additive residual error models in population pharmacokinetic modelling.

PubMed

Proost, Johannes H

2017-11-15

In pharmacokinetic modelling, a combined proportional and additive residual error model is often preferred over a proportional or additive residual error model. Different approaches have been proposed, but a comparison between approaches is still lacking. The theoretical background of the methods is described. Method VAR assumes that the variance of the residual error is the sum of the statistically independent proportional and additive components; this method can be coded in three ways. Method SD assumes that the standard deviation of the residual error is the sum of the proportional and additive components. Using datasets from literature and simulations based on these datasets, the methods are compared using NONMEM. The different coding of methods VAR yield identical results. Using method SD, the values of the parameters describing residual error are lower than for method VAR, but the values of the structural parameters and their inter-individual variability are hardly affected by the choice of the method. Both methods are valid approaches in combined proportional and additive residual error modelling, and selection may be based on OFV. When the result of an analysis is used for simulation purposes, it is essential that the simulation tool uses the same method as used during analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Communities on the Move: Pedestrian-Oriented Zoning as a Facilitator of Adult Active Travel to Work in the United States.

PubMed

Chriqui, Jamie F; Leider, Julien; Thrun, Emily; Nicholson, Lisa M; Slater, Sandy

2016-01-01

Communities across the United States have been reforming their zoning codes to create pedestrian-friendly neighborhoods with increased street connectivity, mixed use and higher density, open space, transportation infrastructure, and a traditional neighborhood structure. Zoning code reforms include new urbanist zoning such as the SmartCode, form-based codes, transects, transportation and pedestrian-oriented developments, and traditional neighborhood developments. To examine the relationship of zoning code reforms and more active living--oriented zoning provisions with adult active travel to work via walking, biking, or by using public transit. Zoning codes effective as of 2010 were compiled for 3,914 municipal-level jurisdictions located in 471 counties and 2 consolidated cities in 48 states and the District of Columbia, and that collectively covered 72.9% of the U.S. population. Zoning codes were evaluated for the presence of code reform zoning and nine pedestrian-oriented zoning provisions (1 = yes): sidewalks, crosswalks, bike-pedestrian connectivity, street connectivity, bike lanes, bike parking, bike-pedestrian trails/paths, mixed-use development, and other walkability/pedestrian orientation. A zoning scale reflected the number of provisions addressed (out of 10). Five continuous outcome measures were constructed using 2010-2014 American Community Survey municipal-level 5-year estimates to assess the percentage of workers: walking, biking, walking or biking, or taking public transit to work OR engaged in any active travel to work. Regression models controlled for municipal-level socioeconomic characteristics and a GIS-constructed walkability scale and were clustered on county with robust standard errors. Adjusted models indicated that several pedestrian-oriented zoning provisions were statistically associated (p < 0.05 or lower) with increased rates of walking, biking, or engaging in any active travel (walking, biking, or any active travel) to work: code reform zoning, bike parking (street furniture), bike lanes, bike-pedestrian trails/paths, other walkability, mixed-use zoning, and a higher score on the zoning scale. Public transit use was associated with code reform zoning and a number of zoning measures in Southern jurisdictions but not in non-Southern jurisdictions. As jurisdictions revisit their zoning and land use policies, they may want to evaluate the pedestrian-orientation of their zoning codes so that they can plan for pedestrian improvements that will help to encourage active travel to work.

Coding update of the SMFM definition of low risk for cesarean delivery from ICD-9-CM to ICD-10-CM.

PubMed

Armstrong, Joanne; McDermott, Patricia; Saade, George R; Srinivas, Sindhu K

2017-07-01

In 2015, the Society for Maternal-Fetal Medicine developed a low risk for cesarean delivery definition based on administrative claims-based diagnosis codes described by the International Classification of Diseases, Ninth Revision, Clinical Modification. The Society for Maternal-Fetal Medicine definition is a clinical enrichment of 2 available measures from the Joint Commission and the Agency for Healthcare Research and Quality measures. The Society for Maternal-Fetal Medicine measure excludes diagnosis codes that represent clinically relevant risk factors that are absolute or relative contraindications to vaginal birth while retaining diagnosis codes such as labor disorders that are discretionary risk factors for cesarean delivery. The introduction of the International Statistical Classification of Diseases, 10th Revision, Clinical Modification in October 2015 expanded the number of available diagnosis codes and enabled a greater depth and breadth of clinical description. These coding improvements further enhance the clinical validity of the Society for Maternal-Fetal Medicine definition and its potential utility in tracking progress toward the goal of safely lowering the US cesarean delivery rate. This report updates the Society for Maternal-Fetal Medicine definition of low risk for cesarean delivery using International Statistical Classification of Diseases, 10th Revision, Clinical Modification coding. Copyright © 2017. Published by Elsevier Inc.

What can we learn from learning models about sensitivity to letter-order in visual word recognition?

PubMed Central

Lerner, Itamar; Armstrong, Blair C.; Frost, Ram

2014-01-01

Recent research on the effects of letter transposition in Indo-European Languages has shown that readers are surprisingly tolerant of these manipulations in a range of tasks. This evidence has motivated the development of new computational models of reading that regard flexibility in positional coding to be a core and universal principle of the reading process. Here we argue that such approach does not capture cross-linguistic differences in transposed-letter effects, nor do they explain them. To address this issue, we investigated how a simple domain-general connectionist architecture performs in tasks such as letter-transposition and letter substitution when it had learned to process words in the context of different linguistic environments. The results show that in spite of of the neurobiological noise involved in registering letter-position in all languages, flexibility and inflexibility in coding letter order is also shaped by the statistical orthographic properties of words in a language, such as the relative prevalence of anagrams. Our learning model also generated novel predictions for targeted empirical research, demonstrating a clear advantage of learning models for studying visual word recognition. PMID:25431521

Correlated prompt fission data in transport simulations

DOE PAGES

Talou, P.; Vogt, R.; Randrup, J.; ...

2018-01-24

Detailed information on the fission process can be inferred from the observation, modeling and theoretical understanding of prompt fission neutron and γ-ray observables. Beyond simple average quantities, the study of distributions and correlations in prompt data, e.g., multiplicity-dependent neutron and γ-ray spectra, angular distributions of the emitted particles, n -n, n - γ, and γ - γ correlations, can place stringent constraints on fission models and parameters that would otherwise be free to be tuned separately to represent individual fission observables. The FREYA and CGMF codes have been developed to follow the sequential emissions of prompt neutrons and γ raysmore » from the initial excited fission fragments produced right after scission. Both codes implement Monte Carlo techniques to sample initial fission fragment configurations in mass, charge and kinetic energy and sample probabilities of neutron and γ emission at each stage of the decay. This approach naturally leads to using simple but powerful statistical techniques to infer distributions and correlations among many observables and model parameters. The comparison of model calculations with experimental data provides a rich arena for testing various nuclear physics models such as those related to the nuclear structure and level densities of neutron-rich nuclei, the γ-ray strength functions of dipole and quadrupole transitions, the mechanism for dividing the excitation energy between the two nascent fragments near scission, and the mechanisms behind the production of angular momentum in the fragments, etc. Beyond the obvious interest from a fundamental physics point of view, such studies are also important for addressing data needs in various nuclear applications. The inclusion of the FREYA and CGMF codes into the MCNP6.2 and MCNPX - PoliMi transport codes, for instance, provides a new and powerful tool to simulate correlated fission events in neutron transport calculations important in nonproliferation, safeguards, nuclear energy, and defense programs. Here, this review provides an overview of the topic, starting from theoretical considerations of the fission process, with a focus on correlated signatures. It then explores the status of experimental correlated fission data and current efforts to address some of the known shortcomings. Numerical simulations employing the FREYA and CGMF codes are compared to experimental data for a wide range of correlated fission quantities. The inclusion of those codes into the MCNP6.2 and MCNPX - PoliMi transport codes is described and discussed in the context of relevant applications. The accuracy of the model predictions and their sensitivity to model assumptions and input parameters are discussed. Lastly, a series of important experimental and theoretical questions that remain unanswered are presented, suggesting a renewed effort to address these shortcomings.« less

Correlated prompt fission data in transport simulations

NASA Astrophysics Data System (ADS)

Talou, P.; Vogt, R.; Randrup, J.; Rising, M. E.; Pozzi, S. A.; Verbeke, J.; Andrews, M. T.; Clarke, S. D.; Jaffke, P.; Jandel, M.; Kawano, T.; Marcath, M. J.; Meierbachtol, K.; Nakae, L.; Rusev, G.; Sood, A.; Stetcu, I.; Walker, C.

2018-01-01

Detailed information on the fission process can be inferred from the observation, modeling and theoretical understanding of prompt fission neutron and γ-ray observables. Beyond simple average quantities, the study of distributions and correlations in prompt data, e.g., multiplicity-dependent neutron and γ-ray spectra, angular distributions of the emitted particles, n - n, n - γ, and γ - γ correlations, can place stringent constraints on fission models and parameters that would otherwise be free to be tuned separately to represent individual fission observables. The FREYA and CGMF codes have been developed to follow the sequential emissions of prompt neutrons and γ rays from the initial excited fission fragments produced right after scission. Both codes implement Monte Carlo techniques to sample initial fission fragment configurations in mass, charge and kinetic energy and sample probabilities of neutron and γ emission at each stage of the decay. This approach naturally leads to using simple but powerful statistical techniques to infer distributions and correlations among many observables and model parameters. The comparison of model calculations with experimental data provides a rich arena for testing various nuclear physics models such as those related to the nuclear structure and level densities of neutron-rich nuclei, the γ-ray strength functions of dipole and quadrupole transitions, the mechanism for dividing the excitation energy between the two nascent fragments near scission, and the mechanisms behind the production of angular momentum in the fragments, etc. Beyond the obvious interest from a fundamental physics point of view, such studies are also important for addressing data needs in various nuclear applications. The inclusion of the FREYA and CGMF codes into the MCNP6.2 and MCNPX - PoliMi transport codes, for instance, provides a new and powerful tool to simulate correlated fission events in neutron transport calculations important in nonproliferation, safeguards, nuclear energy, and defense programs. This review provides an overview of the topic, starting from theoretical considerations of the fission process, with a focus on correlated signatures. It then explores the status of experimental correlated fission data and current efforts to address some of the known shortcomings. Numerical simulations employing the FREYA and CGMF codes are compared to experimental data for a wide range of correlated fission quantities. The inclusion of those codes into the MCNP6.2 and MCNPX - PoliMi transport codes is described and discussed in the context of relevant applications. The accuracy of the model predictions and their sensitivity to model assumptions and input parameters are discussed. Finally, a series of important experimental and theoretical questions that remain unanswered are presented, suggesting a renewed effort to address these shortcomings.

Correlated prompt fission data in transport simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Talou, P.; Vogt, R.; Randrup, J.

Detailed information on the fission process can be inferred from the observation, modeling and theoretical understanding of prompt fission neutron and γ-ray observables. Beyond simple average quantities, the study of distributions and correlations in prompt data, e.g., multiplicity-dependent neutron and γ-ray spectra, angular distributions of the emitted particles, n -n, n - γ, and γ - γ correlations, can place stringent constraints on fission models and parameters that would otherwise be free to be tuned separately to represent individual fission observables. The FREYA and CGMF codes have been developed to follow the sequential emissions of prompt neutrons and γ raysmore » from the initial excited fission fragments produced right after scission. Both codes implement Monte Carlo techniques to sample initial fission fragment configurations in mass, charge and kinetic energy and sample probabilities of neutron and γ emission at each stage of the decay. This approach naturally leads to using simple but powerful statistical techniques to infer distributions and correlations among many observables and model parameters. The comparison of model calculations with experimental data provides a rich arena for testing various nuclear physics models such as those related to the nuclear structure and level densities of neutron-rich nuclei, the γ-ray strength functions of dipole and quadrupole transitions, the mechanism for dividing the excitation energy between the two nascent fragments near scission, and the mechanisms behind the production of angular momentum in the fragments, etc. Beyond the obvious interest from a fundamental physics point of view, such studies are also important for addressing data needs in various nuclear applications. The inclusion of the FREYA and CGMF codes into the MCNP6.2 and MCNPX - PoliMi transport codes, for instance, provides a new and powerful tool to simulate correlated fission events in neutron transport calculations important in nonproliferation, safeguards, nuclear energy, and defense programs. Here, this review provides an overview of the topic, starting from theoretical considerations of the fission process, with a focus on correlated signatures. It then explores the status of experimental correlated fission data and current efforts to address some of the known shortcomings. Numerical simulations employing the FREYA and CGMF codes are compared to experimental data for a wide range of correlated fission quantities. The inclusion of those codes into the MCNP6.2 and MCNPX - PoliMi transport codes is described and discussed in the context of relevant applications. The accuracy of the model predictions and their sensitivity to model assumptions and input parameters are discussed. Lastly, a series of important experimental and theoretical questions that remain unanswered are presented, suggesting a renewed effort to address these shortcomings.« less

Uncertainty Assessment of Hypersonic Aerothermodynamics Prediction Capability

NASA Technical Reports Server (NTRS)

Bose, Deepak; Brown, James L.; Prabhu, Dinesh K.; Gnoffo, Peter; Johnston, Christopher O.; Hollis, Brian

2011-01-01

The present paper provides the background of a focused effort to assess uncertainties in predictions of heat flux and pressure in hypersonic flight (airbreathing or atmospheric entry) using state-of-the-art aerothermodynamics codes. The assessment is performed for four mission relevant problems: (1) shock turbulent boundary layer interaction on a compression corner, (2) shock turbulent boundary layer interaction due a impinging shock, (3) high-mass Mars entry and aerocapture, and (4) high speed return to Earth. A validation based uncertainty assessment approach with reliance on subject matter expertise is used. A code verification exercise with code-to-code comparisons and comparisons against well established correlations is also included in this effort. A thorough review of the literature in search of validation experiments is performed, which identified a scarcity of ground based validation experiments at hypersonic conditions. In particular, a shortage of useable experimental data at flight like enthalpies and Reynolds numbers is found. The uncertainty was quantified using metrics that measured discrepancy between model predictions and experimental data. The discrepancy data is statistically analyzed and investigated for physics based trends in order to define a meaningful quantified uncertainty. The detailed uncertainty assessment of each mission relevant problem is found in the four companion papers.

Comprehensive Benchmark Suite for Simulation of Particle Laden Flows Using the Discrete Element Method with Performance Profiles from the Multiphase Flow with Interface eXchanges (MFiX) Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Peiyuan; Brown, Timothy; Fullmer, William D.

Five benchmark problems are developed and simulated with the computational fluid dynamics and discrete element model code MFiX. The benchmark problems span dilute and dense regimes, consider statistically homogeneous and inhomogeneous (both clusters and bubbles) particle concentrations and a range of particle and fluid dynamic computational loads. Several variations of the benchmark problems are also discussed to extend the computational phase space to cover granular (particles only), bidisperse and heat transfer cases. A weak scaling analysis is performed for each benchmark problem and, in most cases, the scalability of the code appears reasonable up to approx. 103 cores. Profiling ofmore » the benchmark problems indicate that the most substantial computational time is being spent on particle-particle force calculations, drag force calculations and interpolating between discrete particle and continuum fields. Hardware performance analysis was also carried out showing significant Level 2 cache miss ratios and a rather low degree of vectorization. These results are intended to serve as a baseline for future developments to the code as well as a preliminary indicator of where to best focus performance optimizations.« less

Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains.

PubMed

Singer, Meromit; Engström, Alexander; Schönhuth, Alexander; Pachter, Lior

2011-09-23

Recent experimental and computational work confirms that CpGs can be unmethylated inside coding exons, thereby showing that codons may be subjected to both genomic and epigenomic constraint. It is therefore of interest to identify coding CpG islands (CCGIs) that are regions inside exons enriched for CpGs. The difficulty in identifying such islands is that coding exons exhibit sequence biases determined by codon usage and constraints that must be taken into account. We present a method for finding CCGIs that showcases a novel approach we have developed for identifying regions of interest that are significant (with respect to a Markov chain) for the counts of any pattern. Our method begins with the exact computation of tail probabilities for the number of CpGs in all regions contained in coding exons, and then applies a greedy algorithm for selecting islands from among the regions. We show that the greedy algorithm provably optimizes a biologically motivated criterion for selecting islands while controlling the false discovery rate. We applied this approach to the human genome (hg18) and annotated CpG islands in coding exons. The statistical criterion we apply to evaluating islands reduces the number of false positives in existing annotations, while our approach to defining islands reveals significant numbers of undiscovered CCGIs in coding exons. Many of these appear to be examples of functional epigenetic specialization in coding exons.

Spatial Correlations in Natural Scenes Modulate Response Reliability in Mouse Visual Cortex

PubMed Central

Rikhye, Rajeev V.

