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Yuki Shiraito

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Yuki Shiraito works primarily in the field of political methodology. His research interests center on the development and applications of Bayesian statistical models and large-scale computational algorithms for data analysis. He has applied these quantitative methods to political science research including a survey experiment on public support for conflicting parties in civil war, heterogeneous effects of indiscriminate state violence, and the detection of text diffusion among a large set of legislative bills.

After completing his undergraduate education at the University of Tokyo, Yuki received his Ph.D. in Politics (2017) from Princeton University. Before joining the University of Michigan as an Assistant Professor in September 2018, he served as a Postdoctoral Fellow in the Program of Quantitative Social Science at Dartmouth College.

Raed Al Kontar

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My research broadly focuses on developing data analytics and decision-making methodologies specifically tailored for Internet of Things (IoT) enabled smart and connected products/systems. I envision that most (if not all) engineering systems will eventually become connected systems in the future. Therefore, my key focus is on developing next-generation data analytics, machine learning, individualized informatics and graphical and network modeling tools to truly realize the competitive advantages that are promised by smart and connected products/systems.

 

Ho-Joon Lee

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Dr. Lee’s research in data science concerns biological questions in systems biology and network medicine by developing algorithms and models through a combination of statistical/machine learning, information theory, and network theory applied to multi-dimensional large-scale data. His projects have covered genomics, transcriptomics, proteomics, and metabolomics from yeast to mouse to human for integrative analysis of regulatory networks on multiple molecular levels, which also incorporates large-scale public databases such as GO for functional annotation, PDB for molecular structures, and PubChem and LINCS for drugs or small compounds. He previously carried out proteomics and metabolomics along with a computational derivation of dynamic protein complexes for IL-3 activation and cell cycle in murine pro-B cells (Lee et al., Cell Reports 2017), for which he developed integrative analytical tools using diverse approaches from machine learning and network theory. His ongoing interests in methodology include machine/deep learning and topological Kolmogorov-Sinai entropy-based network theory, which are applied to (1) multi-level dynamic regulatory networks in immune response, cell cycle, and cancer metabolism and (2) mass spectrometry-based omics data analysis.

Figure 1. Proteomics and metabolomics analysis of IL-3 activation and cell cycle (Lee et al., Cell Reports 2017). (A) Multi-omics abundance profiles of proteins, modules/complexes, intracellular metabolites, and extracellular metabolites over one cell cycle (from left to right columns) in response to IL-3 activation. Red for proteins/modules/intracellular metabolites up-regulation or extracellular metabolites release; Green for proteins/modules/intracellular metabolites down-regulation or extracellular metabolites uptake. (B) Functional module network identified from integrative analysis. Red nodes are proteins and white nodes are functional modules. Expression profile plots are shown for literature-validated functional modules. (C) Overall pathway map of IL-3 activation and cell cycle phenotypes. (D) IL-3 activation and cell cycle as a cancer model along with candidate protein and metabolite biomarkers. (E) Protein co-expression scale-free network. (F) Power-low degree distribution of the network E. (G) Protein entropy distribution by topological Kolmogorov-Sinai entropy calculated for the network E.

 

Erhan Bayraktar

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Erhan Bayraktar, PhD, the holder of the Susan Smith Chair, is a full professor of Mathematics at the University of Michigan, where he has been since 2004. Professor Bayraktar’s research is in stochastic analysis, control, applied probability and mathematical finance. He has over 120 publications in top journals in these areas.

Professor Bayraktar is recognized as a leader in his areas of research: he is a corresponding editor in the SIAM Journal on Control and Optimization and also serves in the editorial boards of Applied Mathematics and Optimization, Mathematics of Operations Research, Mathematical Finance. His research has been also been continually funded by the National Science Foundation; in particular, he received a CAREER grant.

Professor Bayraktar has also been devoting his time to teaching and synergistic activities: Professor Bayraktar has been the director of the Risk Management and Quantitative Finance Masters program since its inception in 2015. As one of the two organizers of the Financial/Actuarial Math seminar which brings about 10-15 speakers every academic year and he has also organized several international workshops in stochastic analysis for finance and insurance in Ann Arbor.

