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Arvind Rao

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Arvind Rao is an Associate Professor in the Department of Computational Medicine and Bioinformatics, and Radiation Oncology in the School of Medicine. 

His research is in:

1. Transcriptional Genomics: A bioinformatics framework that identifies tissue‐specific enhancers by integrating multi‐modal genomic data has been developed previously [Rao2010]. There is interest to integrate other sources of information (like epigenomic and ChIP datasets) to improve the efficacy of enhancer prediction. We have also participated in the TCGA Glioma groups’ work [Brat2015, Ceccarelli2016] on identifying transcriptional regulators underlying gliomagenesis.

2. Image Informatics: In order to quantify the phenotypic aspects of disease and their relationships with outcome and their genetic context, we have developed methods for the analysis of histopathology [ Mousavi2015, Vu2016] and radiology [Yang2015] images, focusing on tumor heterogeneity. One direction of our group is to develop image analysis tools to delineate tumor image features from radiology data and to develop predictive models to relate them along with underlying genomic measurements to outcomes in low grade gliomas. Further, we have also investigated methodologies to link tumor imaging, genetics and immune status in gliomas. More recently, my group has been studying the relationship between image-derived features, genetics and cognitive status in glioblastoma patients. Further, we have also developed methods for the analysis of multiparametric MR datasets in Radiation Oncology.

3. Heterogeneous Data Integration: Integrative decision making in the clinical domain involves the need for principled formalisms that can integrate pathology, imaging and genomic data sets to drive hypothesis generation and clinical action. We have focused on developing high throughput measurement pipelines from this diverse array of data sources and methods for their integration. Simultaneously, methods for visualization are also under investigation. A more recent interest of our group is to integrate genomics, imaging and (online) behavioral data from patient to assess their evolving response to treatment, in the context of learning healthcare platforms. This could also enable the development of hybrid diagnostics.

4. Informatics for Combinatorial Drug Screens: the availability of multimodal data sources (cell line genomics, drug assays) coupled with high throughput, high content imaging platforms have created the need for informatics frameworks to identify rational drug combinations capable of modulating disease-associated phenotype. In this context, we have worked with the Gulf Coast Consortium to create analysis platforms that jointly mine imaging and genomics data for combinatorial drug discovery.

 

The overall goal is to link different data sources, such as imaging-derived phenotypes with genomic alteration for clinical predictive models. This has prompted work in AI/ML models for image processing &computer vision, data integration and genomic analysis.

 

Kamran Diba

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Kamran Diba is an Associate Professor in the Department of Anesthesiology in the School of Medicine. His research group is interested in how the brain computes, coordinates, stores and transfers information. Neuronal networks generate an assortment of neuronal oscillations that vary depending on the behavior and state of an animal, from active exploration to resting and different stages of sleep and anesthesia. Accordingly, in their recordings of large populations of spiking neurons in rodents, they observe state-dependent temporal relationships at multiple timescales. What role do these unique spike patterns play and what do they tell us about the function and limitations of each brain state? To answer these and related questions, they combine behavioral studies of freely moving, learning and exploring rats, multi-channel recordings of the simultaneous electrical (spiking) activity from hundreds of neurons during behavior and sleep, neural network models of this behavior, statistical and machine learning tools to uncover deep structure within high-dimensional spike trains and chemogenetics and optogenetics to manipulate protein signaling and action potentials in specific neural populations in precise time windows.

Camille Avestruz

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Dr. Avestruz is a computational cosmologist. She uses simulations to model, predict, and interpret observed large-scale cosmic structures. Her primary focus is to understand the evolution of galaxy clusters. These are the most massive gravitationally collapsed structures in our universe, comprised of hundreds to thousands of galaxies. Other aspects of her work prepare for the next decade of observations, which will produce unprecedented volumes of data. In particular, she is leading software development efforts within the clusters working group of the Large Synoptic Survey Telescope to calibrate galaxy cluster masses from simulation data. Dr. Avestruz also incorporates big data methods, including machine learning, to extract gravitational lensing signatures that probe the mass distribution of massive galaxies and galaxy clusters.

[Click on image to see video] Image projection of various components and properties of a simulated galaxy cluster in its last 8 gigayears of formation. The top left panel shows the underlying dark matter content, the top middle image shows the distribution of stars, and the remaining four panels are properties of the gas content: density, temperature, entropy, and metallicity. To model the evolution of galaxy clusters in a cosmological volume, the simulation uses adaptive refinement in space and time in order to span the relevant dynamic range of the system.

Aaron Towne

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Aaron Towne is an Assistant Professor in the Department of Mechanical Engineering. His research develops simple models that can be used to understand, predict, and control turbulent fluid dynamical systems. His approach focuses on identifying and modeling coherent flow structures, i.e., organized motions within otherwise chaotic flows. These structures provide building blocks for an improved theoretical understanding of turbulence and also contribute significantly to engineering quantities of interest such as drag, heat transfer, and noise emission. Consequently, strategically manipulating coherent structures can potentially lead to vast performance improvements in a wide range of engineering applications. Realizing this potential requires new data mining and analysis methods that can be used to identify and extract these organized motions from the large data sets produced by high fidelity simulations and experiments, as well as new theoretical and computational approaches for modeling and controlling them. Aaron’s research focuses on developing these tools for turbulent flow applications, while also contributing more broadly to the emerging areas of large-scale data mining and machine learning.

Temperature (color) and pressure (gray scale) from a simulation of a turbulent jet. The pressure field exhibits organized patterns (alternating black and white regions) that can be leveraged to understand, predict, and control the noise produced by the jet. Image courtesy of Guillaume Brès.

