December 2017

Department of Defense Visits Stony Brook University

On Thursday, December 14, Dr. Robin Staffin, Director of Basic Research for the Department of Defense (DOD) visited Stony Brook University along with four of his DOD colleagues.

This visit was organized by the Office of the Vice President for Research and the Office of Government Relations to provide Stony Brook researchers with a strategic networking opportunity to learn about a wide range of disciplinary funding opportunities for basic research activities from the Department of Defense.

“The visit by DoD’s Director of Basic Research reflects our outstanding reputation for fundamental research at Stony Brook,” said Richard Reeder, Vice President for Research at Stony Brook University. “The new insights gained during the visit will allow us to expand our research across a broad range of disciplines, a goal that’s vitally important at a time when some federal funding agencies are facing possible cuts.”

During his visit, Dr. Staffin provided a presentation to Stony Brook researchers and faculty members, participated in a working lunch with deans and department chairs, and joined faculty for an open session for targeted research connections. DOD visitors toured Dr. Gabor Balazsi’s Synthetic Biology lab and Dr. Eden Figueroa’s Quantum Technology lab at Stony Brook as well.

DOD basic and applied research underpins the innovative health treatments and technologies that help save lives on the battlefield and speed recovery from injuries. Stony Brook University is proud to partner with DOD to address complex challenges requiring innovation and engineering basic research performed at world-class research institutions like Stony Brook.

Recent highlights of Stony Brook’s DOD-funded research include researching algorithm diversity to prevent cyberattacks as well as developing a new super-resolution light microscopy system to enhance the study of cells, tissues and organ systems in order to better address infectious diseases and chemical agents that our American troops may encounter.

Stony Brook recently established its first DC-based federal relations office, demonstrating the University’s strong commitment to working closely with federal agencies like DOD.

Strengthening Application Resilience: Professor Barbara Chapman Wins NSF SPX Award

Significant research in the area of computational power and large-scale application efficiency is being conducted by Professor Barbara Chapman, one of the latest computer science faculty members to receive a National Science Foundation (NSF) funding award.

Chapman won the NSF Scalable Parallelism in the Extreme, otherwise known as an SPX award, for her research, Cross-layer Application-Aware Resilience at Extreme Scale (CAARES).

The funded research addresses the challenges imposed by future extreme-scale architectures that will require dynamic programming approaches, where different software layers, potentially developed using different programming paradigms, will have to closely interact with each other.

“I’m extremely excited to represent Stony Brook University by winning this award thanks to the NSF,” Chapman said. “The SPX award is one of the most prestigious in the industry, and it means the world to me to be named a recipient.”

Chapman’s work quantifies from a theoretical standpoint what the possible benefits are of gathering two well-understood resilience mechanisms, along with ABFT numerical libraries, in one representative application. Never proposed before, the target application is representative of computational science domains.

“In this project we will explore an in-staging data management runtime that combines multiple strategies using them appropriately at execution time based on data locality and/or importance,” the proposal states. “For example, spatial/temporal data locality and user provided hints can be used to classify data based on its access pattern and access mode (read only, write only, or both), and this classification can be used to select appropriate data resilience strategies based on desired cost-benefit ratios.”

The three-year project received more than $300K in funding and will conclude in July 2020. In total, three graduate students will be hired to participate in the SPX project, and they will work closely with the project lead, Anthony Curtis.

A faculty member at Stony Brook University since 2015, Chapman is a core part of the Institute for Advanced Computational Science and the Department of Computer Science. Additionally, she is a professor in the Department of Applied Mathematics and Statistics (AMS).

Prior to joining Stony Brook’s College of Engineering and Applied Sciences, she served as the director of the Center for Advanced Computing and Data Systems at the University of Houston. While working in Houston, her research group developed OpenUH, a state-of-the-art open source compiler that is used to explore language, compiler and runtime techniques, with a special focus on multi-threaded programming.

Chapman also leads the Exascale Programming Models Laboratory, which aims to increase programmer productivity, enhance application performance, develop novel implementation technologies that anticipate architectural changes and emerging user needs, and provide reference implementations of our ideas.

— Joseph Wolkin

Wealth Inequality Increased in Ancient Times with Animal Domestication

Wealth inequality increased over the past 11,000 years and was tied to the rise of animal domestication, according to an analysis by a team of international scientists, including Elizabeth Stone from Stony Brook’s Department of Anthropology.

Published in Nature, the study focused on 63 archeological sites across North America, Europe, Asia and Africa, using house size as a measure of wealth. The sites included a range of economic systems – from ancient cities to hunter-gatherer communities – and spanned the past 11,000 years.

“The houses that I looked at often have cuneiform tablets within them which document the inheritance, sale and exchange of real estate, including houses,” Stone said. “From my data it is clear that house size reflected both wealth and the maturity of the family living in it.”

Stone explains that the team expected wealth inequality to increase over time as societies and ruling systems developed but found Old Word societies experienced more wealth inequality than those in the New World. And unexpectedly, this inequality increased much more in Eurasia than in North America.

The reason for this disparity, according to the authors, is the presence of large domesticated animals, such as horses and cattle that were present in Eurasia but absent in North America in Old World societies. Such animals provided the abilities to plow fields for food product and transportation to move, develop and create mounted armies, all of which enabled Eurasian Old Word societies to extend territory and acquire wealth. The research was supported in part by the National Science Foundation.

