Statistics and Probability Commons^™

Application Of Transfer Learning For Cancer Drug Sensitivity Prediction, Saugato Rahman Dhruba, Raziur Rahman, Kevin Matlock, Souparno Ghosh, Ranadip Pal

Department of Statistics: Faculty Publications

Background: In precision medicine, scarcity of suitable biological data often hinders the design of an appropriate predictive model. In this regard, large scale pharmacogenomics studies, like CCLE and GDSC hold the promise to mitigate the issue. However, one cannot directly employ data from multiple sources together due to the existing distribution shift in data. One way to solve this problem is to utilize the transfer learning methodologies tailored to fit in this specific context.

Results: In this paper, we present two novel approaches for incorporating information from a secondary database for improving the prediction in a target database. The first …

Investigation Of Model Stacking For Drug Sensitivity Prediction, Kevin Matlock, Carlos De Niz, Raziur Rahman, Souparno Ghosh, Ranadip Pal

Department of Statistics: Faculty Publications

Background: A significant problem in precision medicine is the prediction of drug sensitivity for individual cancer cell lines. Predictive models such as Random Forests have shown promising performance while predicting from individual genomic features such as gene expressions. However, accessibility of various other forms of data types including information on multiple tested drugs necessitates the examination of designing predictive models incorporating the various data types.

Results: We explore the predictive performance of model stacking and the effect of stacking on the predictive bias and squarred error. In addition we discuss the analytical underpinnings supporting the advantages of stacking in reducing …

Analysis Of Praxis Physics Subject Assessment Examinees And Performance: Who Are Our Prospective Physics Teachers?, Herman Ray

Faculty Articles

A generally agreed upon tenant of the physics teaching community is the centrality of subject-specific expertise in effective teaching. However, studies which assess the content knowledge of incoming K–12 physics teachers in the U.S. have not yet been reported. Similarly lacking are studies on if or how the demographic makeup of aspiring physics educators is different from previously reported analyses of the actual high school physics teaching workforce. Here we present findings about the demographics and subject knowledge of prospective high school physics teachers using data from Praxis physics subject assessments administered between 2006 and 2016. Our analysis reveals significant …

Self-Reported Vs. Measured Height, Weight, And Bmi In Young Adults, Melissa D. Olfert, Makenzie L. Barr, Camille M. Charlier, Oluremi A. Famodu, Wenjun Zhou, Anne E. Mathews, Carol Byrd-Bredbenner, Sarah E. Colby

Faculty & Staff Scholarship

Self-reported height and weight, if accurate, provide a simple and economical method to track changes in body weight over time. Literature suggests adults tend to under-report their own weight and that the gap between self-reported weight and actual weight increases with obesity. This study investigates the extent of discrepancy in self-reported height, weight, and subsequent Body Mass Index (BMI) versus actual measurements in young adults. Physically measured and self-reported height and weight were taken from 1562 students. Male students marginally overestimated height, while females were closer to target. Males, on average, closely self-reported weight. Self-reported anthropometrics remained statistically correlated to …

Gene × Environment Interaction: What Exactly Are We Talking About?, David S. Moore

Pitzer Faculty Publications and Research

An ambiguity exists in how psychological scientists use the word “interaction.” This word can refer to physical interactions between components that constitute the mechanisms in complex systems, but it can also refer to statistical interactions revealed by General Linear Statistical Models (e.g., Analyses of Variance). Statistical interactions indicate that the nature of the relationship between two variables depends on a third variable, but the discovery of such interactions does not constitute evidence of physical interactions between components in a system. Studies conducted using traditional behavioral genetics methods sometimes reveal statistical interactions between genes and environments, but the presence or absence …

Systematic Review And Meta-Analysis: Tuberculosis, Tnfα Inhibitors, And Crohn's Disease, Brent L. Cao

Honors Undergraduate Theses

Inflammation is often a protective reaction against harmful foreign agents. However, in many disease conditions, the mechanisms behind the inflammatory response are poorly understood. Often times, the inflammation causes adverse effects, such as joint pain, abdominal pain, fever, fatigue, and loss of appetite. Thus, many treatments aim to inhibit the inflammatory response in order to control adverse symptoms. Such treatments include TNFα inhibitors. However, a major risk associated with drugs inhibiting tumor necrosis factor alpha (TNFα) is serious infection, including tuberculosis (TB).

