Digital Commons Network^™

Improving Mixed Variable Optimization Of Computational And Model Parameters Using Multiple Surrogate Functions, David Bethea

Theses and Dissertations

This research focuses on reducing computational time in parameter optimization by using multiple surrogates and subprocess CPU times without compromising the quality of the results. This is motivated by applications that have objective functions with expensive computational times at high fidelity solutions. Applying, matching, and tuning optimization techniques at an algorithm level can reduce the time spent on unprofitable computations for parameter optimization. The objective is to recover known parameters of a flow property reference image by comparing to a template image that comes from a computational fluid dynamics simulation, followed by a numerical image registration and comparison process. Mixed …

The Construction And Analysis Of Adaptive Group Sequential Designs, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

In order to answer scientific questions of interest one often carries out an ordered sequence of experiments generating the appropriate data over time. The design of each experiment involves making various decisions such as 1) What variables to measure on the randomly sampled experimental unit?, 2) How regularly to monitor the unit, and for how long?, 3) How to randomly assign a treatment or drug-dose to the unit?, among others. That is, the design of each experiment involves selecting a so called treatment mechanism/monitoring mechanism/ missingness/censoring mechanism, where these mechanisms represent a formally defined conditional distribution of one of these …

Delay-Induced Instabilities In Self-Propelling Swarms, Eric Forgoston, Ira B. Schwartz

Department of Applied Mathematics and Statistics Faculty Scholarship and Creative Works

We consider a general model of self-propelling particles interacting through a pairwise attractive force in the presence of noise and communication time delay. Previous work by Erdmann [Phys. Rev. E 71, 051904 (2005)] has shown that a large enough noise intensity will cause a translating swarm of individuals to transition to a rotating swarm with a stationary center of mass. We show that with the addition of a time delay, the model possesses a transition that depends on the size of the coupling amplitude. This transition is independent of the initial swarm state (traveling or rotating) and is characterized by …

Data-Adaptive Selection Of The Truncation Level For Inverse-Probability-Of-Treatment-Weighted Estimators, Oliver Bembom, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Inverse-Probability-of-Treatment-Weighted (IPTW) estimators are becoming a popular analysis tool in causal inference. It is well known that these estimators suffer from high variability if some treatment probabilities are estimated to be close to zero. While it is a common recommendation for such situations to truncate the weights in order to reduce the mean squared error of the estimator, the current literature gives little guidance on how to select an appropriate truncation level. In this article, we develop a closed-form estimate for the mean squared error of a truncated IPTW estimator that can be used to select this truncation level data-adaptively. …

Data-Adaptive Selection Of The Adjustment Set In Variable Importance Estimation, Oliver Bembom, Jeffrey W. Fessel, Robert W. Shafer, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

If estimates of the effect of a treatment variable on an outcome of interest are to be adjusted for a set of possible confounding factors, it is necessary to rely on the assumption of experimental treatment assignment (ETA) according to which each experimental unit has positive probability of being observed at any of the possible levels of the treatment variable regardless of the values the confounding factors may take on. Even if this assumption is only practically violated in the sense that certain values of the confounding factors cause some treatment levels to become not impossible, but at least highly …

Skill Evaluation In Women's Volleyball, Lindsay Walker Florence

Theses and Dissertations

The Brigham Young University Women's Volleyball Team recorded and rated all skills (pass, set, attack, etc.) and recorded rally outcomes (point for BYU, rally continues, point for opponent) for the entire 2006 home volleyball season. Only sequences of events occurring on BYU's side of the net were considered. Events followed one of these general patterns: serve-outcome, pass-set-attack-outcome, or block-dig-set-attack-outcome. These sequences of events were assumed to be first-order Markov chains where the quality of each contact depended only explicitly on the quality of the previous contact but not on contacts further removed in the sequence. We represented these sequences in …

An Overview Of Conditionals And Biconditionals In Probability, Nataniel Greene

Publications and Research

Conditional and biconditional statements are a standard part of symbolic logic but they have only recently begun to be explored in probability for applications in artificial intelligence. Here we give a brief overview of the major theorems involved and illustrate them using two standard model problems from conditional probability.

