Newsletter of the Department of Computer Science CHAIR’S MESSAGE The summer was a welcome break for all of Volume 13 / Number 2 / Fall 2009 us after a busy spring semester. As we begin the new academic year, we welcome our www.cs.duke.edu new members. It gives me great pleasure to announce the arrival of our newest faculty member, Bruce Maggs. A world renowned leader in parallel and distributed systems, Bruce moved here from Carnegie Mellon University. He also works as VP of Research and Development of Akamai Technologies. We are also delighted to have new students—both graduate and undergraduate. Congratulations to our recent graduates. We

threads wish them all the best as they start a new phase in their lives. I am always proud to share the Pankaj K. Agarwal, Chair accomplishments of the members of the Department. Xiaobai Sun was promoted to the rank of Full Professor. A highly regarded computational scientist, she is well known for blending mathematical, algorithmic, and engineering issues. Kamesh Munagala received a prestigious Alfred P. Sloan Fellowship. Last year he received an NSF CAREER award for his work on stochastic optimization. Alex Hartemink was named a Bass Professor for his excellence in research and teaching. Currently on a sabbatical leave, Alex is spending a year teaching at a school in Kenya. Spring 2009 graduates Alex Keybl, John Pena, and Tiffany Yam received the Department’s Alex Vasilos Memorial Award for threads their excellence in academic achievement and undergraduate program support. As always, we were busy hosting several events during the spring and summer. Two new students, Sophia Cui and Peng Shi, 2009 fall joined our C-SURF program, a program designed to provide undergraduates with an intensive research experience. Building on the success of the last year’s workshop, Susan Rodger once again organized a threads contents: workshop on Alice, educational software that provides innovative methods for teaching computer programming. Jeff Forbes organized the RoboCup Junior Regional Competition, in which eleven middle- and 2

threads high-school teams participated. The faculty Department also hosted a vibrant summer

threads internship program for undergraduates. The students conducted a wide variety of research in computational economics, 4 , networking, research and . Others assisted with the HarambeeNet and Alice workshops. All agree it was a valuable and rewarding experience. 6 Be sure to check out our website to learn the outreach latest news about the Department and to be

threads a part of our community. If you are in the RTP area, we hope you will stop by for a visit. 7 We look forward to hearing from you. students Best wishes, Pankaj K. Agarwal 12 back page threads 2 Sponsor: NSF Internet Architecture CT-ER: ADoS-Resistant Xiaowei Yang Sponsor: NSF User-Controlled Routes NETS-FIND: AnInternetArchitecturefor Xiaowei Yang Sponsor: NSF Dissemination (REUSupplement) Unifying DataProcessingand III-COR: Wide-AreaPublish/Subscribe: Jun Yang Sponsor: NSF (REU Supplement) Information AcquisitionandExploitation Stochastic ControlPolicies for CAREER: Light-weightNear-Optimal Kamesh Munagala Sponsor: AlfredP. SloanFoundation Alfred P. SloanResearchFellowship Kamesh Munagala Sponsor: OfficeofNavalResearch Fabrication Approaches the Top-down andBottom-up Bioenabled Electronics:Bridging Thom LaBean Sponsor: NorthCarolinaStateUniversity Architectures forNanoengineering of ComplexNucleic-acid-based CDI-Type II:ComputationalDiscovery Thom LaBean(PI-StephenCraig) Sponsor: DARPA During theEukaryotic CellCycle Elucidating Transcriptional Regulation New ComputationalMethodsfor Alexander Hartemink Sponsor: NSF Domains (REUSupplement) PreferencesinCombinatorial Aggregating Computational SocialChoice: Vince Conitzer Sponsor: NSF Systems (REUSupplement) CAREER: QueryingandControlling Shivnath Babu N www e threadsfaculty w G w .csdukeedu ran t s Aw