Anti-TNFα therapy is used to treat patients with Crohn’s disease, for which the risk of tuberculosis may be …

Sequential Probing With A Random Start, Joshua Miller

HMC Senior Theses

Processing user requests quickly requires not only fast servers, but also demands methods to quickly locate idle servers to process those requests. Methods of finding idle servers are analogous to open addressing in hash tables, but with the key difference that servers may return to an idle state after having been busy rather than staying busy. Probing sequences for open addressing are well-studied, but algorithms for locating idle servers are less understood. We investigate sequential probing with a random start as a method for finding idle servers, especially in cases of heavy traffic. We present a procedure for finding the …

Improving The Detection Limit Of Tau Aggregates For Use With Biological Samples, Emily Rickman Hager

Electronic Theses and Dissertations

The protein Tau is found in neurofibrillary tangles in Alzheimer's disease and over 20 other neurodegenerative diseases. An assay has been developed to detect minute amounts of fibrils from human brain tissue. This assay subjects brain tissue extract and recombinant Tau to several rounds of sonication and incubation. Incubation allows recombinant Tau to add itself to the ends of the existing fibrils in brain tissue extract. Sonication breaks the existing fibrils in the brain tissue extract offering more ends for Tau to add onto. Cycles of sonication and incubation have been shown to allow for amplification of Tau fibrils from …

Risk Behaviors And Hiv Care Continuum Outcomes Among Criminal Justice-Involved Hiv-Infected Transgender Women And Cisgender Men: Data From The Seek, Test, Treat, And Retain Harmonization Initiative., Curt G Beckwith, Irene Kuo, Rob J Fredericksen, Lauren Brinkley-Rubinstein, William E Cunningham, Sandra A Springer, Kelsey B Loeliger, Julie Franks, Katerina Christopoulos, Jennifer Lorvick, Shoshana Y Kahana, Rebekah Young, David W Seal, Chad Zawitz, Joseph A Delaney, Heidi M Crane, Mary L Biggs

Epidemiology Faculty Publications

BACKGROUND: Transgender persons are highly victimized, marginalized, disproportionately experience incarceration, and have alarmingly increased rates of HIV infection compared to cis-gender persons. Few studies have examined the HIV care continuum outcomes among transgender women (TW), particularly TW who are involved with the criminal justice (CJ) system.

METHODS: To improve our understanding of HIV care continuum outcomes and risk behaviors among HIV-infected TW who are involved with the CJ system, we analyzed data from the National Institute on Drug Abuse-supported Seek, Test, Treat, Retain (STTR) Data Harmonization Initiative. Baseline data were pooled and analyzed from three U.S. STTR studies to examine …

A Checklist For Clinical Trials In Rare Disease: Obstacles And Anticipatory Actions-Lessons Learned From The For-Dmd Trial, R Crow, K Hart, M Mcdermott, R Tawil, W Martens, Mathula Thangarajh, +Several Additional Authors

Neurology Faculty Publications

Background: Trials in rare diseases have many challenges, among which are the need to set up multiple sites in different countries to achieve recruitment targets and the divergent landscape of clinical trial regulations in those countries. Over the past years, there have been initiatives to facilitate the process of international study set-up, but the fruits of these deliberations require time to be operationally in place. FOR-DMD (Finding the Optimum Steroid Regimen for Duchenne Muscular Dystrophy) is an academic-led clinical trial which aims to find the optimum steroid regimen for Duchenne muscular dystrophy, funded by the National Institutes of Health (NIH) …

Pre- And Post-Diagnosis Physical Activity, Television Viewing, And Mortality Among Hematologic Cancer Survivors., Daniela Schmid, Gundula Behrens, Hannah Arem, Christina Hart, Wolfgang Herr, Carmen Jochem, Charles E Matthews, Michael F Leitzmann

Epidemiology Faculty Publications

PURPOSE: The associations of physical activity and television (TV) viewing with mortality risk among individuals with hematologic malignancies remain unclear.

