Aug 03

Alum Bryan Perozzi, now a research scientist at Google, won the Association of Computing Machinery SIGKDD, KDD 2017 Doctoral Dissertation award for his work at Stony Brook University. The annual award acknowledges excellent doctoral research in the field of data mining and knowledge discovery.

Bryan Perozzi and Steven Skiena

Perozzi thesis, Local Modeling of Attributed Graphs: Algorithms and Applications, was recognized as the best dissertation of the year in the data science community. His work involves graph embeddings — ways of representing the knowledge encoded in the structure of networks to make them accessible for machine learning models.

Focused on developing scalable algorithms and models for attributed graphs, Perozzi presented an online learning algorithm utilizing recent advances in deep learning to result in rich graph embeddings. The applications of this research are far reaching for the fields of data mining, information retrieval, profiling and demographic inference, online advertising and fraud detection.

Perozzi, whose advisor was Stony Brook Professor Steven Skiena, defended his thesis in May 2016. Upon learning of the award, he said, “Wow, what an honor! I’m humbled to have my work recognized by this prestigious early career award, and I am looking forward to giving a talk during the Doctoral Dissertation Award session on August 15.” The KDD 2017 Conference takes place in Nova Scotia, August 13-17.

Professor Skiena is especially proud of Perozzi’s research accomplishments, and they are collaborators on a number of published works. Their paper on DeepWalk graph embeddings has already been cited 270 times in Google Scholar since its publication in 2014.

“Bryan was a very creative, hardworking and independent graduate student here at Stony Brook, and his work on DeepWalk has proven extremely influential in the data science and machine learning communities. They got the right man for this award,” said Skiena.

At Google, Perozzi’s research relates to the intersection of data mining, machine learning, graph theory, and network science with a particular focus on local graph algorithms. In January 2017, he published and presented Ties that Bind: Characterizing Classes by Attributes and Social Ties, a collaboration with Stony Brook PhD student Aria Rezaei and Carnegie Melon faculty Leman Akoglu.

Perozzi is the first PhD student in the Department of Computer Science, which is part of the College of Engineering and Applied Sciences at Stony Brook University, to receive this award.

About the Association for Computing Machinery
Founded in 1947, the ACM is the largest and oldest scientific and industrial computing society. SIGKDD is the ACM’s Special Interest Group on Knowledge Discovery and Data Mining. SIGKDD selects one winner and two runner-ups each year to receive the award. Selections are based on the relevance to KDD, originality, scientific significance, technical depth and soundness, and overall presentation and readability.

Aug 11

Researchers in the Departments of Computer Science, and Applied Mathematics and Statistics awarded $449k through the National Science Foundation’s NeTS program.

Anshul Gandhi, left, and Zhenhua Liu

Even for the personal smartphone or home computer user there is no avoiding the use of cloud computing. Cloud computing is low in cost, easily available, and offers access to useful services that would otherwise be out of reach. Services such as Netflix, Amazon Fire, and Expedia are only some of the popular online services being hosted on the cloud. On the backend, dynamic applications in the cloud are more lucrative if their deployments grow through dynamic capacity provisioning. Software deployments must be carefully provisioned to meet their performance requirements without wasting resources.

Most resource provisioning solutions today employ predictions to estimate demand and provide resources, accordingly. At times, this process could be fraught with errors. With the support of a National Science Foundation (NSF) Networking Technology and Systems (NeTS) award of $449k researchers Anshul Gandhi and Zhenhua Liu, seek to bridge the gap between predictors and provisioning solutions.

The goal of their NeTS project, Demystifying the Role of Prediction Models: Bridging Prediction Algorithms and Resource Provisioning, is to develop and leverage error models to fully realize the potential of predictors. According to Gandhi, “Our research will allow businesses to maximize resource utilization despite prediction errors.”