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billions of Web interactions every day for billions ofWebinteractionseverydayfor delivery networkthathandleshundredsof Today, Akamaiisaninternationalcontent up companycalledAkamaiTechnologies. sabbatical atMIT, hehelpedlauncha start- joined CarnegieMellon.In1998,whileon Research InstituteinPrinceton,Maggs working asaresearchscientistattheNEC Bruce Maggs Duke communityafterfifteenyears of Professor Bruce Maggs. Maggs joins the welcomes its newest faculty member, With greapleasure, the Department CS Welcomes continuous models to digital computer continuous modelstodigitalcomputer along thecomputationalspectrumfrom performance in size, speed, and weight The project works to better application State and Pennsylvania State University. conjunction with researchers at Arizona by Sun and Professor Nikos Pitsianis in Transforms On Microchips, developed Framework For Accelerating Numerical grant currentlyfundstheFANTOM project, U.S. Defense Department Agency. The on a $2.6 million grant from DARPA, the deserved recognition.” “I amthrilledtoseehergettingthiswell- says DepartmentChairPankaj Agarwal. algorithmic, andengineeringissues,” well knownforblendingmathematical, as well as breadth of her work, and she is discrete modelsforcomputation. relationships between continuous and with a focus on the differences and Sun specializesinnumericalanalysis the scientificcomputingfacultyatDuke, to the rank of full Professor. A member of Duke University has promoted Xiaobai Sun The departmen proudly announces that Xiaobai Sun Sun is currently Principal Investigator “Xiaobai ishighlyregardedforthedepth degrees from MIT and degrees fromMITand his SB,SM,andPhD University. at Carnegie Mellon distributed systems in paralleland research andteaching After receiving After receiving ProfessBruceMaggs Promoted to Professor electric scooter. zipping aroundChapelHillonhistrusty the hockeyrinkorsoftballfield,out not inhisoffice,youon cancatchMaggs endowed chairinhisname.Whenhe’s University, whichproudlysupportsan grandfather wasalawprofessoratthe faculty totheranks. able to actively recruit additional strong testament to the Department that it is faculty member, sheadds,anditisa leadership brings out the best in each inspirational,” she says. Department the other faculty members are very recognize herpeers.“Inthisdepartment, of being promoted, Sun was eager to Physics, onMRIimageprocessing. Johnson, Professor of Radiology and reconstruction, andanotherwithG.Allan Program, on optical imaging and spectral of the Duke Imaging and Spectroscopy with ECE professor David Brady, leader used to automate and speed hardware other achievements, the system has been software needsandconstraints.Among architecture, tackling both hardware and fantastic andbright.” 2008 schoolyear. “And thestudentsare visiting professoratDukeduringthe2007- who metmanyofhisnewcolleaguesasa respect fortheDukefaculty,” saysMaggs, page fiveofthisissue.)“Ihavetremendous researchprojectson more aboutMaggs’ major focusofhisresearchtoday. (Read interestinmassivedatasets,a Maggs’ VP ofResearchandDevelopmentsparked Windows Update.WorkingatAkamaias websites likeAppleiTunes andMicrosoft Xiaobai Sun Maggs isnostrangertoDuke:His Maggs When congratulated on the honor collaborations, one collaborations, one on-campus maintain active and herstudents image processing. accelerate signaland development and to Additionally, Sun faculty

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Alexander Hartemink Named Bass

Joining a select group of Duke faculty, “A brilliant scholar, Alex has earned the Alexander Hartemink has been named a admiration and respect of everyone,” says distinguished Bass Professor for excellence Department Chair Pankaj Agarwal. “This in research and teaching. His new title prestigious professorship is the perfect way will be Alexander F. Hehmeyer Associate of recognizing his extraordinary teaching Professor of Computer Science. and research accomplishments.” “I am incredibly honored and grateful In addition to distinction in research, the to have been nominated and selected,” Bass Professorship recognizes excellence says Hartemink, who joined the faculty in in undergraduate teaching. Each year, 2001 after completing his PhD in electrical Hartemink teaches an undergraduate class engineering and computer science at the in computational genomics that attracts Massachusetts Institute of Technology. a wide variety of students, including A member of Duke’s Institute for Genome computer science, biology, engineering, Alexander Hartemink and Provost Peter Lange at the awards ceremony Sciences and Policy, Hartemink uses math, and chemistry majors. Additionally, novel computational methods to study undergraduates often work in Hartemink’s term and attend annual dinners at which transcriptional regulation, a complex cellular research group, attending lab meetings they interact with other from around process in which proteins originally encoded alongside Master’s and PhD students. campus. “They are a great group of people,” by the genome return to the nucleus and turn “Giving undergraduates opportunities to says Hartemink, who attended his first on and off the transcription of other genes. do research can be invaluable for their dinner this April. “I’m looking forward to He has recently published in Nature, Genome intellectual development,” he says. deeper interactions with my colleagues over Research, and PLoS Computational Biology. Bass Fellows are chosen for a five-year the next few years.”

