Explore ARCExplore ARC

Ho-Joon Lee

By |

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.

 

Somangshu Mukherji

By |

Somangshu (Sam) Mukherji, PhD, is Assistant Professor of Music Theory in the School of Music, Theatre & Dance at the University of Michigan, Ann Arbor.

Sam Mukherji‘s work lies at the interface of traditional Western tonal theory, the theory and practice of popular and non-Western idioms, and the cognitive science of music. Within this framework, the main focus of his research has been on the prolongational, grammatical aspects of Western tonality, and their connection to the tonal structures of Indian music, and the blues-based traditions within rock and metal. This emphasis makes his work similar to that of a linguist who explores relationships between the world’s languages-and, therefore, Mukherji’s research has been influenced in particular by ideas from linguistic theory as well, especially the Minimalist Program in contemporary generative linguistics. For this reason, he has investigated connections not only between different musical idioms but also between music and language-and musical and linguistic theory-more generally. Much of his work explores overlaps between Minimalist linguistics, and related, generative approaches within music theory (such as those found in the writings of Heinrich Schenker), and he has also written extensively about what such ‘musicolinguistic’ connections imply for the wider study of human musical behavior, cognition, and evolution.

Lu Wei

By |

Lu Wei, DSc,  is Assistant Professor in the Department of Electrical and Computer Engineering at the University of Michigan, Dearborn.

Prof. Wei studies the analytical properties of interacting particle systems relevant to both classical and quantum information theory.

 

Charu Chandra

By |

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

Emanuel Gull

By |

Professor Gull works in the general area of computational condensed matter physics with a focus on the study of correlated electronic systems in and out of equilibrium. He is an expert on Monte Carlo methods for quantum systems and one of the developers of the diagrammatic ‘continuous-time’ quantum Monte Carlo methods. His recent work includes the study of the Hubbard model using large cluster dynamical mean field methods, the development of vertex function methods for optical (Raman and optical conductivity) probes, and the development of bold line diagrammatic algorithms for quantum impurities out of equilibrium. Professor Gull is involved in the development of open source computer programs for strongly correlated systems.

Quantum impurities are small confined quantum systems coupled to wide leads. An externally applied time-dependent magnetic field induces a change in the population of spins on the impurity, leading to time-dependent switching behavior. The system's equations of motion are determined by a many-body quantum field theory and solved using a diagrammatic Monte Carlo approach. The computations were performed at Columbia University and the University of Michigan.

Quantum impurities are small confined quantum systems coupled to wide leads. An externally applied time-dependent magnetic field induces a change in the population of spins on the impurity, leading to time-dependent switching behavior. The system’s equations of motion are determined by a many-body quantum field theory and solved using a diagrammatic Monte Carlo approach. The computations were performed at Columbia University and the University of Michigan.

Vijay Subramanian

By |

Professor Subramanian is interested in a variety of stochastic modeling, decision and control theoretic, and applied probability questions concerned with networks. Examples include analysis of random graphs, analysis of processes like cascades on random graphs, network economics, analysis of e-commerce systems, mean-field games, network games, telecommunication networks, load-balancing in large server farms, and information assimilation, aggregation and flow in networks especially with strategic users.

Issam El Naqa

By |

Our lab’s research interests are in the areas of oncology bioinformatics, multimodality image analysis, and treatment outcome modeling. We operate at the interface of physics, biology, and engineering with the primary motivation to design and develop novel approaches to unravel cancer patients’ response to chemoradiotherapy treatment by integrating physical, biological, and imaging information into advanced mathematical models using combined top-bottom and bottom-top approaches that apply techniques of machine learning and complex systems analysis to first principles and evaluating their performance in clinical and preclinical data. These models could be then used to personalize cancer patients’ chemoradiotherapy treatment based on predicted benefit/risk and help understand the underlying biological response to disease. These research interests are divided into the following themes:

  • Bioinformatics: design and develop large-scale datamining methods and software tools to identify robust biomarkers (-omics) of chemoradiotherapy treatment outcomes from clinical and preclinical data.
  • Multimodality image-guided targeting and adaptive radiotherapy: design and develop hardware tools and software algorithms for multimodality image analysis and understanding, feature extraction for outcome prediction (radiomics), real-time treatment optimization and targeting.
  • Radiobiology: design and develop predictive models of tumor and normal tissue response to radiotherapy. Investigate the application of these methods to develop therapeutic interventions for protection of normal tissue toxicities.

Laura Balzano

By |

Professor Balzano and her students investigate problems in statistical signal processing and optimization, particularly dealing with large and messy data. Her applications typically have missing, corrupted, and uncalibrated data as well as heterogeneous data in terms of sensors, sensor quality, and scale in both time and space. Her theoretical interests involve classes of non-convex problems that include Principal Components Analysis (or the Singular Value Decomposition) and many interesting variants such as PCA with sparse or structured principal components, orthogonality and non-negativity constraints, nonlinear variants such as low-dimensional algebraic variety models, and even categorical data or human preference data. She concentrates on fast gradient methods and related optimization methods that are scalable to real-time operation and massive data. Her work provides algorithmic and statistical guarantees for these algorithms on the aforementioned non-convex problems, and she focuses carefully on assumptions that are realistic for the relevant applications. She has worked in the areas of online algorithms, real-time computer vision, compressed sensing and matrix completion, network inference, and sensor networks.

Real-time dynamic background tracking and foreground separation. At time t = 101, the virtual camera slightly pans to right 20 pixels. We show how GRASTA quickly adapts to the new subspace by t = 125. The first row is the original video frame; the middle row is the tracked background; the bottom row is the separated foreground.

Real-time dynamic background tracking and foreground separation. At time t = 101, the virtual camera slightly pans to right 20 pixels. We show how GRASTA quickly adapts to the new subspace by t = 125. The first row is the original video frame; the middle row is the tracked background; the bottom row is the separated foreground.

Jeffrey C. Lagarias

By |

Jeffrey C. Lagarias is the Harold Mead Stark Collegiate Professor of Mathematics in the College of Literature, Science, and the Arts at the University of Michigan, Ann Arbor.

Prof. Lagarias’ research interests are diverse. His initial training was in analytic and algebraic number theory. After receiving his PhD in 1974, he worked at Bell Laboratories and AT &T Labs until 2003, on problems in many pure and applied fields. Besides number theory, Prof. Lagarias has made contributions in harmonic analysis (wavelets and fractals), mathematical optimization (interior point methods), discrete geometry (tilings and quasicrystals), ergodic theory, low-dimensional topology (complexity of unknotting), and theoretical computer science.

At Michigan Prof. Lagarias has been active in the number theory group over the last few years, with additional work in other fields. His last 25 postings on the arXiv were in: Number Theory (16), Dynamical Systems (3), Classical Analysis and ODE?s (3), Metric Geometry (1), Optimization and Control (1), Spectral Theory (1). His doctoral students typically work on their own topics. Some have worked in topics in number theory: integer factorial ratios, character sum estimates, Diophantine equations with two separated variables; Others have worked in topics in discrete geometry: packings of regular tetrahedra, rigidity of circle configurations.

 

Jon Lee

By |

Jon’s research focus is on nonlinear discrete optimization (NDO). Many practical engineering problems have physical aspects which are naturally modeled through smooth nonlinear functions, as well as design aspects which are often modeled with discrete variables. Research in NDO seeks to marry diverse techniques from classical areas of optimization, for example methods for smooth nonlinear optimization and methods for integer linear programming, with the idea of successfully attacking natural NDO models for practical engineering problems.  On particular area of applied interest is environmental monitoring and the framework of maximum-entropy sampling.