“This is the kind of cross-cutting research we encourage among our faculty, to advance technologies that push the boundaries and challenge traditional thinking,” said Fotis Sotiropoulos, Dean of the College of Engineering and Applied Sciences. “I applaud Professors Gandhi and Liu on their collaborative approach to this research, and congratulate them on this recognition from the NSF. I look forward to following the progress of their research.”

Gandhi and Liu will investigate the prediction error model which includes constructing models that capture the structure of prediction errors; developing an algorithmic framework; and designing systems to exploit the new prediction error-aware algorithms.

Joseph Mitchell, chair of the Department of Applied Mathematics and Statistics, said, “This is a compelling project that requires collective expertise from computer science, optimization, probability, and statistics, and represents an ideal collaboration between Computer Science and Applied Mathematics and Statistics, both in research and in educational impact.”

Gandhi and Liu will realize additional benefits of their research through technology transfer opportunities with industrial partners.

NSF identified this NeTS project as “transformative research” related to fundamental scientific and technological advances in networking as well as systems research. NSF funds projects such as these in the hope that it will lead to “the development of future-generation, high-performance networks and future internet architectures”.

Arie E. Kaufman, chair of the Department of Computer Science, said, “In addition to finding the answer to network performance challenges, this project is especially interesting because it will directly contribute to interdisciplinary courses taught in two major departments on campus.”

About the Researchers
Anshul Gandhi is an assistant professor in the Department of Computer Science and he is affiliated with the Department of Applied Mathematics and Statistics, and Stony Brook University’s Smart Energy Technologies Cluster. He earned his PhD in computer science from Carnegie Mellon University, where he was advised by Prof. Mor Harchol-Balter. Prior to joining Stony Brook, he spent a year as a post-doctoral researcher in the Cloud Optimization and Analytics group at the IBM T.J. Watson Research Center.

Assistant Professor Zhenhua Liu is currently based in the Department of Applied Mathematics and Statistics, and he is affiliated with Department of Computer Science, and Smart Energy Technology Cluster. He was recently on leave for the ITRI-Rosenfeld Fellowship in the Energy and Environmental Technology Division at Lawrence Berkeley National Laboratory during the year 2014-2015. Dr. Liu earned his PhD in computer science at the California Institute of Technology.

Gandhi and Liu also recently received another NSF award, titled Enhancing the Parasol Experimental Testbed for Sustainable Computing, as part of an infrastructure grant led by Rutgers University to study sustainable computing in datacenters, which is aligned with the Smart Energy Technology cluster’s objectives.

Both the Department of Computer Science and the Department of Applied Mathematics and Statistics are part of the College of Engineering and Applied Sciences at Stony Brook University.

–Christine Cesaria

Jul 19

Scientists have traced the emergence of the modern dog to the domestication of a population of gray wolves that took place in Europe between 20,000 and 40,000 years ago.

By analyzing the DNA of two prehistoric dogs from Germany, an international research team led by Krishna R. Veeramah, PhD, Assistant Professor of Ecology & Evolution in the College of Arts & Sciences at Stony Brook University, has determined that their genomes were the probable ancestors of modern European dogs. The finding was published in Nature Communications.

Dogs were the first animal to be domesticated by humans. The oldest dog fossils that can be clearly distinguished from wolves are from the region of what is now Germany from around 15,000 years ago. However, the archeological record is ambiguous, with claims of ancient domesticated dog bones as far east as Siberia. Recent analysis of genetic data from modern dogs adds to mystery, with some scientists suggesting many areas of Europe, Central Asia, South Asia and the Middle East as possible origins of dog domestication.

Department of Ecology and Evolution Assistant Professor Krishna Veeramah with colleagues Shyamalika Gopalan and Dean Bobo.

In 2016, research by scientists using emerging paleogenomics techniques proved effective for sequencing the genome of a 5,000-year-old ancient dog from Ireland. The results of the study led the research team to suggest dogs were domesticated not once but twice. The team from Oxford University also hypothesized that an indigenous dog population domesticated in Europe was replaced by incoming migrants domesticated independently in East Asia sometime during the Neolithic era.