Predicting Cost And Schedule Growth For Military And Civil Space Systems, Christina F. Rusnock

Theses and Dissertations

Military and civil space acquisitions have received much criticism for their inability to produce realistic cost and schedule estimates. This research seeks to provide space systems cost estimators with a forecasting tool for space system cost and schedule growth by identifying factors contributing to growth, quantifying the relative impact of these factors, and establishing a set of models for predicting space system cost and schedule growth. The analysis considers data from both Department of Defense (DoD) and National Aeronautics and Space Administration (NASA) space programs. The DoD dataset includes 21 space programs that submitted developmental Selected Acquisition Reports between 1969 …

Statistical Approach To The Characterization And Recognition Of Human Gaits, Derrick M. Chelliah

Theses and Dissertations

This thesis addresses the final portion of a complete process for human gait recognition. The thesis takes as input information that has been generated from videotaping walking individuals and converting their gaits into numerical data that measures the locations of various points on the body through time. Beginning with this data, this thesis uses a variety of mathematical and statistical methods to create identifying signatures for each individual and identify them on the basis of that signature. The end goal is to achieve under controlled laboratory conditions human gait recognition, an identification method which does not require contact or cooperation …

A Method For Visualizing Multivariate Time Series Data, Roger D. Peng

Johns Hopkins University, Dept. of Biostatistics Working Papers

Visualization and exploratory analysis is an important part of any data analysis and is made more challenging when the data are voluminous and high-dimensional. One such example is environmental monitoring data, which are often collected over time and at multiple locations, resulting in a geographically indexed multivariate time series. Financial data, although not necessarily containing a geographic component, present another source of high-volume multivariate time series data. We present the mvtsplot function which provides a method for visualizing multivariate time series data. We outline the basic design concepts and provide some examples of its usage by applying it to a …

Empirical Null And False Discovery Rate Inference For Exponential Families, Armin Schwartzman

Harvard University Biostatistics Working Paper Series

No abstract provided.

Marginal Structural Models For Partial Exposure Regimes, Stijn Vansteelandt, Karl Mertens, Carl Suetens, Els Goetghebeur

Harvard University Biostatistics Working Paper Series

Intensive care unit (ICU) patients are ell known to be highly susceptible for nosocomial (i.e. hospital-acquired) infections due to their poor health and many invasive therapeutic treatments. The effects of acquiring such infections in ICU on mortality are however ill understood. Our goal is to quantify these effects using data from the National Surveillance Study of Nosocomial Infections in Intensive Care

Units (Belgium). This is a challenging problem because of the presence of time-dependent confounders (such as exposure to mechanical ventilation)which lie on the causal path from infection to mortality. Standard statistical analyses may be severely misleading in such settings …

Multiple Imputation Of Timing Of Mother-To-Child Transmission Of Hiv, Elizabeth Brown, Ying Qing Chen

UW Biostatistics Working Paper Series

In this paper, we present a model for imputing timing of mother-to- child transmission (MTCT) of HIV. The method re ects the three modes of MTCT of HIV: in utero, during delivery and via breastfeeding and can accomodate shapes for the baseline hazard that vary between infants. Ad- ditionally, it allows that the majority of infants do not experience MTCT of HIV. Final analyses from the imputed data sets are combined in a mul- tiple imputation framework. The methods is illustrated on a large trial designed to assess the use of antibiotics in preventing MTCT of HIV and is validated …

Jointly Modeling Continuous And Binary Outcomes For Boolean Outcomes: An Application To Modeling Hypertension, Xianbin Li, Brian S. Caffo, Elizabeth Stuart

Johns Hopkins University, Dept. of Biostatistics Working Papers

Binary outcomes defined by logical (Boolean) "and" or "or" operations on original continuous and discrete outcomes arise commonly in medical diagnoses and epidemiological research. In this manuscript,we consider applying the “or” operator to two continuous variables above a threshold and a binary variable, a setting that occurs frequently in the modeling of hypertension. Rather than modeling the resulting composite outcome defined by the logical operator, we present a method that models the original outcomes thus utilizing all information in the data, yet continues to yield conclusions on the composite scale. A stratified propensity score adjustment is proposed to account for …

