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


Jodyn Platt

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Our team leads research on the Ethical, Legal, and Social Implications (ELSI) of learning health systems and related enterprises. Our research uses mixed methods to understand policies and practices that make data science methods (data collection and curation, AI, computable algorithms) trustworthy for patients, providers, and the public. Our work engages multiple stakeholders including providers and health systems, as well as the general public and minoritized communities on issues such as AI-enabled clinical decision support, data sharing and privacy, and consent for data use in precision oncology.

Sophia Brueckner

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Sophia Brueckner is a futurist artist/designer/engineer. Inseparable from computers since the age of two, she believes she is a cyborg. As an engineer at Google, she designed and built products used by millions. At RISD and the MIT Media Lab, she researched the simultaneously empowering and controlling nature of technology with a focus on haptics and social interfaces. Her work has been featured internationally by Artforum, SIGGRAPH, The Atlantic, Wired, the Peabody Essex Museum, Portugal’s National Museum of Contemporary Art, and more. Brueckner is the founder and creative director of Tomorrownaut, a creative studio focusing on speculative futures and sci-fi-inspired prototypes. She is currently an artist-in-residence at Nokia Bell Labs, was previously an artist-in-residence at Autodesk, and is an assistant professor at the University of Michigan teaching Sci-Fi Prototyping, a course combining sci-fi, prototyping, and ethics. Her ongoing objective is to combine her background in art, design, and engineering to inspire a more positive future.

Todd Hollon

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A major focus of the MLiNS lab is to combine stimulated Raman histology (SRH), a rapid label-free, optical imaging method, with deep learning and computer vision techniques to discover the molecular, cellular, and microanatomic features of skull base and malignant brain tumors. We are using SRH in our operating rooms to improve the speed and accuracy of brain tumor diagnosis. Our group has focused on deep learning-based computer vision methods for automated image interpretation, intraoperative diagnosis, and tumor margin delineation. Our work culminated in a multicenter, prospective, clinical trial, which demonstrated that AI interpretation of SRH images was equivalent in diagnostic accuracy to pathologist interpretation of conventional histology. We were able to show, for the first time, that a deep neural network is able to learn recognizable and interpretable histologic image features (e.g. tumor cellularity, nuclear morphology, infiltrative growth pattern, etc) in order to make a diagnosis. Our future work is directed at going beyond human-level interpretation towards identifying molecular/genetic features, single-cell classification, and predicting patient prognosis.

Wei Lu

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Dr. Lu brings expertise in machine learning, particularly integrating human knowledge into machine learning and explainable machine learning. He has applied machine learning in a range of domain applications, such as autonomous driving and machine learning for optimized design and control of energy storage systems.

Omar Jamil Ahmed

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The Ahmed lab studies behavioral neural circuits and attempts to repair them when they go awry in neurological disorders. Working with patients and with transgenic rodent models, we focus on how space, time and speed are encoded by the spatial navigation and memory circuits of the brain. We also focus on how these same circuits go wrong in Alzheimer’s disease, Parkinson’s disease and epilepsy. Our research involves the collection of massive volumes of neural data. Within these terabytes of data, we work to identify and understand irregular activity patterns at the sub-millisecond level. This requires us to leverage high performance computing environments, and to design custom algorithmic and analytical signal processing solutions. As part of our research, we also discover new ways for the brain to encode information (how neurons encode sequences of space and time, for example) – and the algorithms utilized by these natural neural networks can have important implications for the design of more effective artificial neural networks.

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.

Mark Steven Cohen

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In his various roles, he has helped develop several educational programs in Innovation and Entrepreneurial Development (the only one of their kind in the world) for medical students, residents, and faculty as well as co-founding 4 start-up companies (including a consulting group, a pharmaceutical company, a device company, and a digital health startup) to improve the care of surgical patients and patients with cancer. He has given over 80 invited talks both nationally and internationally, written and published over 110 original scientific articles, 12 book chapters, as well as a textbook on “Success in Academic Surgery: Innovation and Entrepreneurship” published in 2019 by Springer-NATURE. His research is focused on drug development and nanoparticle drug delivery for cancer therapeutic development as well as evaluation of circulating tumor cells, tissue engineering for development of thyroid organoids, and evaluating the role of mixed reality technologies, AI and ML in surgical simulation, education and clinical care delivery as well as directing the Center for Surgical Innovation at Michigan. He has been externally funded for 13 consecutive years by donors and grants from Susan G. Komen Foundation, the American Cancer Society, and he currently has funding from three National Institute of Health R-01 grants through the National Cancer Institute. He has served on several grant study sections for the National Science Foundation, the National Institute of Health, the Department of Defense, and the Susan G. Komen Foundation. He also serves of several scientific journal editorial boards and has serves on committees and leadership roles in the Association for Academic Surgery, the Society of University Surgeons and the American Association of Endocrine Surgeons where he was the National Program Chair in 2013. For his innovation efforts, he was awarded a Distinguished Faculty Recognition Award by the University of Michigan in 2019. His clinical interests and national expertise are in the areas of Endocrine Surgery: specifically thyroid surgery for benign and malignant disease, minimally invasive thyroid and parathyroid surgery, and adrenal surgery, as well as advanced Melanoma Surgery including developing and running the hyperthermic isolated limb perfusion program for in transit metastatic melanoma (the only one in the state of Michigan) which is now one of the largest in the nation.

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.