“Contrary to the results of this previous analysis, we found that our ancient dogs from the same time period were very similar to modern European dogs, including the majority of breed dogs people keep as pets,” explained Dr. Veeramah. “This suggests that there was no mass Neolithic replacement that occurred on the continent and that there was likely only a single domestication event for the dogs observed in the fossil record from the Stone Age and that we also see and live with today.”

In the paper, titled “Ancient European dog genomes reveal continuity since the Early Neolithic,” Veeramah and colleagues used the older 7,000 year old dog to narrow the timing of dog domestication to the 20,000 to 40,000 years ago range.

They also found evidence of the younger 5,000 year old dog to be a mixture of European dogs and something that resembles current central Asian/Indian dogs. This finding may reflect that people moving into Europe from the Asian Steppes at the beginning of the Bronze Age brought their own dogs with them.

    Jul 27

    An extraordinary gathering of scientists and dignitaries broke ground on July 21, 1017, for the Deep Underground Neutrino Experiment (DUNE), a leading-edge, international experiment for neutrino science and proton decay studies in which Stony Brook University will play an important role.

    Discoveries over the past half-century have put neutrinos, the most abundant matter particles in the universe, in the spotlight for further research into several fundamental questions about the nature of matter and the evolution of the universe — questions that DUNE will seek to answer.

    Stony Brook University’s Nucleon Decay and Neutrino (NN) research group, led by SUNY Distinguished Professor Chang Kee Jung, has been playing a leading role in the nucleon decay and neutrino physics community for two decades in the realization of next-generation NN experiments.

    Starting in 2014, Prof. Jung played a major role in the reformulation process of the Long Baseline Neutrino Experiment (LBNE) to the Deep Underground Neutrino Experiment (DUNE)/Long Baseline Neutrino Facility (LBNF). He was a member of the interim International Executive Board (iIEB), and chaired the committee that drafted the governance section of the DUNE Collaboration document. During 2015-2016, he served as DUNE Resource Coordinator, and currently serves as a DUNE Executive Committee (EC) member.

    Earlier, the Stony Brook group worked on the 35t prototype of the planned DUNE far detector, a liquid argon Time Projection Chamber (TPC). Currently the group is involved in the DUNE far detector and ProtoDUNE-SP at CERN in the areas of cold electronics and field cage (led by Assistant Prof. Michael Wilking), and in the near detector design studies (Profs. Jung and McGrew).

    DUNE will consist of two neutrino detectors placed in the world’s most intense neutrino beam. One detector will record particle interactions near the source of the beam, at the Fermi National Accelerator Laboratory in Batavia, Illinois. A second, much larger, detector will be installed more than a kilometer underground at the Sanford Underground Research Laboratory in Lead, South Dakota — 1,300 kilometers downstream of the source. These detectors will enable scientists to search for new subatomic phenomena and potentially transform our understanding of neutrinos and their role in the universe.

    DUNE prototype detectors are under construction at the European research center CERN. The Long-Baseline Neutrino Facility will provide the neutrino beamline and the infrastructure that will support the DUNE detectors.

    Jul 10

    Stony Brook Linguistics PhD candidate Paola Cepeda has been recognized with a 2017 Mellon/American Council of Learned Societies (ACLS) Dissertation Completion Fellowship for her thesis research entitled “Negation and Time. Against expletive negation in temporal clauses.” Cepeda is an international student from Peru.

    Scholars previously thought that this type of negation, which is present in a variety of natural languages, had no meaning (e.g., a speaker saying, “I missed not seeing you last summer” when he/she actually missed was “seeing you” and not “not seeing you”). Cepeda’s groundbreaking research suggests otherwise. In addition to addressing an open question in her field, her findings could have broader impacts on language processing by artificial personal assistants like Siri or Cortana.

