Michael Loadenthal reviews work performed by Prosecution Project team members at a work session

The Prosecution Project aided by Research Computing Support group

Prosecution Project team members (from left) Sarah Carrier, Olivia Sellegren, Meekael Hailu, and Morgan Demboski, discuss data at a work session.

For all the time, effort, and resources devoted to thwarting terrorism, it’s surprisingly difficult to get a complete view of sociopolitical violence in the United States. The Anti-Defamation League and the Southern Poverty Law Center monitor racist and white nationalist violence. The Center for Biomedical Research collects data on attacks against animal testing facilities. The University of Maryland tracks international incidents of terrorism in its Global Terrorism Database. But because none of these groups’ datasets interface with any other’s, information remains siloed and analysis of broader relationships is stymied.

Michael Loadenthal is trying to break down those silos. A visiting assistant professor of sociology and social justice studies at Miami University, Loadenthal directs the Prosecution Project, which seeks to understand how terrorism, extremism, and hate crimes are prosecuted in the U.S. justice system. The Prosecution Project’s dataset includes all crimes of political violence, without regard to the identity of the targets or the ideology of the perpetrators, so it paints a uniquely comprehensive picture.

“We’re looking to understand the patterns that exist between who a criminal defendant is, who commits crimes motivated by sociopolitical violence, and how that relates to the crime they committed and the way it’s prosecuted,” Loadenthal says.

Altogether, Loadenthal and his project team — which consists entirely of his current and former undergraduate students — account for 46 variables in each case they add to their dataset. Each case is coded by two members of the project’s coding team. After review of the initial coding by at least two senior members of the analysis team, the data are then reviewed by an auditor. So far, the team has fully coded and reviewed about 40% of the 5,000 cases they have identified. Once the dataset is fully processed, Loadenthal intends to make it available to the public.

Working toward that goal has required Loadenthal to figure a way around some technical roadblocks. One place he turned for help is Miami’s Research Computing Support group, particularly Greg Reese, senior research computing support specialist.

Among other things, Reese developed a custom audit program that Loadenthal says “helps machine some of the irregularity out of the data.” Reese’s program reads the data the project team has collected and checks it against a set of defined rules — about 30 in all — to find irregularities or incongruences. Certain mistakes, like an extra space typed after a defendant’s name, will cause a computer to classify data incorrectly. (A computer treats “John Jones ” — with a space after “Jones” — and “John Jones” — no space after “Jones” — as two different people, for instance.) Reese’s audit program searches for such mistakes and flags them so they can be corrected to improve the integrity of the overall dataset.

Loadenthal is grateful for Reese’s willingness not only to listen to the specific challenges the Prosecution Project faces, but also to develop custom solutions.

“I’ve seen Greg learn different aspects of new computer languages in order to code what we need,” Loadenthal says. “He’s taught himself new skill sets in order to accommodate us. Instead of trying to use something he’s already familiar with — let’s say C++ — he adapted and learned Python, which is better suited to what we’re doing.”

Reese’s impulse for inclusivity fits something of a theme for the Prosecution Project, which has remarkably diverse personnel. Although most members of Loadenthal’s 60-person team identify as female, they otherwise represent the gamut of student demographics and identities.

“We have a highly diverse research team that closely resembles the world off-campus,” Loadenthal says. “Our students represent a variety of races, ethnicities, nationalities, and religions. They don’t all conform to binary notions of gender. In addition, they represent a broad set of academic majors, from biology to English to political science to sociology.”

Loadenthal isn’t sure why the Prosecution Project’s team is so diverse. Diversity is more common in the social justice studies and upper-level sociology classes Loadenthal teaches than in the university as a whole, but beyond that, the team’s diversity doesn’t result from any active recruiting strategy. Students self-select to participate in the project — he waits for them to approach him.

The key to the team’s diversity may lie in diverse students’ inherent interest in finding answers to questions about systemic inequalities, which tend not to work out in their favor. Loadenthal says one of his early goals for the Prosecution Project was to explain sentencing disparities. He acknowledges that many members of his team expected to find that nationality, religion, and race play a role. And while they did find that African-, Asian-, and Middle Eastern-born, Muslim defendants with foreign-sounding names often receive harsher sentences than American-born, Christian defendants of European descent, they also found that simple xenophobia didn’t fully explain the differences. Loadenthal is committed to making Prosecution Project data available to other researchers who can help develop more nuanced explanations.

“This project is the only one that co-mingles and assimilates data points so you can make comparisons between ideologies and not restrict it to one particular movement,” Loadenthal says. “That’s the main goal, to ask questions that aren’t specific to one interest group.”


Written by Heather Beattey Johnston, Associate Director of Research Communications, Office for the Advancement of Research and Scholarship, Miami University.

Photos by Miami University Photo Services.