Multiple NSF Awards Fund Jie Gao’s Algorithm Research

The National Science Foundation (NSF) is one of the most prestigious organizations in the American science realm. With its dedication to supporting colleges throughout the nation, the NSF continues to help advance computer science research at Stony Brook University.

Professor Jie Gao is the latest Stony Brook faculty member to earn not one, but two awards from the NSF. Gao has been awarded $250,000 for the NeTS grant (Research in Networking Technology and Systems) along with $100,000 for the Algorithms for Threat Detection (ATD) grant.

“We at the Computer Science Department are very proud of Jie for her exceptional work,” said Interim Department Chair Samir Das. “Serving as one of the lead women researchers, we hope these grants push her forward as she continues to make a difference not only at Stony Brook, but nationally and internationally.”

The ATD grant was awarded to Gao for her project, “Theory and Algorithms for Discrete Curvatures on Network Data from Human Mobility and Monitoring.” The focus of the research is on developing mathematical tools and algorithms for understanding community structures and anomalies in human mobility data that can be of crucial value in many applications.

“The cool thing about this project is to use geometric features, such as the Ollivier Ricci curvature for graph analysis, and we believe that this has a huge potential,” said Gao.

Gao wants to extract stable groups in human mobility patterns to serve as the traffic norm for detecting the abnormal patterns that can be tied to criminal or terrorism events. In doing so, she will also examine how information can spread among the mobile users by exploiting their physical colocation events.

As part of the project, graduate students and postdoctoral fellows will receive training, and Gao will disseminate results through lectures and conference presentations. In the end, software will be developed for practical use.

Gao’s newly awarded NeTS grant from the NSF is also underway. This research seeks to increase privacy protection — an urgent matter with wide impact. Through the use of NeTS funding, new models will be developed to characterize the performance of algorithms in terms of privacy protection effectiveness and data utility.

“We are concerned about the privacy issues in trajectory data collected by wireless devices in an open environment and would like to propose new algorithms to remove the sensitive information while still enabling the mining of useful statistical information for applications,” explained Gao.

About Jie Gao
Jie Gao is an associate professor in the Department of Computer Science at Stony Brook University. She earned a PhD from Stanford University, and her research focuses on algorithms, computational geometry and networks (sensor, wireless and social). Gao spent a year at the Center for the Mathematics of Information at the California Institute of Technology. She is the recipient of an NSF CAREER award and IBM Fellowship. In addition to the ATD and NeTS projects, Gao is also working with students on a number of social contagion and influence studies that examine behavioral changes and influence.

Skin Pigmentation is Genetically Complex, Researchers Find

While skin pigmentation is nearly 100 percent heritable, it is far more genetically complex than previously thought.

South African individuals in a household that exemplifies the substantial skin pigmentation variability in the Khomani and Nama populations.

According to a new study published in Cell, co-authored by Stony Brook’s Brenna Henn, the genetics of skin pigmentation become progressively complex as populations reside closer to the equator, with an increasing number of genes—known and unknown—involved, each making a smaller overall contribution.

Researchers from SBU, Stanford University and the Broad Institute of MIT and Harvard worked closely with the KhoeSan, a group of populations indigenous to southern Africa. They found that earlier studies of the genetics of skin pigmentation are misleading because they rely on datasets that heavily favor northern Eurasian populations.

According to Henn, the findings highlight a previously unsuspected strong role for polygenecity – many genes playing a role in skin pigmentation, as well as the need for scientists to study diverse and understudied populations worldwide to get the full picture of the genetic architecture of human skin pigmentation.

“We need to spend more time focusing on these understudied populations in order to gain deeper genetic insights,” said Brenna Henn, assistant professor in the Department of Ecology and Evolution in the College of Arts and Sciences at Stony Brook University.

Brenna Henn

The paper is a culmination of seven years of research that spanned several institutions, starting with a collaboration between Stellenbosch University in South Africa and Stanford University in Carlos Bustamante’s lab, where Henn and co-author Alicia Martin, a postdoctoral scientist at the Broad Institute, trained. Martin, Henn, and their colleagues spent a great deal of time with the KhoeSan, interviewing individuals, and taking anthropometric measurements (height, age, gender), and using a reflectometer to quantitatively measure skin color. In total, they accumulated data for approximately 400 individuals.

The researchers genotyped each sample — looking at hundreds of  thousands of sites across the genome to identify genetic markers linked with pigmentation measures — and sequenced particular areas of interest. They took this information and compared it to a dataset that comprised nearly 5,000 individuals representing globally diverse populations throughout Africa, Asia, and Europe.

What they found offers a counter-narrative to the common view on pigmentation.

The prevailing theory is that “directional selection” pushes pigmentation in a single direction, from dark to light in high latitudes and from light to dark in lower latitudes. But Martin and Henn’s data showed that the trajectory is more complex. Directional selection, as a guiding principle, seems to hold in far northern latitudes. But as populations move closer to the equator, a dynamic called “stabilizing selection” takes effect. Here, an increasing number of genes begins to influence variability. Only about 10 percent of this variation can be attributed to genes known to affect pigmentation.

“The full picture of the genetic architecture of skin pigmentation will not be complete unless we can represent diverse populations worldwide,” said Henn.

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