2015-01-01

Intrinsic neuronal variability significantly limits information encoding in the primary visual cortex (V1). Certain stimuli can suppress this intertrial variability to increase the reliability of neuronal responses. In particular, responses to natural scenes, which have broadband spatiotemporal statistics, are more reliable than responses to stimuli such as gratings. However, very little is known about which stimulus statistics modulate reliable coding and how this occurs at the neural ensemble level. Here, we sought to elucidate the role that spatial correlations in natural scenes play in reliable coding. We developed a novel noise-masking method to systematically alter spatial correlations in natural movies, without altering their edge structure. Using high-speed two-photon calcium imaging in vivo, we found that responses in mouse V1 were much less reliable at both the single neuron and population level when spatial correlations were removed from the image. This change in reliability was due to a reorganization of between-neuron correlations. Strongly correlated neurons formed ensembles that reliably and accurately encoded visual stimuli, whereas reducing spatial correlations reduced the activation of these ensembles, leading to an unreliable code. Together with an ensemble-specific normalization model, these results suggest that the coordinated activation of specific subsets of neurons underlies the reliable coding of natural scenes. SIGNIFICANCE STATEMENT The natural environment is rich with information. To process this information with high fidelity, V1 neurons have to be robust to noise and, consequentially, must generate responses that are reliable from trial to trial. While several studies have hinted that both stimulus attributes and population coding may reduce noise, the details remain unclear. Specifically, what features of natural scenes are important and how do they modulate reliability? This study is the first to investigate the role of spatial correlations, which are a fundamental attribute of natural scenes, in shaping stimulus coding by V1 neurons. Our results provide new insights into how stimulus spatial correlations reorganize the correlated activation of specific ensembles of neurons to ensure accurate information processing in V1. PMID:26511254

Version 2.0 Visual Sample Plan (VSP): UXO Module Code Description and Verification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilbert, Richard O.; Wilson, John E.; O'Brien, Robert F.

2003-05-06

The Pacific Northwest National Laboratory (PNNL) is developing statistical methods for determining the amount of geophysical surveys conducted along transects (swaths) that are needed to achieve specified levels of confidence of finding target areas (TAs) of anomalous readings and possibly unexploded ordnance (UXO) at closed, transferring and transferred (CTT) Department of Defense (DoD) ranges and other sites. The statistical methods developed by PNNL have been coded into the UXO module of the Visual Sample Plan (VSP) software code that is being developed by PNNL with support from the DoD, the U.S. Department of Energy (DOE, and the U.S. Environmental Protectionmore » Agency (EPA). (The VSP software and VSP Users Guide (Hassig et al, 2002) may be downloaded from http://dqo.pnl.gov/vsp.) This report describes and documents the statistical methods developed and the calculations and verification testing that have been conducted to verify that VSPs implementation of these methods is correct and accurate.« less

Application of JAERI quantum molecular dynamics model for collisions of heavy nuclei

NASA Astrophysics Data System (ADS)

Ogawa, Tatsuhiko; Hashimoto, Shintaro; Sato, Tatsuhiko; Niita, Koji

2016-06-01

The quantum molecular dynamics (QMD) model incorporated into the general-purpose radiation transport code PHITS was revised for accurate prediction of fragment yields in peripheral collisions. For more accurate simulation of peripheral collisions, stability of the nuclei at their ground state was improved and the algorithm to reject invalid events was modified. In-medium correction on nucleon-nucleon cross sections was also considered. To clarify the effect of this improvement on fragmentation of heavy nuclei, the new QMD model coupled with a statistical decay model was used to calculate fragment production cross sections of Ag and Au targets and compared with the data of earlier measurement. It is shown that the revised version can predict cross section more accurately.

PROM7: 1D modeler of solar filaments or prominences

NASA Astrophysics Data System (ADS)

Gouttebroze, P.

2018-05-01

PROM7 is an update of PROM4 (ascl:1306.004) and computes simple models of solar prominences and filaments using Partial Radiative Distribution (PRD). The models consist of plane-parallel slabs standing vertically above the solar surface. Each model is defined by 5 parameters: temperature, density, geometrical thickness, microturbulent velocity and height above the solar surface. It solves the equations of radiative transfer, statistical equilibrium, ionization and pressure equilibria, and computes electron and hydrogen level population and hydrogen line profiles. Moreover, the code treats calcium atom which is reduced to 3 ionization states (Ca I, Ca II, CA III). Ca II ion has 5 levels which are useful for computing 2 resonance lines (H and K) and infrared triplet (to 8500 A).

Cormack Research Project: Glasgow University

NASA Technical Reports Server (NTRS)

Skinner, Susan; Ryan, James M.

1998-01-01

The aim of this project was to investigate and improve upon existing methods of analysing data from COMITEL on the Gamma Ray Observatory for neutrons emitted during solar flares. In particular, a strategy for placing confidence intervals on neutron energy distributions, due to uncertainties on the response matrix has been developed. We have also been able to demonstrate the superior performance of one of a range of possible statistical regularization strategies. A method of generating likely models of neutron energy distributions has also been developed as a tool to this end. The project involved solving an inverse problem with noise being added to the data in various ways. To achieve this pre-existing C code was used to run Fortran subroutines which performed statistical regularization on the data.

Method and System for Temporal Filtering in Video Compression Systems

NASA Technical Reports Server (NTRS)

Lu, Ligang; He, Drake; Jagmohan, Ashish; Sheinin, Vadim

2011-01-01

Three related innovations combine improved non-linear motion estimation, video coding, and video compression. The first system comprises a method in which side information is generated using an adaptive, non-linear motion model. This method enables extrapolating and interpolating a visual signal, including determining the first motion vector between the first pixel position in a first image to a second pixel position in a second image; determining a second motion vector between the second pixel position in the second image and a third pixel position in a third image; determining a third motion vector between the first pixel position in the first image and the second pixel position in the second image, the second pixel position in the second image, and the third pixel position in the third image using a non-linear model; and determining a position of the fourth pixel in a fourth image based upon the third motion vector. For the video compression element, the video encoder has low computational complexity and high compression efficiency. The disclosed system comprises a video encoder and a decoder. The encoder converts the source frame into a space-frequency representation, estimates the conditional statistics of at least one vector of space-frequency coefficients with similar frequencies, and is conditioned on previously encoded data. It estimates an encoding rate based on the conditional statistics and applies a Slepian-Wolf code with the computed encoding rate. The method for decoding includes generating a side-information vector of frequency coefficients based on previously decoded source data and encoder statistics and previous reconstructions of the source frequency vector. It also performs Slepian-Wolf decoding of a source frequency vector based on the generated side-information and the Slepian-Wolf code bits. The video coding element includes receiving a first reference frame having a first pixel value at a first pixel position, a second reference frame having a second pixel value at a second pixel position, and a third reference frame having a third pixel value at a third pixel position. It determines a first motion vector between the first pixel position and the second pixel position, a second motion vector between the second pixel position and the third pixel position, and a fourth pixel value for a fourth frame based upon a linear or nonlinear combination of the first pixel value, the second pixel value, and the third pixel value. A stationary filtering process determines the estimated pixel values. The parameters of the filter may be predetermined constants.

Exploration of ICD-9-CM Coding of Chronic Disease within the Elixhauser Comorbidity Measure in Patients with Chronic Heart Failure

PubMed Central

Garvin, Jennifer Hornung; Redd, Andrew; Bolton, Dan; Graham, Pauline; Roche, Dominic; Groeneveld, Peter; Leecaster, Molly; Shen, Shuying; Weiner, Mark G.

2013-01-01

Introduction International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes capture comorbidities that can be used to risk adjust nonrandom patient groups. We explored the accuracy of capturing comorbidities associated with one risk adjustment method, the Elixhauser Comorbidity Measure (ECM), in patients with chronic heart failure (CHF) at one Veterans Affairs (VA) medical center. We explored potential reasons for the differences found between the original codes assigned and conditions found through retrospective review. Methods This descriptive, retrospective study used a cohort of patients discharged with a principal diagnosis coded as CHF from one VA medical center in 2003. One admission per patient was used in the study; with multiple admissions, only the first admission was analyzed. We compared the assignment of original codes assigned to conditions found in a retrospective, manual review of the medical record conducted by an investigator with coding expertise as well as by physicians. Members of the team experienced with assigning ICD-9-CM codes and VA coding processes developed themes related to systemic reasons why chronic conditions were not coded in VA records using applied thematic techniques. Results In the 181-patient cohort, 388 comorbid conditions were identified; 305 of these were chronic conditions, originally coded at the time of discharge with an average of 1.7 comorbidities related to the ECM per patient. The review by an investigator with coding expertise revealed a total of 937 comorbidities resulting in 618 chronic comorbid conditions with an average of 3.4 per patient; physician review found 872 total comorbidities with 562 chronic conditions (average 3.1 per patient). The agreement between the original and the retrospective coding review was 88 percent. The kappa statistic for the original and the retrospective coding review was 0.375 with a 95 percent confidence interval (CI) of 0.352 to 0.398. The kappa statistic for the retrospective coding review and physician review was 0.849 (CI, 0.823–0.875). The kappa statistic for the original coding and the physician review was 0.340 (CI, 0.316–0.364). Several systemic factors were identified, including familiarity with inpatient VA and non-VA guidelines, the quality of documentation, and operational requirements to complete the coding process within short time frames and to identify the reasons for movement within a given facility. Conclusion Comorbidities within the ECM representing chronic conditions were significantly underrepresented in the original code assignment. Contributing factors potentially include prioritization of codes related to acute conditions over chronic conditions; coders’ professional training, educational level, and experience; and the limited number of codes allowed in initial coding software. This study highlights the need to evaluate systemic causes of underrepresentation of chronic conditions to improve the accuracy of risk adjustment used for health services research, resource allocation, and performance measurement. PMID:24159270

Performance simulation in high altitude platforms (HAPs) communications systems

NASA Astrophysics Data System (ADS)

Ulloa-Vásquez, Fernando; Delgado-Penin, J. A.

2002-07-01

This paper considers the analysis by simulation of a digital narrowband communication system for an scenario which consists of a High-Altitude aeronautical Platform (HAP) and fixed/mobile terrestrial transceivers. The aeronautical channel is modelled considering geometrical (angle of elevation vs. horizontal distance of the terrestrial reflectors) and statistical arguments and under these circumstances a serial concatenated coded digital transmission is analysed for several hypothesis related to radio-electric coverage areas. The results indicate a good feasibility for the communication system proposed and analysed.

Verification and Validation Plan for Three-Dimensional Probability of Incapacitation Methodology for Masonry Structures (3DPIMMS)

DTIC Science & Technology

2011-01-01

all panels of a test were recorded, it was reduced into text format and then input into the code. B. Current Development The capabilities...due to fragmentation. Any or all of these models can be activated for a particular lethality assessment. Incapacitation criteria of different times...defined for all fragments represented in the file. Only the fragment material density needs to be set by the user. 3DPIMMS accounts for some statistical

Computer modelling of grain microstructure in three dimensions

NASA Astrophysics Data System (ADS)

Narayan, K. Lakshmi

We present a program that generates the two-dimensional micrographs of a three dimensional grain microstructure. The code utilizes a novel scanning, pixel mapping technique to secure statistical distributions of surface areas, grain sizes, aspect ratios, perimeters, number of nearest neighbors and volumes of the randomly nucleated particles. The program can be used for comparing the existing theories of grain growth, and interpretation of two-dimensional microstructure of three-dimensional samples. Special features have been included to minimize the computation time and resource requirements.

The usefulness of administrative databases for identifying disease cohorts is increased with a multivariate model.

PubMed

van Walraven, Carl; Austin, Peter C; Manuel, Douglas; Knoll, Greg; Jennings, Allison; Forster, Alan J

2010-12-01

Administrative databases commonly use codes to indicate diagnoses. These codes alone are often inadequate to accurately identify patients with particular conditions. In this study, we determined whether we could quantify the probability that a person has a particular disease-in this case renal failure-using other routinely collected information available in an administrative data set. This would allow the accurate identification of a disease cohort in an administrative database. We determined whether patients in a randomly selected 100,000 hospitalizations had kidney disease (defined as two or more sequential serum creatinines or the single admission creatinine indicating a calculated glomerular filtration rate less than 60 mL/min/1.73 m²). The independent association of patient- and hospitalization-level variables with renal failure was measured using a multivariate logistic regression model in a random 50% sample of the patients. The model was validated in the remaining patients. Twenty thousand seven hundred thirteen patients had kidney disease (20.7%). A diagnostic code of kidney disease was strongly associated with kidney disease (relative risk: 34.4), but the accuracy of the code was poor (sensitivity: 37.9%; specificity: 98.9%). Twenty-nine patient- and hospitalization-level variables entered the kidney disease model. This model had excellent discrimination (c-statistic: 90.1%) and accurately predicted the probability of true renal failure. The probability threshold that maximized sensitivity and specificity for the identification of true kidney disease was 21.3% (sensitivity: 80.0%; specificity: 82.2%). Multiple variables available in administrative databases can be combined to quantify the probability that a person has a particular disease. This process permits accurate identification of a disease cohort in an administrative database. These methods may be extended to other diagnoses or procedures and could both facilitate and clarify the use of administrative databases for research and quality improvement. Copyright © 2010 Elsevier Inc. All rights reserved.

ab initio MD simulations of geomaterials with ~1000 atoms

NASA Astrophysics Data System (ADS)

Martin, G. B.; Kirtman, B.; Spera, F. J.

2009-12-01

In the last two decades, ab initio studies of materials using Density Functional Theory (DFT) have increased exponentially in popularity. DFT codes are now used routinely to simulate properties of geomaterials--mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only ~100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it is statistically marginal for duplicating physical properties of the liquid state like transport and structure. In MD simulations in the NEV ensemble, temperature (T), and pressure (P) fluctuations scale as N-1/2; small particle number (N) systems are therefore characterized by greater statistical state point location uncertainty than large N systems. Previous studies have used codes such as VASP where CPU time increases with N2, making calculations with N much greater than 100 impractical. SIESTA (Soler, et al. 2002) is a DFT code that enables electronic structure and MD computations on larger systems (N~103) by making some approximations, such as localized numerical orbitals, that would be useful in modeling some properties of geomaterials. Here we test the applicability of SIESTA to simulate geosilicates, both hydrous and anhydrous, in the solid and liquid state. We have used SIESTA for lattice calculations of brucite, Mg(OH)2, that compare very well to experiment and calculations using CRYSTAL, another DFT code. Good agreement between more classical DFT calculations and SIESTA is needed to justify study of geosilicates using SIESTA across a range of pressures and temperatures relevant to the Earth’s interior. Thus, it is useful to adjust parameters in SIESTA in accordance with calculations from CRYSTAL as a check on feasibility. Results are reported here that suggest SIESTA may indeed be useful to model silicate liquids at very high T and P.

Early Warning Signs of Suicide in Service Members Who Engage in Unauthorized Acts of Violence

DTIC Science & Technology

2016-06-01

observable to military law enforcement personnel. Statistical analyses tested for differences in warning signs between cases of suicide, violence, or...indicators, (2) Behavioral Change indicators, (3) Social indicators, and (4) Occupational indicators. Statistical analyses were conducted to test for...6 Coding _________________________________________________________________ 7 Statistical

Statistical Learning as a Key to Cracking Chinese Orthographic Codes

ERIC Educational Resources Information Center

He, Xinjie; Tong, Xiuli

2017-01-01

This study examines statistical learning as a mechanism for Chinese orthographic learning among children in Grades 3-5. Using an artificial orthography, children were repeatedly exposed to positional, phonetic, and semantic regularities of radicals. Children showed statistical learning of all three regularities. Regularities' levels of consistency…

Open-access programs for injury categorization using ICD-9 or ICD-10.