Kamesh Munagala Wins Sloan Fellowship the department is pleased to announce Hartemink, and Mauro Maggioni. that Kamesh Munagala, Assistant Professor “It is a great honor to be named a Sloan of Computer Science, has been awarded a Fellow, and it will contribute to increased prestigious Sloan Research Fellowship. He national recognition for the entire is one of only sixteen computer scientists Department,” says Munagala. “I am very from across the U.S. and Canada to be grateful to my department and colleagues honored with the award this year. for their support and encouragement.” Established in 1955, the Sloan Research Fellows receive $50,000 over a two-year Fellowships are designed to “stimulate period to fund research of their choice. fundamental research Munagala plans to use the funding to by early-career continue his research in approximation scientists and scholars , particularly for stochastic of outstanding control problems with applications to promise,” according managing uncertainty and incomplete to the Alfred P. information in databases, communication Sloan Foundation systems, and multi-agent systems. Much Kamesh Munagala website. Past Sloan of the funding will be used to support Fellows have gone on to win numerous graduate students and for travel. awards later in their careers, including This past April, Munagala also received thirty-eight Nobel Prizes and sixteen Fields the Best Paper Award at the 18th Medals, the top honor in mathematics. International World Wide Web Conference Past Department recipients of the Sloan (WWW) for Hybrid Keyword Search Auctions, Fellowship are Professors Pankaj Agarwal, a publication written with Ashish Goel of Vincent Conitzer, Ronald Parr, Alexander . Bruce Donald 4

threadsresearchwww .csdukeedu software program created by theK* Model ofanenzyme natural antibiotics. the machinerythatbacteriausetomake can showexperimentalistshowtochange laboratory-tested acomputerprogramthat and biochemistshavedeveloped Working together, computerscientists race betweenantibioticsandgerms. software tothenever-endingarms A Duke-ledteam has broughtpowerful Speeds EnzymeDesign S shape into the and telling it what shape intothealgorithmandtelling itwhat enzyme simplyby inputtingthe protein’s in principle,bepossibletoredesignany purely experimentaltechniques.Itshould, that wouldtakeaverylongtimethrough might beabletoquicklydiscoverthings flexibility, itembracesit,” hesays. “Sowe shape shifting.“Thusitnotonlyaddresses “an entirealbum,orensemble,” ofpossible simultaneously evaluateswhatDonaldcalls like theywouldinreallife.Moreover, it more backbones andsidechainswiggle But thelatestversionofK*letsprotein proteins movearoundinthreedimensions. to accountforthewaykeypartsofreal proposed, andsomeofthoseevenattempt experiments alone.” magnitude morevariationsthanlaboratory but thealgorithmcantestoutordersof possible changesyou canmaketoaprotein, antibiotics,” saysDonald.“Therearemany essentially anewpathwaytomakenovel and cheaperforthebestdesigns.“Itis making microbe,usingK*tosearchfaster mutations toenzymesfromanantibiotic- compounds. Buthisgroupinsteadpredicted begins by directlymodifyingexisting National InstitutesofHealth. The workwasfundedby agrantfromthe said Donald,wholeadstheresearcheffort. laboratory, andhavethemworkasplanned,” enzymes onacomputer, maketheminthe drugs tofoildrug-resistanceingerms. way towardmoreautomatedredesignofold Donald. Thenewtechniquemightpavethe called gramicidinS,saysProfessorBruce enzyme thatproducesanaturalantibiotic possible shapesandchangesofakey K Star)—isabletosortthroughallthe known asthealgorithm“K*”(pronounced Other algorithms have been Other proteindesignalgorithmshavebeen The searchfornewantibioticsusually “It reallyexcitesusthatwecanredesign The program—asetofcomputerrules oftware D ramatically dozen subsequentstepsdownstream.” beginning workonredesigningthehalf achievement,” saysDonald.“Wearenow “Redesigning thatfirststepisabig line neededtomaketheantibiotic. first stepinthebiochemicalassembly version ofthealgorithmtoredesign and oneofK*’s designers,usedthelatest Ivelin Georgiev, arecentCSPhDgraduate of SciencesreportpublishedlastFebruary, on February17,2009. Adapted from a Duke News article published such aspenicillinandvancomycin. workhorse enzymesingramicidin’s family, revamping themachinerythatmakesother to redesignanyenzyme.” Thatmight include Donald. “Itshould,inprinciple,bepossible we knowalotaboutits3-Dshape,” says studying howsuchenzymeswork,because diseases, it’s agreatmodelsystem for useful antibioticagainstemerging infectious of eachproteinwaseventrickier.” trivial todothat,andtestingthefunctions proteins,” saysDonald.“Itwasnotatall synthesize some“quitebigandtricky biochemical wetlab,usingbacteriato algorithm’s predicteddesignsinDonald’s Donald’s graduatestudents,confirmedthe biochemist Cheng-Yu Chen,anotherof all thecalculationswerecompleted, housed inDonald’s lab,hesays.After in the230-processorcomputercluster just oneredesignmighttakeuptoaweek out scenariosthatcannotwork.Calculating flexible moleculararchitecturestoweed all possiblechemicalinteractionsand elimination” featurethatcanrunthough antibiotic inBacillusbrevisbacteria. enzyme system, whichproducesthenatural accuracy usingtheGramicidinSSynthetase to biochemicallytestthealgorithm’s Anderson oftheUniversityConnecticut fostered alongcollaborationwithAmy says Donald.Intheprocess,hisgrouphas develop reliableenzymedesignalgorithms, researchers toevaluateanduse. is availableasopensourcecodeforother you wantittodo.” TheK*algorithmsoftware The algorithm includes a “dead-end The algorithmincludesa“dead-end “While gramicidin S is probably not a really “While gramicidinSisprobablynotareally In aProceedingsoftheNationalAcademy It hasbeennearlyaten-year effortto Building the right system