Crop Updates 2008 - Cereals, Christine M. Zaicou-Kunesch, Shahajahan Miyan, Brenda Shackley, Steve Penny, Sarah Ellis, Darshan Sharma, Blakely Paynter, Jeff Russell, Andrea Hills, Glen Riethmuller, Bill Bowden, Paul Blackwell, Harmohinder Dhammu, Vince Lambert, Chris Roberts, David Cox, Sally Cox, Jeremy Lemon, Paul Damon, Zed Rengel, Geoff J. Thomas, Ciara Beard, Anne Smith, Kithsiri Jayasena, Sean Kelly, Rob Loughman, Bill Macleod, Raj Malik, Ravjit Khangura, Vivien Vanstone, Colin Hanbury, Mehreteab Aberra, Gordon Masnish, Brenda A. Coutts, Geoff Strickland, Monica Kehoe, Dustin Severtson, Roger A C Jones, Dominie Wright, Megan Jordan, Xinhua He, Eli Manyol, Song-Ai Nio, Imran Malik, Tina Botwright-Acuña, Len Wade, Nigel Metz, Linda Price, Dean A. Diepeveen, Leisa Armstrong, Peter Clarke, Doug Abrecht, Rudi Appels, Matthew Bellgard

Crop Updates

This session covers twenty four papers from different authors:

WHEAT AGRONOMY

1. Wheat variety performance in the Northern Agricultural Region in 2007, Christine Zaicou, Department of Agriculture and Food

2. Wheat variety performance on the Central Agricultural Region in 2007, Shahajahan Miyan, Department of Agriculture and Food

3. Response of wheat varieties to sowing time in the Great Southern and Lakes Region in 2007, Brenda Shackley and Steve Penny, Department of Agriculture and Food

4. Wheat variety performance in the South Coastal Region in 2007, Sarah Ellis, Department of Agriculture and Food

5. Flowering dates of wheat varieties in Western …

Covariate Adjustment For The Intention-To-Treat Parameter With Empirical Efficiency Maximization, Daniel B. Rubin, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

In randomized experiments, the intention-to-treat parameter is defined as the difference in expected outcomes between groups assigned to treatment and control arms. There is a large literature focusing on how (possibly misspecified) working models can sometimes exploit baseline covariate measurements to gain precision, although covariate adjustment is not strictly necessary. In Rubin and van der Laan (2008), we proposed the technique of empirical efficiency maximization for improving estimation by forming nonstandard fits of such working models. Considering a more realistic randomization scheme than in our original article, we suggest a new class of working models for utilizing covariate information, show …

Medical Progress Depends On Animal Models - Doesn't It?, Robert A. J. Matthews

Validation of Animal Experimentation Collection

Animal models are widely recognized as being essential to the progress of medical science. In countering the critics’ arguments of the use of animals in medicine, one statement has acquired almost talismanic importance:

‘Virtually every medical achievement of the last century has depended directly or indirectly on research with animals.’

In this essay, the origins and justification of this oft-repeated statement are examined. Despite its endorsement by leading academic bodies, it is far from clear that the statement has been, or even could be, formally validated.

Infant Feeding Decisions Among Pregnant Black Wic Participants And The Role Of Peer Support, Astrid D. Mickens

Loma Linda University Electronic Theses, Dissertations & Projects

The purpose of this study was to identify the important factors that impact infant feeding decisions among Black women, and to determine whether peer support influences the relationship among theoretical constructs of the social learning theory. A convenience sample of 110 Black pregnant women, ages 18-45, attending Women, Infant and Children (WIC) clinics throughout Riverside and San Bernardino Counties were recruited to participate in the study through the Nutrition Services Department. Eligible participants included pregnant Black WIC clients in any stage of pregnancy.