PubMed

Clark, David E; Black, Adam W; Skavdahl, David H; Hallagan, Lee D

2018-04-09

The article introduces Programs for Injury Categorization, using the International Classification of Diseases (ICD) and R statistical software (ICDPIC-R). Starting with ICD-8, methods have been described to map injury diagnosis codes to severity scores, especially the Abbreviated Injury Scale (AIS) and Injury Severity Score (ISS). ICDPIC was originally developed for this purpose using Stata, and ICDPIC-R is an open-access update that accepts both ICD-9 and ICD-10 codes. Data were obtained from the National Trauma Data Bank (NTDB), Admission Year 2015. ICDPIC-R derives CDC injury mechanism categories and an approximate ISS ("RISS") from either ICD-9 or ICD-10 codes. For ICD-9-coded cases, RISS is derived similar to the Stata package (with some improvements reflecting user feedback). For ICD-10-coded cases, RISS may be calculated in several ways: The "GEM" methods convert ICD-10 to ICD-9 (using General Equivalence Mapping tables from CMS) and then calculate ISS with options similar to the Stata package; a "ROCmax" method calculates RISS directly from ICD-10 codes, based on diagnosis-specific mortality in the NTDB, maximizing the C-statistic for predicting NTDB mortality while attempting to minimize the difference between RISS and ISS submitted by NTDB registrars (ISSAIS). Findings were validated using data from the National Inpatient Survey (NIS, 2015). NTDB contained 917,865 cases, of which 86,878 had valid ICD-10 injury codes. For a random 100,000 ICD-9-coded cases in NTDB, RISS using the GEM methods was nearly identical to ISS calculated by the Stata version, which has been previously validated. For ICD-10-coded cases in NTDB, categorized ISS using any version of RISS was similar to ISSAIS; for both NTDB and NIS cases, increasing ISS was associated with increasing mortality. Prediction of NTDB mortality was associated with C-statistics of 0.81 for ISSAIS, 0.75 for RISS using the GEM methods, and 0.85 for RISS using the ROCmax method; prediction of NIS mortality was associated with C-statistics of 0.75-0.76 for RISS using the GEM methods, and 0.78 for RISS using the ROCmax method. Instructions are provided for accessing ICDPIC-R at no cost. The ideal methods of injury categorization and injury severity scoring involve trained personnel with access to injured persons or their medical records. ICDPIC-R may be a useful substitute when this ideal cannot be obtained.

Knowledge and Performance about Nursing Ethic Codes from Nurses' and Patients' Perspective in Tabriz Teaching Hospitals, Iran.

PubMed

Mohajjel-Aghdam, Alireza; Hassankhani, Hadi; Zamanzadeh, Vahid; Khameneh, Saied; Moghaddam, Sara

2013-09-01

Nursing profession requires knowledge of ethics to guide performance. The nature of this profession necessitates ethical care more than routine care. Today, worldwide definition of professional ethic code has been done based on human and ethical issues in the communication between nurse and patient. To improve all dimensions of nursing, we need to respect ethic codes. The aim of this study is to assess knowledge and performance about nursing ethic codes from nurses' and patients' perspective. A descriptive study Conducted upon 345 nurses and 500 inpatients in six teaching hospitals of Tabriz, 2012. To investigate nurses' knowledge and performance, data were collected by using structured questionnaires. Statistical analysis was done using descriptive and analytic statistics, independent t-test and ANOVA and Pearson correlation coefficient, in SPSS13. Most of the nurses were female, married, educated at BS degree and 86.4% of them were aware of Ethic codes also 91.9% of nurses and 41.8% of patients represented nurses respect ethic codes. Nurses' and patients' perspective about ethic codes differed significantly. Significant relationship was found between nurses' knowledge of ethic codes and job satisfaction and complaint of ethical performance. According to the results, consideration to teaching ethic codes in nursing curriculum for student and continuous education for staff is proposed, on the other hand recognizing failures of the health system, optimizing nursing care, attempt to inform patients about Nursing ethic codes, promote patient rights and achieve patient satisfaction can minimize the differences between the two perspectives.

Knowledge and Performance about Nursing Ethic Codes from Nurses' and Patients' Perspective in Tabriz Teaching Hospitals, Iran

PubMed Central

Mohajjel-Aghdam, Alireza; Hassankhani, Hadi; Zamanzadeh, Vahid; Khameneh, Saied; Moghaddam, Sara

2013-01-01

Introduction: Nursing profession requires knowledge of ethics to guide performance. The nature of this profession necessitates ethical care more than routine care. Today, worldwide definition of professional ethic code has been done based on human and ethical issues in the communication between nurse and patient. To improve all dimensions of nursing, we need to respect ethic codes. The aim of this study is to assess knowledge and performance about nursing ethic codes from nurses' and patients' perspective. Methods: A descriptive study Conducted upon 345 nurses and 500 inpatients in six teaching hospitals of Tabriz, 2012. To investigate nurses' knowledge and performance, data were collected by using structured questionnaires. Statistical analysis was done using descriptive and analytic statistics, independent t-test and ANOVA and Pearson correlation coefficient, in SPSS13. Results: Most of the nurses were female, married, educated at BS degree and 86.4% of them were aware of Ethic codes also 91.9% of nurses and 41.8% of patients represented nurses respect ethic codes. Nurses' and patients' perspective about ethic codes differed significantly. Significant relationship was found between nurses' knowledge of ethic codes and job satisfaction and complaint of ethical performance. Conclusion: According to the results, consideration to teaching ethic codes in nursing curriculum for student and continuous education for staff is proposed, on the other hand recognizing failures of the health system, optimizing nursing care, attempt to inform patients about Nursing ethic codes, promote patient rights and achieve patient satisfaction can minimize the differences between the two perspectives. PMID:25276730

ICD Social Codes: An Underutilized Resource for Tracking Social Needs.

PubMed

Torres, Jacqueline M; Lawlor, John; Colvin, Jeffrey D; Sills, Marion R; Bettenhausen, Jessica L; Davidson, Amber; Cutler, Gretchen J; Hall, Matt; Gottlieb, Laura M

2017-09-01

Social determinants of health (SDH) data collected in health care settings could have important applications for clinical decision-making, population health strategies, and the design of performance-based incentives and penalties. One source for cataloging SDH data is the International Statistical Classification of Diseases and Related Health Problems (ICD). To explore how SDH are captured with ICD Ninth revision SDH V codes in a national inpatient discharge database. Data come from the 2013 Healthcare Cost and Utilization Project (HCUP) National Inpatient Sample, a national stratified sample of discharges from 4363 hospitals from 44 US states. We estimate the rate of ICD-9 SDH V code utilization overall and by patient demographics and payer categories. We additionally estimate the rate of SDH V code utilization for: (a) the 5 most common reasons for hospitalization; and (b) the 5 conditions with the highest rates of SDH V code utilization. Fewer than 2% of overall discharges in the National Inpatient Sample were assigned an SDH V code. There were statistically significant differences in the rate of overall SDH V code utilization by age categories, race/ethnicity, sex, and payer (all P<0.001). Nevertheless, SDH V codes were assigned to <7% of discharges in any demographic or payer subgroup. SDH V code utilization was highest for major diagnostic categories related to mental health and alcohol/substance use-related discharges. SDH V codes are infrequently utilized in inpatient settings for discharges other than those related to mental health and alcohol/substance use. Utilization incentives will likely need to be developed to realize the potential benefits of cataloging SDH information.

28 CFR 36.608 - Guidance concerning model codes.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Guidance concerning model codes. 36.608... Codes § 36.608 Guidance concerning model codes. Upon application by an authorized representative of a... relevant model code and issue guidance concerning whether and in what respects the model code is consistent...

ON THE FOURIER AND WAVELET ANALYSIS OF CORONAL TIME SERIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Auchère, F.; Froment, C.; Bocchialini, K.

Using Fourier and wavelet analysis, we critically re-assess the significance of our detection of periodic pulsations in coronal loops. We show that the proper identification of the frequency dependence and statistical properties of the different components of the power spectra provides a strong argument against the common practice of data detrending, which tends to produce spurious detections around the cut-off frequency of the filter. In addition, the white and red noise models built into the widely used wavelet code of Torrence and Compo cannot, in most cases, adequately represent the power spectra of coronal time series, thus also possibly causingmore » false positives. Both effects suggest that several reports of periodic phenomena should be re-examined. The Torrence and Compo code nonetheless effectively computes rigorous confidence levels if provided with pertinent models of mean power spectra, and we describe the appropriate manner in which to call its core routines. We recall the meaning of the default confidence levels output from the code, and we propose new Monte-Carlo-derived levels that take into account the total number of degrees of freedom in the wavelet spectra. These improvements allow us to confirm that the power peaks that we detected have a very low probability of being caused by noise.« less

On the Fourier and Wavelet Analysis of Coronal Time Series

NASA Astrophysics Data System (ADS)

Auchère, F.; Froment, C.; Bocchialini, K.; Buchlin, E.; Solomon, J.

2016-07-01

Using Fourier and wavelet analysis, we critically re-assess the significance of our detection of periodic pulsations in coronal loops. We show that the proper identification of the frequency dependence and statistical properties of the different components of the power spectra provides a strong argument against the common practice of data detrending, which tends to produce spurious detections around the cut-off frequency of the filter. In addition, the white and red noise models built into the widely used wavelet code of Torrence & Compo cannot, in most cases, adequately represent the power spectra of coronal time series, thus also possibly causing false positives. Both effects suggest that several reports of periodic phenomena should be re-examined. The Torrence & Compo code nonetheless effectively computes rigorous confidence levels if provided with pertinent models of mean power spectra, and we describe the appropriate manner in which to call its core routines. We recall the meaning of the default confidence levels output from the code, and we propose new Monte-Carlo-derived levels that take into account the total number of degrees of freedom in the wavelet spectra. These improvements allow us to confirm that the power peaks that we detected have a very low probability of being caused by noise.

An Ensemble Approach to Building Mercer Kernels with Prior Information

NASA Technical Reports Server (NTRS)

Srivastava, Ashok N.; Schumann, Johann; Fischer, Bernd

2005-01-01

This paper presents a new methodology for automatic knowledge driven data mining based on the theory of Mercer Kernels, which are highly nonlinear symmetric positive definite mappings from the original image space to a very high, possibly dimensional feature space. we describe a new method called Mixture Density Mercer Kernels to learn kernel function directly from data, rather than using pre-defined kernels. These data adaptive kernels can encode prior knowledge in the kernel using a Bayesian formulation, thus allowing for physical information to be encoded in the model. Specifically, we demonstrate the use of the algorithm in situations with extremely small samples of data. We compare the results with existing algorithms on data from the Sloan Digital Sky Survey (SDSS) and demonstrate the method's superior performance against standard methods. The code for these experiments has been generated with the AUTOBAYES tool, which automatically generates efficient and documented C/C++ code from abstract statistical model specifications. The core of the system is a schema library which contains templates for learning and knowledge discovery algorithms like different versions of EM, or numeric optimization methods like conjugate gradient methods. The template instantiation is supported by symbolic-algebraic computations, which allows AUTOBAYES to find closed-form solutions and, where possible, to integrate them into the code.

Chroma intra prediction based on inter-channel correlation for HEVC.

PubMed

Zhang, Xingyu; Gisquet, Christophe; François, Edouard; Zou, Feng; Au, Oscar C

2014-01-01

In this paper, we investigate a new inter-channel coding mode called LM mode proposed for the next generation video coding standard called high efficiency video coding. This mode exploits inter-channel correlation using reconstructed luma to predict chroma linearly with parameters derived from neighboring reconstructed luma and chroma pixels at both encoder and decoder to avoid overhead signaling. In this paper, we analyze the LM mode and prove that the LM parameters for predicting original chroma and reconstructed chroma are statistically the same. We also analyze the error sensitivity of the LM parameters. We identify some LM mode problematic situations and propose three novel LM-like modes called LMA, LML, and LMO to address the situations. To limit the increase in complexity due to the LM-like modes, we propose some fast algorithms with the help of some new cost functions. We further identify some potentially-problematic conditions in the parameter estimation (including regression dilution problem) and introduce a novel model correction technique to detect and correct those conditions. Simulation results suggest that considerable BD-rate reduction can be achieved by the proposed LM-like modes and model correction technique. In addition, the performance gain of the two techniques appears to be essentially additive when combined.

Bubbles and denaturation in DNA

NASA Astrophysics Data System (ADS)

van Erp, T. S.; Cuesta-López, S.; Peyrard, M.

2006-08-01

The local opening of DNA is an intriguing phenomenon from a statistical-physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code cannot take place without the unwinding of the DNA double helix. Although these biological processes are driven by proteins, there might well be a relation between these biological openings and the spontaneous bubble formation due to thermal fluctuations. Mesoscopic models, like the Peyrard-Bishop-Dauxois (PBD) model, have fairly accurately reproduced some experimental denaturation curves and the sharp phase transition in the thermodynamic limit. It is, hence, tempting to see whether these models could be used to predict the biological activity of DNA. In a previous study, we introduced a method that allows to obtain very accurate results on this subject, which showed that some previous claims in this direction, based on molecular-dynamics studies, were premature. This could either imply that the present PBD model should be improved or that biological activity can only be predicted in a more complex framework that involves interactions with proteins and super helical stresses. In this article, we give a detailed description of the statistical method introduced before. Moreover, for several DNA sequences, we give a thorough analysis of the bubble-statistics as a function of position and bubble size and the so-called l-denaturation curves that can be measured experimentally. These show that some important experimental observations are missing in the present model. We discuss how the present model could be improved.

GAMBIT: the global and modular beyond-the-standard-model inference tool

NASA Astrophysics Data System (ADS)

Athron, Peter; Balazs, Csaba; Bringmann, Torsten; Buckley, Andy; Chrząszcz, Marcin; Conrad, Jan; Cornell, Jonathan M.; Dal, Lars A.; Dickinson, Hugh; Edsjö, Joakim; Farmer, Ben; Gonzalo, Tomás E.; Jackson, Paul; Krislock, Abram; Kvellestad, Anders; Lundberg, Johan; McKay, James; Mahmoudi, Farvah; Martinez, Gregory D.; Putze, Antje; Raklev, Are; Ripken, Joachim; Rogan, Christopher; Saavedra, Aldo; Savage, Christopher; Scott, Pat; Seo, Seon-Hee; Serra, Nicola; Weniger, Christoph; White, Martin; Wild, Sebastian

2017-11-01

We describe the open-source global fitting package GAMBIT: the Global And Modular Beyond-the-Standard-Model Inference Tool. GAMBIT combines extensive calculations of observables and likelihoods in particle and astroparticle physics with a hierarchical model database, advanced tools for automatically building analyses of essentially any model, a flexible and powerful system for interfacing to external codes, a suite of different statistical methods and parameter scanning algorithms, and a host of other utilities designed to make scans faster, safer and more easily-extendible than in the past. Here we give a detailed description of the framework, its design and motivation, and the current models and other specific components presently implemented in GAMBIT. Accompanying papers deal with individual modules and present first GAMBIT results. GAMBIT can be downloaded from gambit.hepforge.org.

Stochastic kinetic mean field model

NASA Astrophysics Data System (ADS)

Erdélyi, Zoltán; Pasichnyy, Mykola; Bezpalchuk, Volodymyr; Tomán, János J.; Gajdics, Bence; Gusak, Andriy M.

2016-07-01

This paper introduces a new model for calculating the change in time of three-dimensional atomic configurations. The model is based on the kinetic mean field (KMF) approach, however we have transformed that model into a stochastic approach by introducing dynamic Langevin noise. The result is a stochastic kinetic mean field model (SKMF) which produces results similar to the lattice kinetic Monte Carlo (KMC). SKMF is, however, far more cost-effective and easier to implement the algorithm (open source program code is provided on http://skmf.eu website). We will show that the result of one SKMF run may correspond to the average of several KMC runs. The number of KMC runs is inversely proportional to the amplitude square of the noise in SKMF. This makes SKMF an ideal tool also for statistical purposes.

DarkBit: a GAMBIT module for computing dark matter observables and likelihoods

NASA Astrophysics Data System (ADS)

Bringmann, Torsten; Conrad, Jan; Cornell, Jonathan M.; Dal, Lars A.; Edsjö, Joakim; Farmer, Ben; Kahlhoefer, Felix; Kvellestad, Anders; Putze, Antje; Savage, Christopher; Scott, Pat; Weniger, Christoph; White, Martin; Wild, Sebastian

2017-12-01

We introduce DarkBit, an advanced software code for computing dark matter constraints on various extensions to the Standard Model of particle physics, comprising both new native code and interfaces to external packages. This release includes a dedicated signal yield calculator for gamma-ray observations, which significantly extends current tools by implementing a cascade-decay Monte Carlo, as well as a dedicated likelihood calculator for current and future experiments ( gamLike). This provides a general solution for studying complex particle physics models that predict dark matter annihilation to a multitude of final states. We also supply a direct detection package that models a large range of direct detection experiments ( DDCalc), and that provides the corresponding likelihoods for arbitrary combinations of spin-independent and spin-dependent scattering processes. Finally, we provide custom relic density routines along with interfaces to DarkSUSY, micrOMEGAs, and the neutrino telescope likelihood package nulike. DarkBit is written in the framework of the Global And Modular Beyond the Standard Model Inference Tool ( GAMBIT), providing seamless integration into a comprehensive statistical fitting framework that allows users to explore new models with both particle and astrophysics constraints, and a consistent treatment of systematic uncertainties. In this paper we describe its main functionality, provide a guide to getting started quickly, and show illustrative examples for results obtained with DarkBit (both as a stand-alone tool and as a GAMBIT module). This includes a quantitative comparison between two of the main dark matter codes ( DarkSUSY and micrOMEGAs), and application of DarkBit 's advanced direct and indirect detection routines to a simple effective dark matter model.