Around the world, Akamai Technologies Another ongoing project in Maggs’ research operates 50,000 servers in over 1,500 repertoire is a study of improving locations, handling twenty percent of bottlenecks at central database servers today’s Web traffic. So it’s no wonder that for websites that use dynamic content— threads 5 as Vice President of Research and images and text generated in real-time Development at Akamai, Bruce Maggs and customized for users. As more and became interested in studying large more websites add dynamic content, from distributed systems and massive data sets. welcome screens to advertisements, it is “The key to innovation in Internet becoming harder to scale the technology. infrastructure is the proper engineering “We need a database scalability service,” of large distributed systems. Working at says Maggs. He and colleagues at Carnegie Akamai, I started to think this would be an Mellon and Google are working to do just interesting area in which to do research,” that by building layers of caches that store says Maggs. As a new faculty member in dynamic content locally, instead of at the Department (see his profile on page distant, backlogged databases. “But it’s two), Maggs arrives on campus with several tricky,” Maggs warns, as researchers must research projects that address large figure out how to maintain local cache distributed systems within various areas consistency as the database is updated. of concern, from business energy costs Last summer, at the 34th International to database bottlenecks to denial of Conference on Very Large Databases (VLDB), capability attacks. the group introduced Ferdinand, a first- In much of his research, Maggs uses an of-its-kind cooperative proxy architecture innovative strategy to analyze data: He for dynamic content delivery that uses collects massive data sets on networking distributed database query result caching behavior from Akamai’s content delivery and scalable consistency maintenance. network (CDN) and combines them with Maggs also has a strong interest in other data sets to gain new perspective in database security and has another project a particular area. For example, in a paper in the works that follows on the heels of presented this summer at the ACM SIGCOMM previous research from Professor Xiaowei 2009 conference, Maggs and colleagues at Yang on network capabilities, a solution Akamai and MIT analyzed the energy costs to denial of service attacks, during which of existing distributed systems. Massive a malicious host can flood a server with Internet-scale and cloud computing unwanted traffic. Capabilities are like systems today utilize hundreds of thousands golden tickets to a website, establishing of servers, which can require megawatts of priority connections for “good” traffic. electricity, enough to power thousands of But attackers have learned to prevent any homes. The cost of such energy can range capabilities from being sent in “denial of Bruce Maggs from $3.7 million per year (eBay) to $38 capability” attacks. As a new way to prevent million per year (Google), the researchers such attacks, Maggs has developed a partial estimate. By comparing historical electricity solution. “It would require all users to prices with network traffic data from provide evidence that they are legitimate the Akamai CDN, the team found that by performing some kind of computational companies might save millions in electricity work, like solving a puzzle,” says Maggs. costs each year by routing client requests Even if attackers can figure out how to solve to locations where energy is cheapest, as some type of short computation, they will energy prices regularly fluctuate from have to invest some of their resources into area to area and hour to hour. The process doing so, effectively slowing the attack. could be done using routing systems that Together with Yang and Professor Landon most large distributed systems already Cox, Maggs plans to continue to explore have in place. network security issues. www.cs.duke.edu