The survey questions contained information about perceived support, cognitive knowledge, abilities and beliefs regarding breastfeeding. The goal …

The Expression Of Microrna Mir-107 Decreases Early In Alzheimer's Disease And May Accelerate Disease Progression Through Regulation Of Β-Site Amyloid Precursor Protein-Cleaving Enzyme 1, Wang-Xia Wang, Bernard W. Rajeev, Arnold J. Stromberg, Na Ren, Guiliang Tang, Qingwei Huang, Isidore Rigoutsos, Peter T. Nelson

Sanders-Brown Center on Aging Faculty Publications

MicroRNAs (miRNAs) are small regulatory RNAs that participate in posttranscriptional gene regulation in a sequence-specific manner. However, little is understood about the role(s) of miRNAs in Alzheimer's disease (AD). We used miRNA expression microarrays on RNA extracted from human brain tissue from the University of Kentucky Alzheimer's Disease Center Brain Bank with near-optimal clinicopathological correlation. Cases were separated into four groups: elderly nondemented with negligible AD-type pathology, nondemented with incipient AD pathology, mild cognitive impairment (MCI) with moderate AD pathology, and AD. Among the AD-related miRNA expression changes, miR-107 was exceptional because miR-107 levels decreased significantly even in patients with …

Rna Genome Annotation With A Focus On T. Brucei, Brett Bucci

Theses

The goal of this project is to identify untranslated regions (UTRs) and UTR-indicating patterns in the genome of T. brucei. T. brucei is an interesting organism, and as the cause of African sleeping sickness -- which infects 300,000-500,000 people and a significant number of cattle annually -- is currently the subject of considerable research. Using existing algorithms, several patterns have been found that may lead to more complete UTR annotations in the T. brucei genome. The most encouraging sequence is the 11-base sequence GAGGGIICG]TGGGG, which appears in five hypothetical genes near the tail. Discovery of several such sequences could guide …

Utr Prediction Programs For Trypanosoma Brucei, Maria Moutafis

Theses

In the past few years, the field of bioinformatics has seen a rapid increase in the need for use of various sequence analysis tools. As we advance in the fields of science and technology, new programs and software are constantly being developed in this field. Rapidly expanding gene sequence databases and rapidly evolving sequence analysis tools are providing researchers with ways to search for highly similar query sequences whether they are nucleotide, protein, or gene databases. This thesis will focus on sequence alignment tools, specifically concentrating on tools that help determine/predict non-coding regions of sequences also known as untranslated regions …

Cluster Mass Inference Method Via Random Field Theory, Hui Zhang, Thomas E. Nichols, Timothy D. Johnson

The University of Michigan Department of Biostatistics Working Paper Series

Cluster extent and voxel intensity are two widely used statistics in neuroimaging inference. Cluster extent is sensitive to spatially extended signals while voxel intensity is better for intense but focal signals. In order to leverage strength from both statistics, several nonparametric permutation methods have been proposed to combine the two methods. Simulation studies have shown that of the different cluster permutation methods, the cluster mass statistic is generally the best. However, to date, there is no parametric cluster mass inference available. In this paper, we propose a cluster mass inference method based on random field theory (RFT). We develop this …

Accommodating Covariates In Roc Analysis, Holly Janes, Gary M. Longton, Margaret Pepe

UW Biostatistics Working Paper Series

Classification accuracy is the ability of a marker or diagnostic test to discriminate between two groups of individuals, cases and controls, and is commonly summarized using the receiver operating characteristic (ROC) curve. In studies of classification accuracy, there are often covariates that should be incorporated into the ROC analysis. We describe three different ways of using covariate informa- tion. For factors that affect marker observations among controls, we present a method for covariate adjustment. For factors that affect discrimination (ie the ROC curve), we describe methods for mod- elling the ROC curve as a function of covariates. Finally, for factors …

Estimation And Comparison Of Receiver Operating Characteristic Curves, Margaret Pepe, Gary M. Longton, Holly Janes

