Statistics and Probability Commons^™

Design Of Probabilistic Random Forests With Applications To Anticancer Drug Sensitivity Prediction, Raziur Rahman, Saad Haider, Souparno Gosh, Ranadip Pal

Department of Statistics: Faculty Publications

Random forests consisting of an ensemble of regression trees with equal weights are frequently used for design of predictive models. In this article, we consider an extension of the methodology by representing the regression trees in the form of probabilistic trees and analyzing the nature of heteroscedasticity. The probabilistic tree representation allows for analytical computation of confidence intervals (CIs), and the tree weight optimization is expected to provide stricter CIs with comparable performance in mean error. We approached the ensemble of probabilistic trees’ prediction from the perspectives of a mixture distribution and as a weighted sum of correlated random variables. …

S1: Supplementary Information For Article: A Copula Based Approach For Design Of Multivariate Random Forests For Drug Sensitivity Prediction, Saad Haider, Raziur Rahman, Souparno Ghosh, Ranadip Pal

Department of Statistics: Faculty Publications

Changes in performance with prior feature selection

Random forest (RF) is designed to create uncorrelated trees using random subsets of features in each node of each tree. RF by itself is a great tool for feature selection from a high dimensional set of features. But we observed that the prediction accuracy is improved when a prior feature selection (RELIEFF) [1] approach is implemented. Table A shows the performance of RF, VMRF and CMRF with and without RELIEFF feature selection in 2 drug sets of GDSC.

Performance Analysis for drugsets consisting of more 8 than two drugs

We have generated empirical …

Voc Emissions From Beef Feedlot Pen Surfaces As Affected By Within-Pen Location, Moisture And Temperature, Bryan L. Woodbury, John E. Gilley, David B. Parker, David B. Marx, Roger A. Eigenberg

Department of Statistics: Faculty Publications

A laboratory study was conducted to evaluate the effects of pen location, moisture, and temperature on emissions of volatile organic compounds (VOC) from surface materials obtained from feedlot pens where beef cattle were fed a diet containing 30% wet distillers grain plus solubles. Surface materials were collected from the feed trough (bunk), drainage, and raised areas (mounds) within three feedlot pens. The surface materials were mixed with water to represent dry, wet, or saturated conditions and then incubated at temperatures of 5, 15, 25 and 35 C. A wind tunnel and gas chromatograph-mass spectrometer were used to collect and quantify …

Equate: Observed-Score Linking And Equating In R, Anthony D. Albano

Department of Educational Psychology: Faculty Publications

Linking and equating are statistical procedures used to convert scores from one measurement scale to another. These procedures are most often used in testing programs that involve multiple test forms, where adjustments are made for form difficulty differences when creating a measurement scale that is common across forms. Linking and equating methods are traditionally distinguished by the type of scores they are applied to, whether observed scores or scores from an item response theory model. Methods are also distinguished by the study design under which measurements are taken. The R package equate (Albano, 2014) is free, open-source software for conducting …

Modeling The Dynamic Processes Of Challenge And Recovery (Stress And Strain) Over Time, Fan Yang

Department of Statistics: Dissertations, Theses, and Student Research

A dynamic process with challenge and recovery is an important branch in the family of stochastic processes. The dependent data of such processes are often observed over time, and hence, are time dependent. The purpose of this dissertation is to develop methods to characterize a dynamic process with challenge and recovery under different dimensionalities and error assumptions. In this dissertation, a univariate dynamic process under Gaussian assumption is discussed first and a bi-logistic model is developed by three different methods: compartment, additive, and Bayesian. Then the discussion is extended to a bivariate hysteresis system with challenge and recovery. Three methods: …

A Reduced Bias Method Of Estimating Variance Components In Generalized Linear Mixed Models, Elizabeth A. Claassen

Department of Statistics: Dissertations, Theses, and Student Research

In small samples it is well known that the standard methods for estimating variance components in a generalized linear mixed model (GLMM), pseudo-likelihood and maximum likelihood, yield estimates that are biased downward. An important consequence of this is that inferences on fixed effects will have inflated Type I error rates because their precision is overstated. We introduce a new method for estimating parameters in GLMMs that applies a Firth bias adjustment to the maximum likelihood-based GLMM estimating algorithm. We apply this technique to one- and two-treatment logistic regression models with a single random effect. We show simulation results that demonstrate …

New Statistical Methods For Analysis Of Historical Data From Wildlife Populations, Trevor Hefley