METHODS: We examined the relations of physical activity and TV viewing time before and after diagnosis with mortality among 5182 U.S. adults aged 50-71 years from the NIH-AARP Diet and Health Study cohort who survived a first primary hematologic cancer between 1995-1996 and 2011.

RESULTS: For the pre- and post-diagnosis analyses, we confirmed 2606 and 613 deaths respectively. In multivariable-adjusted Cox proportional hazard regression models, comparing high (≥4 hrs/wk) versus low (/wk) activity levels, pre-diagnosis physical activity was associated with …

Impact Of Chronic Sexual Abuse And Depression On Inflammation And Wound Healing In The Female Reproductive Tract Of Hiv-Uninfected And Hiv-Infected Women., Mimi Ghosh, Jason Daniels, Maria Pyra, Monika Juzumaite, Mariel Jais, Kerry Murphy, Tonya N Taylor, Seble Kassaye, Lorie Benning, Mardge Cohen, Kathleen Weber

Epidemiology Faculty Publications

Sexual violence is associated with increased risk of HIV acquisition/transmission in women. Forced sex can result in physical trauma to the reproductive tract as well as severe psychological distress. However, immuno-biological mechanisms linking sexual violence and HIV susceptibility are incompletely understood. Using the Women's Interagency HIV Study repository, a total of 77 women were selected to form 4 groups, stratified by HIV serostatus, in the following categories: 1) no sexual abuse history and low depressive symptom score (below clinically significant cut-off, scores

Piloting Very Early Infant Diagnosis Of Hiv In Lesotho: Acceptability And Feasibility Among Mothers, Health Workers And Laboratory Personnel., Michelle M Gill, Lynne M Mofenson, Mamakhetha Phalatse, Vincent Tukei, Laura Guay, Matsepeli Nchephe

Epidemiology Faculty Publications

INTRODUCTION: Mortality associated with in-utero HIV infection rises rapidly within weeks after birth. Very early infant diagnosis of HIV (VEID)-testing within 2 weeks of birth-followed by immediate initiation of antiretroviral therapy has potential to avert mortality associated with in-utero transmission. However, our understanding of acceptability and feasibility of VEID is limited.

METHODS: VEID was piloted in an observational prospective cohort of HIV-positive pregnant women and their infants in 13 Lesotho health facilities. Between March-July 2016, semi-structured interviews were conducted with HIV-positive women attending 6-week or 14-week postnatal visits and health workers (HWs) in 8 study facilities in 3 districts as …

Sexually Transmitted Infections Among Hiv-Infected Individuals In The District Of Columbia And Estimated Hiv Transmission Risk: Data From The Dc Cohort, Jose Lucar, Rachel Hart, Nabil Rayeed, Arpi Terzian, Amy Weintrob, Amanda D. Castel, Debra A. Benator, Dc Cohort Executive Committee

Epidemiology Faculty Publications

Background

Washington, DC, has one of the highest rates of HIV infection in the United States. Sexual intercourse is the leading mode of HIV transmission, and sexually transmitted infections (STIs) are a risk factor for HIV acquisition and transmission.

Methods

We evaluated the incidence and demographic factors associated with chlamydia, gonorrhea, and syphilis among HIV-infected persons enrolled at 13 DC Cohort sites from 2011 to 2015. Using Poisson regression, we assessed covariates of risk for incident STIs. We also examined HIV viral loads (VLs) at the time of STI diagnosis as a proxy for HIV transmission risk.

