Survival Analysis Commons^™

Novel R Shiny Tool For Survival Analysis With Time-Varying Covariate In Oncology Studies: Overcoming Biases And Enhancing Collaboration, Yimei Li, Yang Qiao, Fei Gao, Jordan Gauthier, Qiang Ed Zhang, Jenna Voutsinas, Wendy Leisenring, Ted Gooley, Corinne Summers, Alexandre Hirayama, Cameron Turtle, Rebecca Gardner, Jarcy Zee, Qian Vicky Wu

Wills Eye Hospital Papers

PURPOSE: Our study is motivated by evaluating the role of hematopoietic cell transplantation (HCT) after chimeric antigen receptor T-cell (CAR-T) therapy for ALL, a debated topic. Because patients may receive HCT at different times after CAR-T infusion or never, HCT post-CAR-T should be considered as a time-varying covariate (TVC).

METHODS: Standard Cox models and Kaplan-Meier (KM) curves (naïve method) assume that TVC status is known and fixed at baseline, which can yield biased estimates. Landmark analysis is a popular alternative but depends on a chosen landmark time. Time-dependent (TD) Cox model is better suited for TVC although visualizing survival curves …

Modeling Musculoskeletal Combat Casualty Care: Nato Trauma System Performance In Large Scale Combat Operations, Mark P. Cote, Kaitlyn E. Holly, Roman J. Schoenfeld, Matthew R. Bryan, Malina O. Hatton, Mitchel B. Harris, Tracey P. Koehlmoos, Andrew J. Schoenfeld

Department of Orthopaedic Surgery Faculty Papers

BACKGROUND: It is unclear whether the current North Atlantic Treaty Organization (NATO) trauma system will be effective in the setting of Large-Scale Combat Operations (LSCO). We sought to model the efficacy of the NATO trauma system in the setting of LSCO. We also intended to model novel scenarios that could better adapt the current system to LSCO.

METHODS: We developed a discrete-event simulation model for patients with combat musculoskeletal injuries treated within the standard NATO system. The primary outcome of the model was survival. The model's health states were characterized as stable, hypovolemia, sepsis, shock, or death. The model simulated …

Unified Hybrid Censoring Samples From Power Pratibha Distribution And Its Applications, Mahmoud Mansour, Hebatalla H. Mohammad Dr, Khalaf S. Sultan Prof.

Basic Science Engineering

This paper suggests an extensive inferential method for the Power Pratibha Distribution (PPD) under Unified Hybrid Censoring Schemes (UHCSs), since there is a growing interest in flexible models in both reliability and service operations. This work studies the PPD model using standard Maximum Likelihood Estimation methods and modern Bayesian approaches too. Using a complex architecture, UHCS simulates tests more closely to what is done in practice than by using more basic censoring schemes. Using analysis, the probability and statistical ranges are carefully calculated for the parameters. Tests demonstrate that Bayesian estimation gives better results than many other methods for estimation, …

Resale Revolution: Trend Implications From Media Presence Transcended To Luxury Retail Markets, Penelope Prochnow

Capstone Projects

This study aims to deepen understanding of fashion trend decline from peak popularity to obsolescence, with implications for sustainability and producer profit margins. It investigates how the attributes and media presence of fashion items influence their journey from high-end editorial coverage to resale platforms. Using survival analysis to model trend lifetimes and cosine similarity metrics to compare resale and magazine keyword frequencies, alongside machine learning for price prediction, the study uncovers critical temporal patterns. Results show that resale trends reflect magazine content with a lag of approximately 18 to 30 months and draw from long-wave revivals spanning 6 to 14 …

Transcriptional Profiles Reveal Physiological Mechanisms For Compensation During A Simulated Marine Heatwave In Yellowtail Kingfish (Seriola Lalandi), Sharon E. Hook, Ryan J. Farr, Jenny Su, Alistair J. Hobday, Catherine Wingate, Lindsey Woolley, Luke Pilmer

Fisheries Research Articles

Background

Changing ocean temperatures are already causing declines in populations of marine organisms. Predicting the capacity of organisms to adjust to the pressures posed by climate change is a topic of much current research effort, particularly for species we farm or harvest. To explore one measure of phenotypic plasticity, the physiological compensations in response to heat stress as might be experienced in a marine heatwave, we exposed Yellowtail Kingfish (Seriola lalandi) to sublethal heat stress, and used the transcriptome in gill and muscle, benchmarked against heat shock proteins and oxidative stress indicators, to characterise the acute heat stress …