Department of Statistics: Dissertations, Theses, and Student Research

Wildlife biologists, many times with the help of ordinary citizens, have developed and maintained long-term datasets for monitoring the status of wildlife populations. These datasets can range from a collection of citizen-reported sightings of a rare species, to datasets collected by biologists using standardized methods. The commonality is that these datasets span a temporal and spatial scale that is beyond the scope of most scientific studies. Ensuring the continued persistence of wildlife populations requires predictions of the impact of human actions. Regardless if the predictions are quantitative or qualitative, the best we can do is use the past data to …

Confidence Intervals For Ranks Of Age-Adjusted Rates Across States Or Counties, Shunpu Zhang, Jun Luo, Li Zhu, David G. Stinchcomb, Dave Campbell, Ginger Carter, Scott Gilkeson, Eric J. Feuer

Department of Statistics: Faculty Publications

Health indices provide information to the general public on the health condition of the community. They can also be used to inform the government’s policy making, to evaluate the effect of a current policy or healthcare program, or for program planning and priority setting. It is a common practice that the health indices across different geographic units are ranked and the ranks are reported as fixed values. We argue that the ranks should be viewed as random and hence should be accompanied by an indication of precision (i.e., the confidence intervals). A technical difficulty in doing so is how to …

Parametric And Nonparametric Statistical Methods For Genomic Selection Of Traits With Additive And Epistatic Genetic Architectures, Reka Howard, Alicia L. Carriquiry, William D. Beavis

Department of Statistics: Faculty Publications

Parametric and nonparametric methods have been developed for purposes of predicting phenotypes. These methods are based on retrospective analyses of empirical data consisting of genotypic and phenotypic scores. Recent reports have indicated that parametric methods are unable to predict phenotypes of traits with known epistatic genetic architectures. Herein, we review parametric methods including least squares regression, ridge regression, Bayesian ridge regression, least absolute shrinkage and selection operator (LASSO), Bayesian LASSO, best linear unbiased prediction (BLUP), Bayes A, Bayes B, Bayes C, and Bayes Cπ. We also review nonparametric methods including Nadaraya-Watson estimator, reproducing kernel Hilbert space, support vector machine regression, …

Native Insect Herbivory Limits Population Growth Rate Of A Non-Native Thistle, James O. Eckberg, Brigitte Tenhumberg, Svata M. Louda

Brigitte Tenhumberg Papers

The influence of native fauna on non-native plant population growth, size, and distribution is not well documented. Previous studies have shown that native insects associated with tall thistle (Cirsium altissimum) also feed on the leaves, stems, and flower heads of the Eurasian congener Cirsium vulgare, thus limiting individual plant performance. In this study, we tested the effects of insect herbivores on the population growth rate of C. vulgare. We experimentally initiated invasions by adding seeds at four unoccupied grassland sites in eastern Nebraska, USA, and recorded plant establishment, survival, and reproduction. Cumulative foliage and floral herbivory …

Random Search Models Of Foraging Behavior: Theory, Simulation, And Observation, Ben C. Nolting

Department of Mathematics: Dissertations, Theses, and Student Research

Many organisms, from bacteria to primates, use stochastic movement patterns to find food. These movement patterns, known as search strategies, have recently be- come a focus of ecologists interested in identifying universal properties of optimal foraging behavior. In this dissertation, I describe three contributions to this field. First, I propose a way to extend Charnov's Marginal Value Theorem to the spatially explicit framework of stochastic search strategies. Next, I describe simulations that compare the efficiencies of sensory and memory-based composite search strategies, which involve switching between different behavioral modes. Finally, I explain a new behavioral analysis protocol for identifying the …

Improving Time Structure Patterns Of Orthogonal Markov Chains And Its Consequences In Hydraulic Simulations, Juan C. Jaimes-Correa

School of Natural Resources: Dissertations, Theses, and Student Research

Rainfall¹ occurrences understood as rain events are relevant for agricultural practices because temporal distribution of rainfall highly affects yield production. A few stochastic models satisfactorily generate daily rainfall events while preserving temporal and spatial dependence among multiple sites. I evaluated an extension on the traditional Orthogonal Markov chain (TOMC) model in reproducing the temporal structure of rainfall events at multiple sites in Florida (FL), Nebraska (NE) and California (CA). In addition, a simulation of watershed runoff from rainfall events, reproduced by a single- and multi-site weather generator, was conducted. Results shows that (i) a temporal structure extended …