50 CFR Figure 1 to Part 679 - Bering Sea and Aleutian Islands Statistical and Reporting Areas

Code of Federal Regulations, 2011 CFR

2011-10-01

... Statistical and Reporting Areas 1 Figure 1 to Part 679 Wildlife and Fisheries FISHERY CONSERVATION AND... Islands Statistical and Reporting Areas ER15NO99.000 b. Coordinates Code Description 300 Russian waters... statistical area is the part of a reporting area contained in the EEZ. [64 FR 61983, Nov. 15, 1999; 65 FR...

50 CFR Figure 1 to Part 679 - Bering Sea and Aleutian Islands Statistical and Reporting Areas

Code of Federal Regulations, 2010 CFR

2010-10-01

... Statistical and Reporting Areas 1 Figure 1 to Part 679 Wildlife and Fisheries FISHERY CONSERVATION AND... Islands Statistical and Reporting Areas ER15NO99.000 b. Coordinates Code Description 300 Russian waters... statistical area is the part of a reporting area contained in the EEZ. [64 FR 61983, Nov. 15, 1999; 65 FR...

A Subband Coding Method for HDTV

NASA Technical Reports Server (NTRS)

Chung, Wilson; Kossentini, Faouzi; Smith, Mark J. T.

1995-01-01

This paper introduces a new HDTV coder based on motion compensation, subband coding, and high order conditional entropy coding. The proposed coder exploits the temporal and spatial statistical dependencies inherent in the HDTV signal by using intra- and inter-subband conditioning for coding both the motion coordinates and the residual signal. The new framework provides an easy way to control the system complexity and performance, and inherently supports multiresolution transmission. Experimental results show that the coder outperforms MPEG-2, while still maintaining relatively low complexity.

Model specification and bootstrapping for multiply imputed data: An application to count models for the frequency of alcohol use

PubMed Central

Comulada, W. Scott

2015-01-01

Stata’s mi commands provide powerful tools to conduct multiple imputation in the presence of ignorable missing data. In this article, I present Stata code to extend the capabilities of the mi commands to address two areas of statistical inference where results are not easily aggregated across imputed datasets. First, mi commands are restricted to covariate selection. I show how to address model fit to correctly specify a model. Second, the mi commands readily aggregate model-based standard errors. I show how standard errors can be bootstrapped for situations where model assumptions may not be met. I illustrate model specification and bootstrapping on frequency counts for the number of times that alcohol was consumed in data with missing observations from a behavioral intervention. PMID:26973439

Accelerated GPU based SPECT Monte Carlo simulations.

PubMed

Garcia, Marie-Paule; Bert, Julien; Benoit, Didier; Bardiès, Manuel; Visvikis, Dimitris

2016-06-07

Monte Carlo (MC) modelling is widely used in the field of single photon emission computed tomography (SPECT) as it is a reliable technique to simulate very high quality scans. This technique provides very accurate modelling of the radiation transport and particle interactions in a heterogeneous medium. Various MC codes exist for nuclear medicine imaging simulations. Recently, new strategies exploiting the computing capabilities of graphical processing units (GPU) have been proposed. This work aims at evaluating the accuracy of such GPU implementation strategies in comparison to standard MC codes in the context of SPECT imaging. GATE was considered the reference MC toolkit and used to evaluate the performance of newly developed GPU Geant4-based Monte Carlo simulation (GGEMS) modules for SPECT imaging. Radioisotopes with different photon energies were used with these various CPU and GPU Geant4-based MC codes in order to assess the best strategy for each configuration. Three different isotopes were considered: (99m) Tc, (111)In and (131)I, using a low energy high resolution (LEHR) collimator, a medium energy general purpose (MEGP) collimator and a high energy general purpose (HEGP) collimator respectively. Point source, uniform source, cylindrical phantom and anthropomorphic phantom acquisitions were simulated using a model of the GE infinia II 3/8" gamma camera. Both simulation platforms yielded a similar system sensitivity and image statistical quality for the various combinations. The overall acceleration factor between GATE and GGEMS platform derived from the same cylindrical phantom acquisition was between 18 and 27 for the different radioisotopes. Besides, a full MC simulation using an anthropomorphic phantom showed the full potential of the GGEMS platform, with a resulting acceleration factor up to 71. The good agreement with reference codes and the acceleration factors obtained support the use of GPU implementation strategies for improving computational efficiency of SPECT imaging simulations.

Computationally efficient methods for modelling laser wakefield acceleration in the blowout regime

NASA Astrophysics Data System (ADS)

Cowan, B. M.; Kalmykov, S. Y.; Beck, A.; Davoine, X.; Bunkers, K.; Lifschitz, A. F.; Lefebvre, E.; Bruhwiler, D. L.; Shadwick, B. A.; Umstadter, D. P.; Umstadter

2012-08-01

Electron self-injection and acceleration until dephasing in the blowout regime is studied for a set of initial conditions typical of recent experiments with 100-terawatt-class lasers. Two different approaches to computationally efficient, fully explicit, 3D particle-in-cell modelling are examined. First, the Cartesian code vorpal (Nieter, C. and Cary, J. R. 2004 VORPAL: a versatile plasma simulation code. J. Comput. Phys. 196, 538) using a perfect-dispersion electromagnetic solver precisely describes the laser pulse and bubble dynamics, taking advantage of coarser resolution in the propagation direction, with a proportionally larger time step. Using third-order splines for macroparticles helps suppress the sampling noise while keeping the usage of computational resources modest. The second way to reduce the simulation load is using reduced-geometry codes. In our case, the quasi-cylindrical code calder-circ (Lifschitz, A. F. et al. 2009 Particle-in-cell modelling of laser-plasma interaction using Fourier decomposition. J. Comput. Phys. 228(5), 1803-1814) uses decomposition of fields and currents into a set of poloidal modes, while the macroparticles move in the Cartesian 3D space. Cylindrical symmetry of the interaction allows using just two modes, reducing the computational load to roughly that of a planar Cartesian simulation while preserving the 3D nature of the interaction. This significant economy of resources allows using fine resolution in the direction of propagation and a small time step, making numerical dispersion vanishingly small, together with a large number of particles per cell, enabling good particle statistics. Quantitative agreement of two simulations indicates that these are free of numerical artefacts. Both approaches thus retrieve the physically correct evolution of the plasma bubble, recovering the intrinsic connection of electron self-injection to the nonlinear optical evolution of the driver.

The Opponent Channel Population Code of Sound Location Is an Efficient Representation of Natural Binaural Sounds

PubMed Central

Młynarski, Wiktor

2015-01-01

In mammalian auditory cortex, sound source position is represented by a population of broadly tuned neurons whose firing is modulated by sounds located at all positions surrounding the animal. Peaks of their tuning curves are concentrated at lateral position, while their slopes are steepest at the interaural midline, allowing for the maximum localization accuracy in that area. These experimental observations contradict initial assumptions that the auditory space is represented as a topographic cortical map. It has been suggested that a “panoramic” code has evolved to match specific demands of the sound localization task. This work provides evidence suggesting that properties of spatial auditory neurons identified experimentally follow from a general design principle- learning a sparse, efficient representation of natural stimuli. Natural binaural sounds were recorded and served as input to a hierarchical sparse-coding model. In the first layer, left and right ear sounds were separately encoded by a population of complex-valued basis functions which separated phase and amplitude. Both parameters are known to carry information relevant for spatial hearing. Monaural input converged in the second layer, which learned a joint representation of amplitude and interaural phase difference. Spatial selectivity of each second-layer unit was measured by exposing the model to natural sound sources recorded at different positions. Obtained tuning curves match well tuning characteristics of neurons in the mammalian auditory cortex. This study connects neuronal coding of the auditory space with natural stimulus statistics and generates new experimental predictions. Moreover, results presented here suggest that cortical regions with seemingly different functions may implement the same computational strategy-efficient coding. PMID:25996373

Decision Process to Identify Lessons for Transition to a Distributed (or Blended) Learning Instructional Format

DTIC Science & Technology

2009-09-01

instructional format. Using a mixed- method coding and analysis approach, the sample of POIs were categorized, coded, statistically analyzed, and a... Method SECURITY CLASSIFICATION OF 19. LIMITATION OF 20. NUMBER 21. RESPONSIBLE PERSON 16. REPORT Unclassified 17. ABSTRACT...transition to a distributed (or blended) learning format. Procedure: A mixed- methods approach, combining qualitative coding procedures with basic

Statistical regularities in art: Relations with visual coding and perception.

PubMed

Graham, Daniel J; Redies, Christoph

2010-07-21

Since at least 1935, vision researchers have used art stimuli to test human response to complex scenes. This is sensible given the "inherent interestingness" of art and its relation to the natural visual world. The use of art stimuli has remained popular, especially in eye tracking studies. Moreover, stimuli in common use by vision scientists are inspired by the work of famous artists (e.g., Mondrians). Artworks are also popular in vision science as illustrations of a host of visual phenomena, such as depth cues and surface properties. However, until recently, there has been scant consideration of the spatial, luminance, and color statistics of artwork, and even less study of ways that regularities in such statistics could affect visual processing. Furthermore, the relationship between regularities in art images and those in natural scenes has received little or no attention. In the past few years, there has been a concerted effort to study statistical regularities in art as they relate to neural coding and visual perception, and art stimuli have begun to be studied in rigorous ways, as natural scenes have been. In this minireview, we summarize quantitative studies of links between regular statistics in artwork and processing in the visual stream. The results of these studies suggest that art is especially germane to understanding human visual coding and perception, and it therefore warrants wider study. Copyright 2010 Elsevier Ltd. All rights reserved.

Joint Source-Channel Decoding of Variable-Length Codes with Soft Information: A Survey

NASA Astrophysics Data System (ADS)

Guillemot, Christine; Siohan, Pierre

2005-12-01

Multimedia transmission over time-varying wireless channels presents a number of challenges beyond existing capabilities conceived so far for third-generation networks. Efficient quality-of-service (QoS) provisioning for multimedia on these channels may in particular require a loosening and a rethinking of the layer separation principle. In that context, joint source-channel decoding (JSCD) strategies have gained attention as viable alternatives to separate decoding of source and channel codes. A statistical framework based on hidden Markov models (HMM) capturing dependencies between the source and channel coding components sets the foundation for optimal design of techniques of joint decoding of source and channel codes. The problem has been largely addressed in the research community, by considering both fixed-length codes (FLC) and variable-length source codes (VLC) widely used in compression standards. Joint source-channel decoding of VLC raises specific difficulties due to the fact that the segmentation of the received bitstream into source symbols is random. This paper makes a survey of recent theoretical and practical advances in the area of JSCD with soft information of VLC-encoded sources. It first describes the main paths followed for designing efficient estimators for VLC-encoded sources, the key component of the JSCD iterative structure. It then presents the main issues involved in the application of the turbo principle to JSCD of VLC-encoded sources as well as the main approaches to source-controlled channel decoding. This survey terminates by performance illustrations with real image and video decoding systems.

Computational Material Processing in Microgravity

NASA Technical Reports Server (NTRS)

2005-01-01

Working with Professor David Matthiesen at Case Western Reserve University (CWRU) a computer model of the DPIMS (Diffusion Processes in Molten Semiconductors) space experiment was developed that is able to predict the thermal field, flow field and concentration profile within a molten germanium capillary under both ground-based and microgravity conditions as illustrated. These models are coupled with a novel nonlinear statistical methodology for estimating the diffusion coefficient from measured concentration values after a given time that yields a more accurate estimate than traditional methods. This code was integrated into a web-based application that has become a standard tool used by engineers in the Materials Science Department at CWRU.

Period variations of Algol-type eclipsing binaries AD And, TWCas and IV Cas

NASA Astrophysics Data System (ADS)

Parimucha, Štefan; Gajdoš, Pavol; Kudak, Viktor; Fedurco, Miroslav; Vaňko, Martin

2018-04-01

We present new analyses of variations in O – C diagrams of three Algol-type eclipsing binary stars: AD And, TW Cas and IV Cas. We have used all published minima times (including visual and photographic) as well as newly determined ones from our and SuperWasp observations. We determined orbital parameters of 3rd bodies in the systems with statistically significant errors, using our code based on genetic algorithms and Markov chain Monte Carlo simulations. We confirmed the multiple nature of AD And and the triple-star model of TW Cas, and we proposed a quadruple-star model of IV Cas.

Security authentication using phase-encoded nanoparticle structures and polarized light.

PubMed

Carnicer, Artur; Hassanfiroozi, Amir; Latorre-Carmona, Pedro; Huang, Yi-Pai; Javidi, Bahram

2015-01-15

Phase-encoded nanostructures such as quick response (QR) codes made of metallic nanoparticles are suggested to be used in security and authentication applications. We present a polarimetric optical method able to authenticate random phase-encoded QR codes. The system is illuminated using polarized light, and the QR code is encoded using a phase-only random mask. Using classification algorithms, it is possible to validate the QR code from the examination of the polarimetric signature of the speckle pattern. We used Kolmogorov-Smirnov statistical test and Support Vector Machine algorithms to authenticate the phase-encoded QR codes using polarimetric signatures.

Information theory of adaptation in neurons, behavior, and mood.

PubMed

Sharpee, Tatyana O; Calhoun, Adam J; Chalasani, Sreekanth H

2014-04-01

The ability to make accurate predictions of future stimuli and consequences of one's actions are crucial for the survival and appropriate decision-making. These predictions are constantly being made at different levels of the nervous system. This is evidenced by adaptation to stimulus parameters in sensory coding, and in learning of an up-to-date model of the environment at the behavioral level. This review will discuss recent findings that actions of neurons and animals are selected based on detailed stimulus history in such a way as to maximize information for achieving the task at hand. Information maximization dictates not only how sensory coding should adapt to various statistical aspects of stimuli, but also that reward function should adapt to match the predictive information from past to future. Copyright © 2013 Elsevier Ltd. All rights reserved.

Spectral analysis of variable-length coded digital signals

NASA Astrophysics Data System (ADS)

Cariolaro, G. L.; Pierobon, G. L.; Pupolin, S. G.

1982-05-01

A spectral analysis is conducted for a variable-length word sequence by an encoder driven by a stationary memoryless source. A finite-state sequential machine is considered as a model of the line encoder, and the spectral analysis of the encoded message is performed under the assumption that the sourceword sequence is composed of independent identically distributed words. Closed form expressions for both the continuous and discrete parts of the spectral density are derived in terms of the encoder law and sourceword statistics. The jump part exhibits jumps at multiple integers of per lambda(sub 0)T, where lambda(sub 0) is the greatest common divisor of the possible codeword lengths, and T is the symbol period. The derivation of the continuous part can be conveniently factorized, and the theory is applied to the spectral analysis of BnZS and HDBn codes.

An open-access CMIP5 pattern library for temperature and precipitation: Description and methodology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lynch, Cary D.; Hartin, Corinne A.; Bond-Lamberty, Benjamin

Pattern scaling is used to efficiently emulate general circulation models and explore uncertainty in climate projections under multiple forcing scenarios. Pattern scaling methods assume that local climate changes scale with a global mean temperature increase, allowing for spatial patterns to be generated for multiple models for any future emission scenario. For uncertainty quantification and probabilistic statistical analysis, a library of patterns with descriptive statistics for each file would be beneficial, but such a library does not presently exist. Of the possible techniques used to generate patterns, the two most prominent are the delta and least squared regression methods. We exploremore » the differences and statistical significance between patterns generated by each method and assess performance of the generated patterns across methods and scenarios. Differences in patterns across seasons between methods and epochs were largest in high latitudes (60-90°N/S). Bias and mean errors between modeled and pattern predicted output from the linear regression method were smaller than patterns generated by the delta method. Across scenarios, differences in the linear regression method patterns were more statistically significant, especially at high latitudes. We found that pattern generation methodologies were able to approximate the forced signal of change to within ≤ 0.5°C, but choice of pattern generation methodology for pattern scaling purposes should be informed by user goals and criteria. As a result, this paper describes our library of least squared regression patterns from all CMIP5 models for temperature and precipitation on an annual and sub-annual basis, along with the code used to generate these patterns.« less

An open-access CMIP5 pattern library for temperature and precipitation: Description and methodology

DOE PAGES

Lynch, Cary D.; Hartin, Corinne A.; Bond-Lamberty, Benjamin; ...

