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

 

Anne Fernandez

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Dr. Fernandez is a clinical psychologist with extensive training in both addiction and behavioral medicine. She is the Clinical Program Director at the University of Michigan Addiction Treatment Service. Her research focuses on the intersection of addiction and health across two main themes: 1) Expanding access to substance use disorder treatment and prevention services particularly in healthcare settings and; 2) applying precision health approaches to addiction-related healthcare questions. Her current grant-funded research includes an NIH-funded randomized controlled pilot trial of a preoperative alcohol intervention, an NIH-funded precision health study to leverage electronic health records to identify high-risk alcohol use at the time of surgery using natural language processing and other machine-learning based approaches, a University of Michigan funded precision health award to understand and prevent new persistent opioid use after surgery using prediction modeling, and a federally-funded evaluation of the state of Michigan’s substance use disorder treatment expansion.

Sara Lafia

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I am a Research Fellow in the Inter-university Consortium for Political and Social Research (ICPSR) at the University of Michigan. My research is currently supported by a NSF project, Developing Evidence-based Data Sharing and Archiving Policies, where I am analyzing curation activities, automatically detecting data citations, and contributing to metrics for tracking the impact of data reuse. I hold a Ph.D. in Geography from UC Santa Barbara and I have expertise in GIScience, spatial information science, and urban planning. My interests also include the Semantic Web, innovative GIS education, and the science of science. I have experience deploying geospatial applications, designing linked data models, and developing visualizations to support data discovery.

Xu Shi

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My methodological research focus on developing statistical methods for routinely collected healthcare databases such as electronic health records (EHR) and claims data. I aim to tackle the unique challenges that arise from the secondary use of real-world data for research purposes. Specifically, I develop novel causal inference methods and semiparametric efficiency theory that harness the full potential of EHR data to address comparative effectiveness and safety questions. I develop scalable and automated pipelines for curation and harmonization of EHR data across healthcare systems and coding systems.

Nambi Nallasamy

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Our team develops machine learning algorithms for the enhancement of outcomes in cataract surgery, the most commonly performed surgery in the world. Our works focuses on developing models for postoperative refraction after cataract surgery and analysis of surgical quality.

Frederick George Conrad

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Fred Conrad’s research concerns the development of new methods and data sources for conducting social research. His work is largely focused on survey methodology, but he also explores the use of social media content as a complement to survey data and as a source of large-scale qualitative insights. His focus is on data quality and reducing measurement error. For example, live video interviews promote more thoughtful responses, e.g., less straightlining – the tendency to give the same answer to a battery of survey questions, but they also promote less candor when answering questions on sensitive topics. Measurement error in social media include misclassification in the automated interpretation of content using methods such as sentiment analysis and topic modeling, as well as selective self-presentation (only posting flattering content). Equally challenging is not knowing the extent to which users differ from the population to which one might wish to generalize results.

Lisa Levinson

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My research interests are in natural language semantics and psycholinguistics, focusing on verbs. I conduct behavioral psycholinguistic experiments with methodologies such as self-paced reading and maze tasks, as well as surveys of linguistic and semantic judgments. I also study semantic variation using corpora and datasets such as the Twitter Decahose, to better understand how words have developed diverging meanings in different communities, age groups, or regions. I use primarily R and Python to collect, manage, and analyze data. I direct the UM WordLab in the linguistics department, working with students (especially undergraduates) on experimental and computational research focusing on lexical representations.

Wenhao Sun

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We are interested in resolving outstanding fundamental scientific problems that impede the computational materials design process. Our group uses high-throughput density functional theory, applied thermodynamics, and materials informatics to deepen our fundamental understanding of synthesis-structure-property relationships, while exploring new chemical spaces for functional technological materials. These research interests are driven by the practical goal of the U.S. Materials Genome Initiative to accelerate materials discovery, but whose resolution requires basic fundamental research in synthesis science, inorganic chemistry, and materials thermodynamics.

Joshua Stein

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As a board-certified ophthalmologist and glaucoma specialist, I have more than 15 years of clinical experience caring for patients with different types and complexities of glaucoma. In addition to my clinical experience, as a health services researcher, I have developed experience and expertise in several disciplines including performing analyses using large health care claims databases to study utilization and outcomes of patients with ocular diseases, racial and other disparities in eye care, associations between systemic conditions or medication use and ocular diseases. I have learned the nuances of various data sources and ways to maximize our use of these data sources to answer important and timely questions. Leveraging my background in HSR with new skills in bioinformatics and precision medicine, over the past 2-3 years I have been developing and growing the Sight Outcomes Research Collaborative (SOURCE) repository, a powerful tool that researchers can tap into to study patients with ocular diseases. My team and I have spent countless hours devising ways of extracting electronic health record data from Clarity, cleaning and de-identifying the data, and making it linkable to ocular diagnostic test data (OCT, HVF, biometry) and non-clinical data. Now that we have successfully developed such a resource here at Kellogg, I am now collaborating with colleagues at > 2 dozen academic ophthalmology departments across the country to assist them with extracting their data in the same format and sending it to Kellogg so that we can pool the data and make it accessible to researchers at all of the participating centers for research and quality improvement studies. I am also actively exploring ways to integrate data from SOURCE into deep learning and artificial intelligence algorithms, making use of SOURCE data for genotype-phenotype association studies and development of polygenic risk scores for common ocular diseases, capturing patient-reported outcome data for the majority of eye care recipients, enhancing visualization of the data on easy-to-access dashboards to aid in quality improvement initiatives, and making use of the data to enhance quality of care, safety, efficiency of care delivery, and to improve clinical operations. .

Feng Zhou

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For human-machine systems, I first collect data from human users, whether it’s an individual, a team, or even a society. Different kinds of methods can be used, including self-report, interview, focus groups, physiological and behavioral data, as well as user-generated data from the Internet.

Based on the data collected, I attempt to understand human contexts, including different aspects of the human users, such as emotion, cognition, needs, preferences, locations and activities. Such understanding can then be applied to different human-machine systems, including healthcare systems, automated driving systems, and product-service systems.

Based on the different design theory and methodology, from the perspective of the machine dimension, I apply knowledge of computing and communication as well as practical and theoretical knowledge of social and behavior to design various systems for human users. From the human dimension, I seek to understand human needs and decision making processes, and then build mathematical models and design tools that facilitate integration of subjective experiences, social contexts, and engineering principles into the design process of human-machine systems.