Thomas Schmidt

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The current goal of our research is to learn enough about the physiology and ecology of microbes and microbial communities in the gut that we are able to engineer the gut microbiome to improve human health. The first target of our engineering is the production of butyrate – a common fermentation product of some gut microbes that is essential for human health. Butyrate is the preferred energy source for mitochondria in the epithelial cells lining the gut and it also regulates their gene expression.

One of the most effective ways to influence the composition and metabolism of the gut microbiota is through diet. In an interventional study, we have tracked responses in the composition and fermentative metabolism of the gut microtiota in >800 healthy individuals. Emerging patterns suggest several configurations of the microbiome that can result in increased production of butyrate acid. We have isolated the microbes that form an anaerobic food web to convert dietary fiber to butyrate and continue to make discoveries about their physiology and interactions. Based on these results, we have initiated a clinical trial in which we are hoping to prevent the development of Graft versus Host Disease following bone marrow transplants by managing butyrate production by the gut microbiota.

We are also beginning to track hundreds of other metabolites from the gut microbiome that may influence human health. We use metagenomes and metabolomes to identify patterns that link the microbiota with their metabolites and then test those models in human organoids and gnotobiotic mice colonized with synthetic communities of microbes. This blend of wet-lab research in basic microbiology, data science and in ecology is moving us closer to engineering the gut microbiome to improve human health.

Salar Fattahi

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Today’s real-world problems are complex and large, often with overwhelmingly large number of unknown variables which render them doomed to the so-called “curse of dimensionality”. For instance, in energy systems, the system operators should solve optimal power flow, unit commitment, and transmission switching problems with tens of thousands of continuous and discrete variables in real time. In control systems, a long standing question is how to efficiently design structured and distributed controllers for large-scale and unknown dynamical systems. Finally, in machine learning, it is important to obtain simple, interpretable, and parsimonious models for high-dimensional and noisy datasets. Our research is motivated by two main goals: (1) to model these problems as tractable optimization problems; and (2) to develop structure-aware and scalable computational methods for these optimization problems that come equipped with certifiable optimality guarantees. We aim to show that exploiting hidden structures in these problems—such as graph-induced or spectral sparsity—is a key game-changer in the pursuit of massively scalable and guaranteed computational methods.

9.9.2020 MIDAS Faculty Research Pitch Video.

My research lies at the intersection of optimization, data analytics, and control.

Alex Gorodetsky

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Alex Gorodetsky’s research is at the intersection of applied mathematics, data science, and computational science, and is focused on enabling autonomous decision making under uncertainty. He is especially interested in controlling, designing, and analyzing autonomous systems that must act in complex environments where observational data and expensive computational simulations must work together to ensure objectives are achieved. Toward this goal, he pursues research in wide-ranging areas including uncertainty quantification, statistical inference, machine learning, control, and numerical analysis. His methodology is to increase scalability of probabilistic modeling and analysis techniques such as Bayesian inference and uncertainty quantification. His current strategies to achieving scalability revolve around leveraging computational optimal transport, developing tensor network learning algorithms, and creating new multi-fidelity information fusion approaches.

Sample workflow for enabling autonomous decision making under uncertainty for a drone operating in a complex environment. We develop algorithms to compress simulation data by exploiting problem structure. We then embed the compressed representations onto onboard computational resources. Finally, we develop approaches to enable the drone to adapt, learn, and refine knowledge by interacting with, and collecting data from, the environment.

Gabor Orosz

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Gabor Orosz is an Associate Professor of Mechanical Engineering and Civil and Environmental Engineering. His theoretical research include dynamical systems, control, and reinforcement learning with particular interests in the roles of nonlinearities and time delays in such systems. In terms of applications he focuses on connected and automated vehicles, traffic flow, and biological networks. His research has been supported by the National Science Foundation and industrial funds. His recent work appeared in journals like IEEE Transactions on Automated Control, IEEE Transactions on Control Systems Technology, IEEE Transactions on Intelligent Transportation Systems, and Transportation Research Part C. For the latter journal he has also be serving as an Editor. WIRED magazine reported on his experimental results when his team built a connected automated vehicle and evaluated it in real traffic. He served as the program chair for the 12th IFAC Workshop on Time Delay Systems and served as the general chair for 3rd IAVSD Workshop on Dynamics of Road Vehicles, Connected and Automated Vehicles.