Leveraging Bayesian And Classical Techniques For Survival Analysis Using The Weibull-Rayleigh Distribution, Mahmoud Mansour, Rashad El-Sagheer, Nagwa Mohamed

Basic Science Engineering

This paper contributes to an extensive analysis of the Weibull-Rayleigh distribution (WRD), including Bayesian inference for randomly censored data. The WRD is a versatile model that fits various types of survival data, especially in situations including censoring, commonly found in biostatistics and engineering reliability research. The research investigates the derivation of the WRD’s probability density and cumulative distribution functions, employing maximum likelihood estimation (MLE) and Bayesian estimating techniques to accurately infer parameters. Gamma priors are utilized in Bayesian analysis, and approximate Bayesian estimates are derived by Gibbs sampling and Lindley’s approximation methods. An actual dataset that represents leukemia-free survival times …

An Analytical Prior Selection Procedure For Empirical Bayesian Analysis Using Resampling Techniques: A Simulation-Based Approach Using The Pancreatic Adenocarcinoma Data From The Seer Database, Aditya Chakraborty, Mohan D. Pant

Epidemiology, Biostatistics, & Environmental Health Faculty Publications

Introduction: In the field of medical research, empirical Bayesian analysis has emerged as an increasingly applicable approach. This statistical framework offers greater flexibility, enabling researchers to incorporate prior information and rigorously estimate parameters of interest. However, the selection of suitable prior distributions can be a challenging endeavor, with profound implications for the resulting inferences. To address this challenge, this study proposes a new analytical procedure that leverages resampling techniques to guide the choice of priors in Bayesian analysis. Subject and Methods: The study group consisted of patients who had been diagnosed and had died of pancreatic adenocarcinoma (cause-specific death) who …

Handwritten Digit Recognition Using Machine Learning Classifiers, Md Ahiduzzaman

Data Science and Data Mining

This project explores and compares the performance of various machine learning classifiers for handwritten digit recognition using the MNIST dataset. The classifiers include Logistic Regression, k-Nearest Neighbors, and Convolutional Neural Networks. Each classifier is evaluated based on accuracy, precision, recall, F1-score, and confusion matrix analysis.

Pediatric Renal Cell Carcinoma (Prcc) Subpopulation Environmental Differentials In Survival Disadvantage Of Black/African American Children In The United States: Large-Cohort Evidence, Laurens Holmes, Phatismo Masire, Arieanna Eaton, Robert Mason, Mackenzie Holmes, Justin William, Maura Poleon, Michael Enwere

College of Population Health Faculty Papers

OBJECTIVE: Renal cell carcinoma (RCC) is a rare but severe and aggressive pediatric malignancy. While incidence is uncommon, survival is relatively low with respect to acute lymphocytic leukemia (ALL), AML, lymphoma, ependymoma, glioblastoma, and Wilms Tumor. The pediatric renal cell carcinoma (pRCC) incidence, cumulative incidence (period prevalence), and mortality vary by health disparities' indicators, namely sex, race, ethnicity, age at tumor diagnosis, and social determinants of health (SDHs) as well as Epigenomic Determinants of Health (EDHs). However, studies are unavailable on some pRCC risk determinants, such as area of residence and socio-economic status (SES). The current study aimed at assessing …

Cane Toad, Department Of Primary Industries And Regional Development, Western Australia

Biosecurity factsheets

This factsheet provides information about the identification, biology, impact, and management of the cane toad.

The cane toad (Rhinella marina), or giant toad, is native to central and South America. It has been introduced to many countries, including northern and eastern Australia. The cane toad is a declared pest under the Biosecurity and Agriculture Management Act 2007 (BAM Act) in Western Australia (WA). The Western Australian Organism List (WAOL), available on the website at dpird.wa.gov.au) contains information on the area(s) in which this pest is declared, and the control and keeping categories to which it has been assigned in WA.