    Cepeda’s advisor, Professor Richard Larson from the Department of Linguistics, explains further: “The artificial languages of logic and computer science have the property that expressions written in them are meaningful in all their parts — they contain no extraneous symbols. As such, one might describe such artificial languages as ‘perfectly’ interpreted. They show a perfect match up between form and meaning. Cepeda’s results suggest that when speakers say a ‘not’ they really do convey a negative meaning, even when it doesn’t seem so. If she is correct, then speakers are more logical and systematic, and natural language more perfect, than initially appears.”

    It is a great honor for Cepeda — and Stony Brook — to be recognized with this prestigious award. Only 65 fellows were selected from a pool of more than 1,000 applicants through a rigorous, multi-stage peer-review process. The fellowship offers promising graduate students a year of support to focus their attention on completing projects that form the foundations of their careers and that will help shape a generation of humanistic scholarship. The program, which is made possible by a grant from The Andrew W. Mellon Foundation, also includes a faculty-led academic job market seminar, hosted by ACLS, to further prepare fellows for their postgraduate careers.

    “The fellows are completing their degrees at 36 different US universities, and their work represents the broad range of disciplines that this program supports, including literature, philosophy, media studies, ethnic studies, linguistics, sociology, and archaeology,” said ACLS Program Officer Rachel Bernard.

    When asked what advice she has for other graduate students pursuing prestigious awards, Cepeda emphasized the importance of crafting one’s proposal with a particular audience in mind. “It’s a delicate balance,” she said, “you want to appear knowledgeable while still ensuring that the subject is approachable for non-experts.” Cepeda carefully tailored her application materials so that a panel of humanists and social scientists unfamiliar with her topic could grasp the significance of her research.

    Click here for more information about the Mellon/ACLS Dissertation Completion Fellowship.

    Jul 11

    New research reveals that sulfur dioxide, a major contributor to air pollution, is removed from the air by concrete surfaces. Stony Brook University researcher Alex Orlov, PhD, and colleagues discovered how concrete interacts and eliminates sulfur and nitrogen oxides. Their findings, published in the July edition of the Journal of Chemical Engineering, could be a significant step toward the practice of using waste concrete to minimize air pollution.

    Alexander Orlov, PhD

    According to the World Health Organization, as many as seven million premature deaths of people worldwide may be linked to poor air quality and pollution. Sulfur dioxide emissions are among the most common pollutants into the air globally, with power plants emitting the most sulfur dioxide. Cement kilns also produce approximately 20 percent of all sulfur dioxide industrial emissions.

    “Even though producing concrete causes air pollution, concrete buildings in urban areas can serve as a kind of sponge adsorbing sulfur dioxide to a high level,” explained Dr. Orlov, Associate Professor of Materials Science and Chemical Engineering in the College of Engineering and Applied Sciences, and a faculty member of the Consortium for Inter-Disciplinary Environmental Research at Stony Brook University. “Our findings open up the possibility that waste concrete coming from building demolitions can be used to adsorb these pollutants.”

    He added that concrete remains the most widely used material in the world and is inexpensive.  Because of this, Dr. Orlov emphasized that “the strategy of using pollution causing material and turning it into an environmental solution could lead to new thinking in urban design and waste management.”

    This electron microscopy image of concrete includes a model of sulfur dioxide interactions with concrete surface – represented by the colored spheres. (photo: Marija Illoska)

    Dr. Orlov cautioned that the capacity for concrete to adsorb pollutants diminishes over time as the material ages. Crushing concrete, however, can expose new surfaces and restore its pollution removing properties.

    The researchers used various cement and cement-based building materials to conduct their experiments, details of which are in the paper, titled “Reactions of SO2  on hydrated cement particle system for atmospheric pollution reduction: A DRIFTS and XANES study.” They employed Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) and X-ray absorption Near Edge Spectroscopy (XANES) to identify the levels of sulfur dioxide adsorption on the materials.

    Experiments were conducted at Stony Brook University, Brookhaven National Laboratory’s National Synchrotron Light Source and Center for Functional Nanomaterials, and the National University of Singapore.