 

Cables plugged into computers at the Center for Nanoscale Materials at the Advanced Photon Source.

Research Computing Support staff member facilitates high performance computing for university’s faculty and students

Jens Mueller and a student look at data on a computer screen.
Jens Mueller (left) is the director of high performance computing services at Miami University and a Campus Champion for the Ohio Supercomputer Center, supporting faculty and students in all stages of their HPC needs.

We’re pleased to run this item, which originally appeared in the Ohio Supercomputer Center’s  2017-2018 Research Report, with the permission of  the Ohio Technology Consortium, a division of the Ohio Department of Higher Education.


The demand for high performance computing at Ohio’s universities has significantly grown and diversified. Jens Mueller, Ph.D., has witnessed that first hand at Miami University.

Mueller is the director of high performance computing services at Miami University and a Campus Champion for the Ohio Supercomputer Center, supporting faculty and students in all stages of their HPC needs.

“In some way, I’m the person for everything,” said Mueller, who has worked with OSC for more than 10 years. “The highlight at Miami is the broad spectrum of fields using computational research. I’ve only gotten busier because everything is more data driven, increasing demands.”

Traditional HPC users at Miami and many Ohio campuses include the engineering departments, computer science, math, physics, chemistry, geography and geology. However, Mueller has witnessed a growing demand from the business school, economics, finance, humanities, political sciences and even the English department.

And the broad spectrum of disciplines also means a broad spectrum of computational skill sets.

“One of the challenges in my role is to identify the proper computational resources based on experience and expressed needs,” Mueller said. “This includes software tools and specific hardware resources.”

Mueller and his team follow a tiered approach to helping researchers meet HPC needs. They start with Miami’s local clusters and, once they are exhausted, Mueller facilitates the transition to OSC.

Mueller also helps facilitate a class partially taught on OSC machines to assist people through the process of using HPC resources, everything from applying for an account to reserving compute nodes to gaining software licenses and even using OSC OnDemand.

“I look at what challenges they’ll face and how they can be eliminated,” he said. “I just want to make sure the transition is smooth.”

Mueller also works one-on-one with research groups and faculty labs. And while he helps Miami’s researchers a great deal, he also helps OSC. He was part of the OnDemand committee to give feedback on its usability and regularly communicates to OSC what is working well and what isn’t.

“We contribute to OSC and that’s beneficial to them, of course the benefit to us is great as well,” he said. “Researchers can get amazing things accomplished using OSC.”

Mueller highlighted a few recent Miami projects in which he helped researchers make the most of OSC’s resources:

  • Graduate student Melvin Ikwubuo, with David Munday, Ph.D., associate professor in mechanical and manufacturing engineering, is studying the effect of geometric features on film cooling efficiency. The project was featured in a poster presentation during the OSC Statewide Users Group in April.
  • Amelie Davis, assistant professor of geography, is in a research collaboration on computational analysis of satellite imagery, using the tool R at OSC to predict forage suitability for honey bees and other pollinators.
  • Graduate student Erik Brodin, with Jessica Sparks, Ph.D., in chemical, paper and biomedical engineering is in a research collaboration on 3D printer syringe modeling.
  • Amy Yousefi, Ph.D., a professor in chemical, paper and biomedical engineering, has a senior design student project attempting to model flow of cell culture fluid in bioreactors with the goal to improve bone growth in artificial scaffolds.
  • Rachel Blum, Ph.D., assistant professor of political science, used automated content analysis to study the dynamics of political parties via a topic model. The sources were a vast collection of blog posts and interview data.
  • Andor Kiss, Ph.D., director of the Center for Bioinformatics and Functional Genomics, had a project studying the genome of the wood frog, a species that freezes in the winter and comes back to life in spring when it thaws.

Photo of high performance computer by Argonne National Laboratory via Wikimedia Commons, used under Creative Commons license. Photo of Jens Mueller by Jeff Sabo, Miami University Photo Services.

Detail of wiring in the high performance computing (HPC) data center at NREL's Energy Systems Integration Facility.

Redhawk3, new high performance computing cluster, now live

DJ Rao stands in front of a screen displaying computer-generated models of Zika virus epidemiology.
Miami faculty, including Dhananjai “DJ” Rao, of the Department of Computer Science and Software Engineering, use the HPC for computer modeling and other research.

Miami University IT Services and Research Computing Support have been implementing a significant portion of the new high performance computing (HPC) cluster, named Redhawk3, over the last few months. The result: Redhawk3 went live for the Miami research community on October 11, at noon. While not at its full capacity yet, Redhawk3 already exceeds the compute power of the old system by far, in terms of available memory and compute speed.

The new machines have state-of-the art Intel processors that work at a clock speed of 2.6GHz, and each has 24 compute cores and about 100GB of shared memory. One large memory node has 1.5 TB of RAM. Now that the new system is being implemented, the old system will be decommissioned.

