HPC training workshops begin Monday, May 15

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series of training workshops in high performance computing will be held May 15, May 17 and May 24, 2017, presented by CSCAR in conjunction with Advanced Research Computing – Technology Services (ARC-TS). All sessions are held at East Hall, Room B254, 530 Church St.

Introduction to the Linux command Line
This course will familiarize the student with the basics of accessing and interacting with Linux computers using the GNU/Linux operating system’s Bash shell, also known as the “command line.”
• Monday, May 15, 9 a.m. – noon. (full descriptionregistration)

Introduction to the Flux cluster and batch computing
This workshop will provide a brief overview of the components of the Flux cluster, including the resource manager and scheduler, and will offer students hands-on experience.
• Wednesday, May 17, 1 – 4:30 p.m. (full description | registration)

Advanced batch computing on the Flux cluster
This course will cover advanced areas of cluster computing on the Flux cluster, including common parallel programming models, dependent and array scheduling, and a brief introduction to scientific computing with Python, among other topics.
• Wednesday, May 24, 1 – 5 p.m. (full description | registration)

NOTE: Additional workshops may be scheduled if demand warrants. Please sign up for the waiting list if the workshops are full, and you will be given first priority for any additional sessions.

U-M students invited to apply for MICDE fellowships — May 19 deadline

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University of Michigan students are invited to apply for Michigan Institute for Computational Discovery and Engineering (MICDE) Fellowships for the 2017-2018 academic year. These $4,000 fellowships are available to students in both the Ph.D in Scientific Computing and the Graduate Certificate Program in Computational Discovery and Engineering. Applicants should be graduate students enrolled in either program, although students not yet enrolled but planning to do so may simultaneously submit program and fellowship applications.

Fellows will receive a $4,000 research fund that can be used to attend a conference, to buy a computer, or for any other approved activity that enhances the Fellow’s graduate experience. We also ask that Fellows attend at least 8 MICDE seminars between Fall 2017 and Winter 2018, attend one MICDE students’ networking event, and present a poster at the MICDE Symposium on March 22, 2018. For more details and to apply please visit http://micde.umich.edu/academic-programs/micde-fellowships/.

Interested students should download and complete the application form, and submit it with a one-page resume as a SINGLE PDF DOCUMENT to MICDE-apps@umich.edu. The due date for applications is May 19, 2017, 5:00 E.T. We expect to announce the awardees onJune 5, 2017.

We encourage applications from all qualified candidates, including women and minorities.

New private insurance claims dataset and analytic support now available to health care researchers

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The Institute for Healthcare Policy and Innovation (IHPI) is partnering with Advanced Research Computing (ARC) to bring two commercial claims datasets to campus researchers.

The OptumInsight and Truven Marketscan datasets contain nearly complete insurance claims and other health data on tens of millions of people representing the US private insurance population. Within each dataset, records can be linked longitudinally for over 5 years.  

To begin working with the data, researchers should submit a brief analysis plan for review by IHPI staff, who will create extracts or grant access to primary data as appropriate.

CSCAR consultants are available to provide guidance on computational and analytic methods for a variety of research aims, including use of Flux and other UM computing infrastructure for working with these large and complex repositories.

Contact Patrick Brady (pgbrady@umich.edu) at IHPI or James Henderson (jbhender@umich.edu) at CSCAR for more information.

The data acquisition and availability was funded by IHPI and the U-M Data Science Initiative.

Designing optimal shunts for newborns with heart defects using computational modeling

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shuntFor babies born with hypoplastic left heart syndrome, several open-heart surgeries are required. During Stage I, a Norwood procedure is performed to construct an appropriate circulation to both the systemic and the pulmonary arteries. The pulmonary arteries receive flow from the systemic circulation, often by using a Blalock-Taussig (BT) shunt between the innominate artery and the right pulmonary artery. This procedure causes significantly disturbed flow in the pulmonary arteries.

A group of researchers led by U-M Drs. Ronald Grifka and Alberto Figueroa used computational hemodynamic simulations to demonstrate its capacity for examining the properties of the flow through and near the BT shunt. Initially, the researchers constructed a computational model which produces blood flow and pressure measurements matching the clinical magnetic resonance imaging (MRI) and catheterization data. Achieving this required us to determine the level of BT shunt occlusion; because the occlusion is below the MRI resolution, this information is difficult to recover without the aid of computational simulations. The researchers determined that the shunt had undergone an effective diameter reduction of 22% since the time of surgery. Using the resulting geometric model, they showed that we can computationally reproduce the clinical data. The researchers then replaced the BT shunt by with a hypothetical alternative shunt design with a flare at the distal end. Investigation of the impact of the shunt design revealed that the flare can increase pulmonary pressure by as much as 7%, and flow by as much as 9% in the main pulmonary branches, which may be beneficial to the pulmonary circulation.