    Co-authors on the paper are Girish Ramakrishnan and Qiyuan Wu of Stony Brook University, and Juhyuk Moon at the National University of Singapore.

    The research was supported in part  by the National Science Foundation CMMI program.

    Jul 11

    Genetics PhD candidate Alex Bott is ready to take his place in the front ranks of the fight against cancer, and he has the grants to prove it.

    Genetics PhD candidate Alex Bott

    This past year, Bott was recognized with two prestigious and highly competitive awards from the National Institutes of Health (NIH): the F31 (Predoctoral Individual National Research Service Award) and the newly-established F99/K00 — the Predoctoral to Postdoctoral Fellow Transition Award, which is designed to encourage and retain outstanding graduate students who have demonstrated potential to pursue careers as independent cancer researchers.

    Bott’s research focuses on Myc, a regulator gene amplified in a wide range of cancers, particularly breast cancer. Since Myc is known to contribute to the genesis of many human cancers, scientists hope that understanding the gene could lead to breakthrough therapies aimed at inhibiting tumor growth.

    Bott’s early success is fueled not only by his enthusiasm for research and innovation, but also by a commitment to effective science communication. In order to improve his skills in this area, he worked with Stony Brook’s Alan Alda Center for Communicating Science, which coaches scientists to talk about their research in a clear, vivid, and engaging way.

    “Writing grants isn’t easy,” Bott said. “The act of sitting down, thinking, and explaining why your research matters is absolutely essential, even if you don’t want to make your career in academia. If every student could talk about their work in the simplest terms, without jargon, we’d have a tremendous effect in promoting scientific literacy.”

    Bott also received help and advice from the Integration of Research, Education, and Professional Development (IREP) Office. According to Jennifer Green, IREP’s External Fellowships Advisor, her office seeks to create a culture where SBU students and postdocs consider applying for nationally competitive fellowships early in their careers.

    “There is a great deal of support for students pursuing external awards, particularly those offered by the NIH,” Green said.

    “Examples include the ‘Writing to Win’ workshops offered by IREP and the Center for Inclusive Education (CIE), as well as the application incentives offered periodically by the SUNY Research Foundation,” she said.

    Green said prospective applicants should contact the IREP Office at for more information.

    Asked his advice for other graduate students pursuing awards of this caliber, Bott emphasized the importance of learning to think critically about one’s own work, for instance by asking questions like: “Why is this important and who can it help?”

    Bott also stressed the importance of persistence. His initial attempt at the F31 was unsuccessful, but then he went on to receive the award on his second attempt and utilized the feedback to tailor his successful F99/K00 application.

    Jun 08

    When pro ballers indulge in late-night tweetstorms, they aren’t just courting controversy: they could also be impacting their performance on-court.

    A new study led by Stony Brook researchers suggests that NBA players had worse personal statistics in games that followed a late-night tweet.

    Players scored on average about 1 point less in games following late-night tweets, and their shooting accuracy dropped 2.5 percentage points compared with their performance in games that did not follow late-night tweeting. After a late-night tweet, players also took fewer shots and had fewer rebounds, steals and blocks. “Using late-night tweeting activity as a proxy for being up late, we interpret these data to show that basketball skills are impaired after getting less sleep,” said lead investigator Jason J. Jones, PhD, Assistant Professor of Sociology at Stony Brook University in New York.

    “While experimental studies have shown the impact of sleep deprivation on performance, this study uses big data to provide interpretable results on real-world performance of basketball players.”

    According to the authors, most of the statistical changes following late-night tweets can be explained by fewer minutes played. Players had an average of 2 minutes less playing time following late-night tweeting.

    “Our findings are relevant beyond just sports science research,” said study co-author Lauren Hale, PhD, Professor of Family, Population and Preventive Medicine in the Program in Public Health at Stony Brook University. “Our results demonstrate a broader phenomenon: to perform at your personal best, you should get a full night of sleep.”

