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.
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.
“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.
Nested partially latent class models for dependent binary data; Estimating disease etiology
on April 1, 2017 at 12:00 am
Nested partially latent class models for dependent binary data; Estimating disease etiologyWu, Z., Deloria-Knoll, M. & Zeger, S. L. Apr 1 2017 In : Biostatistics. 18, 2, p. 200-213 14 p.Research output: Contribution to journal › Artic […]
Bayesian estimation of pneumonia etiology: Epidemiologic considerations and applications to the pneumonia etiology research for child health study
on January 1, 2017 at 12:00 am
Bayesian estimation of pneumonia etiology: Epidemiologic considerations and applications to the pneumonia etiology research for child health studyKnoll, M. D. , Fu, W. , Shi, Q. , Prosperi, C. , Wu, Z. , Hammitt, L. L. , Feikin, D. R. , Baggett, H. C. , Howie, S. R. C. , Scott, J. A. G. , Murdoch, D. R. , Madhi, S. A. , Thea, D. M. , Brooks, W. A. , Kotloff, K. L. , Li, M. , Park, D. E. , Lin, W. , Levine, O. S. , O'Brien, K. L. & 1 others Zeger, S. L. Jan 1 2017 In : Clinical Infectious Diseases. 64, p. S213-S227Research output: Contribution to journal › Artic […]
Partially latent class models for case-control studies of childhood pneumonia aetiology
on January 1, 2016 at 12:00 am
Partially latent class models for case-control studies of childhood pneumonia aetiologyWu, Z., Deloria-Knoll, M., Hammitt, L. L. & Zeger, S. L. Jan 1 2016 In : Journal of the Royal Statistical Society. Series C: Applied Statistics. 65, 1, p. 97-114 18 p.Research output: Contribution to journal › Artic […]
Daniel Forger is a Professor in the Department of Mathematics. He is devoted to understanding biological clocks. He uses techniques from many fields, including computer simulation, detailed mathematical modeling and mathematical analysis, to understand biological timekeeping. His research aims to generate predictions that can be experimentally verified.
My research focus is on the development and application of machine learning tools to large scale financial and unstructured (textual) data to extract, quantify and predict risk profiles and investment grade rating of private and public companies. Example datasets include social media and financial aggregators such as Bloomberg, Pitchbook, and Privco.
My research spans security, privacy, and optimization of data collection particularly as applied to the Smart Grid, an augmented and enhanced paradigm for the conventional power grid. I am particularly interested in optimization approaches that take a notion of security and/or privacy into the modeling explicitly. At the intersection of the Intelligent Transportation Systems, Smart Grid, and Smart Cities, I am interested in data privacy and energy usage in smart parking lots. Protection of data and availability, especially under assault through a Denial-of-Service attacks, represents another dimension of my area of research interests. I am working on developing data privacy-aware bidding applications for the Smart Grid Demand Response systems without relying on trusted third parties. Finally, I am interested in educational and pedagogical research about teaching computer science, Smart Grid, cyber security, and data privacy.
Necmiye Ozay, PhD, is Assistant Professor of Electrical Engineering and Computer Science, College of Engineering, at the University of Michigan, Ann Arbor.
Prof. Ozay and her team develop the scientific foundations and associated algorithmic tools for compactly representing and analyzing heterogeneous data streams from sensor/information-rich networked dynamical systems. They take a unified dynamics-based and data-driven approach for the design of passive and active monitors for anomaly detection in such systems. Dynamical models naturally capture temporal (i.e., causal) relations within data streams. Moreover, one can use hybrid and networked dynamical models to capture, respectively, logical relations and interactions between different data sources. They study structural properties of networks and dynamics to understand fundamental limitations of anomaly detection from data. By recasting information extraction problem as a networked hybrid system identification problem, they bring to bear tools from computer science, system and control theory and convex optimization to efficiently and rigorously analyze and organize information. The applications include diagnostics, anomaly and change detection in critical infrastructure such as building management systems, transportation and energy networks.
Jingwen Hu, PhD, is Associate Research Scientist in the University of Michigan Transportation Research Institute (UMTRI) with a secondary appointment as Associate Research Scientist in Mechanical Engineering in the College of Engineering at the University of Michigan, Ann Arbor.
