Jonathan Ozik
YOU?
Author Swipe
View article: Adaptive Grid-Based Thompson Sampling for Efficient Trajectory Discovery
Adaptive Grid-Based Thompson Sampling for Efficient Trajectory Discovery Open
Bayesian optimization (BO) is a powerful framework for estimating parameters of computationally expensive simulation models, particularly in settings where the likelihood is intractable and evaluations are costly. In stochastic models ever…
View article: Modeling of hepatitis B virus infection spread in primary human hepatocytes
Modeling of hepatitis B virus infection spread in primary human hepatocytes Open
Chronic hepatitis B virus (HBV) infection poses a significant global health threat, causing severe liver diseases including cirrhosis and hepatocellular carcinoma. We characterized HBV DNA kinetics in primary human hepatocytes (PHHs) over …
View article: Neighborhood sociome factors and pediatric asthma exacerbations: Protective role of tree crown density and importance of pharmacy access in Chicago's south side
Neighborhood sociome factors and pediatric asthma exacerbations: Protective role of tree crown density and importance of pharmacy access in Chicago's south side Open
Background Pediatric asthma exacerbations remain a critical public health concern, particularly in historically underserved urban settings. Objective This study investigates sociome factors—the social context of disease—associated with ast…
View article: Benefits of colorectal cancer screening using fecal immunochemical testing with varying positivity thresholds by age and sex
Benefits of colorectal cancer screening using fecal immunochemical testing with varying positivity thresholds by age and sex Open
Background Fecal immunochemical test (FIT) performance for colorectal cancer screening varies by age and sex, yet most FIT-based screening programs use uniform positivity thresholds. This study assessed the potential benefits of stratifyin…
View article: AERO: An autonomous platform for continuous research
AERO: An autonomous platform for continuous research Open
The COVID-19 pandemic highlighted the need for new data infrastructure, as epidemiologists and public health workers raced to harness rapidly evolving data, analytics, and infrastructure in support of cross-sector investigations. To meet t…
View article: Developing and deploying a use-inspired metapopulation modeling framework for detailed tracking of stratified health outcomes
Developing and deploying a use-inspired metapopulation modeling framework for detailed tracking of stratified health outcomes Open
Public health experts studying infectious disease spread often seek granular insights into population health outcomes. Metapopulation models offer an effective framework for analyzing disease transmission through subpopulation mixing. Thes…
View article: Stress-Testing US Colorectal Cancer Screening Guidelines: Decennial Colonoscopy from Age 45 is Robust to Natural History Uncertainty and Colonoscopy Sensitivity Assumptions
Stress-Testing US Colorectal Cancer Screening Guidelines: Decennial Colonoscopy from Age 45 is Robust to Natural History Uncertainty and Colonoscopy Sensitivity Assumptions Open
Purpose The 2023 American College of Physicians (ACP) guidelines for colorectal cancer (CRC) screening are at odds with the United States Preventive Task Force (USPSTF) guidelines, with the former recommending screening starting at age 50 …
View article: Bayesian Calibration of Stochastic Agent Based Model via Random Forest
Bayesian Calibration of Stochastic Agent Based Model via Random Forest Open
Agent‐based models (ABM) provide an excellent framework for modeling outbreaks and interventions in epidemiology by explicitly accounting for diverse individual interactions and environments. However, these models are usually stochastic an…
View article: A taxonomy of social support interventions for People experiencing a syndemic of substance use disorder, criminal legal involvement, and downstream Health sequelae
A taxonomy of social support interventions for People experiencing a syndemic of substance use disorder, criminal legal involvement, and downstream Health sequelae Open
View article: Incorporating social determinants of health into agent-based models of HIV transmission: methodological challenges and future directions
Incorporating social determinants of health into agent-based models of HIV transmission: methodological challenges and future directions Open
There is much focus in the field of HIV prevention research on understanding the impact of social determinants of health (e.g., housing, employment, incarceration) on HIV transmission and developing interventions to address underlying stru…