Read more in Frontiers in Pediatrics.

MICDE awards four Catalyst Grants

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The Michigan Institute for Computational Discovery and Engineering has awarded its first round of Catalyst Grants, providing $75,000 each to four innovative projects in computational science. The proposals were judged on novelty, likelihood of success, potential for external funding, and potential to leverage ARC’s existing computing resources.

The funded projects are:

Title: From Spiking Patterns to Memory formation — Tools for Analysis and Modeling of Network-wide Cognitive Dynamics of the Brain
Researchers: Sara Aton, Department of Molecular, Cellular and Developmental Biology and Michal Zochowski, Department of Physics, Biophysics Program
Description: The aim of the research is to develop models as well as analysis tools to understand network-wide spatio-temporal patterning underlying experimentally observed neural spiking activity. The research team has developed novel tools to analyze dynamics of neuronal representations across time, before during and after learning. These tools, for the first time, compare the stability of network dynamics before and after memory encoding.

Title: Integral Equation Based Methods for Scientific Computing
Researcher: Robert Krasny, Department of Mathematics
Description: This project expands the application of numerical methods in which the differential equation is first converted into an integral equation by convolution with the Green’s function, followed by discretization and linear solution. Recent advances in numerical analysis and computing resources make this expansion possible, and the research team believes that integral equation-based numerical methods are superior to traditional methods in both serial and parallel computations. The project will attempt to apply these numerical methods to studies of viscous fluid flow, protein/solvent electrostatics, and electronic structure.

Title: Computational Energy Systems
Researchers: Pascal Van Hentenryck, Industrial and Operations Engineering (IOE); E. Byon, IOE; R. Jiang, IOE; J. Lee, IOE; and J. Mathieu, Electrical Engineering and Computer Science
Description: The research team aims to develop new algorithms for the U.S. electrical power grid that integrate renewable energy sources, electrification of transportation systems, the increasing frequency of extreme weather events, and other emerging contingencies.

Title: Black Swans, Dragon Kings, and the Science of Rare Events: Problems for the Exascale Era and Beyond
Researchers: Venkat Raman, Aerospace Engineering; Jacqueline Chen, Sandia National Laboratory; and Ramanan Sankaran, Oak Ridge National Laboratory.
Description: The purpose of the project is to develop the computational frameworks for exploring the tails of distributions, which lead to rare but consequential (and often catastrophic) outcomes. Two such rare events are “Black Swans” (occurring from pre-existing but unencountered events) and “Dragon Kings (occurring due to an external shock to the system). The methods developed are expected to have application in aerospace sciences, power generation and utilization, chemical processing, weather prediction, computational chemistry, and other fields.

Another round of Catalyst Grants will be awarded next year.

MIDAS starting research group on mobile sensor analytics

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The Michigan Institute for Data Science (MIDAS) is convening a research working group on mobile sensor analytics. Mobile sensors are taking on an increasing presence in our lives. Wearable devices allow for physiological and cognitive monitoring, and behavior modeling for health maintenance, exercise, sports, and entertainment. Sensors in vehicles measure vehicle kinematics, record driver behavior, and increase perimeter awareness. Mobile sensors are becoming essential in areas such as environmental monitoring and epidemiological tracking.

There are significant data science opportunities for theory and application in mobile sensor analytics, including real-time data collection, streaming data analysis, active on-line learning, mobile sensor networks, and energy efficient mobile computing.

Our working group welcomes researchers with interest in mobile sensor analytics in any scientific domain, including but not limited to health, transportation, smart cities, ecology and the environment.

Where and When:

Noon to 2 pm, April 13, 2017

School of Public Health I, Room 7625

Lunch provided


  • Brief presentations about challenges and opportunities in mobile sensor analytics (theory and application);

  • A brief presentation of a list of funding opportunities;

  • Discussion of research ideas and collaboration in the context of grant application and industry partnership.

Future Plans: Based on the interest of participants, MIDAS will alert researchers to relevant funding opportunities, hold follow-up meetings for continued discussion and team formation as ideas crystalize for grant applications, and work with the UM Business Engagement Center to bring in industry partnership.

Please RSVP.  For questions, please contact Jing Liu, Ph.D, MIDAS research specialist (ljing@umich.edu; 734-764-2750).

U-M, Toyota Research Institute partner in $2.4M battery project

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With a $2.4 million investment from the Toyota Research Institute, University of Michigan researchers will develop computer simulation tools to predict automotive battery performance.