Rollicking Robots outreach On four wheels, a robot haltingly programming, measurement, and other navigates a corner, guided only by light engineering principles. “My kids were great,” sensors attached to its base tracking a says Stephanie Tepperberg, a mentor for 6 threads black strip of tape on the ground. The ‘Team Awesome’ from the Durham School of device’s designers, students in bright the Arts. “You can already tell some of them blue RoboCup Junior T-shirts, cheer for want to be engineers.” their creation. Supported by a grant from the Burroughs It was an enthused crowed at this year’s Wellcome Fund Student Science Enrichment annual RoboCup Junior (RCJ) Regional Program, each team receives a LEGO Competition, hosted by Duke on a sunny MINDSTORMS NXT kit from which to assemble Saturday in April. Students from middle a robot. Over the course of ten weeks, and high schools in Durham, Raleigh, South students must pick a category, begin Carolina, and Pennsylvania flocked to the construction and programming, and learn to Levine Science Research Center to compete work as a team. “They are given materials in three robotics competitions: search and and a timeline,” says Forbes. “Then they rescue, dance, and soccer. must ask, how do you make a plan to build But the experience was more than a what you want to build, and how do you single-day competition for many of them. Of have each team member contribute?” The the eleven participating teams, most were program encourages students to learn Students participate in the 2009 RoboCup Junior involved in the RCJ after-school program, mechanical engineering, programming, and Competition at Duke organized by Professor Jeffrey Forbes. time management, says Forbes, and exposes Once a week, local Durham students met them to careers in science through lectures with undergraduate Duke mentors to learn from faculty and graduate students.

Alice is Back With great anticipation, Adventures in Rodger. At the same time, Wanda Dann of Alice Programming returned to Duke! Carnegie Mellon University and Steve Cooper Making a difference, After a successful three-week workshop of Saint Joseph’s University, Rodger’s co- one laptop at a time last year led by Professor Susan Rodger, recipients of an NSF grant for Alice, ran One Laptop Per Child is a worldwide middle and high school teachers again filled workshops on Alice 3.0, the new version of effort to provide rugged, low-cost, the Department this summer to learn how the program. connected laptops to children in to teach Alice, an educational software Following the initial workshops, a day-long developing countries. But in 2007, a group that encourages students to program Alice Symposium welcomed educators from of Duke CS undergraduates realized the by building virtual worlds populated by around the country to present papers on project could also benefit the Durham animated 3D objects. Alice. Duke’s own Rachael Brady, director of community, a county where the majority Funded by the National Science the Visualization Technology Group, gave the of school-age children come from low- Foundation and IBM, the summer began keynote address. income homes, and few use computers at with a follow-up workshop for previously The summer concluded with three one- school or home. participating teachers. “Last summer they week workshops to introduce new teachers “We wanted to bridge the technological developed lesson plans to use during the to the software. “I had over 400 teachers divide in Durham,” says Alex Keybl, co- school year, and now they’ve come back to apply for the 120 spots,” says Rodger. “There founder of the Duke University Chapter talk about what they’ve been doing,” says is a lot of interest in Alice.” of OLPC. With fifty laptops donated by Professor Dan Ariely of the Fuqua School of Business and the help of their advisor Professor Jeff Forbes, Keybl and classmates John Pena and Justin Mullen initiated a pilot OLPC program in a fourth grade classroom at the Carter Community School in Durham. Over fifteen Duke undergraduates participated in the program, visiting Carter two to three times a week to teach lessons on the laptops. “Hopefully this will prove OLPC is a viable option for a community in the United States,” says Keybl. The three founders graduated this past Susan Rodger and Alice workshop participants spring, but the program will continue with other Duke undergrads at the helm, expanding into a second classroom at Carter this fall. Alumni Profile: Susan Athey students Susan Athey remembers her first foray to receive the award. After Duke, Athey coding, writing efficient programs, and into economics. In 1988, then a young CS attended the Stanford Graduate School conceptualizing which problems will be undergrad at Duke, Athey landed a job of Business and graduated with a PhD in easy or difficult to solve are important administering a Unix workstation for an economics and an entourage of two dozen skills for me.” Last year, Athey took leave 7 economics professor. universities eager to hire her. Athey chose from Harvard to work full-time as chief Though she was hired MIT, where she made tenure in only six years. economist at Microsoft, designing online for her computing She returned to Stanford in 2001 and finally advertising auctions for the company. skills, it wasn’t settled at Harvard in 2006. “I was working very closely with a lot of long before Athey’s Athey has been called an “applied computer scientists and engineers. Being talent in another theorist” for her work in both extremes of fluent in technical discussions as well as field began to shine. the economics spectrum: applied economics economics discussions made me a lot more Susan Athey “I had always been and basic research. She has investigated a effective,” she says. interested in programming,” recalls Athey, wide variety of topics, including diversity Athey’s list of accomplishments is long, now a Professor of Economics at Harvard and mentoring at organizations, U.S. timber including an honorary doctorate from Duke, University, “but the business aspects of auctions, and secret industry agreements. but she still remembers the early days of her computing were very compelling.” Athey’s But her research is united by a single goal—to career. “Duke professors really reached out first research project was a study of how create tools that enable economists to make to me and were excited when I was interested computers are bought and sold at auctions, and test predictions about how organizations in research,” she says, recalling Professors and in 1991 she graduated magna cum will act in the marketplace. Currently, Athey Owen Astrachan, Donald Rose, and Carla laude with a triple major in economics, is studying auctions and online advertising, Ellis. “I felt like they saw something in me mathematics, and computer science. working to develop auctions that will that I didn’t necessarily see in myself, and Today, only thirty-eight years old, Athey promote the best quality matches between they took the initiative to encourage my is a world-renowned economist and winner advertisers and consumers online. studies.” Such encouragement certainly of the 2007 John Bates Clark Medal, a Computing remains an important part paid off, as there is no end in sight for this prestigious economics award second only of Athey’s work. “I still write my own talented computer-savvy economist. to the Nobel Prize. She is the first female programs,” she says. “Having expertise in