2017-05-15

Pattern scaling is used to efficiently emulate general circulation models and explore uncertainty in climate projections under multiple forcing scenarios. Pattern scaling methods assume that local climate changes scale with a global mean temperature increase, allowing for spatial patterns to be generated for multiple models for any future emission scenario. For uncertainty quantification and probabilistic statistical analysis, a library of patterns with descriptive statistics for each file would be beneficial, but such a library does not presently exist. Of the possible techniques used to generate patterns, the two most prominent are the delta and least squared regression methods. We exploremore » the differences and statistical significance between patterns generated by each method and assess performance of the generated patterns across methods and scenarios. Differences in patterns across seasons between methods and epochs were largest in high latitudes (60-90°N/S). Bias and mean errors between modeled and pattern predicted output from the linear regression method were smaller than patterns generated by the delta method. Across scenarios, differences in the linear regression method patterns were more statistically significant, especially at high latitudes. We found that pattern generation methodologies were able to approximate the forced signal of change to within ≤ 0.5°C, but choice of pattern generation methodology for pattern scaling purposes should be informed by user goals and criteria. As a result, this paper describes our library of least squared regression patterns from all CMIP5 models for temperature and precipitation on an annual and sub-annual basis, along with the code used to generate these patterns.« less

Evaluation of seismic design spectrum based on UHS implementing fourth-generation seismic hazard maps of Canada

NASA Astrophysics Data System (ADS)

Ahmed, Ali; Hasan, Rafiq; Pekau, Oscar A.

2016-12-01

Two recent developments have come into the forefront with reference to updating the seismic design provisions for codes: (1) publication of new seismic hazard maps for Canada by the Geological Survey of Canada, and (2) emergence of the concept of new spectral format outdating the conventional standardized spectral format. The fourth -generation seismic hazard maps are based on enriched seismic data, enhanced knowledge of regional seismicity and improved seismic hazard modeling techniques. Therefore, the new maps are more accurate and need to incorporate into the Canadian Highway Bridge Design Code (CHBDC) for its next edition similar to its building counterpart National Building Code of Canada (NBCC). In fact, the code writers expressed similar intentions with comments in the commentary of CHBCD 2006. During the process of updating codes, NBCC, and AASHTO Guide Specifications for LRFD Seismic Bridge Design, American Association of State Highway and Transportation Officials, Washington (2009) lowered the probability level from 10 to 2% and 10 to 5%, respectively. This study has brought five sets of hazard maps corresponding to 2%, 5% and 10% probability of exceedance in 50 years developed by the GSC under investigation. To have a sound statistical inference, 389 Canadian cities are selected. This study shows the implications of the changes of new hazard maps on the design process (i.e., extent of magnification or reduction of the design forces).

Extending R packages to support 64-bit compiled code: An illustration with spam64 and GIMMS NDVI3g data

NASA Astrophysics Data System (ADS)

Gerber, Florian; Mösinger, Kaspar; Furrer, Reinhard

2017-07-01

Software packages for spatial data often implement a hybrid approach of interpreted and compiled programming languages. The compiled parts are usually written in C, C++, or Fortran, and are efficient in terms of computational speed and memory usage. Conversely, the interpreted part serves as a convenient user-interface and calls the compiled code for computationally demanding operations. The price paid for the user friendliness of the interpreted component is-besides performance-the limited access to low level and optimized code. An example of such a restriction is the 64-bit vector support of the widely used statistical language R. On the R side, users do not need to change existing code and may not even notice the extension. On the other hand, interfacing 64-bit compiled code efficiently is challenging. Since many R packages for spatial data could benefit from 64-bit vectors, we investigate strategies to efficiently pass 64-bit vectors to compiled languages. More precisely, we show how to simply extend existing R packages using the foreign function interface to seamlessly support 64-bit vectors. This extension is shown with the sparse matrix algebra R package spam. The new capabilities are illustrated with an example of GIMMS NDVI3g data featuring a parametric modeling approach for a non-stationary covariance matrix.

Parallelization of a Monte Carlo particle transport simulation code

NASA Astrophysics Data System (ADS)

Hadjidoukas, P.; Bousis, C.; Emfietzoglou, D.

2010-05-01

We have developed a high performance version of the Monte Carlo particle transport simulation code MC4. The original application code, developed in Visual Basic for Applications (VBA) for Microsoft Excel, was first rewritten in the C programming language for improving code portability. Several pseudo-random number generators have been also integrated and studied. The new MC4 version was then parallelized for shared and distributed-memory multiprocessor systems using the Message Passing Interface. Two parallel pseudo-random number generator libraries (SPRNG and DCMT) have been seamlessly integrated. The performance speedup of parallel MC4 has been studied on a variety of parallel computing architectures including an Intel Xeon server with 4 dual-core processors, a Sun cluster consisting of 16 nodes of 2 dual-core AMD Opteron processors and a 200 dual-processor HP cluster. For large problem size, which is limited only by the physical memory of the multiprocessor server, the speedup results are almost linear on all systems. We have validated the parallel implementation against the serial VBA and C implementations using the same random number generator. Our experimental results on the transport and energy loss of electrons in a water medium show that the serial and parallel codes are equivalent in accuracy. The present improvements allow for studying of higher particle energies with the use of more accurate physical models, and improve statistics as more particles tracks can be simulated in low response time.

PopCORN: Hunting down the differences between binary population synthesis codes

NASA Astrophysics Data System (ADS)

Toonen, S.; Claeys, J. S. W.; Mennekens, N.; Ruiter, A. J.

2014-02-01

Context. Binary population synthesis (BPS) modelling is a very effective tool to study the evolution and properties of various types of close binary systems. The uncertainty in the parameters of the model and their effect on a population can be tested in a statistical way, which then leads to a deeper understanding of the underlying (sometimes poorly understood) physical processes involved. Several BPS codes exist that have been developed with different philosophies and aims. Although BPS has been very successful for studies of many populations of binary stars, in the particular case of the study of the progenitors of supernovae Type Ia, the predicted rates and ZAMS progenitors vary substantially between different BPS codes. Aims: To understand the predictive power of BPS codes, we study the similarities and differences in the predictions of four different BPS codes for low- and intermediate-mass binaries. We investigate the differences in the characteristics of the predicted populations, and whether they are caused by different assumptions made in the BPS codes or by numerical effects, e.g. a lack of accuracy in BPS codes. Methods: We compare a large number of evolutionary sequences for binary stars, starting with the same initial conditions following the evolution until the first (and when applicable, the second) white dwarf (WD) is formed. To simplify the complex problem of comparing BPS codes that are based on many (often different) assumptions, we equalise the assumptions as much as possible to examine the inherent differences of the four BPS codes. Results: We find that the simulated populations are similar between the codes. Regarding the population of binaries with one WD, there is very good agreement between the physical characteristics, the evolutionary channels that lead to the birth of these systems, and their birthrates. Regarding the double WD population, there is a good agreement on which evolutionary channels exist to create double WDs and a rough agreement on the characteristics of the double WD population. Regarding which progenitor systems lead to a single and double WD system and which systems do not, the four codes agree well. Most importantly, we find that for these two populations, the differences in the predictions from the four codes are not due to numerical differences, but because of different inherent assumptions. We identify critical assumptions for BPS studies that need to be studied in more detail. Appendices are available in electronic form at http://www.aanda.org

Summary statistics in the attentional blink.

PubMed

McNair, Nicolas A; Goodbourn, Patrick T; Shone, Lauren T; Harris, Irina M

2017-01-01

We used the attentional blink (AB) paradigm to investigate the processing stage at which extraction of summary statistics from visual stimuli ("ensemble coding") occurs. Experiment 1 examined whether ensemble coding requires attentional engagement with the items in the ensemble. Participants performed two sequential tasks on each trial: gender discrimination of a single face (T1) and estimating the average emotional expression of an ensemble of four faces (or of a single face, as a control condition) as T2. Ensemble coding was affected by the AB when the tasks were separated by a short temporal lag. In Experiment 2, the order of the tasks was reversed to test whether ensemble coding requires more working-memory resources, and therefore induces a larger AB, than estimating the expression of a single face. Each condition produced a similar magnitude AB in the subsequent gender-discrimination T2 task. Experiment 3 additionally investigated whether the previous results were due to participants adopting a subsampling strategy during the ensemble-coding task. Contrary to this explanation, we found different patterns of performance in the ensemble-coding condition and a condition in which participants were instructed to focus on only a single face within an ensemble. Taken together, these findings suggest that ensemble coding emerges automatically as a result of the deployment of attentional resources across the ensemble of stimuli, prior to information being consolidated in working memory.

A system for classifying wood-using industries and recording statistics for automatic data processing.

Treesearch

E.W. Fobes; R.W. Rowe

1968-01-01

A system for classifying wood-using industries and recording pertinent statistics for automatic data processing is described. Forms and coding instructions for recording data of primary processing plants are included.

Method and system for efficient video compression with low-complexity encoder

NASA Technical Reports Server (NTRS)

Chen, Jun (Inventor); He, Dake (Inventor); Sheinin, Vadim (Inventor); Jagmohan, Ashish (Inventor); Lu, Ligang (Inventor)

2012-01-01

Disclosed are a method and system for video compression, wherein the video encoder has low computational complexity and high compression efficiency. The disclosed system comprises a video encoder and a video decoder, wherein the method for encoding includes the steps of converting a source frame into a space-frequency representation; estimating conditional statistics of at least one vector of space-frequency coefficients; estimating encoding rates based on the said conditional statistics; and applying Slepian-Wolf codes with the said computed encoding rates. The preferred method for decoding includes the steps of; generating a side-information vector of frequency coefficients based on previously decoded source data, encoder statistics, and previous reconstructions of the source frequency vector; and performing Slepian-Wolf decoding of at least one source frequency vector based on the generated side-information, the Slepian-Wolf code bits and the encoder statistics.

29 CFR 510.21 - SIC codes.

Code of Federal Regulations, 2012 CFR

2012-07-01

... annual Census of Manufacturing Industries as a source of average hourly wage data by industry. Industries in that census are organized by Standard Industrial Classification (SIC), the statistical... stated that data “should be at a level of specificity comparable to the four digit Standard Industry Code...

29 CFR 510.21 - SIC codes.

Code of Federal Regulations, 2014 CFR

2014-07-01

... annual Census of Manufacturing Industries as a source of average hourly wage data by industry. Industries in that census are organized by Standard Industrial Classification (SIC), the statistical... stated that data “should be at a level of specificity comparable to the four digit Standard Industry Code...

29 CFR 510.21 - SIC codes.

Code of Federal Regulations, 2013 CFR

2013-07-01

... annual Census of Manufacturing Industries as a source of average hourly wage data by industry. Industries in that census are organized by Standard Industrial Classification (SIC), the statistical... stated that data “should be at a level of specificity comparable to the four digit Standard Industry Code...

29 CFR 510.21 - SIC codes.

Code of Federal Regulations, 2011 CFR

2011-07-01

... annual Census of Manufacturing Industries as a source of average hourly wage data by industry. Industries in that census are organized by Standard Industrial Classification (SIC), the statistical... stated that data “should be at a level of specificity comparable to the four digit Standard Industry Code...

Cracking the Neural Code for Sensory Perception by Combining Statistics, Intervention, and Behavior.

PubMed

Panzeri, Stefano; Harvey, Christopher D; Piasini, Eugenio; Latham, Peter E; Fellin, Tommaso

2017-02-08

The two basic processes underlying perceptual decisions-how neural responses encode stimuli, and how they inform behavioral choices-have mainly been studied separately. Thus, although many spatiotemporal features of neural population activity, or "neural codes," have been shown to carry sensory information, it is often unknown whether the brain uses these features for perception. To address this issue, we propose a new framework centered on redefining the neural code as the neural features that carry sensory information used by the animal to drive appropriate behavior; that is, the features that have an intersection between sensory and choice information. We show how this framework leads to a new statistical analysis of neural activity recorded during behavior that can identify such neural codes, and we discuss how to combine intersection-based analysis of neural recordings with intervention on neural activity to determine definitively whether specific neural activity features are involved in a task. Copyright © 2017 Elsevier Inc. All rights reserved.

The discounting model selector: Statistical software for delay discounting applications.

PubMed

Gilroy, Shawn P; Franck, Christopher T; Hantula, Donald A

2017-05-01

Original, open-source computer software was developed and validated against established delay discounting methods in the literature. The software executed approximate Bayesian model selection methods from user-supplied temporal discounting data and computed the effective delay 50 (ED50) from the best performing model. Software was custom-designed to enable behavior analysts to conveniently apply recent statistical methods to temporal discounting data with the aid of a graphical user interface (GUI). The results of independent validation of the approximate Bayesian model selection methods indicated that the program provided results identical to that of the original source paper and its methods. Monte Carlo simulation (n = 50,000) confirmed that true model was selected most often in each setting. Simulation code and data for this study were posted to an online repository for use by other researchers. The model selection approach was applied to three existing delay discounting data sets from the literature in addition to the data from the source paper. Comparisons of model selected ED50 were consistent with traditional indices of discounting. Conceptual issues related to the development and use of computer software by behavior analysts and the opportunities afforded by free and open-sourced software are discussed and a review of possible expansions of this software are provided. © 2017 Society for the Experimental Analysis of Behavior.

Clusters in irregular areas and lattices.

PubMed

Wieczorek, William F; Delmerico, Alan M; Rogerson, Peter A; Wong, David W S

2012-01-01

Geographic areas of different sizes and shapes of polygons that represent counts or rate data are often encountered in social, economic, health, and other information. Often political or census boundaries are used to define these areas because the information is available only for those geographies. Therefore, these types of boundaries are frequently used to define neighborhoods in spatial analyses using geographic information systems and related approaches such as multilevel models. When point data can be geocoded, it is possible to examine the impact of polygon shape on spatial statistical properties, such as clustering. We utilized point data (alcohol outlets) to examine the issue of polygon shape and size on visualization and statistical properties. The point data were allocated to regular lattices (hexagons and squares) and census areas for zip-code tabulation areas and tracts. The number of units in the lattices was set to be similar to the number of tract and zip-code areas. A spatial clustering statistic and visualization were used to assess the impact of polygon shape for zip- and tract-sized units. Results showed substantial similarities and notable differences across shape and size. The specific circumstances of a spatial analysis that aggregates points to polygons will determine the size and shape of the areal units to be used. The irregular polygons of census units may reflect underlying characteristics that could be missed by large regular lattices. Future research to examine the potential for using a combination of irregular polygons and regular lattices would be useful.

Envelope statistics of self-motion signals experienced by human subjects during everyday activities: Implications for vestibular processing.

PubMed

Carriot, Jérome; Jamali, Mohsen; Cullen, Kathleen E; Chacron, Maurice J

2017-01-01

There is accumulating evidence that the brain's neural coding strategies are constrained by natural stimulus statistics. Here we investigated the statistics of the time varying envelope (i.e. a second-order stimulus attribute that is related to variance) of rotational and translational self-motion signals experienced by human subjects during everyday activities. We found that envelopes can reach large values across all six motion dimensions (~450 deg/s for rotations and ~4 G for translations). Unlike results obtained in other sensory modalities, the spectral power of envelope signals decreased slowly for low (< 2 Hz) and more sharply for high (>2 Hz) temporal frequencies and thus was not well-fit by a power law. We next compared the spectral properties of envelope signals resulting from active and passive self-motion, as well as those resulting from signals obtained when the subject is absent (i.e. external stimuli). Our data suggest that different mechanisms underlie deviation from scale invariance in rotational and translational self-motion envelopes. Specifically, active self-motion and filtering by the human body cause deviation from scale invariance primarily for translational and rotational envelope signals, respectively. Finally, we used well-established models in order to predict the responses of peripheral vestibular afferents to natural envelope stimuli. We found that irregular afferents responded more strongly to envelopes than their regular counterparts. Our findings have important consequences for understanding the coding strategies used by the vestibular system to process natural second-order self-motion signals.

The FORTRAN static source code analyzer program (SAP) system description

NASA Technical Reports Server (NTRS)

Decker, W.; Taylor, W.; Merwarth, P.; Oneill, M.; Goorevich, C.; Waligora, S.

1982-01-01

A source code analyzer program (SAP) designed to assist personnel in conducting studies of FORTRAN programs is described. The SAP scans FORTRAN source code and produces reports that present statistics and measures of statements and structures that make up a module. The processing performed by SAP and of the routines, COMMON blocks, and files used by SAP are described. The system generation procedure for SAP is also presented.

Statistical inference of static analysis rules

NASA Technical Reports Server (NTRS)

Engler, Dawson Richards (Inventor)

2009-01-01

Various apparatus and methods are disclosed for identifying errors in program code. Respective numbers of observances of at least one correctness rule by different code instances that relate to the at least one correctness rule are counted in the program code. Each code instance has an associated counted number of observances of the correctness rule by the code instance. Also counted are respective numbers of violations of the correctness rule by different code instances that relate to the correctness rule. Each code instance has an associated counted number of violations of the correctness rule by the code instance. A respective likelihood of the validity is determined for each code instance as a function of the counted number of observances and counted number of violations. The likelihood of validity indicates a relative likelihood that a related code instance is required to observe the correctness rule. The violations may be output in order of the likelihood of validity of a violated correctness rule.