Practical Guidelines For The Comprehensive Analysis Of Chip-Seq Data, Timonthy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang

Department of Statistics: Faculty Publications

Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the key tasks of modern biology, as evidenced by the Encyclopedia of DNA Elements (ENCODE) Project. To this end, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the standard methodology. Mapping such protein-DNA interactions in vivo using ChIP-seq presents multiple challenges not only in sample preparation and sequencing but also for computational analysis. Here, we present step-by-step guidelines for the computational analysis of ChIP-seq data. We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality …

A Test For Detecting Changes In Closed Networks Based On The Number Of Communications Between Nodes, Christopher S. Wichman

Department of Statistics: Dissertations, Theses, and Student Research

This dissertation presents a formal method for detecting changes in a closed communications network based on an “abnormal” shift in the number of communications between some of the nodes. The method relies on the analyst’s ability to define the network of interest; capture the number of communications between nodes; and to establish a history of normal communications flow between nodes over fixed intervals of time. A metric multi-dimensional scaling technique is then used to represent the network at each time interval with a k-dimensional (k = 1, 2, …) configuration. The affine bi-dimensional regression coefficient of determination (aR²) …

Informative Retesting For Hierarchical Group Testing, Michael S. Black

Department of Statistics: Dissertations, Theses, and Student Research

Group testing is the process of pooling samples (e.g., blood, chemical compounds) from multiple sources and testing the pooled material for some binary characteristic. It is used in pathogen screening for humans and animals, drug discovery studies, electrical systems testing, and many other applications. Group testing has traditionally been used for two main types of investigations: 1) the identification of positive specimens and 2) the estimation of a characteristic’s prevalence in a population. This dissertation focuses on the identification process. We propose new identification procedures that exploit the heterogeneity among samples in order to reduce the number of tests needed …

Environmentally Friendly Sizing Agent From Corn Distillers Dried Grains, Yue Zhang

College of Education and Human Sciences: Dissertations, Theses, and Student Research

Distillers dried grains (DDGS), the coproducts of corn ethanol production, were used as a textile sizing agent on cotton, polyester and polyester/cotton blends in an effort to find inexpensive and biodegradable alternatives to sizing agents such as poly(vinyl alcohol) that are currently used. Although DDGS is an inexpensive, biodegradable and abundant co-product, it has limited industrial applications. DDGS is a mixture of carbohydrates, proteins and oil which are used as sizing agents or as size additives. The effects of DDGS extraction conditions on sizing evaluation parameters such as fiber adhesion, film properties, viscosity and fabric abrasion were studied in comparison …

Assessment Of Tillage Practices Using Landsat-Tm 5 In Nebraska., Sonisa Sharma

School of Natural Resources: Dissertations, Theses, and Student Research

Tillage management practices are an important component to crop production and to federal and state conservation efforts and crop subsidy programs. Crop residue created by conservation tillage reduces soil erosion and reduce evaporation from exposed soil. Agro-hydrological models require information on tillage practices to estimate their impacts on soil-water-holding capacity, total evapotranspiration, carbon sequestration, water runoff and water and wind erosion for agricultural lands. Classification of tillage practices using remote sensing offers promise for the rapid collection of tillage information on individual fields over large areas. Using satellite imagery proves to be challenging due to the similarity in spectral signatures …

New Tools For Quantitative Decision Analysis In Applied Ecology And Conservation, Adam W. Schapaugh

School of Natural Resources: Dissertations, Theses, and Student Research

Scientists have generated a massive body of theory aimed at predicting and managing the impacts of anthropogenic activities on populations, species, and ecosystems. Transforming this research into knowledge that informs complex decision-making problems remains a major challenge in environmental management and conservation. My dissertation research aims to address this issue through the development and application of mathematical and statistical models. I integrate tools, concepts, and techniques from ecology, applied mathematics, computer science, and statistics to build structured decision-making frameworks for spatial prioritization, resource allocation, and optimal scheduling. I also tackle several of the technical challenges limiting the utility of such …

Drosophila Melanogaster Selection For Survival After Infection With Bacillus Cereus Spores: Evolutionary Genetic And Phenotypic Investigations Of Respiration And Movement, Junjie Ma, Andrew K. Benson, Stephen D. Kachman, Deidra J. Jacobsen, Lawrence G. Harshman