Ronald Gary Larson

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Larson’s research has been in the area of “Complex Fluids,” which include polymers, colloids, surfactant-containing fluids, liquid crystals, and biological macromolecules such as DNA, proteins, and lipid membranes. He has also contributed extensively to fluid mechanics, including microfluidics, and transport modeling. He has also has carried out research over the past 16 years in the area of molecular simulations for biomedical applications. The work has involved determining the structure and dynamics of lipid membranes, trans-membrane peptides, anti-microbial peptides, the conformation and functioning of ion channels, interactions of excipients with drugs for drug delivery, interactions of peptides with proteins including MHC molecules, resulting in more than 50 publications in these areas, and in the training of several Ph.D. students and postdocs. Many of these studies involve heavy use of computer simulations and methods of statistical analysis of simulations, including umbrella sampling, forward flux sampling, and metadynamics, which involve statistical weighting of results. He also has been engaged in analysis of percolation processes on lattices, including application to disease propagation.

Alpha helical peptide bridging lipid bilayer in molecular dynamics simulations of “hydrophobic mismatch.”

Joseph Eisenberg

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Dr. Eisenberg studies infectious disease epidemiology with a focus on waterborne pathogens. His expertise are in the areas of water sanitation and hygiene (WASH), quantitative microbial risk assessment (QMRA) and disease transmission modeling. Dr. Eisenberg has a long-standing research platform in northern coastal Ecuador, examining how changes in the social and natural environments, mediated by road construction, affect the epidemiology of enteric pathogens. Specific studies focus on enteric pathogens, antimicrobial resistance, the microbiome and dengue. He is also The NIGMS consortium, Models of Infectious Disease Agent Study (MIDAS), to examine mechanisms of transmission and potential intervention and control of enteric pathogens through water and sanitation interventions.

Robert Hampshire

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He develops and applies operations research, data science, and systems approaches to public and private service industries. His research focuses on the management and policy analysis of emerging networked industries and innovative mobility services such as smart parking, connected vehicles, autonomous vehicles, ride-hailing, bike sharing, and car sharing. He has worked extensively with both public and private sector partners worldwide. He is a queueing theorist that uses statistics, stochastic modeling, simulation and dynamic optimization.

Anna G. Stefanopoulou

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Energy Transportation related topics: data and simulations of various cleaner and ultimately cost-effective options for transit. exploring techno-economic and environmental issues in electric ride-sharing/hailing vehicles to create clean and convenient alternatives to single-occupancy vehicles. investigation of the location and integration of chargers with energy storage and bi-directional services, along with the connection to distributed renewable power generation such as solar arrays as well as the centralized electric grid.

Powertrain related topics: measurements, models and management of batteries, fuel cells, and engines in automotive and stationary applications.

Jing Sun

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My areas of interest are control, estimation, and optimization, with applications to energy systems in transportation, automotive, and marine domains. My group develops model-based and data-driven tools to explore underlying system dynamics and understand the operational environments. We develop computational frameworks and numerical algorithms to achieve real-time optimization and explore connectivity and data analytics to reduce uncertainties and improve performance through predictive control and planning.

Lili Zhao

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I have broad interests and expertise in developing statistical methodology and applying it in biomedical research. I have adapted methodologies, including Bayesian data analysis, categorical data analysis, generalized linear models, longitudinal data analysis, multivariate analysis, RNA-Seq data analysis, survival data analysis and machine learning methods, in response to the unique needs of individual studies and objectives without compromising the integrity of the research and results. Two main methods recently developed:
1) A risk prediction model for a survival outcome using predictors of a large dimension
I have develop a simple, fast yet sufficiently flexible statistical method to estimate the updated risk of renal disease over time using longitudinal biomarkers of a high dimension. The goal is to utilize all sources of data of a large dimension (e.g., routine clinical features, urine and serum markers measured at baseline and all follow-up time points) to efficiently and accurately estimate the updated ESRD risk.
2) A safety mining tool for vaccine safety study
I developed an algorithm for vaccine safety surveillance while incorporating adverse event ontology. Multiple adverse events may individually be rare enough to go undetected, but if they are related, they can borrow strength from each other to increase the chance of being flagged. Furthermore, borrowing strength induces shrinkage of related AEs, thereby also reducing headline-grabbing false positives.