Robert Dick

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Robert Dick is an Associate Professor in the Department of Electrical Engineering and Computer Science, in the Electrical and Computer Engineering division. He also co-founded and served as CEO of Stryd, Inc., which produces wearable electronics for athletes. He received his Ph.D. degree from Princeton University in 2002 and his B.S. degree from Clarkson University in 1996. He worked as a Visiting Professor at Tsinghua University’s Department of Electronic Engineering in 2002, as a Visiting Researcher at NEC Labs America in 1999, and was on the faculty of Northwestern University from 2003-2008.

Prof. Dick has published in the areas of embedded operating systems, data compression, embedded system synthesis, dynamic power management, low-power and temperature-aware integrated circuit design, wireless sensor networks, human perception aware computer design, reliability, embedded system security, and behavioral synthesis. He especially likes projects in which a deep understanding of a particular application leads to a new fundamental concept or technology with broader application. He is a principal investigator in MICDE’s catalyst grant titled “Embedded Machine Learning Systems To Sense and Understand Pollinator Behavior”.

He received an NSF CAREER award and won his department’s Best Teacher of the Year award in 2004. In 2007, his technology won a Computerworld Horizon Award and his paper was selected as one of the 30 in a special collection of DATE papers appearing during the past 10 years. His 2010 work won a Best Paper Award at DATE.

Fernanda Valdovinos

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Fernanda Valdovinos is an Assistant Professor in the department of Ecology and Evolutionary Biology and Complex Systems. She received her Ph.D. in Ecology and Evolutionary Biology from the Faculty of Science, University of Chile in 2008. Before joining the University of Michigan, she was a researcher in the Estación Biológica de Doñana, Spain, at the Pacific Ecoinformatics and Computational Lab in Berkeley, CA and at the department of Ecology and Evolutionary Biology at the University of Arizona.

Her lab studies the structure and dynamics of ecological networks at ecological and evolutionary scales; including their resilience to biodiversity loss, biological invasions, climate change, and exploitation by humans. She is a principal investigator in MICDE Catalyst Grant: “Embedded Machine Learning Systems To Sense and Understand Pollinator Behavior”.

Jianzhi (George) Zhang

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Jianzhi (George) Zhang is a Professor of Ecology and Evolutionary Biology interested in the relative roles of chance and necessity in evolution. He got his B. S. from Fudan University in Shanghai, China, and his Ph. D. in Genetics from Pennsylvania State University. He was a  Fogarty postdoctoral fellow at the National Institute of Allergy and Infectious Diseases before moving to the University of Michigan.

Professor Zhang’s research focuses on two main research areas:  (1) yeast as an experimental system for studying evolution, where his research group uses the budding yeast Saccharomyces cerevisiae and its relatives as model organisms to understand a variety of evolutionary processes such as the genetic basis of phenotypic variations among strains and species, or molecular and genomic bases of heterosis; and (2) computational evolutionary genomics where they use evolutionary, genomic, and/or systemic approaches to analyze publicly available data to characterize and understand pleiotropy, robustness, epistasis, gene-environment interaction, gene expression noise, translational regulation, RNA editing, convergent evolution, adaptation, origin of new genes, among-protein evolutionary rate variation, and other important genetic and evolutionary phenomena. Projects may also involve modeling and simulation, including the MICDE catalyst grant project where the team is using deep neural networks to infer molecular phylogenies and extract phylogenetically useful patterns from amino acid or nucleotide sequences, which will help understand evolutionary mechanisms and build evolutionary models for a variety of analyses.

Yuanfang Guan

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Yuanfang Guan is an associate professor of Computational Medicine and Bioinformatics. She got her B.S. from the University of Hong Kong, and her Ph.D. in Molecular Biology from Princeton University.

Prof. Guan is interested in machine learning in biology and medicine. Her team has written the majority of the best-performing algorithms in DREAM challenges, the largest systems biology benchmark study. Prof. Guan was awarded the ‘Consistent Best Technical Performer’ for her groups achievements in the DREAM challenges and in recognition of the open source software that they have contributed to the bioinformatics field. She is one of the very few people globally who own multiple gold medals in the annual Data Science Bowl by Kaggle.

Her team has written many award-winning deep learning methods. In traditional machine learning, she is the inventor of GuanRank, adaptive GPR and several other algorithms that are often used as the reference algorithms in benchmark studies/challenges.

Xun Huan

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Xun (Ryan) Huan is an Assistant Professor in the Department of Mechanical Engineering. His research broadly revolves around uncertainty quantification, data-driven modeling, and numerical optimization. His expertise focuses on bridging models and data: optimal experimental design, Bayesian methods for statistical inference, uncertainty propagation in high-dimensional settings, and methods that are robust to model misspecification. He seeks to develop efficient computational methods that integrate realistic models with big data, and combine uncertainty quantification with machine learning to enable robust prediction, design, and decision-making. He is interested in collaborative opportunities in various applications that can benefit from a better understanding of uncertainty and modeling. Current research activities include assessing uncertainty in deep neural networks, and developing sequential experimental design methods for improving autonomy.

Optimal experimental design seeks to identify experiments that produce the most valuable data, and can lead to substantial resource savings. For example, in the design of a shock-tube combustion experiment, design condition A maximizes the expected information gain. When Bayesian inference is performed on data from this experiment, we obtain “tighter” posteriors (with less uncertainty) compared to those obtained from suboptimal design conditions B and C.

Raed Al Kontar

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Rael Al Kontar is an Assistant Professor in the department of Industrial & Operations Engineering. His research broadly focuses on developing data analytics and decision-making methodologies specifically tailored for Internet of Things (IoT) enabled smart and connected products/systems. He envisions that most (if not all) engineering systems will eventually become connected systems in the future. Therefore, his 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.

Towards smart and connected systems