Areas of interest: Mathematical finance, applied probability, stochastic analysis, stochastic control, optimal stopping.

Samuel K Handelman

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Samuel K Handelman, Ph.D., is Research Assistant Professor in the department of Internal Medicine, Gastroenterology, of Michigan Medicine at the University of Michigan, Ann Arbor. Prof. Handelman is focused on multi-omics approaches to drive precision/personalized-therapy and to predict population-level differences in the effectiveness of interventions. He tends to favor regression-style and hierarchical-clustering approaches, partially because he has a background in both statistics and in cladistics. His scientific monomania is for compensatory mechanisms and trade-offs in evolution, but he has a principled reason to focus on translational medicine: real understanding of these mechanisms goes all the way into the clinic. Anything less that clinical translation indicates that we don’t understand what drove the genetics of human populations.

Romesh Saigal

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Professor Saigal has held faculty positions at the Haas School of Business, Berkeley and the department of Industrial Engineering and Management Sciences at Northwestern University, has been a researcher at the Bell Telephone Laboratories and numerous short term visiting positions. He currently teaches courses in Financial Engineering. In the recent past he taught courses in optimization, and Management Science. His current research involves data based studies of operational problems in the areas of Finance, Transportation, Renewable Energy and Healthcare, with an emphasis on the management and pricing of risks. This involves the use of data analytics, optimization, stochastic processes and financial engineering tools. His earlier research involved theoretical investigation into interior point methods, large scale optimization and software development for mathematical programming. He is an author of two books on optimization and large set of publications in top refereed journals. He has been an associate editor of Management Science and is a member of SIAM, AMS and AAAS. He has served as the Director of the interdisciplinary Financial Engineering Program and as the Director of Interdisciplinary Professional Programs (now Integrative Design + Systems) at the College of Engineering.

Zhenke Wu

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Zhenke Wu is an Assistant Professor of Biostatistics, and a core faculty member in the Michigan Institute of Data Science (MIDAS). He received his Ph.D. in Biostatistics from the Johns Hopkins University in 2014 and then stayed at Hopkins for his postdoctoral training before joining the University of Michigan. Dr. Wu’s research focuses on the design and application of statistical methods that inform health decisions made by individuals, or precision medicine. The original methods and software developed by Dr. Wu are now used by investigators from research institutes such as CDC and Johns Hopkins, as well as site investigators from developing countries, e.g., Kenya, South Africa, Gambia, Mali, Zambia, Thailand and Bangladesh.

 

Profile: At a “sweet spot” of data science

By Dan Meisler
Communications Manager, ARC

If you had to name two of the more exciting, emerging fields of data science, electronic health records (EHR) and mobile health might be near the top of the list.

Zhenke Wu, one of the newest MIDAS core faculty members, has one foot firmly in each field.

“These two fields share the common goal of learning from the experience of the population in the past to advance health and clinical decisions for those to follow. I am looking forward to more work that will bring the two fields closer to continuously generate insights about human health.” Wu said. “I’m in a sweet spot.”

Wu joined U-M in Fall 2016, after earning a PhD in Biostatistics from Johns Hopkins University, and a bachelor’s in Mathematics from Fudan University. He said the multitude of large-scale studies going on at U-M and access to EHR databases were factors in his coming to Michigan.

“The University of Michigan is an exciting place that has a diversity of large-scale databases and supportive research groups in the fields I’m interested in,” he said.

Wu is collaborating with the Michigan Genomics Initiative, which is a biorepository effort at Michigan Medicine to integrate genome-wide information with EHR from approximately 40,000 patients undergoing anesthesia prior to surgery or diagnostic procedures. He’s also collaborating with Dr. Srijan Sen, Associate Professor, Department of Psychiatry and Molecular and Behavioral Neuroscience Institute, on the MIDAS-supported project “Identifying Real-Time Data Predictors of Stress and Depression Using Mobile Technology,” the preliminary results of which recently matured into an NIH-funded R01 project “Mobile Technology to Identify Mechanisms Linking Genetic Variation and Depression” that will draw broad expertise from a multi-disciplinary team of medical and data science researchers.