Undergraduate Student Profile: Sophia Cui

Sophia Cui had a plan: study economics, Cui continued to work with Brady into her become an investment banker, make sophomore year and was accepted into the millions. But during her first semester at C-SURF program. As part of the program, Duke, sitting miserably in an introductory Cui began a research project with Brady and economics class, Cui had a revelation. “If mentor Eric Monson last summer developing you’re going to spend a tool for organization and visualization of four years studying massive data sets. Ambitious, Cui crammed something, you might a full nine weeks of research into six weeks as well enjoy it,” she so she could spend the rest of the summer thought. Drawn to doing research and development at a the problem-solving start-up in Silicon Valley. “I tend to do a challenges of CS—“You lot of things,” laughs Cui, bright-eyed and Sophia Cui have to get the cogs enthusiastic despite her busy lifestyle. turning,” she says with a smile—Cui switched A Canadian-American with a talent for her major to computer science. graphic design, Cui is Duke’s resident T-shirt Right after freshman year, Cui began her designer, winner of three campus design first CS project with Rachael Brady, director competitions, including the Last Day of of Duke’s Visualization Technology Group. Classes shirt. She is also the design talent At the soundSpace exhibit at the North behind the wall of screens in the Link!, a Carolina Museum of Life and Science, an studying and teaching facility in the lower interactive room that translates movement level of the Perkins library. Looking into the into sound, Cui undertook the challenge of future, Cui hopes she can keep combining additionally translating the movement into her many interests and talents in graduate images of birds fluttering across a screen. school. “I want to continue to be creative “From there, I started to develop an interest and still do programming,” she says. in visualization and design,” says Cui.

Graphic art by Sophia Cui www.cs.duke.edu

Graduate Student Profile: Lirong Xia Lirong Xia made a decision: he would system, lying about their real preferences study mathematics in college, for which he in the hopes of strategically altering the had a natural affinity. But his father had result. Xia studies how to prevent such other ideas. Mr. Xia brought a computer manipulation by students scientist home to meet his son, and both adding computational urged the young man to try computing complexity to voting