Department of Statistics: Faculty Publications

Laboratory populations of D.melanogaster have been subjected to selection for survival after live spores of B. cereus were introduced as a pathogenic agent. The present study was designed to investigate correlated traits: respiration as ametabolic trait and movement as a behavioral trait.An underlying hypothesiswas that the evolution of increased survival after B. cereus infection exerts ametabolic cost associated with elevated immunity and this would be detected by increased respiration rates. There was support for this hypothesis in the male response to selection, but not for selected-line females. Two phenotypic effects were also observed in the study. Females especially showed a …

The Change In Differing Leukocyte Populations During Vaccination To Bovine Respiratory Disease And Their Correlations With Lung Scores, Health Records, And Average Daily Gain, R. J. Leach, C. G. Chitko-Mckown, G. L. Bennett, S. A. Jones, Stephen D. Kachman, J. W. Keele, K. A. Leymaster, R. M. Thallman, L. A. Kuehn

Department of Statistics: Faculty Publications

Bovine respiratory disease (BRD) is the most economically important disease in U.S. feedlots. Infection can result in morbidity, mortality, and reduced average daily gain. Cheap and reliable genetic methods of prediction and protection from BRD would be highly advantageous to the industry. The immune response may correlate with BRD incidence. Cattle (n = 2,182) were vaccinated against common viral and bacterial pathogens of BRD. Two blood samples were collected, one during booster vaccination and one 21d later, enabling 3 phenotypes for each trait [prebooster (pre), postbooster (post), and delta (post minus pre)]. From the blood samples innate and adaptive responses …

Prediction In M-Complete Problems With Limited Sample Size, Jennifer Lynn Clarke, Bertrand Clarke, Chi-Wai Yu

Department of Statistics: Faculty Publications

We define a new Bayesian predictor called the posterior weighted median (PWM) and compare its performance to several other predictors including the Bayes model average under squared error loss, the Barbieri-Berger median model predictor, the stacking predictor, and the model average predictor based on Akaike's information criterion. We argue that PWM generally gives better performance than other predictors over a range of M-complete problems. This range is between the M-closed-M-complete boundary and the M-complete- M-open boundary. Indeed, as a problem gets closer to M-open, it seems that M-complete predictive methods begin to break down. Our comparisons rest on extensive simulations …

Comparison Of Molecular Breeding Values Based On Within- And Across-Breed Training In Beef Cattle, Stephen D. Kachman, Matthew L. Spangler, Gary L. Bennett, Kathryn J. Hanford, Larry A. Kuehn, Warren M. Snelling, Mark Thallman, Mahdi Saatchi, Dorian J. Garrick, Robert D. Schnabel, Jeremy F. Taylor, E John Pollak

Department of Statistics: Faculty Publications

Background: Although the efficacy of genomic predictors based on within-breed training looks promising, it is necessary to develop and evaluate across-breed predictors for the technology to be fully applied in the beef industry. The efficacies of genomic predictors trained in one breed and utilized to predict genetic merit in differing breeds based on simulation studies have been reported, as have the efficacies of predictors trained using data from multiple breeds to predict the genetic merit of purebreds. However, comparable studies using beef cattle field data have not been reported.

Methods: Molecular breeding values for weaning and yearling weight …

Patron-Driven Acquisition And Circulation At An Academic Library: Interaction Effects And Circulation Performance Of Print Books Acquired Via Librarians’ Orders, Approval Plans, And Patrons’ Interlibrary Loan Requests, David C. Tyler, Christina D. Falci, Joyce C. Melvin, Marylou Epp, Anita M. Kreps

University of Nebraska-Lincoln Libraries: Faculty Publications

Numerous publications on patron-driven acquisition (PDA) for print books and similar materials have reported that patron-requested materials circulate more. Tying circulation to selector may be failing to address the complex of factors that contributes to items’ circulation. In the present study, the authors revisit a PDA program’s data and to determine whether PDA print books’ circulation advantage persists when the potential interactions of several additional variables are taken into account. As with prior studies, library patrons were significantly better predictors of circulation than were librarians or approval plans. However, librarians proved to be significantly better predictors than were approval plans.

Do Non-Response Follow-Ups Improve Or Reduce Data Quality?: A Review Of The Existing Literature, Kristen Olson

Department of Sociology: Faculty Publications

The paper systematically reviews existing literature on the relationship between the level of effort to recruit a sampled person and the measurement quality of survey data. Hypotheses proposed for this relationship are reviewed. Empirical findings for the relationship between level of effort as measured by paradata (the number of follow-up attempts, refusal conversion and time in the field) and question-specific item non-response rates, aggregate measures of item non-response rates, response accuracy and various measurement errors on attitudinal questions are examined through a qualitative review.