Genomic Population Structure Of Great Hammerhead Sharks (Sphyrna Mokarran) Across The Indo-Pacific, Naomi L. Brunjes, Samuel M. Williams, Alexis L. Levengood, Matt K. Broadhurst, Vincent Raoult, Alastair V. Harry, Matias Braccini, Madeline E. Green, Julia L. Y. Spaet, Michael J. Travers, Bonnie J. Holmes

Fisheries Research Articles

Context

Currently, little information exists describing the population structure of great hammerhead sharks (Sphyrna mokarran) in Australian waters. Aims

This study used single nucleotide polymorphisms to investigate fine-scale population structure in S. mokarran across the Indo-Pacific. Methods

DNA was extracted from 235 individuals across six Australian locations and a Red Sea outgroup. Population parameters were calculated and visualised to test structuring across locations. Key results

No fine-scale population structuring was observed for S. mokarran across the Indo-Pacific. However, population structuring occurred for all Australian locations when compared to the Red Sea outgroup. Conclusions

Findings suggest a single stock …

The Social And Economic Dimensions Of One Of The World’S Longest-Operating Shark Fisheries, Matias Braccini, Maddison Watt, Clinton Syers, Nick Blay, Matthew Navarro, Michael Burton

Fisheries Research Articles

Context

Social and economic information is limited for coastal commercial and recreational fisheries, particularly shark fisheries, which are perceived as unsustainable and as targeting sharks for fins.

Aims

To characterise the social and economic dimensions of one of the world’s few long-standing sustainable shark fisheries.

Methods

We reviewed historic data and surveyed stakeholders to understand the economic and social dimensions of the shark fishery currently operating in Western Australia.

Key results

Since the fishery’s historic peak, there has been a substantial reduction in the number of operating vessels and ports due to management intervention. For the vessels that have remained, …

Formulating An Efficient Statistical Test Using The Goodness Of Fit Approach With Applications To Real-Life Data, S. A. Qaid, S. E. Abo Youssef Prof., Mahmoud Mansour

Basic Science Engineering

Statistical tests are very important for researchers to make decisions. In particular, when the tests are non-parametric, they are of greater importance because they can be applied to a wide range of data sets regardless of knowing the distribution of these data. Researchers are therefore racing to obtain efficient tests for making good decisions based on the results of these tests. In this study, NBU (2)L was used based on the goodness of fit approach to present an efficient statistical test. The efficiency of the proposed test was computed, and the results were compared to those of other tests. Critical …

A Nonparametric Test For Comparing Survival Functions Based On Restricted Distance Correlation, Quinyang Zhang

Mathematical Sciences Faculty Publications and Presentations

In this article, we propose an omnibus test for comparing two survival functions under non-proportional hazards. The test statistic is based on a product-limit estimate of the restricted distance correlation, which is closely related to the L₂ distance between survival curves. The strong consistency is established under mild regularity conditions. Our simulation studies show that the new test has satisfactory power under proportional hazard and various non-proportional hazards settings including delayed treatment effect, diminishing effect, and crossing survival curves; therefore, it can be a competitive alternative to the existing omnibus tests such as Kolmogorov-Smirnov test, Cramer-von Mises test, two-stage …

Forecasting Remission Time Of A Treatment Method For Leukemia As An Application To Statistical Inference Approach, Ahmed Galal Atia, Mahmoud Mansour, Rashad Mohamed El-Sagheer, B. S. El-Desouky

Basic Science Engineering

In this paper, Weibull-Linear Exponential distribution (WLED) has been investigated whether being it is a well-fit distribution to a clinical real data. These data represent the duration of remission achieved by a certain drug used in the treatment of leukemia for a group of patients. The statistical inference approach is used to estimate the parameters of the WLED through the set of the fitted data. The estimated parameters are utilized to evaluate the survival and hazard functions and hence assessing the treatment method through forecasting the duration of remission times of patients. A two-sample prediction approach has been applied to …

Survivability Analysis In The Shadow Of Apollo: Part Ii - Spacecraft Charging Vulnerability Near The Stable Earth-Moon Lagrange Points, Robert A. Bettinger, Nathan R. Boone, Nicholas S. Hamilton, Bryan D. Little

Faculty Publications

Though the reality of routine travel and sustained operations in space likely remains several decades away, the building blocks of space exploration and space system development necessary to realize this reality are currently being laid by peer, near-peer, and emerging space-faring nations. The pursuance of sustained cislunar space operations will necessitate a renewed examination of spacecraft survivability and the capability of spacecraft to avoid and/or withstand the natural and manmade environmental risks posed by this “new” ultimate high ground.