threads instead. “At the time, I didn’t know which rules, so even if 8 was better, but I decided to follow their it is possible to advice,” says Xia, now a CS PhD candidate at manipulate a system, Duke. He remains pleased with his decision, it will be impossibly “but I still prefer theoretical problems to Lirong Xia difficult (NP hard) to programming,” he laughs. do so. For most CS researchers, unsolvable Xia completed his undergraduate degree problems are bad news. For Xia, they are the Undergraduate Awards in CS at Tsinghua University, the MIT of ideal solution. Friends and colleagues of the late Alex China, and stayed on for graduate work In a second line of research, Xia studies Vasilos donated the Alex Vasilos Memorial until 2007. But he first set his sights on voting in multi-issue situations, in which Award to the Department of Computer Duke in 2006. One day while browsing parties make a variety of decisions, each Science to recognize deserving students. through conference papers, Xia came conditional on the one before it. For This year’s recipients are: across a study on voting theory by the example, if a group of people are going out Alexander Keybl Department’s own Vincent Conitzer. Voting for dinner, a person’s vote for a restaurant John Pena theory, the design and analysis of rules may change depending on the day and Tiffany Yam applied to group decisions, appealed to time the group chooses to eat. With many Xia’s interests in both CS and math. “I choices, multi-issue voting rapidly becomes Graduation with High Distinction realized I could apply a lot of mathematics computationally complex. Xia is working to to voting problems,” he recalls. find solutions that speed up the process, Alexander Keybl Xia received a James B. Duke fellowship to hoping that an efficient system for multi- Perry Nelson attend Duke, a competitive campus-wide issue voting will make the procedure more John Pena merit scholarship, and joined Conitzer’s useful in real life situations. Advisor for all three: Jeffrey Forbes lab in the fall of 2007. Once on campus, This year, Xia co-authored an unpre- One Laptop Per Child (OLPC) Computer Xia decided to study computational social cedented five papers at the prestigious Science Course choice, the computational aspects of voting 21st International Joint Conference on when overwhelming amounts of information Artificial Intelligence (IJCAI-09). “He’s had are involved. “He’s very independent, driven, an extremely successful year,” says Conitzer. and motivated,” says Conitzer. “We’re very Xia, who is also pursuing a Master’s degree lucky to have him here.” in economics, attributes that success to Xia’s research spans two major topics: Department support, especially from his manipulation of voting systems and multi- advisor. “Vince gives me a lot of freedom to issue domains. During any type of voting, develop my research,” says Xia. “I owe him participants may try and manipulate the thanks for his help and support.”

It’s Raining Recruits! Rain showers ushered in the arrival of recruitment committee. this year’s troop of prospective graduate In the afternoon, guests enjoyed a students, but the clouds soon scattered campus tour led by Professor Alexander for what would be a sunny and successful Hartemink, followed by a reception with recruitment weekend. Prospectives from faculty, students, and staff in the Hall as far as Romania and China braved the of Science. Saturday was the annual showers on Thursday night to join current Department picnic: Past and present graduate students for pizza, pool, and drinks faculty, families, and students met at the in downtown Durham. As the sun came out Duke Faculty Club for heaps of barbeque, on Friday, the prospective students visited a fierce basketball game, and a chance labs around campus to hear presentations to chat with the visiting students. The day from the Department’s research groups concluded with a women’s dinner hosted and to meet one-on-one with potential by graduate student Brittany Fasy and future advisors. “The weekend is designed Professor Xiaobai Sun, and a party at the to encourage prospectives to meet faculty home of graduate student Gavin Taylor. and see if their research interests align with Overall, the weekend went swimmingly, says current projects in the Department,” says Hartemink. “The prospectives were great. Justin Manweiler, a second year PhD student They were engaged, interested, and excited and co-chair of this year’s graduate student about the program.”

Left: Scenes from the 2009 graduate recruitment weekend Recent GRADUA William Horning Nicholas Ho John Hartzog Darrell Gaspar Daniel Garrison Peter Franklin Julia Foran Bryan Fleming Gregory Filpus Ashley DeMass Edward CronauerIV Andrew Cook Matthew Colabrese Ruijun Chen Zachary Cancio Aneesh Butani Grant Bond Majors Undergradua System SupportforStrongAccountability Advisor: JeffreyChase Aydan Yumerefendi Computing Molecular Scale Integrated Sensing and Structures, Circuits and Architectures for Co-advisors: AlvinLebeckandChrisDwyer Constantin Pistol Problems Distributions for Geometric Statistical Small andStableDescriptorsof Advisor: Pankaj K.Agarwal Jeff Phillips Self-Assembly Molecular ComputingwithDNA Co-advisors: JohnReifandThomLaBean Urmi Majumder Verification-Aware ProcessorDesign Advisor: DanielSorin Anita Lungu from IndirectInteractions Motifs and Distinguishing Direct Protein-DNA Binding:Discovering Advisor: AlexanderHartemink Raluca Gordan Inhibitor Design Enzyme Redesign and Small-Molecule Protein Design with Applications to Novel Algorithms for Computational Advisor: BruceDonald Ivelin Georgiev P h D egrees te Degrees