View article: Advancing calibration for stochastic agent-based models in epidemiology with Stein variational inference and Gaussian process surrogates
Advancing calibration for stochastic agent-based models in epidemiology with Stein variational inference and Gaussian process surrogates Open
Accurate calibration of stochastic agent-based models (ABMs) in epidemiology is crucial to make them useful in public health policy decisions and interventions. Traditional calibration methods, e.g., Markov Chain Monte Carlo (MCMC), that y…
View article: Modeling of hepatitis B virus infection spread in primary human hepatocytes
Modeling of hepatitis B virus infection spread in primary human hepatocytes Open
Chronic hepatitis B virus (HBV) infection poses a significant global health threat, causing severe liver diseases including cirrhosis and hepatocellular carcinoma. We characterized HBV DNA kinetics in primary human hepatocytes (PHH) over 3…
View article: A Portfolio Approach to Massively Parallel Bayesian Optimization
A Portfolio Approach to Massively Parallel Bayesian Optimization Open
One way to reduce the time of conducting optimization studies is to evaluate designs in parallel rather than just one-at-a-time. For expensive-to-evaluate black-boxes, batch versions of Bayesian optimization have been proposed. They work b…
View article: Theoretical modeling of hepatitis C acute infection in liver-humanized mice support pre-clinical assessment of candidate viruses for controlled-human-infection studies
Theoretical modeling of hepatitis C acute infection in liver-humanized mice support pre-clinical assessment of candidate viruses for controlled-human-infection studies Open
View article: Optimal Stopping Ages for Colorectal Cancer Screening
Optimal Stopping Ages for Colorectal Cancer Screening Open
Importance Prior studies have shown that the benefits, harms, and costs of colorectal cancer (CRC) screening at older ages are associated with a patient’s sex, health, and screening history. However, these studies were hypothetical exercis…
View article: Modeling of randomized hepatitis C vaccine trials: Bridging the gap between controlled human infection models and real-word testing
Modeling of randomized hepatitis C vaccine trials: Bridging the gap between controlled human infection models and real-word testing Open
Global elimination of chronic hepatitis C (CHC) remains difficult without an effective vaccine. Since injection drug use is the leading cause of hepatitis C virus (HCV) transmission in Western Europe and North America, people who inject dr…
View article: Agent-Based Model of Combined Community- and Jail-Based Take-Home Naloxone Distribution
Agent-Based Model of Combined Community- and Jail-Based Take-Home Naloxone Distribution Open
Importance Opioid-related overdose accounts for almost 80 000 deaths annually across the US. People who use drugs leaving jails are at particularly high risk for opioid-related overdose and may benefit from take-home naloxone (THN) distrib…
View article: Spatial inequities in access to medications for treatment of opioid use disorder highlight scarcity of methadone providers under counterfactual scenarios
Spatial inequities in access to medications for treatment of opioid use disorder highlight scarcity of methadone providers under counterfactual scenarios Open
Access to treatment and medication for opioid use disorder (MOUD) is essential in reducing opioid use and associated behavioral risks, such as syringe sharing among persons who inject drugs (PWID). Syringe sharing among PWID carries high r…
View article: Bayesian calibration of stochastic agent based model via random forest
Bayesian calibration of stochastic agent based model via random forest Open
Agent-based models (ABM) provide an excellent framework for modeling outbreaks and interventions in epidemiology by explicitly accounting for diverse individual interactions and environments. However, these models are usually stochastic an…
View article: Emulator-Based Bayesian Calibration of the CISNET Colorectal Cancer Models
Emulator-Based Bayesian Calibration of the CISNET Colorectal Cancer Models Open
Purpose To calibrate Cancer Intervention and Surveillance Modeling Network (CISNET)’s SimCRC, MISCAN-Colon, and CRC-SPIN simulation models of the natural history colorectal cancer (CRC) with an emulator-based Bayesian algorithm and interna…
View article: Characteristics of a cost-effective blood test for colorectal cancer screening