The primary goal of Prof. Hu’s research is to reduce the incidence of injuries and fatalities in motor-vehicle crashes and other injurious events using a multidisciplinary approach. It involves 1) collecting and analyzing large-scale injury data to identify the injury problems and assess the performance of safety designs, 2) performing physical tests and computational simulations to investigate human impact responses, injury mechanisms, and injury tolerances for various body regions under field-relevant loading conditions, and 3) developing tools for large-scale computational simulations to explore the best solutions for reducing impact-induced injuries.
My research interests are in developing inter-disciplinary knowledge in System Informatics, as the basis for study of complex system problems with the fusion of theory, computation, and application components adopted from Systems and Informatics fields. In this framework, a complex system such as the supply chain is posited as a System-of-Systems; i.e., a collection of individual business entities organized as a composite system with their resources and capabilities pooled to obtain an interoperable and synergistic system, possessing common and shared goals and objectives. Informatics facilitates coordination and integration in the system by processing and sharing information among supply chain entities for improved decision-making.
A common theme of my research is the basic foundation of universality of system and the realization that what makes it unique is its environment. This has enabled to categorize problems, designs, models, methodologies, and solution techniques at macro and micro levels and develop innovative solutions by coordinating these levels in an integrated environment.
My goal is to study the efficacy of the body of knowledge available in Systems Theory, Information Science, Artificial Intelligence & Knowledge Management, Management Science, Industrial Engineering and Operations Research fields; applied uniquely to issues and problems of complex systems in the manufacturing and service sectors.
Theoretical work investigated by me in this research thrust relates to:
- Developing Generalized System Taxonomies and Ontologies for complex systems management.
- Experimenting with Problem Taxonomies for design and modeling efficiencies in complex system networks.
- Developing methodologies, frameworks and reference models for complex systems management.
- Computation and application development focused on developing algorithms and software development for:
- Supply chain information system and knowledge library using Web-based technology as a dissemination tool.
- Integration with Enterprise Resource Planning modules in SAP software.
- Supply chain management problem-solving through application of problem specific simulation and optimization.
My research has extended to application domains in healthcare, textiles, automotive, and defense sectors. Problems and issues addressed relate to health care management, operationalizing of sustainability, energy conservation, global logistics management, mega-disaster recovery, humanitarian needs management, and entrepreneurship management.
Currently, my application focus is on expanding the breadth and depth of inquiry in the healthcare domain. Among the topics being investigated are: (1) the organization and structure of health care enterprises; and (2) operations and strategies that relate to management of critical success factors, such as costs, quality, innovation and technology adoption by health care providers. Two significant topics that I have chosen to study with regard to care for elderly patients suffering from chronic congestive heart failure and hypertension are: (1) the design of patient-centered health care delivery to improve quality of care; and (2) managing enhanced care costs due to readmission of these patients.
Data science applications: Real-time data processing in supply chains, Knowledge portals for decision-making in supply chains, information sharing for optimizing patient-centered healthcare delivery
Luis Ortiz, PhD, is Assistant Professor of Computer and Information Science, College of Engineering and Computer Science, The University of Michigan, Dearborn
The study of large complex systems of structured strategic interaction, such as economic, social, biological, financial, or large computer networks, provides substantial opportunities for fundamental computational and scientific contributions. Luis’ research focuses on problems emerging from the study of systems involving the interaction of a large number of “entities,” which is my way of abstractly and generally capturing individuals, institutions, corporations, biological organisms, or even the individual chemical components of which they are made (e.g., proteins and DNA). Current technology has facilitated the collection and public availability of vasts amounts of data, particularly capturing system behavior at fine levels of granularity. In Luis’ group, they study behavioral data of strategic nature at big data levels. One of their main objectives is to develop computational tools for data science, and in particular learning large-population models from such big sources of behavioral data that we can later use to study, analyze, predict and alter future system behavior at a variety of scales, and thus improve the overall efficiency of real-world complex systems (e.g., the smart grid, social and political networks, independent security and defense systems, and microfinance markets, to name a few).