Group Testing Regression Models, Boan Zhang

Department of Statistics: Dissertations, Theses, and Student Research

Group testing, where groups of individual specimens are composited to test for the presence or absence of a disease (or some other binary characteristic), is a procedure commonly used to reduce the costs of screening a large number of individuals. Statistical research in group testing has traditionally focused on a homogeneous population, where individuals are assumed to have the same probability of having a disease. However, individuals often have different risks of positivity, so recent research has examined regression models that allow for heterogeneity among individuals within the population. This dissertation focuses on two problems involving group testing regression models. …

Retrieval Of Sub-Pixel-Based Fire Intensity And Its Application For Characterizing Smoke Injection Heights And Fire Weather In North America, David Peterson

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

For over two decades, satellite sensors have provided the locations of global fire activity with ever-increasing accuracy. However, the ability to measure fire intensity, know as fire radiative power (FRP), and its potential relationships to meteorology and smoke plume injection heights, are currently limited by the pixel resolution. This dissertation describes the development of a new, sub-pixel-based FRP calculation (FRP_f) for fire pixels detected by the MODerate Resolution Imaging Spectroradiometer (MODIS) fire detection algorithm (Collection 5), which is subsequently applied to several large wildfire events in North America. The methodology inherits an earlier bi-spectral algorithm for retrieving sub-pixel …

Significant Themes In 19th-Century Literature, Matthew L. Jockers, David Mimno

Department of English: Faculty Publications

External factors such as author gender, author nationality, and date of publication affect both the choice of literary themes in novels and the expression of those themes, but the extent of this association is difficult to quantify. In this work, we apply statistical methods to identify and extract hundreds of "topics" from a corpus of 3,346 works of 19th-century British, Irish, and American fiction. We use these topics as a measurable, data-driven proxy for literary themes. External factors may predict fluctuations in the use of themes and the individual word choices within themes. We use topics to measure the evidence …

Modeling And Mathematical Analysis Of Plant Models In Ecology, Eric A. Eager

Department of Mathematics: Dissertations, Theses, and Student Research

Population dynamics tries to explain in a simple mechanistic way the variations of the size and structure of biological populations. In this dissertation we use mathematical modeling and analysis to study the various aspects of the dynamics of plant populations and their seed banks.

In Chapter 2 we investigate the impact of structural model uncertainty by considering different nonlinear recruitment functions in an integral projection model for Cirsium canescens. We show that, while having identical equilibrium populations, these two models can elicit drastically different transient dynamics. We then derive a formula for the sensitivity of the equilibrium population to …

Murine Gut Microbiota Is Defined By Host Genetics And Modulates Variation Of Metabolic Traits, Autumn M. Mcknite, Maria Elisa Perez-Munoz, Lu Lu, Evan G. Williams, Simon Brewer, Penelope A. Andreux, John W. M. Bastiaansen, Xusheng Wang, Stephen D. Kachman, Johan Auwerx, Robert W. Williams, Andrew K. Benson, Daniel A. Peterson, Daniel C. Ciobanu

Department of Statistics: Faculty Publications

The gastrointestinal tract harbors a complex and diverse microbiota that has an important role in host metabolism. Microbial diversity is influenced by a combination of environmental and host genetic factors and is associated with several polygenic diseases. In this study we combined next-generation sequencing, genetic mapping, and a set of physiological traits of the BXD mouse population to explore genetic factors that explain differences in gut microbiota and its impact on metabolic traits. Molecular profiling of the gut microbiota revealed important quantitative differences in microbial composition among BXD strains. These differences in gut microbial composition are influenced by host-genetics, which …

Transcriptome-Wide Changes In Chlamydomonas Reinhardtii Gene Expression Regulated By Carbon Dioxide And The Co2-Concentrating Mechanism Regulator Cia5/Ccm1, Wei Fang, Yaqing Si, Stephen Douglass, David Casero, Sabeeha S. Merchant, Matteo Pellegrini, Istvan Ladunga, Peng Liu, Martin H. Spalding

Department of Statistics: Faculty Publications

Copyright (c) 2012 American Society of Plant Biologists. Used by permission.