    The research team led by Jones and Hale merged two public sources of data for the study, analyzing Twitter account activity from 112 verified NBA players as well as basketball statistics from Yahoo Sports. The data, which included more than 30,000 tweets, were compiled across 7 basketball seasons from 2009 to 2016. To reduce the potential performance effects of changing time zones, the analysis included only games within the same time zone as the player’s home.

    “Twitter is currently an untapped resource for late-night behavior data that can be used as a proxy for not sleeping,” said Jones. “We hope this will encourage further studies making use of time-stamped online behavior to study the effects of sleep deprivation on real-world performance.”

    Jun 09

    SUNY ranked 38th in the “Top 100 Worldwide Universities Granted U.S. Utility Patents for 2016,” according to the National Academy of Inventors and Intellectual Property Owners Association, which publishes the ranking annually based on U.S. Patent and Trademark Office data.

    SUNY campuses overall were awarded 57 U.S. utility patents. Among those from Stony Brook University is a redesigned a catheter developed by a multidisciplinary team led by Annie Rohan from the School of Nursing. The catheter incorporates LED lights to reduce the likelihood of infection after the device is inserted into a patient’s body.

    “Catheter-related infections are a multibillion-dollar-a-year problem,” says Rohan. “Healthcare providers have addressed it with prophylactic antibiotics, handwashing, and techniques to maintain sterility, but up until now there hasn’t been a product that can successfully reduce infection risk once the device is in the body.”

    “Across SUNY, our faculty and students partner to make groundbreaking discoveries in a broad spectrum of areas,” said SUNY Chancellor Nancy L. Zimpher. “Through more than 1,300 U.S. patents earned to date, SUNY research has led to hundreds of new technologies and advances that address society’s greatest challenges and have a positive impact on quality of life in New York and beyond. Congratulations to all those at SUNY whose important work has elevated us to this prominent world ranking.”

    Jun 22

    Jamie Sommer, a PhD candidate in the Department of Sociology at Stony Brook University, has received a research grant from the Horowitz Foundation for Social Policy for her work, “Is Bilateral Environmental Aid Effective? A Cross-National Analysis of Forest Loss.” Sommer is one of 20 award winners chosen by the board of trustees from 535 applications.

    “I am honored to receive the Horowitz Foundation research grant to continue my work on analyzing the effectiveness of bilateral aid at reducing environmental harms cross-nationally,” said Sommer. “This project is part of my larger research narrative, which aims to understand the role of the state in reducing forest loss. In particular, this grant will help me theoretically and empirically test what types of foreign bilateral environmental aid are most effective, considering the internal political and economic characteristics of receiving nations. The findings will help donors implement policies to ensure the delivery of their funds and that projects are improving the environment and reducing forest loss. I hope my research will help inform the U.S. and other high-income nations in how to increase the effectiveness of their aid to limit the loss of our world’s forests.”

    “This year the foundation saw a marked increase in not just the number of applications, but also the number of applicants holding citizenship in other countries, although surprisingly all recipients attend U.S. institutions,” said Horowitz Foundation Chair Mary E. Curtis. “The winners were chosen by the trustees for their potential to contribute to social policy on both a global and local level. As we look forward to celebrating our 20th year in 2018, we hope to continue aiding international scholars at home and abroad.”

    About the Horowitz Foundation for Social Policy
    The Horowitz Foundation for Social Policy was established in 1997 by Irving Louis Horowitz and Mary E. Curtis. Its general purpose is to support the advancement of research and understanding in the major fields of the social sciences. Since inception, the foundation has awarded grants to more than 200 scholars from over 100 different universities around the world.

    Applications for 2017 Awards
    Award applications for next year open July 1, 2017, and all application materials are due on December 1, 2017. Applicants are encouraged to begin their application online as early as possible. Award winners for 2017 will be announced in May 2018. Additional information, including a list of previous recipients, is available on the Horowitz Foundation website.


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