Noise Estimation and Adaptive Encoding for Asymmetric Quantum Error Correcting Codes

NASA Astrophysics Data System (ADS)

Florjanczyk, Jan; Brun, Todd; CenterQuantum Information Science; Technology Team

We present a technique that improves the performance of asymmetric quantum error correcting codes in the presence of biased qubit noise channels. Our study is motivated by considering what useful information can be learned from the statistics of syndrome measurements in stabilizer quantum error correcting codes (QECC). We consider the case of a qubit dephasing channel where the dephasing axis is unknown and time-varying. We are able to estimate the dephasing angle from the statistics of the standard syndrome measurements used in stabilizer QECC's. We use this estimate to rotate the computational basis of the code in such a way that the most likely type of error is covered by the highest distance of the asymmetric code. In particular, we use the [ [ 15 , 1 , 3 ] ] shortened Reed-Muller code which can correct one phase-flip error but up to three bit-flip errors. In our simulations, we tune the computational basis to match the estimated dephasing axis which in turn leads to a decrease in the probability of a phase-flip error. With a sufficiently accurate estimate of the dephasing axis, our memory's effective error is dominated by the much lower probability of four bit-flips. Aro MURI Grant No. W911NF-11-1-0268.

The Role of Margin in Link Design and Optimization

NASA Technical Reports Server (NTRS)

Cheung, K.

2015-01-01

Link analysis is a system engineering process in the design, development, and operation of communication systems and networks. Link models that are mathematical abstractions representing the useful signal power and the undesirable noise and attenuation effects (including weather effects if the signal path transverses through the atmosphere) that are integrated into the link budget calculation that provides the estimates of signal power and noise power at the receiver. Then the link margin is applied which attempts to counteract the fluctuations of the signal and noise power to ensure reliable data delivery from transmitter to receiver. (Link margin is dictated by the link margin policy or requirements.) A simple link budgeting approach assumes link parameters to be deterministic values typically adopted a rule-of-thumb policy of 3 dB link margin. This policy works for most S- and X-band links due to their insensitivity to weather effects. But for higher frequency links like Ka-band, Ku-band, and optical communication links, it is unclear if a 3 dB link margin would guarantee link closure. Statistical link analysis that adopted the 2-sigma or 3-sigma link margin incorporates link uncertainties in the sigma calculation. (The Deep Space Network (DSN) link margin policies are 2-sigma for downlink and 3-sigma for uplink.) The link reliability can therefore be quantified statistically even for higher frequency links. However in the current statistical link analysis approach, link reliability is only expressed as the likelihood of exceeding the signal-to-noise ratio (SNR) threshold that corresponds to a given bit-error-rate (BER) or frame-error-rate (FER) requirement. The method does not provide the true BER or FER estimate of the link with margin, or the required signalto-noise ratio (SNR) that would meet the BER or FER requirement in the statistical sense. In this paper, we perform in-depth analysis on the relationship between BER/FER requirement, operating SNR, and coding performance curve, in the case when the channel coherence time of link fluctuation is comparable or larger than the time duration of a codeword. We compute the "true" SNR design point that would meet the BER/FER requirement by taking into account the fluctuation of signal power and noise power at the receiver, and the shape of the coding performance curve. This analysis yields a number of valuable insights on the design choices of coding scheme and link margin for the reliable data delivery of a communication system - space and ground. We illustrate the aforementioned analysis using a number of standard NASA error-correcting codes.

Entraining IDyOT: Timing in the Information Dynamics of Thinking

PubMed Central

Forth, Jamie; Agres, Kat; Purver, Matthew; Wiggins, Geraint A.

2016-01-01

We present a novel hypothetical account of entrainment in music and language, in context of the Information Dynamics of Thinking model, IDyOT. The extended model affords an alternative view of entrainment, and its companion term, pulse, from earlier accounts. The model is based on hierarchical, statistical prediction, modeling expectations of both what an event will be and when it will happen. As such, it constitutes a kind of predictive coding, with a particular novel hypothetical implementation. Here, we focus on the model's mechanism for predicting when a perceptual event will happen, given an existing sequence of past events, which may be musical or linguistic. We propose a range of tests to validate or falsify the model, at various different levels of abstraction, and argue that computational modeling in general, and this model in particular, can offer a means of providing limited but useful evidence for evolutionary hypotheses. PMID:27803682

Comparison of heavy-ion transport simulations: Collision integral in a box

NASA Astrophysics Data System (ADS)

Zhang, Ying-Xun; Wang, Yong-Jia; Colonna, Maria; Danielewicz, Pawel; Ono, Akira; Tsang, Manyee Betty; Wolter, Hermann; Xu, Jun; Chen, Lie-Wen; Cozma, Dan; Feng, Zhao-Qing; Das Gupta, Subal; Ikeno, Natsumi; Ko, Che-Ming; Li, Bao-An; Li, Qing-Feng; Li, Zhu-Xia; Mallik, Swagata; Nara, Yasushi; Ogawa, Tatsuhiko; Ohnishi, Akira; Oliinychenko, Dmytro; Papa, Massimo; Petersen, Hannah; Su, Jun; Song, Taesoo; Weil, Janus; Wang, Ning; Zhang, Feng-Shou; Zhang, Zhen

2018-03-01

Simulations by transport codes are indispensable to extract valuable physical information from heavy-ion collisions. In order to understand the origins of discrepancies among different widely used transport codes, we compare 15 such codes under controlled conditions of a system confined to a box with periodic boundary, initialized with Fermi-Dirac distributions at saturation density and temperatures of either 0 or 5 MeV. In such calculations, one is able to check separately the different ingredients of a transport code. In this second publication of the code evaluation project, we only consider the two-body collision term; i.e., we perform cascade calculations. When the Pauli blocking is artificially suppressed, the collision rates are found to be consistent for most codes (to within 1 % or better) with analytical results, or completely controlled results of a basic cascade code. In orderto reach that goal, it was necessary to eliminate correlations within the same pair of colliding particles that can be present depending on the adopted collision prescription. In calculations with active Pauli blocking, the blocking probability was found to deviate from the expected reference values. The reason is found in substantial phase-space fluctuations and smearing tied to numerical algorithms and model assumptions in the representation of phase space. This results in the reduction of the blocking probability in most transport codes, so that the simulated system gradually evolves away from the Fermi-Dirac toward a Boltzmann distribution. Since the numerical fluctuations are weaker in the Boltzmann-Uehling-Uhlenbeck codes, the Fermi-Dirac statistics is maintained there for a longer time than in the quantum molecular dynamics codes. As a result of this investigation, we are able to make judgements about the most effective strategies in transport simulations for determining the collision probabilities and the Pauli blocking. Investigation in a similar vein of other ingredients in transport calculations, like the mean-field propagation or the production of nucleon resonances and mesons, will be discussed in the future publications.

Evaluation of the flame propagation within an SI engine using flame imaging and LES

NASA Astrophysics Data System (ADS)

He, Chao; Kuenne, Guido; Yildar, Esra; van Oijen, Jeroen; di Mare, Francesca; Sadiki, Amsini; Ding, Carl-Philipp; Baum, Elias; Peterson, Brian; Böhm, Benjamin; Janicka, Johannes

2017-11-01

This work shows experiments and simulations of the fired operation of a spark ignition engine with port-fuelled injection. The test rig considered is an optically accessible single cylinder engine specifically designed at TU Darmstadt for the detailed investigation of in-cylinder processes and model validation. The engine was operated under lean conditions using iso-octane as a substitute for gasoline. Experiments have been conducted to provide a sound database of the combustion process. A planar flame imaging technique has been applied within the swirl- and tumble-planes to provide statistical information on the combustion process to complement a pressure-based comparison between simulation and experiments. This data is then analysed and used to assess the large eddy simulation performed within this work. For the simulation, the engine code KIVA has been extended by the dynamically thickened flame model combined with chemistry reduction by means of pressure dependent tabulation. Sixty cycles have been simulated to perform a statistical evaluation. Based on a detailed comparison with the experimental data, a systematic study has been conducted to obtain insight into the most crucial modelling uncertainties.

Computing and Visualizing the Complex Dynamics of Earthquake Fault Systems: Towards Ensemble Earthquake Forecasting

NASA Astrophysics Data System (ADS)

Rundle, J.; Rundle, P.; Donnellan, A.; Li, P.

2003-12-01

We consider the problem of the complex dynamics of earthquake fault systems, and whether numerical simulations can be used to define an ensemble forecasting technology similar to that used in weather and climate research. To effectively carry out such a program, we need 1) a topological realistic model to simulate the fault system; 2) data sets to constrain the model parameters through a systematic program of data assimilation; 3) a computational technology making use of modern paradigms of high performance and parallel computing systems; and 4) software to visualize and analyze the results. In particular, we focus attention of a new version of our code Virtual California (version 2001) in which we model all of the major strike slip faults extending throughout California, from the Mexico-California border to the Mendocino Triple Junction. We use the historic data set of earthquakes larger than magnitude M > 6 to define the frictional properties of all 654 fault segments (degrees of freedom) in the model. Previous versions of Virtual California had used only 215 fault segments to model the strike slip faults in southern California. To compute the dynamics and the associated surface deformation, we use message passing as implemented in the MPICH standard distribution on a small Beowulf cluster consisting of 10 cpus. We are also planning to run the code on significantly larger machines so that we can begin to examine much finer spatial scales of resolution, and to assess scaling properties of the code. We present results of simulations both as static images and as mpeg movies, so that the dynamical aspects of the computation can be assessed by the viewer. We also compute a variety of statistics from the simulations, including magnitude-frequency relations, and compare these with data from real fault systems.

PAKDD Data Mining Competition 2009: New Ways of Using Known Methods

NASA Astrophysics Data System (ADS)

Linhart, Chaim; Harari, Guy; Abramovich, Sharon; Buchris, Altina

The PAKDD 2009 competition focuses on the problem of credit risk assessment. As required, we had to confront the problem of the robustness of the credit-scoring model against performance degradation caused by gradual market changes along a few years of business operation. We utilized the following standard models: logistic regression, KNN, SVM, GBM and decision tree. The novelty of our approach is two-fold: the integration of existing models, namely feeding the results of KNN as an input variable to the logistic regression, and re-coding categorical variables as numerical values that represent each category's statistical impact on the target label. The best solution we obtained reached 3rd place in the competition, with an AUC score of 0.655.

A Sub-filter Scale Noise Equation far Hybrid LES Simulations

NASA Technical Reports Server (NTRS)

Goldstein, Marvin E.

2006-01-01

Hybrid LES/subscale modeling approaches have an important advantage over the current noise prediction methods in that they only involve modeling of the relatively universal subscale motion and not the configuration dependent larger scale turbulence . Previous hybrid approaches use approximate statistical techniques or extrapolation methods to obtain the requisite information about the sub-filter scale motion. An alternative approach would be to adopt the modeling techniques used in the current noise prediction methods and determine the unknown stresses from experimental data. The present paper derives an equation for predicting the sub scale sound from information that can be obtained with currently available experimental procedures. The resulting prediction method would then be intermediate between the current noise prediction codes and previously proposed hybrid techniques.

A Hebbian learning rule gives rise to mirror neurons and links them to control theoretic inverse models.

PubMed

Hanuschkin, A; Ganguli, S; Hahnloser, R H R

2013-01-01

Mirror neurons are neurons whose responses to the observation of a motor act resemble responses measured during production of that act. Computationally, mirror neurons have been viewed as evidence for the existence of internal inverse models. Such models, rooted within control theory, map-desired sensory targets onto the motor commands required to generate those targets. To jointly explore both the formation of mirrored responses and their functional contribution to inverse models, we develop a correlation-based theory of interactions between a sensory and a motor area. We show that a simple eligibility-weighted Hebbian learning rule, operating within a sensorimotor loop during motor explorations and stabilized by heterosynaptic competition, naturally gives rise to mirror neurons as well as control theoretic inverse models encoded in the synaptic weights from sensory to motor neurons. Crucially, we find that the correlational structure or stereotypy of the neural code underlying motor explorations determines the nature of the learned inverse model: random motor codes lead to causal inverses that map sensory activity patterns to their motor causes; such inverses are maximally useful, by allowing the imitation of arbitrary sensory target sequences. By contrast, stereotyped motor codes lead to less useful predictive inverses that map sensory activity to future motor actions. Our theory generalizes previous work on inverse models by showing that such models can be learned in a simple Hebbian framework without the need for error signals or backpropagation, and it makes new conceptual connections between the causal nature of inverse models, the statistical structure of motor variability, and the time-lag between sensory and motor responses of mirror neurons. Applied to bird song learning, our theory can account for puzzling aspects of the song system, including necessity of sensorimotor gating and selectivity of auditory responses to bird's own song (BOS) stimuli.

A Hebbian learning rule gives rise to mirror neurons and links them to control theoretic inverse models

PubMed Central

Hanuschkin, A.; Ganguli, S.; Hahnloser, R. H. R.

2013-01-01

Mirror neurons are neurons whose responses to the observation of a motor act resemble responses measured during production of that act. Computationally, mirror neurons have been viewed as evidence for the existence of internal inverse models. Such models, rooted within control theory, map-desired sensory targets onto the motor commands required to generate those targets. To jointly explore both the formation of mirrored responses and their functional contribution to inverse models, we develop a correlation-based theory of interactions between a sensory and a motor area. We show that a simple eligibility-weighted Hebbian learning rule, operating within a sensorimotor loop during motor explorations and stabilized by heterosynaptic competition, naturally gives rise to mirror neurons as well as control theoretic inverse models encoded in the synaptic weights from sensory to motor neurons. Crucially, we find that the correlational structure or stereotypy of the neural code underlying motor explorations determines the nature of the learned inverse model: random motor codes lead to causal inverses that map sensory activity patterns to their motor causes; such inverses are maximally useful, by allowing the imitation of arbitrary sensory target sequences. By contrast, stereotyped motor codes lead to less useful predictive inverses that map sensory activity to future motor actions. Our theory generalizes previous work on inverse models by showing that such models can be learned in a simple Hebbian framework without the need for error signals or backpropagation, and it makes new conceptual connections between the causal nature of inverse models, the statistical structure of motor variability, and the time-lag between sensory and motor responses of mirror neurons. Applied to bird song learning, our theory can account for puzzling aspects of the song system, including necessity of sensorimotor gating and selectivity of auditory responses to bird's own song (BOS) stimuli. PMID:23801941

*K-means and cluster models for cancer signatures.

PubMed

Kakushadze, Zura; Yu, Willie

2017-09-01

We present *K-means clustering algorithm and source code by expanding statistical clustering methods applied in https://ssrn.com/abstract=2802753 to quantitative finance. *K-means is statistically deterministic without specifying initial centers, etc. We apply *K-means to extracting cancer signatures from genome data without using nonnegative matrix factorization (NMF). *K-means' computational cost is a fraction of NMF's. Using 1389 published samples for 14 cancer types, we find that 3 cancers (liver cancer, lung cancer and renal cell carcinoma) stand out and do not have cluster-like structures. Two clusters have especially high within-cluster correlations with 11 other cancers indicating common underlying structures. Our approach opens a novel avenue for studying such structures. *K-means is universal and can be applied in other fields. We discuss some potential applications in quantitative finance.

Comparison of transform coding methods with an optimal predictor for the data compression of digital elevation models

NASA Technical Reports Server (NTRS)

Lewis, Michael

1994-01-01

Statistical encoding techniques enable the reduction of the number of bits required to encode a set of symbols, and are derived from their probabilities. Huffman encoding is an example of statistical encoding that has been used for error-free data compression. The degree of compression given by Huffman encoding in this application can be improved by the use of prediction methods. These replace the set of elevations by a set of corrections that have a more advantageous probability distribution. In particular, the method of Lagrange Multipliers for minimization of the mean square error has been applied to local geometrical predictors. Using this technique, an 8-point predictor achieved about a 7 percent improvement over an existing simple triangular predictor.

24 CFR 200.926c - Model code provisions for use in partially accepted code jurisdictions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... Minimum Property Standards § 200.926c Model code provisions for use in partially accepted code... partially accepted, then the properties eligible for HUD benefits in that jurisdiction shall be constructed..., those portions of one of the model codes with which the property must comply. Schedule for Model Code...

24 CFR 200.926c - Model code provisions for use in partially accepted code jurisdictions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... Minimum Property Standards § 200.926c Model code provisions for use in partially accepted code... partially accepted, then the properties eligible for HUD benefits in that jurisdiction shall be constructed..., those portions of one of the model codes with which the property must comply. Schedule for Model Code...

Planetarium instructional efficacy: A research synthesis

NASA Astrophysics Data System (ADS)

Brazell, Bruce D.

