Elle O’Brien

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My research focuses on building infrastructure for public health and health science research organizations to take advantage of cloud computing, strong software engineering practices, and MLOps (machine learning operations). By equipping biomedical research groups with tools that facilitate automation, better documentation, and portable code, we can improve the reproducibility and rigor of science while scaling up the kind of data collection and analysis possible.

Research topics include:
1. Open source software and cloud infrastructure for research,
2. Software development practices and conventions that work for academic units, like labs or research centers, and
3. The organizational factors that encourage best practices in reproducibility, data management, and transparency

The practice of science is a tug of war between competing incentives: the drive to do a lot fast, and the need to generate reproducible work. As data grows in size, code increases in complexity and the number of collaborators and institutions involved goes up, it becomes harder to preserve all the “artifacts” needed to understand and recreate your own work. Technical AND cultural solutions will be needed to keep data-centric research rigorous, shareable, and transparent to the broader scientific community.

View MIDAS Faculty Research Pitch, Fall 2021

 

Marie O’Neill

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My research interests include health effects of air pollution, temperature extremes and climate change (mortality, asthma, hospital admissions, birth outcomes and cardiovascular endpoints); environmental exposure assessment; and socio-economic influences on health.
Data science tools and methodologies include geographic information systems and spatio-temporal analysis, epidemiologic study design and data management.

Sardar Ansari

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I build data science tools to address challenges in medicine and clinical care. Specifically, I apply signal processing, image processing and machine learning techniques, including deep convolutional and recurrent neural networks and natural language processing, to aid diagnosis, prognosis and treatment of patients with acute and chronic conditions. In addition, I conduct research on novel approaches to represent clinical data and combine supervised and unsupervised methods to improve model performance and reduce the labeling burden. Another active area of my research is design, implementation and utilization of novel wearable devices for non-invasive patient monitoring in hospital and at home. This includes integration of the information that is measured by wearables with the data available in the electronic health records, including medical codes, waveforms and images, among others. Another area of my research involves linear, non-linear and discrete optimization and queuing theory to build new solutions for healthcare logistic planning, including stochastic approximation methods to model complex systems such as dispatch policies for emergency systems with multi-server dispatches, variable server load, multiple priority levels, etc.

Kevin Bakker

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Kevin’s research is focused on to identifying and interpreting the mechanisms responsible for the complex dynamics we observe in ecological and epidemiological systems using data science and modeling approaches. He is primarily interested in emerging and endemic pathogens, such as SARS-CoV-2, influenza, vampire bat rabies, and a host of childhood infectious diseases such as chickenpox. He uses statistical and mechanistic models to fit, forecast, and occasionally back-cast expected disease dynamics under a host of conditions, such as vaccination or other control mechanisms.

Jesse Hamilton

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My research focuses on the development of novel Magnetic Resonance Imaging (MRI) technology for imaging the heart. We focus in particular on quantitative imaging techniques, in which the signal intensity at each pixel in an image represents a measurement of an inherent property of a tissue. Much of our research is based on cardiac Magnetic Resonance Fingerprinting (MRF), which is a class of methods for simultaneously measuring multiple tissue properties from one rapid acquisition.

Our group is exploring novel ways to combine physics-based modeling of MRI scans with deep learning algorithms for several purposes. First, we are exploring the use of deep learning to design quantitative MRI scans with improved accuracy and precision. Second, we are developing deep learning approaches for image reconstruction that will allow us to reduce image noise, improve spatial resolution and volumetric coverage, and enable highly accelerated acquisitions to shorten scan times. Third, we are exploring ways of using artificial intelligence to derive physiological motion signals directly from MRI data to enable continuous scanning that is robust to cardiac and breathing motion. In general, we focus on algorithms that are either self-supervised or use training data generated in computer simulations, since the collection of large amounts of training data from human subjects is often impractical when designing novel imaging methods.

Kathryn Luker

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As an expert in molecular imaging of single cell signaling in cancer, I develop integrated systems of molecular, cellular, optical, and custom image processing tools to extract rich data sets for biochemical and behavioral functions in living cells over minutes to days. Data sets composed of thousands to millions of cells enable us to develop predictive models of cellular function through a variety of computational approaches, including ODE, ABM, and IRL modeling.

Rajiv Saran

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Dr. Saran is an internationally recognized expert in kidney disease research – specifically, in the area of kidney disease surveillance and epidemiology. From 2014 – 2019, he served as Director of the United States Renal Data System (USRDS; www.usrds.org), a ‘gold standard’ for kidney disease data systems, worldwide. Since 2006 he has been Co-Principal Investigator for the Centers for the Disease Control and Prevention’s (CDC’s) National CKD Surveillance System for the US, a one of a kind project that complements the USRDS, while focusing on upstream surveillance of CKD and its risk factors (www.cdc.org/ckd/surveillance). Both projects have influenced policy related to kidney disease in the US and were cited extensively in the July 2019 Advancing American Kidney Health Federal policy document. Dr. Saran led the development of the first National Kidney Disease Information System (VA-REINS), for the Department of Veterans Affairs (VA), funded by the VA’s Center for Innovation, and one that led to the VA recognizing the importance of kidney disease as a health priority for US veterans. Dr. Saran has recently (2018-2021) been funded on a spin off project from VA REINS for investigation of ‘hot-spot’ of kidney disease among US Veterans involving both risk-prediction and geospatial analyses – a modern approach to health system big data being used for prevention and population health improvement, using kidney disease as an example. This approach has broad application for prevention and optimizing management of major chronic diseases.

Nicholas Henderson

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My research primarily focuses on the following main themes: 1) development of methods for risk prediction and analyzing treatment effect heterogeneity, 2) Bayesian nonparametrics and Bayesian machine learning methods with a particular emphasis on the use of these methods in the context of survival analysis, 3) statistical methods for analyzing heterogeneity in risk-benefit profiles and for supporting individualized treatment decisions, and 4) development of empirical Bayes and shrinkage methods for high-dimensional statistical applications. I am also broadly interested in collaborative work in biomedical research with a focus on the application of statistics in cancer research.

Catherine Hausman

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Catherine H. Hausman is an Associate Professor in the School of Public Policy and a Research Associate at the National Bureau of Economic Research. She uses causal inference, related statistical methods, and microeconomic modeling to answer questions at the intersection of energy markets, environmental quality, climate change, and public policy.

Recent projects have looked at inequality and environmental quality, the natural gas sector’s role in methane leaks, the impact of climate change on the electricity grid, and the effects of nuclear power plant closures. Her research has appeared in the American Economic Journal: Applied Economics, the American Economic Journal: Economic Policy, the Brookings Papers on Economic Activity, and the Proceedings of the National Academy of Sciences.