A visualization of data from the Michigan Genomics Initiative

“One of my goals is to use an integrated and rigorous approach to predict how a person’s health status will be in the near future,” Wu said.

Wu applies hierarchical Bayesian models to these problems, which he hopes will shed light on phenomena he describes as latent constructs that are “well-known, but less quantitatively understood, e.g., intelligence quotient (IQ) in psychology.”

As another example, he cites the current challenge in active surveillance of prostate cancer patients for aggressive tumors requiring removal and/or radiation, or indolent tumors permitting continued surveillance.

“The underlying status of aggressive versus indolent cancer is not observed, which needs to be learned from the results of biopsy and other clinical measurements,” he said. “The decisions and experience of urologists and their patients will greatly benefit from more accurate understanding of the tumor status… There are lots of scientific problems in clinical, biomedical, behavioral and social sciences where you have well-known but less quantitatively understood latent constructs. These are problems that Bayesian latent variable methods can formulate and address.”

Just as Wu has a hand in two hot-button big data areas, he also sees himself as straddling the line between application and methodology.

He says the large number of data sources — sensors, mobile apps, test results, and questionnaires, to name just a few — results in richness as well as some “messiness” that needs new methodologies to adjust, integrate and translate to new scientific insights. At the same time, a valid new methodology for dealing with, for example, electronic health data, will likely find numerous different applications.

Wu says his approach was heavily influenced by his work in the Pneumonia Etiology Research for Child Health (PERCH) funded by the Gates Foundation while he was at Johns Hopkins. Pneumonia is a clinical syndrome due to lung infection that can be caused by more than 30 different species of pathogens, including bacteria, viruses and fungi. The goal of the seven-country study that enrolled more than 5,000 cases and 5,000 controls from Africa and Southeast Asia is to estimate the frequency with which each pathogen caused pneumonia in the population and the probability of each individual being infected by the list of pathogens in the lung.

“In most settings, it is extremely difficult to identify the pathogen by directly sampling from the site of infection – the child’s lung. PERCH therefore looked for other sources of evidence by standardizing and comprehensively testing biofluids collected from sites peripheral to the lung. Using hierarchical Bayesian models to infer disease etiology by integrating such a large trove of data was extremely fun and exciting”, he said.

Wu’s initial interest in math, leading to biostatistics and now data science, stems from what he called a “greedy” desire to learn the guiding principles of how the world works by rigorous data science.

“If you have new problems, you can wait for other people to ask a clean math question, or you can go work with these messy problems and figure out interesting questions and their answers,” he said.

For more on Dr. Wu, see his profile on Michigan Experts.

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    Bhramar Mukherjee

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    Bhramar Mukherjee is  a Professor in the Department of Biostatistics, joining the department in Fall, 2006. Bhramar is also a Professor in the Department of Epidemiology. Bhramar completed her Ph.D. in 2001 from Purdue University. Bhramar’s principal research interests lie in Bayesian methods in epidemiology and studies of gene-environment interaction. She is also interested in modeling missingness in exposure, categorical data models, Bayesian nonparametrics, and the general area of statistical inference under outcome/exposure dependent sampling schemes. Bhramar’s methodological research is funded by NSF and NIH.   Bhramar is involved as a co-investigator in several R01s led by faculty in Internal Medicine, Epidemiology and Environment Health sciences at UM. Her collaborative interests focus on genetic and environmental epidemiology, ranging from investigating the genetic architecture of colorectal cancer in relation to environmental exposures to studies of air pollution on pediatric Asthma events in Detroit. She is actively engaged in Global Health Research.

    Ding Zhao

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    Ding Zhao, PhD, is Assistant Research Scientist in the department of Mechanical Engineering, College of Engineering with a secondary appointment in the Robotics Institute at The University of Michigan, Ann Arbor.

    Dr. Zhao’s research interests include autonomous vehicles, intelligent/connected transportation, traffic safety, human-machine interaction, rare events analysis, dynamics and control, machine learning, and big data analysis