The project is part of a four-year, $35 million investment with research entities, universities and companies on research that uses artificial intelligence to help accelerate the design and discovery of advanced materials, TRI has announced.

Initially, the program will aim to help revolutionize materials science and identify new advanced battery materials and fuel cell catalysts that can power future zero-emissions and carbon-neutral vehicles.

“Toyota recognizes that artificial intelligence is a vital basic technology that can be leveraged across a range of industries, and we are proud to use it to expand the boundaries of materials science,” said Eric Krotkov, TRI chief science officer.

“Accelerating the pace of materials discovery will help lay the groundwork for the future of clean energy and bring us even closer to achieving Toyota’s vision of reducing global average new-vehicle CO2 emissions by 90 percent by 2050.”

The project, under the auspices of the Michigan Institute for Computational Discovery and Engineering at U-M, will combine mathematical models of the atomic nature and physics of materials with artificial intelligence.

“At the University of Michigan, we look forward to collaborating with TRI to advance computational materials science using machine learning principles,” said principal investigator Krishna Garikipati, professor of mechanical engineering and mathematics.

Also involved from U-M are Vikram Gavini, associate professor of mechanical engineering and materials science and engineering, and Karthik Duraisamy, assistant professor of aerospace engineering.

“The timing and goals of this program are well-aligned with the paradigm of data-enabled science that we have been promoting via the Michigan Institute for Computational Discovery and Engineering, and the Center for Data-Driven Computational Physics,” Duraisamy said.

The U-M project will use the ConFlux cluster, an innovative, new computing platform that enables computational simulations to interface with large datasets.

In addition to U-M, TRI’s newly funded research projects include collaborations with Stanford University, the Massachusetts Institute of Technology, University at Buffalo, University of Connecticut and the U.K.-based materials science company Ilika. TRI is also in ongoing discussions with additional research partners.

Research will merge advanced computational materials modeling, new sources of experimental data, machine learning and artificial intelligence in an effort to reduce the time scale for new materials development from a period that has historically been measured in decades.

Research programs will follow parallel paths, working to identify new materials for use in future energy systems as well as to develop tools and processes that can accelerate the design and development of new materials more broadly, according to TRI.

In support of these goals, TRI will partner on projects focused on areas including:

  • The development of new models and materials for batteries and fuel cells.
  • Broader programs to pursue novel uses of machine learning, artificial intelligence and materials informatics approaches for the design and development of new materials.
  • New automated materials discovery systems that integrate simulation, machine learning, artificial intelligence or robotics.

Accelerating materials science discovery represents one of four core focus areas for TRI, which was launched in 2015 with mandates to also enhance auto safety with automated technologies, increase access to mobility for those who otherwise cannot drive and help translate outdoor mobility technology into products for indoor mobility.

Gilbert, Rudelson, Wu named Simons Foundation Fellows in Mathematics

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Three University of Michigan professors have been named Simons Fellows in Mathematics by the Simons Foundation:

  • Anna Gilbert, the Herman H. Goldstine Collegiate Professor of Mathematics, core faculty member at the Michigan Institute for Data Science (MIDAS), and Professor of Electrical and Computer Engineering
  • Mark Rudelson, Professor of Mathematics
  • Sijue Wu, Robert W. and Lynn H. Browne Professor of Science and Professor of Mathematics.

Forty fellows were named in all.

The fellowships provide funding that allows faculty to take up to a semester-long research leave from teaching and administrative duties. The foundation also gives fellowships in Theoretical Physics.

For more information, see www.simonsfoundation.org.

Workshop co-chaired by MIDAS co-director Prof. Hero releases proceedings on inference in big data

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The National Academies Committee on Applied and Theoretical Statistics has released proceedings from its June 2016 workshop titled “Refining the Concept of Scientific Inference When Working with Big Data,” co-chaired by Alfred Hero, MIDAS co-director and the John H Holland Distinguished University Professor of Electrical Engineering and Computer Science.

The report can be downloaded from the National Academies website.

The workshop explored four key issues in scientific inference:

  • Inference about causal discoveries driven by large observational data
  • Inference about discoveries from data on large networks
  • Inference about discoveries based on integration of diverse datasets
  • Inference when regularization is used to simplify fitting of high-dimensional models.

The workshop brought together statisticians, data scientists and domain researchers from different biomedical disciplines in order to identify new methodological developments that hold significant promise, and to highlight potential research areas for the future. It was partially funded by the National Institutes of Health Big Data to Knowledge Program, and the National Science Foundation Division of Mathematical Sciences.