UW Biostatistics Working Paper Series

The receiver operating characteristic (ROC) curve displays the capacity of a marker or diagnostic test to discriminate between two groups of subjects, cases versus controls. We present a comprehensive suite of Stata commands for performing ROC analysis. Non-parametric, semiparametric and parametric estimators are calculated. Comparisons between curves are based on the area or partial area under the ROC curve. Alternatively pointwise comparisons between ROC curves or inverse ROC curves can be made. Options to adjust these analyses for covariates, and to perform ROC regression are described in a companion article. We use a unified framework by representing the ROC curve …

A Bayesian Approach To Effect Estimation Accounting For Adjustment Uncertainty, Chi Wang, Giovanni Parmigiani, Ciprian Crainiceanu, Francesca Dominici

Johns Hopkins University, Dept. of Biostatistics Working Papers

Adjustment for confounding factors is a common goal in the analysis of both observational and controlled studies. The choice of which confounding factors should be included in the model used to estimate an effect of interest is both critical and uncertain. For this reason it is important to develop methods that estimate an effect, while accounting not only for confounders, but also for the uncertainty about which confounders should be included. In a recent article, Crainiceanu et al. (2008) have identified limitations and potential biases of Bayesian Model Averaging (BMA) (Raftery et al., 1997; Hoeting et al., 1999)when applied to …

Estimation Of Controlled Direct Effects, Sylvie Goetgeluk, Stijn Vansteelandt, Els Goetghebeur

Harvard University Biostatistics Working Paper Series

No abstract provided.

Using Regression Models To Analyze Randomized Trials: Asymptotically Valid Hypothesis Tests Despite Incorrectly Specified Models, Michael Rosenblum, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Regression models are often used to test for cause-effect relationships from data collected in randomized trials or experiments. This practice has deservedly come under heavy scrutiny, since commonly used models such as linear and logistic regression will often not capture the actual relationships between variables, and incorrectly specified models potentially lead to incorrect conclusions. In this paper, we focus on hypothesis test of whether the treatment given in a randomized trial has any effect on the mean of the primary outcome, within strata of baseline variables such as age, sex, and health status. Our primary concern is ensuring that such …

On The Merits Of Voxel-Based Morphometric Path-Analysis For Investigating Volumetric Mediation Of A Toxicant's Influence On Cognitive Function, Shu-Chih Su, Brian S. Caffo, Lynn E. Eberly, Elizabeth Garrett-Mayer, Walter F. Stewart, Sining Chen, David Yousem, Christos Davatzikos, Brian Schwartz

Johns Hopkins University, Dept. of Biostatistics Working Papers

We previously showed that lifetime cumulative lead dose, measured as lead concentration in the tibia bone by X-ray fluorescence, was associated with persistent and progressive declines in cognitive function and with decreases in MRI-based brain volumes in former lead workers. Moreover, larger region-specific brain volumes were associated with better cognitive function. These findings motivated us to explore a novel application of path analysis to evaluate effect mediation. Voxel-wise path analysis, at face value, represents the natural evolution of voxel-based morphometry methods to answer questions of mediation. Application of these methods to the former lead worker data demonstrated potential limitations in …

Geostatistical Inference Under Preferential Sampling, Peter J. Diggle, Raquel Menezes, Ting-Li Su

Johns Hopkins University, Dept. of Biostatistics Working Papers

Geostatistics involves the fitting of spatially continuous models to spatially discrete data (Chil`es and Delfiner, 1999). Preferential sampling arises when the process that determines the data-locations and the process being modelled are stochastically dependent. Conventional geostatistical methods assume, if only implicitly, that sampling is non-preferential. However, these methods are often used in situations where sampling is likely to be preferential. For example, in mineral exploration samples may be concentrated in areas thought likely to yield high-grade ore. We give a general expression for the likelihood function of preferentially sampled geostatistical data and describe how this can be evaluated approximately using …

Radiometric Clocks, Gary B. Hughes

Statistics

This paper provides and introduction to radioactivity, and how geologists exploit radioactive decay to determine the age of rocks.