When users access the new cluster, they will find their home space and files from the old system transferred and readily available to them.

A new security feature will require users to authenticate with two-factor authorization, in line with the new Miami security policy. Current users of the HPC cluster can request detailed instructions on how to access the new cluster by emailing Research Computing Support.


By Jens Mueller, Senior Research Computing Specialist, Research Computing Support, Miami University.

HPC detail wiring photo by U.S. Department of Energy via Flickr, public domain. Photo of DJ Rao by Jeff Sabo, Miami University Photo Services.

Scott Hartley and two of his graduate students work in the lab.

Miami University to implement new high performance computing cluster

 

DJ Rao works on a computer in his office. A model of a mosquito sits in the foreground.
Among the research that will be enabled by the new Redhawk3 cluster is DJ Rao’s work on forecasting emergent epidemics in humans and livestock, including Zika, chikungunya, dengue, and avian influenza.

Miami University is purchasing a new high performance computing (HPC) cluster this spring. It will serve Miami researchers — both faculty and students — who have extensive computational needs that typically cannot be met by personal or lab computers. Named Redhawk3, the cluster will be made up of machines with the latest Intel processor architecture as core components. Compute nodes will have 24 Intel Skylake Xeon Gold 6126 cores with a clock speed of 2.6GHz.

The new system will be much faster than the current Redhawk, with most computations completing several times faster. The compute nodes are equipped with 96GB of RAM, making it possible to target bigger and more challenging computational problems. Redhawk3 will have two large memory nodes, each with 1.5TB of RAM. These nodes are meant to support researchers who have an interest in big data analytics or machine learning. In addition, the new cluster will have several nodes with general purpose graphics processing units (GPGPUs). GPUs have become increasingly popular because they can significantly speed up computations in a wide array of disciplines, including bioinformatics, engineering, physics, chemistry and many more.

Redhawk3 will facilitate the work of researchers like Scott Hartley, professor of chemistry and biochemistry;  DJ Rao, assistant professor of computer science and software engineering; and Nam Vu, assistant professor of economics.

Scott Hartley

One of the key projects in Hartley’s group focuses on understanding how molecules fold, and how that folding can be controlled to give predictable structural complexity. Hartley says computational chemistry calculations — which demand a lot of computing power — are an invaluable resource for this sort of work.

“They let us predict behavior before embarking on time-consuming synthesis, and then allow us to relate our experimental data to molecular structure,” Hartley says.  “As our understanding of our system has increased, so have our computational needs. The new cluster will allow us to explore ever-more sophisticated molecular architectures.”

DJ Rao

Rao and his team of undergraduate and graduate students are developing a novel computational methodology for predicting and forecasting emergent epidemics in humans and livestock, including Zika, chikungunya, dengue, and avian influenza. The computational method focuses on parallel simulations and machine learning using detailed mechanistic models that simulate the lifecycle of almost a billion humans in 51 countries in the Americas, along with mosquito lifecycles, weather, and air traffic. Rao says such a large and complex model would require over three months of run-time on a conventional desktop, making it impractical. However, with supercomputing, processing time is reduced to under 24 hours, enabling global health research that is of national and international importance.

Nam Vu

Vu’s research focuses on understanding the extent to which fiscal and monetary policy can impact the economy. Like Rao’s, Vu’s work typically requires computations that would take multiple days to process, even on a very powerful desktop computer.

“The old Redhawk cluster has been critical in my research agenda in terms of computing time and precision,” he says. “I have no doubt that the new Redhawk3 cluster, along with the wonderful support provided by the Research Computing Support group, will benefit my research for years to come.”

Redhawk3 is projected to be fully operational by the beginning of the fall semester, after an initial testing period.


Written by Jens Mueller, Senior Research Computing Specialist, Research Computing Support, Miami University.

Photos of Scott Hartley and DJ Rao by Jeff Sabo, Miami University Photo Services.

 

Research Computing Support joins the OARS family

Head-and-shoulders portraits of Jens Mueller, Greg Reese, and Jon Patton
Research Computing Support staff Jens Mueller, Greg Reese, and Jon Patton have extensive experience in scientific computing.

I’m very pleased to announce that Research Computing Support (RCS) is now part of the OARS family. This change in reporting line brings Miami’s centralized research support services together under a single umbrella, making it easier for researchers to identify and access them.

RCS will continue its mission to assist researchers with their use of technology so that they have more time to spend on core activities. The staff and the services they offer will also remain the same.

To learn more about RCS, visit their website or contact any of the staff:

Jens Mueller, Senior Research Computing Specialist
Greg Reese, Senior Research Computing Specialist
Jon Patton, Senior Research Computing Specialist


Mathematical chaos image by By Anders Sandberg via Flickr, used under Creative Commons license. Photos of RCS staff courtesy of RCS.