Survivability Analysis In The Shadow Of Apollo: Part I - Cislunar Debris Propagation And Spacecraft Vulnerability, Nathan R. Boone, Robert A. Bettinger

Faculty Publications

Although the reality of routine travel and sustained operations and habitation in space likely remains several decades away, the building blocks of space exploration and space system development necessary to realize this reality are currently being laid by peer, near-peer, and emerging space-faring nations. Traditionally, global space operations were notionally limited to near-Earth space, with mission altitudes extending to geosynchronous or even highly elliptical orbits. During the 2010s, however, space operations began moving beyond this paradigm to encompass cislunar space with reinvigorated U.S. initiatives to return to the Moon via the Artemis program, planned commercial space projects, and an accelerated …

Inferences For Weibull-Gamma Distribution In Presence Of Partially Accelerated Life Test, Mahmoud Mansour, M A W Mahmoud Prof., Rashad El-Sagheer

Basic Science Engineering

In this paper, the point at issue is to deliberate point and interval estimations for the parameters of Weibull-Gamma distribution (WGD) using progressively Type-II censored (PROG-II-C) sample under step stress partially accelerated life test (SSPALT) model. The maximum likelihood (ML), Bayes, and four parametric bootstrap methods are used to obtain the point estimations for the distribution parameters and the acceleration factor. Furthermore, the approximate confidence intervals (ACIs), four bootstrap confidence intervals and credible intervals of the estimators have been gotten. The results of Bayes estimators are computed under the squared error loss (SEL) function using Markov Chain Monte Carlo (MCMC) …

Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease's process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous data sets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards …

Non Parametric Test For Testing Exponentiality Against Exponential Better Than Used In Laplace Transform Order, Mahmoud Mansour, M A W Mahmoud Prof.

Basic Science Engineering

In this paper, the test statistic for testing exponentiality against exponential better than used in Laplace transform order (EBUL) based on the Laplace transform technique is proposed. Pitman’s asymptotic efficiency of our test is calculated and compared with other tests. The percentiles of this test are tabulated. The powers of the test are estimated for famously used distributions in aging problems. In the case of censored data, our test is applied and the percentiles are also calculated and tabulated. Finally, real examples in different areas are utilized as practical applications for the proposed test.

The Utility Of Bioenergetics Modelling In Quantifying Predation Rates Of Marine Apex Predators: Ecological And Fisheries Implications, A. Barnett, M. Braccini, C. L. Dudgeon, N. L. Payne, K. G. Abrantes, M. Sheaves, E. P. Snelling

Fisheries Research Articles

Predators play a crucial role in the structure and function of ecosystems. However, the magnitude of this role is often unclear, particularly for large marine predators, as predation rates are difficult to measure directly. If relevant biotic and abiotic parameters can be obtained, then bioenergetics modelling offers an alternative approach to estimating predation rates, and can provide new insights into ecological processes. We integrate demographic and ecological data for a marine apex predator, the broadnose sevengill shark Notorynchus cepedianus, with energetics data from the literature, to construct a bioenergetics model to quantify predation rates on key fisheries species in …

Inference On The Stress-Strength Model From Weibull Gamma Distribution, Mahmoud Mansour, Rashad El-Sagheer, M. A. W. Mahmoud Prof.

Basic Science Engineering

No abstract provided.