The purpose of the current study was to explore the instructional effectiveness of the planetarium in astronomy education using meta-analysis. A review of the literature revealed 46 studies related to planetarium efficacy. However, only 19 of the studies satisfied selection criteria for inclusion in the meta-analysis. Selected studies were then subjected to coding procedures, which extracted information such as subject characteristics, experimental design, and outcome measures. From these data, 24 effect sizes were calculated in the area of student achievement and five effect sizes were determined in the area of student attitudes using reported statistical information. Mean effect sizes were calculated for both the achievement and the attitude distributions. Additionally, each effect size distribution was subjected to homogeneity analysis. The attitude distribution was found to be homogeneous with a mean effect size of -0.09, which was not significant, p = .2535. The achievement distribution was found to be heterogeneous with a statistically significant mean effect size of +0.28, p < .05. Since the achievement distribution was heterogeneous, the analog to the ANOVA procedure was employed to explore variability in this distribution in terms of the coded variables. The analog to the ANOVA procedure revealed that the variability introduced by the coded variables did not fully explain the variability in the achievement distribution beyond subject-level sampling error under a fixed effects model. Therefore, a random effects model analysis was performed which resulted in a mean effect size of +0.18, which was not significant, p = .2363. However, a large random effect variance component was determined indicating that the differences between studies were systematic and yet to be revealed. The findings of this meta-analysis showed that the planetarium has been an effective instructional tool in astronomy education in terms of student achievement. However, the meta-analysis revealed that the planetarium has not been a very effective tool for improving student attitudes towards astronomy.

KEWPIE: A dynamical cascade code for decaying exited compound nuclei

NASA Astrophysics Data System (ADS)

Bouriquet, Bertrand; Abe, Yasuhisa; Boilley, David

2004-05-01

A new dynamical cascade code for decaying hot nuclei is proposed and specially adapted to the synthesis of super-heavy nuclei. For such a case, the interesting channel is of the tiny fraction that will decay through particles emission, thus the code avoids classical Monte-Carlo methods and proposes a new numerical scheme. The time dependence is explicitely taken into account in order to cope with the fact that fission decay rate might not be constant. The code allows to evaluate both statistical and dynamical observables. Results are successfully compared to experimental data.

Mapping Quantitative Traits in Unselected Families: Algorithms and Examples

PubMed Central

Dupuis, Josée; Shi, Jianxin; Manning, Alisa K.; Benjamin, Emelia J.; Meigs, James B.; Cupples, L. Adrienne; Siegmund, David

2009-01-01

Linkage analysis has been widely used to identify from family data genetic variants influencing quantitative traits. Common approaches have both strengths and limitations. Likelihood ratio tests typically computed in variance component analysis can accommodate large families but are highly sensitive to departure from normality assumptions. Regression-based approaches are more robust but their use has primarily been restricted to nuclear families. In this paper, we develop methods for mapping quantitative traits in moderately large pedigrees. Our methods are based on the score statistic which in contrast to the likelihood ratio statistic, can use nonparametric estimators of variability to achieve robustness of the false positive rate against departures from the hypothesized phenotypic model. Because the score statistic is easier to calculate than the likelihood ratio statistic, our basic mapping methods utilize relatively simple computer code that performs statistical analysis on output from any program that computes estimates of identity-by-descent. This simplicity also permits development and evaluation of methods to deal with multivariate and ordinal phenotypes, and with gene-gene and gene-environment interaction. We demonstrate our methods on simulated data and on fasting insulin, a quantitative trait measured in the Framingham Heart Study. PMID:19278016

Estimating population diversity with CatchAll

PubMed Central

Bunge, John; Woodard, Linda; Böhning, Dankmar; Foster, James A.; Connolly, Sean; Allen, Heather K.

2012-01-01

Motivation: The massive data produced by next-generation sequencing require advanced statistical tools. We address estimating the total diversity or species richness in a population. To date, only relatively simple methods have been implemented in available software. There is a need for software employing modern, computationally intensive statistical analyses including error, goodness-of-fit and robustness assessments. Results: We present CatchAll, a fast, easy-to-use, platform-independent program that computes maximum likelihood estimates for finite-mixture models, weighted linear regression-based analyses and coverage-based non-parametric methods, along with outlier diagnostics. Given sample ‘frequency count’ data, CatchAll computes 12 different diversity estimates and applies a model-selection algorithm. CatchAll also derives discounted diversity estimates to adjust for possibly uncertain low-frequency counts. It is accompanied by an Excel-based graphics program. Availability: Free executable downloads for Linux, Windows and Mac OS, with manual and source code, at www.northeastern.edu/catchall. Contact: jab18@cornell.edu PMID:22333246

On the uncertain nature of the core of α Cen A

NASA Astrophysics Data System (ADS)

Bazot, M.; Christensen-Dalsgaard, J.; Gizon, L.; Benomar, O.

2016-08-01

High-quality astrometric, spectroscopic, interferometric and, importantly, asteroseismic observations are available for α Cen A, which is the closest binary star system to earth. Taking all these constraints into account, we study the internal structure of the star by means of theoretical modelling. Using the Aarhus STellar Evolution Code (ASTEC) and the tools of Computational Bayesian Statistics, in particular a Markov chain Monte Carlo algorithm, we perform statistical inferences for the physical characteristics of the star. We find that α Cen A has a probability of approximately 40 per cent of having a convective core. This probability drops to few per cent if one considers reduced rates for the 14N(p,γ)15O reaction. These convective cores have fractional radii less than 8 per cent when overshoot is neglected. Including overshooting also leads to the possibility of a convective core mostly sustained by the ppII chain energy output. We finally show that roughly 30 per cent of the stellar models describing α Cen A are in the subgiant regime.

PyEvolve: a toolkit for statistical modelling of molecular evolution.

PubMed

Butterfield, Andrew; Vedagiri, Vivek; Lang, Edward; Lawrence, Cath; Wakefield, Matthew J; Isaev, Alexander; Huttley, Gavin A

2004-01-05

Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences - ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from approximately 10 days to approximately 6 hours. PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be used interactively or by writing and executing scripts. The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. PyEvolve can be readily adapted in response to changing computational demands and hardware configurations to maximise performance. PyEvolve is released under the GPL and can be downloaded from http://cbis.anu.edu.au/software.

Relational machine learning for electronic health record-driven phenotyping.

PubMed

Peissig, Peggy L; Santos Costa, Vitor; Caldwell, Michael D; Rottscheit, Carla; Berg, Richard L; Mendonca, Eneida A; Page, David

2014-12-01

Electronic health records (EHR) offer medical and pharmacogenomics research unprecedented opportunities to identify and classify patients at risk. EHRs are collections of highly inter-dependent records that include biological, anatomical, physiological, and behavioral observations. They comprise a patient's clinical phenome, where each patient has thousands of date-stamped records distributed across many relational tables. Development of EHR computer-based phenotyping algorithms require time and medical insight from clinical experts, who most often can only review a small patient subset representative of the total EHR records, to identify phenotype features. In this research we evaluate whether relational machine learning (ML) using inductive logic programming (ILP) can contribute to addressing these issues as a viable approach for EHR-based phenotyping. Two relational learning ILP approaches and three well-known WEKA (Waikato Environment for Knowledge Analysis) implementations of non-relational approaches (PART, J48, and JRIP) were used to develop models for nine phenotypes. International Classification of Diseases, Ninth Revision (ICD-9) coded EHR data were used to select training cohorts for the development of each phenotypic model. Accuracy, precision, recall, F-Measure, and Area Under the Receiver Operating Characteristic (AUROC) curve statistics were measured for each phenotypic model based on independent manually verified test cohorts. A two-sided binomial distribution test (sign test) compared the five ML approaches across phenotypes for statistical significance. We developed an approach to automatically label training examples using ICD-9 diagnosis codes for the ML approaches being evaluated. Nine phenotypic models for each ML approach were evaluated, resulting in better overall model performance in AUROC using ILP when compared to PART (p=0.039), J48 (p=0.003) and JRIP (p=0.003). ILP has the potential to improve phenotyping by independently delivering clinically expert interpretable rules for phenotype definitions, or intuitive phenotypes to assist experts. Relational learning using ILP offers a viable approach to EHR-driven phenotyping. Copyright © 2014 Elsevier Inc. All rights reserved.

Structural Life and Reliability Metrics: Benchmarking and Verification of Probabilistic Life Prediction Codes

NASA Technical Reports Server (NTRS)

Litt, Jonathan S.; Soditus, Sherry; Hendricks, Robert C.; Zaretsky, Erwin V.

2002-01-01

Over the past two decades there has been considerable effort by NASA Glenn and others to develop probabilistic codes to predict with reasonable engineering certainty the life and reliability of critical components in rotating machinery and, more specifically, in the rotating sections of airbreathing and rocket engines. These codes have, to a very limited extent, been verified with relatively small bench rig type specimens under uniaxial loading. Because of the small and very narrow database the acceptance of these codes within the aerospace community has been limited. An alternate approach to generating statistically significant data under complex loading and environments simulating aircraft and rocket engine conditions is to obtain, catalog and statistically analyze actual field data. End users of the engines, such as commercial airlines and the military, record and store operational and maintenance information. This presentation describes a cooperative program between the NASA GRC, United Airlines, USAF Wright Laboratory, U.S. Army Research Laboratory and Australian Aeronautical & Maritime Research Laboratory to obtain and analyze these airline data for selected components such as blades, disks and combustors. These airline data will be used to benchmark and compare existing life prediction codes.

Modeling of Radiotherapy Linac Source Terms Using ARCHER Monte Carlo Code: Performance Comparison for GPU and MIC Parallel Computing Devices

NASA Astrophysics Data System (ADS)

Lin, Hui; Liu, Tianyu; Su, Lin; Bednarz, Bryan; Caracappa, Peter; Xu, X. George

2017-09-01

Monte Carlo (MC) simulation is well recognized as the most accurate method for radiation dose calculations. For radiotherapy applications, accurate modelling of the source term, i.e. the clinical linear accelerator is critical to the simulation. The purpose of this paper is to perform source modelling and examine the accuracy and performance of the models on Intel Many Integrated Core coprocessors (aka Xeon Phi) and Nvidia GPU using ARCHER and explore the potential optimization methods. Phase Space-based source modelling for has been implemented. Good agreements were found in a tomotherapy prostate patient case and a TrueBeam breast case. From the aspect of performance, the whole simulation for prostate plan and breast plan cost about 173s and 73s with 1% statistical error.

Applications of just-noticeable depth difference model in joint multiview video plus depth coding

NASA Astrophysics Data System (ADS)

Liu, Chao; An, Ping; Zuo, Yifan; Zhang, Zhaoyang

2014-10-01

A new multiview just-noticeable-depth-difference(MJNDD) Model is presented and applied to compress the joint multiview video plus depth. Many video coding algorithms remove spatial and temporal redundancies and statistical redundancies but they are not capable of removing the perceptual redundancies. Since the final receptor of video is the human eyes, we can remove the perception redundancy to gain higher compression efficiency according to the properties of human visual system (HVS). Traditional just-noticeable-distortion (JND) model in pixel domain contains luminance contrast and spatial-temporal masking effects, which describes the perception redundancy quantitatively. Whereas HVS is very sensitive to depth information, a new multiview-just-noticeable-depth-difference(MJNDD) model is proposed by combining traditional JND model with just-noticeable-depth-difference (JNDD) model. The texture video is divided into background and foreground areas using depth information. Then different JND threshold values are assigned to these two parts. Later the MJNDD model is utilized to encode the texture video on JMVC. When encoding the depth video, JNDD model is applied to remove the block artifacts and protect the edges. Then we use VSRS3.5 (View Synthesis Reference Software) to generate the intermediate views. Experimental results show that our model can endure more noise and the compression efficiency is improved by 25.29 percent at average and by 54.06 percent at most compared to JMVC while maintaining the subject quality. Hence it can gain high compress ratio and low bit rate.

An introduction to using Bayesian linear regression with clinical data.

PubMed

Baldwin, Scott A; Larson, Michael J

2017-11-01

Statistical training psychology focuses on frequentist methods. Bayesian methods are an alternative to standard frequentist methods. This article provides researchers with an introduction to fundamental ideas in Bayesian modeling. We use data from an electroencephalogram (EEG) and anxiety study to illustrate Bayesian models. Specifically, the models examine the relationship between error-related negativity (ERN), a particular event-related potential, and trait anxiety. Methodological topics covered include: how to set up a regression model in a Bayesian framework, specifying priors, examining convergence of the model, visualizing and interpreting posterior distributions, interval estimates, expected and predicted values, and model comparison tools. We also discuss situations where Bayesian methods can outperform frequentist methods as well has how to specify more complicated regression models. Finally, we conclude with recommendations about reporting guidelines for those using Bayesian methods in their own research. We provide data and R code for replicating our analyses. Copyright © 2017 Elsevier Ltd. All rights reserved.

Generalized gas-solid adsorption modeling: Single-component equilibria

DOE PAGES

Ladshaw, Austin; Yiacoumi, Sotira; Tsouris, Costas; ...

2015-01-07

Over the last several decades, modeling of gas–solid adsorption at equilibrium has generally been accomplished through the use of isotherms such as the Freundlich, Langmuir, Tóth, and other similar models. While these models are relatively easy to adapt for describing experimental data, their simplicity limits their generality to be used with many different sets of data. This limitation forces engineers and scientists to test each different model in order to evaluate which one can best describe their data. Additionally, the parameters of these models all have a different physical interpretation, which may have an effect on how they can bemore » further extended into kinetic, thermodynamic, and/or mass transfer models for engineering applications. Therefore, it is paramount to adopt not only a more general isotherm model, but also a concise methodology to reliably optimize for and obtain the parameters of that model. A model of particular interest is the Generalized Statistical Thermodynamic Adsorption (GSTA) isotherm. The GSTA isotherm has enormous flexibility, which could potentially be used to describe a variety of different adsorption systems, but utilizing this model can be fairly difficult due to that flexibility. To circumvent this complication, a comprehensive methodology and computer code has been developed that can perform a full equilibrium analysis of adsorption data for any gas-solid system using the GSTA model. The code has been developed in C/C++ and utilizes a Levenberg–Marquardt’s algorithm to handle the non-linear optimization of the model parameters. Since the GSTA model has an adjustable number of parameters, the code iteratively goes through all number of plausible parameters for each data set and then returns the best solution based on a set of scrutiny criteria. Data sets at different temperatures are analyzed serially and then linear correlations with temperature are made for the parameters of the model. The end result is a full set of optimal GSTA parameters, both dimensional and non-dimensional, as well as the corresponding thermodynamic parameters necessary to predict the behavior of the system at temperatures for which data were not available. It will be shown that this code, utilizing the GSTA model, was able to describe a wide variety of gas-solid adsorption systems at equilibrium.In addition, a physical interpretation of these results will be provided, as well as an alternate derivation of the GSTA model, which intends to reaffirm the physical meaning.« less

Spatial transformations between superior colliculus visual and motor response fields during head-unrestrained gaze shifts.

PubMed

Sadeh, Morteza; Sajad, Amirsaman; Wang, Hongying; Yan, Xiaogang; Crawford, John Douglas

2015-12-01

We previously reported that visuomotor activity in the superior colliculus (SC)--a key midbrain structure for the generation of rapid eye movements--preferentially encodes target position relative to the eye (Te) during low-latency head-unrestrained gaze shifts (DeSouza et al., 2011). Here, we trained two monkeys to perform head-unrestrained gaze shifts after a variable post-stimulus delay (400-700 ms), to test whether temporally separated SC visual and motor responses show different spatial codes. Target positions, final gaze positions and various frames of reference (eye, head, and space) were dissociated through natural (untrained) trial-to-trial variations in behaviour. 3D eye and head orientations were recorded, and 2D response field data were fitted against multiple models by use of a statistical method reported previously (Keith et al., 2009). Of 60 neurons, 17 showed a visual response, 12 showed a motor response, and 31 showed both visual and motor responses. The combined visual response field population (n = 48) showed a significant preference for Te, which was also preferred in each visual subpopulation. In contrast, the motor response field population (n = 43) showed a preference for final (relative to initial) gaze position models, and the Te model was statistically eliminated in the motor-only population. There was also a significant shift of coding from the visual to motor response within visuomotor neurons. These data confirm that SC response fields are gaze-centred, and show a target-to-gaze transformation between visual and motor responses. Thus, visuomotor transformations can occur between, and even within, neurons within a single frame of reference and brain structure. © 2015 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Design Oriented Structural Modeling for Airplane Conceptual Design Optimization

NASA Technical Reports Server (NTRS)

Livne, Eli

1999-01-01

The main goal for research conducted with the support of this grant was to develop design oriented structural optimization methods for the conceptual design of airplanes. Traditionally in conceptual design airframe weight is estimated based on statistical equations developed over years of fitting airplane weight data in data bases of similar existing air- planes. Utilization of such regression equations for the design of new airplanes can be justified only if the new air-planes use structural technology similar to the technology on the airplanes in those weight data bases. If any new structural technology is to be pursued or any new unconventional configurations designed the statistical weight equations cannot be used. In such cases any structural weight estimation must be based on rigorous "physics based" structural analysis and optimization of the airframes under consideration. Work under this grant progressed to explore airframe design-oriented structural optimization techniques along two lines of research: methods based on "fast" design oriented finite element technology and methods based on equivalent plate / equivalent shell models of airframes, in which the vehicle is modelled as an assembly of plate and shell components, each simulating a lifting surface or nacelle / fuselage pieces. Since response to changes in geometry are essential in conceptual design of airplanes, as well as the capability to optimize the shape itself, research supported by this grant sought to develop efficient techniques for parametrization of airplane shape and sensitivity analysis with respect to shape design variables. Towards the end of the grant period a prototype automated structural analysis code designed to work with the NASA Aircraft Synthesis conceptual design code ACS= was delivered to NASA Ames.