Characteristics of a cost-effective blood test for colorectal cancer screening Open
Background Blood-based biomarker tests can potentially change the landscape of colorectal cancer (CRC) screening. We characterize the conditions under which blood test screening would be as effective and cost-effective as annual fecal immu…
View article: Reducing Sample Size While Improving Equity in Vaccine Clinical Trials: A Machine Learning-Based Recruitment Methodology with Application to Improving Trials of Hepatitis C Virus Vaccines in People Who Inject Drugs
Reducing Sample Size While Improving Equity in Vaccine Clinical Trials: A Machine Learning-Based Recruitment Methodology with Application to Improving Trials of Hepatitis C Virus Vaccines in People Who Inject Drugs Open
Despite the availability of direct-acting antivirals that cure individuals infected with the hepatitis C virus (HCV), developing a vaccine is critically needed in achieving HCV elimination. HCV vaccine trials have been performed in populat…
View article: Towards Improved Uncertainty Quantification of Stochastic Epidemic Models Using Sequential Monte Carlo
Towards Improved Uncertainty Quantification of Stochastic Epidemic Models Using Sequential Monte Carlo Open
Sequential Monte Carlo (SMC) algorithms represent a suite of robust computational methodologies utilized for state estimation and parameter inference within dynamical systems, particularly in real-time or online environments where data arr…
View article: Sociome Data Commons: A scalable and sustainable platform for investigating the full social context and determinants of health – ERRATUM
Sociome Data Commons: A scalable and sustainable platform for investigating the full social context and determinants of health – ERRATUM Open
[This corrects the article DOI: 10.1017/cts.2023.670.].
View article: A Community Roadmap for Scientific Workflows Research and Development
A Community Roadmap for Scientific Workflows Research and Development Open
The landscape of workflow systems for scientific applications is notoriously convoluted with hundreds of seemingly equivalent workflow systems, many isolated research claims, and a steep learning curve. To address some of these challenges …
View article: Impact of post-incarceration care engagement interventions on HIV transmission among young Black men who have sex with men and their sexual partners: an agent-based network modeling study
Impact of post-incarceration care engagement interventions on HIV transmission among young Black men who have sex with men and their sexual partners: an agent-based network modeling study Open
This work was supported by the following grants from the National Institutes of Health: R01DA039934; P20 GM 130414; P30 AI 042853; P30MH058107; T32 DA 043469; U2C DA050098 and the California HIV/AIDS Research Program: OS17-LA-003; H21PC346…
View article: PSI/J: A Portable Interface for Submitting, Monitoring, and Managing Jobs
PSI/J: A Portable Interface for Submitting, Monitoring, and Managing Jobs Open
It is generally desirable for high-performance computing (HPC) applications to be portable between HPC systems, for example to make use of more performant hardware, make effective use of allocations, and to co-locate compute jobs with larg…
View article: NSF RESUME EcoEpi Workshop: One Health Surveillance and Predictive Intelligence for Eco-Epidemiological Modeling
NSF RESUME EcoEpi Workshop: One Health Surveillance and Predictive Intelligence for Eco-Epidemiological Modeling Open
The NSF-funded Robust Epidemic Surveillance and Modeling (RESUME) project successfully convened a workshop entitled, “One Health surveillance and predictive intelligence for eco-epidemiological modeling” at the University of Chicago on Apr…
View article: NSF RESUME HPC Workshop: High-Performance Computing and Large-Scale Data Management in Service of Epidemiological Modeling
NSF RESUME HPC Workshop: High-Performance Computing and Large-Scale Data Management in Service of Epidemiological Modeling Open
The NSF-funded Robust Epidemic Surveillance and Modeling (RESUME) project successfully convened a workshop entitled "High-performance computing and large-scale data management in service of epidemiological modeling" at the University of Ch…
View article: Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics
Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics Open
Hepatitis B virus (HBV) infection kinetics in immunodeficient mice reconstituted with humanized livers from inoculation to steady state is highly dynamic despite the absence of an adaptive immune response. To recapitulate the multiphasic v…