Conditional Screening For Ultra-High Dimensional Covariates With Survival Outcomes, Hyokyoung Grace Hong, Jian Kang, Yi Li

The University of Michigan Department of Biostatistics Working Paper Series

Identifying important biomarkers that are predictive for cancer patients' prognosis is key in gaining better insights into the biological influences on the disease and has become a critical component of precision medicine. The emergence of large-scale biomedical survival studies, which typically involve excessive number of biomarkers, has brought high demand in designing efficient screening tools for selecting predictive biomarkers. The vast amount of biomarkers defies any existing variable selection methods via regularization. The recently developed variable screening methods, though powerful in many practical setting, fail to incorporate prior information on the importance of each biomarker and are less powerful in …

A Transformation Class For Spatio-Temporal Survival Data With A Cure Fraction, Sandra M. Hurtado Rua, Dipak K. Dey

Mathematics and Statistics Faculty Publications

We propose a hierarchical Bayesian methodology to model spatially or spatio-temporal clustered survival data with possibility of cure. A flexible continuous transformation class of survival curves indexed by a single parameter is used. This transformation model is a larger class of models containing two special cases of the well-known existing models: the proportional hazard and the proportional odds models. The survival curve is modeled as a function of a baseline cumulative distribution function, cure rates, and spatio-temporal frailties. The cure rates are modeled through a covariate link specification and the spatial frailties are specified using a conditionally autoregressive model with …

Models For Hsv Shedding Must Account For Two Levels Of Overdispersion, Amalia Magaret

UW Biostatistics Working Paper Series

We have frequently implemented crossover studies to evaluate new therapeutic interventions for genital herpes simplex virus infection. The outcome measured to assess the efficacy of interventions on herpes disease severity is the viral shedding rate, defined as the frequency of detection of HSV on the genital skin and mucosa. We performed a simulation study to ascertain whether our standard model, which we have used previously, was appropriately considering all the necessary features of the shedding data to provide correct inference. We simulated shedding data under our standard, validated assumptions and assessed the ability of 5 different models to reproduce the …

A Pairwise Likelihood Augmented Estimator For The Cox Model Under Left-Truncation, Fan Wu, Sehee Kim, Jing Qin, Rajiv Saran, Yi Li

The University of Michigan Department of Biostatistics Working Paper Series

Survival data collected from prevalent cohorts are subject to left-truncation and the analysis is challenging. Conditional approaches for left-truncated data under the Cox model are inefficient as they typically ignore the information in the marginal likelihood of the truncation times. Length-biased sampling methods can improve the estimation efficiency but only when the stationarity assumption of the disease incidence holds, i.e., the truncation distribution is uniform; otherwise they may generate biased estimates. In this paper, we propose a semi-parametric method for the Cox model under general left-truncation, where the truncation distribution is unspecified. Our approach is to make inference based on …

Preparedness Of Hospitals In The Republic Of Ireland For An Influenza Pandemic, An Infection Control Perspective, Mary Reidy, Fiona Ryan, Dervla Hogan, Seán Lacey, Claire Buckley

Department of Mathematics Publications

When an influenza pandemic occurs most of the population is susceptible and attack rates can range as high as 40–50 %. The most important failure in pandemic planning is the lack of standards or guidelines regarding what it means to be ‘prepared’. The aim of this study was to assess the preparedness of acute hospitals in the Republic of Ireland for an influenza pandemic from an infection control perspective.

Cox Regression Models With Functional Covariates For Survival Data, Jonathan E. Gellar, Elizabeth Colantuoni, Dale M. Needham, Ciprian M. Crainiceanu

Johns Hopkins University, Dept. of Biostatistics Working Papers

We extend the Cox proportional hazards model to cases when the exposure is a densely sampled functional process, measured at baseline. The fundamental idea is to combine penalized signal regression with methods developed for mixed effects proportional hazards models. The model is fit by maximizing the penalized partial likelihood, with smoothing parameters estimated by a likelihood-based criterion such as AIC or EPIC. The model may be extended to allow for multiple functional predictors, time varying coefficients, and missing or unequally-spaced data. Methods were inspired by and applied to a study of the association between time to death after hospital discharge …

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 …

Hypothesis Testing For An Extended Cox Model With Time-Varying Coefficients, Takumi Saegusa, Chongzhi Di, Ying Qing Chen

UW Biostatistics Working Paper Series

The log-rank test has been widely used to test a treatment effect under the Cox model for censored time-to-event outcomes, though it may lose power substantially when the model's proportional hazards assumption does not hold. In this paper, we consider an extended Cox model that uses B-splines or smoothing splines to model a time-varying treatment effect and propose score test statistics for the treatment effect. Our proposed new tests combine statistical evidence from both the magnitude and the shape of the time-varying hazard ratio function, and thus are omnibus and powerful against various types of alternatives. In addition, the new …