Results

Six point …

Cluster-Based Network Proximities For Arbitrary Nodal Subsets, Kenneth S. Berenhaut, Peter S. Barr, Alyssa M. Kogel, Ryan L. Melvin

Faculty & Staff Scholarship

The concept of a cluster or community in a network context has been of considerable interest in a variety of settings in recent years. In this paper, employing random walks and geodesic distance, we introduce a unified measure of cluster-based proximity between nodes, relative to a given subset of interest. The inherent simplicity and informativeness of the approach could make it of value to researchers in a variety of scientific fields. Applicability is demonstrated via application to clustering for a number of existent data sets (including multipartite networks). We view community detection (i.e. when the full set of network nodes …

Synthesis And Large-Scale Textual Corpora: A Nested Topic Model Of Britain's Debates Over Landed Property In The Nineteenth Century, Jo Guldi, Benjamin Williams

History Faculty Publications

Scholars need tools that will allow them to generalize about the fit of themes, events, and rhetorical styles represented in a body of texts. In this article, we introduce the concept of “nested topics,” an approach to topic modeling large-scale textual corpora that highlights implicit ontologies and relationships within the texts themselves. This tool exploits the fact that topic modeling can be used to generalize about topics on an aggregate level as well as a fine-grained level, an approach that has the consequences of revealing overarching themes that appear across all texts as well as more idosyncratic events and rehtorical …

Mixture Models With Grouping Structure: Retail Analytics Applications, Haidar Almohri

Wayne State University Dissertations

Growing competitiveness and increasing availability of data is generating tremendous interest in data-driven analytics across industries. In the retail sector, stores need targeted guidance to improve both the efficiency and effectiveness of individual stores based on their specific location, demographics, and environment. We propose an effective data-driven framework for internal benchmarking that can lead to targeted guidance for individual stores. In particular, we propose an objective method for segmenting stores using a model-based clustering technique that accounts for similarity in store performance dynamics. It relies on effective Finite Mixture of Regression (FMR) techniques for carrying out the model-based clustering with …

Iterative Matrix Factorization Method For Social Media Data Location Prediction, Natchanon Suaysom

HMC Senior Theses

Since some of the location of where the users posted their tweets collected by social media company have varied accuracy, and some are missing. We want to use those tweets with highest accuracy to help fill in the data of those tweets with incomplete information. To test our algorithm, we used the sets of social media data from a city, we separated them into training sets, where we know all the information, and the testing sets, where we intentionally pretend to not know the location. One prediction method that was used in (Dukler, Han and Wang, 2016) requires appending one-hot …

Borrowing Capacity, Financial Instability, And Contagion: Case Study Of The U.S. Subprime Mortgage Crisis, Youngna Choi

Department of Applied Mathematics and Statistics Faculty Scholarship and Creative Works

We use the case of the 2007 United States subprime mortgage crisis to investigate the impact of borrowing capacity limitations on financial instability and contagion. We divide an economy into agents that interact via flow of funds and express the financial instability level of each agent as a function of time derivatives of its wealth, cash inflows, and borrowing capacity. We show that among these factors, the borrowing capacity, which is determined by other economic constraints, has the largest impact on financial instability. It is suggested that borrowing capacity limitations could even cause contagion through feedback loop formed by flow …

The Impact Of Truncating Data On The Predictive Ability For Single-Step Genomic Best Linear Unbiased Prediction, Jeremy T. Howard, Thomas A. Rathje, Caitlyn E. Bruns, Danielle F. Wilson-Wells, Stephen D. Kachman, Matthew L. Spangler

Department of Animal Science: Faculty Publications

Simulated and swine industry data sets were utilized to assess the impact of removing older data on the predictive ability of selection candidate estimated breeding values (EBV) when using single-step genomic best linear unbiased prediction (ssGBLUP). Simulated data included thirty replicates designed to mimic the structure of swine data sets. For the simulated data, varying amounts of data were truncated based on the number of ancestral generations back from the selection candidates. The swine data sets consisted of phenotypic and genotypic records for three traits across two breeds on animals born from 2003 to 2017. Phenotypes and genotypes were iteratively …