Integrated design and manufacturing for the high speed civil transport (a combined aerodynamics/propulsion optimization study)

NASA Technical Reports Server (NTRS)

Baecher, Juergen; Bandte, Oliver; DeLaurentis, Dan; Lewis, Kemper; Sicilia, Jose; Soboleski, Craig

1995-01-01

This report documents the efforts of a Georgia Tech High Speed Civil Transport (HSCT) aerospace student design team in completing a design methodology demonstration under NASA's Advanced Design Program (ADP). Aerodynamic and propulsion analyses are integrated into the synthesis code FLOPS in order to improve its prediction accuracy. Executing the integrated product and process development (IPPD) methodology proposed at the Aerospace Systems Design Laboratory (ASDL), an improved sizing process is described followed by a combined aero-propulsion optimization, where the objective function, average yield per revenue passenger mile ($/RPM), is constrained by flight stability, noise, approach speed, and field length restrictions. Primary goals include successful demonstration of the application of the response surface methodolgy (RSM) to parameter design, introduction to higher fidelity disciplinary analysis than normally feasible at the conceptual and early preliminary level, and investigations of relationships between aerodynamic and propulsion design parameters and their effect on the objective function, $/RPM. A unique approach to aircraft synthesis is developed in which statistical methods, specifically design of experiments and the RSM, are used to more efficiently search the design space for optimum configurations. In particular, two uses of these techniques are demonstrated. First, response model equations are formed which represent complex analysis in the form of a regression polynomial. Next, a second regression equation is constructed, not for modeling purposes, but instead for the purpose of optimization at the system level. Such an optimization problem with the given tools normally would be difficult due to the need for hard connections between the various complex codes involved. The statistical methodology presents an alternative and is demonstrated via an example of aerodynamic modeling and planform optimization for a HSCT.

High-Order Local Pooling and Encoding Gaussians Over a Dictionary of Gaussians.

PubMed

Li, Peihua; Zeng, Hui; Wang, Qilong; Shiu, Simon C K; Zhang, Lei

2017-07-01

Local pooling (LP) in configuration (feature) space proposed by Boureau et al. explicitly restricts similar features to be aggregated, which can preserve as much discriminative information as possible. At the time it appeared, this method combined with sparse coding achieved competitive classification results with only a small dictionary. However, its performance lags far behind the state-of-the-art results as only the zero-order information is exploited. Inspired by the success of high-order statistical information in existing advanced feature coding or pooling methods, we make an attempt to address the limitation of LP. To this end, we present a novel method called high-order LP (HO-LP) to leverage the information higher than the zero-order one. Our idea is intuitively simple: we compute the first- and second-order statistics per configuration bin and model them as a Gaussian. Accordingly, we employ a collection of Gaussians as visual words to represent the universal probability distribution of features from all classes. Our problem is naturally formulated as encoding Gaussians over a dictionary of Gaussians as visual words. This problem, however, is challenging since the space of Gaussians is not a Euclidean space but forms a Riemannian manifold. We address this challenge by mapping Gaussians into the Euclidean space, which enables us to perform coding with common Euclidean operations rather than complex and often expensive Riemannian operations. Our HO-LP preserves the advantages of the original LP: pooling only similar features and using a small dictionary. Meanwhile, it achieves very promising performance on standard benchmarks, with either conventional, hand-engineered features or deep learning-based features.

Accelerating execution of the integrated TIGER series Monte Carlo radiation transport codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, L.M.; Hochstedler, R.D.

1997-02-01

Execution of the integrated TIGER series (ITS) of coupled electron/photon Monte Carlo radiation transport codes has been accelerated by modifying the FORTRAN source code for more efficient computation. Each member code of ITS was benchmarked and profiled with a specific test case that directed the acceleration effort toward the most computationally intensive subroutines. Techniques for accelerating these subroutines included replacing linear search algorithms with binary versions, replacing the pseudo-random number generator, reducing program memory allocation, and proofing the input files for geometrical redundancies. All techniques produced identical or statistically similar results to the original code. Final benchmark timing of themore » accelerated code resulted in speed-up factors of 2.00 for TIGER (the one-dimensional slab geometry code), 1.74 for CYLTRAN (the two-dimensional cylindrical geometry code), and 1.90 for ACCEPT (the arbitrary three-dimensional geometry code).« less

Mode-dependent templates and scan order for H.264/AVC-based intra lossless coding.

PubMed

Gu, Zhouye; Lin, Weisi; Lee, Bu-Sung; Lau, Chiew Tong; Sun, Ming-Ting

2012-09-01

In H.264/advanced video coding (AVC), lossless coding and lossy coding share the same entropy coding module. However, the entropy coders in the H.264/AVC standard were original designed for lossy video coding and do not yield adequate performance for lossless video coding. In this paper, we analyze the problem with the current lossless coding scheme and propose a mode-dependent template (MD-template) based method for intra lossless coding. By exploring the statistical redundancy of the prediction residual in the H.264/AVC intra prediction modes, more zero coefficients are generated. By designing a new scan order for each MD-template, the scanned coefficients sequence fits the H.264/AVC entropy coders better. A fast implementation algorithm is also designed. With little computation increase, experimental results confirm that the proposed fast algorithm achieves about 7.2% bit saving compared with the current H.264/AVC fidelity range extensions high profile.

LakeMetabolizer: An R package for estimating lake metabolism from free-water oxygen using diverse statistical models

USGS Publications Warehouse

Winslow, Luke; Zwart, Jacob A.; Batt, Ryan D.; Dugan, Hilary; Woolway, R. Iestyn; Corman, Jessica; Hanson, Paul C.; Read, Jordan S.

2016-01-01

Metabolism is a fundamental process in ecosystems that crosses multiple scales of organization from individual organisms to whole ecosystems. To improve sharing and reuse of published metabolism models, we developed LakeMetabolizer, an R package for estimating lake metabolism from in situ time series of dissolved oxygen, water temperature, and, optionally, additional environmental variables. LakeMetabolizer implements 5 different metabolism models with diverse statistical underpinnings: bookkeeping, ordinary least squares, maximum likelihood, Kalman filter, and Bayesian. Each of these 5 metabolism models can be combined with 1 of 7 models for computing the coefficient of gas exchange across the air–water interface (k). LakeMetabolizer also features a variety of supporting functions that compute conversions and implement calculations commonly applied to raw data prior to estimating metabolism (e.g., oxygen saturation and optical conversion models). These tools have been organized into an R package that contains example data, example use-cases, and function documentation. The release package version is available on the Comprehensive R Archive Network (CRAN), and the full open-source GPL-licensed code is freely available for examination and extension online. With this unified, open-source, and freely available package, we hope to improve access and facilitate the application of metabolism in studies and management of lentic ecosystems.

Building integral projection models: a user's guide

PubMed Central

Rees, Mark; Childs, Dylan Z; Ellner, Stephen P; Coulson, Tim

2014-01-01

In order to understand how changes in individual performance (growth, survival or reproduction) influence population dynamics and evolution, ecologists are increasingly using parameterized mathematical models. For continuously structured populations, where some continuous measure of individual state influences growth, survival or reproduction, integral projection models (IPMs) are commonly used. We provide a detailed description of the steps involved in constructing an IPM, explaining how to: (i) translate your study system into an IPM; (ii) implement your IPM; and (iii) diagnose potential problems with your IPM. We emphasize how the study organism's life cycle, and the timing of censuses, together determine the structure of the IPM kernel and important aspects of the statistical analysis used to parameterize an IPM using data on marked individuals. An IPM based on population studies of Soay sheep is used to illustrate the complete process of constructing, implementing and evaluating an IPM fitted to sample data. We then look at very general approaches to parameterizing an IPM, using a wide range of statistical techniques (e.g. maximum likelihood methods, generalized additive models, nonparametric kernel density estimators). Methods for selecting models for parameterizing IPMs are briefly discussed. We conclude with key recommendations and a brief overview of applications that extend the basic model. The online Supporting Information provides commented R code for all our analyses. PMID:24219157

SiGN-SSM: open source parallel software for estimating gene networks with state space models.

PubMed

Tamada, Yoshinori; Yamaguchi, Rui; Imoto, Seiya; Hirose, Osamu; Yoshida, Ryo; Nagasaki, Masao; Miyano, Satoru

2011-04-15

SiGN-SSM is an open-source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by a statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles. SiGN-SSM is distributed under GNU Affero General Public Licence (GNU AGPL) version 3 and can be downloaded at http://sign.hgc.jp/signssm/. The pre-compiled binaries for some architectures are available in addition to the source code. The pre-installed binaries are also available on the Human Genome Center supercomputer system. The online manual and the supplementary information of SiGN-SSM is available on our web site. tamada@ims.u-tokyo.ac.jp.

Benchmarking the MCNP code for Monte Carlo modelling of an in vivo neutron activation analysis system.

PubMed

Natto, S A; Lewis, D G; Ryde, S J

1998-01-01

The Monte Carlo computer code MCNP (version 4A) has been used to develop a personal computer-based model of the Swansea in vivo neutron activation analysis (IVNAA) system. The model included specification of the neutron source (252Cf), collimators, reflectors and shielding. The MCNP model was 'benchmarked' against fast neutron and thermal neutron fluence data obtained experimentally from the IVNAA system. The Swansea system allows two irradiation geometries using 'short' and 'long' collimators, which provide alternative dose rates for IVNAA. The data presented here relate to the short collimator, although results of similar accuracy were obtained using the long collimator. The fast neutron fluence was measured in air at a series of depths inside the collimator. The measurements agreed with the MCNP simulation within the statistical uncertainty (5-10%) of the calculations. The thermal neutron fluence was measured and calculated inside the cuboidal water phantom. The depth of maximum thermal fluence was 3.2 cm (measured) and 3.0 cm (calculated). The width of the 50% thermal fluence level across the phantom at its mid-depth was found to be the same by both MCNP and experiment. This benchmarking exercise has given us a high degree of confidence in MCNP as a tool for the design of IVNAA systems.

A neuronal model of predictive coding accounting for the mismatch negativity.

PubMed

Wacongne, Catherine; Changeux, Jean-Pierre; Dehaene, Stanislas

2012-03-14

The mismatch negativity (MMN) is thought to index the activation of specialized neural networks for active prediction and deviance detection. However, a detailed neuronal model of the neurobiological mechanisms underlying the MMN is still lacking, and its computational foundations remain debated. We propose here a detailed neuronal model of auditory cortex, based on predictive coding, that accounts for the critical features of MMN. The model is entirely composed of spiking excitatory and inhibitory neurons interconnected in a layered cortical architecture with distinct input, predictive, and prediction error units. A spike-timing dependent learning rule, relying upon NMDA receptor synaptic transmission, allows the network to adjust its internal predictions and use a memory of the recent past inputs to anticipate on future stimuli based on transition statistics. We demonstrate that this simple architecture can account for the major empirical properties of the MMN. These include a frequency-dependent response to rare deviants, a response to unexpected repeats in alternating sequences (ABABAA…), a lack of consideration of the global sequence context, a response to sound omission, and a sensitivity of the MMN to NMDA receptor antagonists. Novel predictions are presented, and a new magnetoencephalography experiment in healthy human subjects is presented that validates our key hypothesis: the MMN results from active cortical prediction rather than passive synaptic habituation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sigeti, David E.; Pelak, Robert A.

We present a Bayesian statistical methodology for identifying improvement in predictive simulations, including an analysis of the number of (presumably expensive) simulations that will need to be made in order to establish with a given level of confidence that an improvement has been observed. Our analysis assumes the ability to predict (or postdict) the same experiments with legacy and new simulation codes and uses a simple binomial model for the probability, {theta}, that, in an experiment chosen at random, the new code will provide a better prediction than the old. This model makes it possible to do statistical analysis withmore » an absolute minimum of assumptions about the statistics of the quantities involved, at the price of discarding some potentially important information in the data. In particular, the analysis depends only on whether or not the new code predicts better than the old in any given experiment, and not on the magnitude of the improvement. We show how the posterior distribution for {theta} may be used, in a kind of Bayesian hypothesis testing, both to decide if an improvement has been observed and to quantify our confidence in that decision. We quantify the predictive probability that should be assigned, prior to taking any data, to the possibility of achieving a given level of confidence, as a function of sample size. We show how this predictive probability depends on the true value of {theta} and, in particular, how there will always be a region around {theta} = 1/2 where it is highly improbable that we will be able to identify an improvement in predictive capability, although the width of this region will shrink to zero as the sample size goes to infinity. We show how the posterior standard deviation may be used, as a kind of 'plan B metric' in the case that the analysis shows that {theta} is close to 1/2 and argue that such a plan B should generally be part of hypothesis testing. All the analysis presented in the paper is done with a general beta-function prior for {theta}, enabling sequential analysis in which a small number of new simulations may be done and the resulting posterior for {theta} used as a prior to inform the next stage of power analysis.« less

Accounting for regional background and population size in the detection of spatial clusters and outliers using geostatistical filtering and spatial neutral models: the case of lung cancer in Long Island, New York

PubMed Central

Goovaerts, Pierre; Jacquez, Geoffrey M

2004-01-01

Background Complete Spatial Randomness (CSR) is the null hypothesis employed by many statistical tests for spatial pattern, such as local cluster or boundary analysis. CSR is however not a relevant null hypothesis for highly complex and organized systems such as those encountered in the environmental and health sciences in which underlying spatial pattern is present. This paper presents a geostatistical approach to filter the noise caused by spatially varying population size and to generate spatially correlated neutral models that account for regional background obtained by geostatistical smoothing of observed mortality rates. These neutral models were used in conjunction with the local Moran statistics to identify spatial clusters and outliers in the geographical distribution of male and female lung cancer in Nassau, Queens, and Suffolk counties, New York, USA. Results We developed a typology of neutral models that progressively relaxes the assumptions of null hypotheses, allowing for the presence of spatial autocorrelation, non-uniform risk, and incorporation of spatially heterogeneous population sizes. Incorporation of spatial autocorrelation led to fewer significant ZIP codes than found in previous studies, confirming earlier claims that CSR can lead to over-identification of the number of significant spatial clusters or outliers. Accounting for population size through geostatistical filtering increased the size of clusters while removing most of the spatial outliers. Integration of regional background into the neutral models yielded substantially different spatial clusters and outliers, leading to the identification of ZIP codes where SMR values significantly depart from their regional background. Conclusion The approach presented in this paper enables researchers to assess geographic relationships using appropriate null hypotheses that account for the background variation extant in real-world systems. In particular, this new methodology allows one to identify geographic pattern above and beyond background variation. The implementation of this approach in spatial statistical software will facilitate the detection of spatial disparities in mortality rates, establishing the rationale for targeted cancer control interventions, including consideration of health services needs, and resource allocation for screening and diagnostic testing. It will allow researchers to systematically evaluate how sensitive their results are to assumptions implicit under alternative null hypotheses. PMID:15272930

National Freight Demand Modeling - Bridging the Gap between Freight Flow Statistics and U.S. Economic Patterns

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chin, Shih-Miao; Hwang, Ho-Ling

2007-01-01

This paper describes a development of national freight demand models for 27 industry sectors covered by the 2002 Commodity Flow Survey. It postulates that the national freight demands are consistent with U.S. business patterns. Furthermore, the study hypothesizes that the flow of goods, which make up the national production processes of industries, is coherent with the information described in the 2002 Annual Input-Output Accounts developed by the Bureau of Economic Analysis. The model estimation framework hinges largely on the assumption that a relatively simple relationship exists between freight production/consumption and business patterns for each industry defined by the three-digit Northmore » American Industry Classification System industry codes (NAICS). The national freight demand model for each selected industry sector consists of two models; a freight generation model and a freight attraction model. Thus, a total of 54 simple regression models were estimated under this study. Preliminary results indicated promising freight generation and freight attraction models. Among all models, only four of them had a R2 value lower than 0.70. With additional modeling efforts, these freight demand models could be enhanced to allow transportation analysts to assess regional economic impacts associated with temporary lost of transportation services on U.S. transportation network infrastructures. Using such freight demand models and available U.S. business forecasts, future national freight demands could be forecasted within certain degrees of accuracy. These freight demand models could also enable transportation analysts to further disaggregate the CFS state-level origin-destination tables to county or zip code level.« less