TES

Justin Mullen Ryan Minogue Jonathan Mathew Ralitsa Markova William Linton Sejin Lim Zoravar Lamba Roy Kwon Nicholas Kurtzman Alexander Keybl T Boyoun Jung Jonathan Jou Micah Jasper Benjamin Isaacson Alexander Hunter Alex Hu Andrew Hsiao

homas K enney (SFLD) Semi-Supervised Fisher Linear Discriminant Advisor: CarloTomasi Seda VuralRemus Reconfigurable Robots Developing ScalableAbilitiesforSelf- Advisor: JohnReif Sam Slee of Tumor andTissue Microvasculature-Adaptive Discretization Advisor: XiaobaiSun Stephen Odaibo Resonance Data Symmetric Proteins from Nuclear Magnetic Algorithms forStructureDeterminationof Advisor: BruceDonald Jeffrey Martin and (Sometimes)Error zTuned: Automated SQL Tuning through Trial Advisor: ShivnathBabu Herodotos Herodotou Using MonteCarloMethods Uncertainty Propogation in Analytic Models Advisor: KishorTrivedi Amita Devaraj Content Swarms The ProblemofHonestShirkingin Advisor: JeffreyChase Kareem Dana mS Degrees David Zhang Ray Zeller Tiffany Yam Wu Congyi Kenneth White Neelamohan Vadoothker Michael T Andrew T Abhishek Thapa Harish Srinivasan Oliver Sherouse Benjamin Shelton George Rossin John Pena T Nicholas Patrick Jonathan Odom Andrew Nelson ristan Patterson remblay unick

Aydan Yumerefendi Anita Lungu Ivelin Georgiev Jeff Phillips Nidhi T Crystal Senko Yang Qin Deborah Nelson Jaymeson Morris Carolyn Meyer Max Masnick Yifan Li Joel Burrill Evan Beard Laura Angle Minors ripathi Urmi Majumder Raluca Gordan Constantin Pistol 9 9 threads students www.cs.duke.edu

welcome new Computer Science students

PhD Ryan Tate

students Andrew Brown US Military Academy—West Point NC State University Networks, Databases Systems

threads Xuting Zhao 10 Qiang Cao Peking University Wuhan University Artificial Intelligence Networks, Security Paper Named Top Pick undergraduate MAJORS Sudhanshu Garg Michael Ansel a network of sensors atop city light I.I.I.T.—Hyderabad Nikhil Arun poles and buildings may someday monitor Theory, Computational Geometry traffic patterns, pollution, and the weather. Maggie Bashford But first, researchers must find ways to Jun Hu Cameron Behar effectively and reliably place sensors in Wuhan University Michael Bell complicated urban environments. Numerical Analysis, Machine Learning Christopher Carlon Haoyu Chen A new publication by PhD candidate Yin Lin Van Dang Shashidhara Ganjugunte, along with Pankaj Shanghai Jiaotong University Se-Gil Feldsott Agarwal and Esther Ezra, presenting an AI, Vision, Robotics efficient and simple algorithm for sensor Jeffrey Forte placement was recently named Best Paper Jeffrey Martin Nicholas Hawthorne on the Algorithms and Analysis track Duke University David Herzka at the fifth annual IEEE International Computational Biology Matthew Jacobson Micah Jasper Conference on Distributed Computing in Matthew Matlock Ga-Young Joung Sensor Systems (DCOSS ‘09). University of Tulsa Kostadin Kostadinov “We modeled the urban environment as a Artificial Intelligence polygon with obstacles,” says Ganjugunte, Lindsay Kubasik “and tried to develop an algorithm to decide Jason Pazis Chengyu Li where the sensors should be placed to cover Technical University of Crete Elizabeth Liang as much area as possible.” Their solution Machine Learning, Robotics Peter Linnartz Patrick Lu demonstrates that, by sampling, one can Ion Valentin Pistol Joshua Lund identify certain ‘’landmark’’ locations, University of Craiova Lakshya Madhok and if sensors are placed to cover these Architecture, Distributed Systems landmarks, then they cover almost the entire Muntasir Natour area. The number of landmarks required is Bi Wu Vitor Olivier surprisingly small, the team found, so only a Duke University Matthew Prorok small number of sensors are needed. Distributed Systems Trevor Reid Daniel Shapiro Ganjugunte presented the paper, Efficient Xin Wu Daniel Sharkey Sensor Placement for Surveillance Problems, Tsinghua University Maxim Sirenko at the June DCOSS conference in Marina Del Systems, Networks Rey, California. Jonathan Su Jie Xu Yin Quan Teo Brandeis University Antony Thomas Computational Biology Tian Tian student wins Dylan Wengert DukeMobile competition Xuanran Zong National University of Singapore undergraduate MINORS Distributed Systems JP Cafaro, a senior with a dual ECE/CS Barbara Bao major, was recently selected as winner of Shwetadwip Chowdhury MS the DukeMobile competition, a contest Justin Goldsmith Liang Dong hosted by the Office of Information Nils Hultgren Beijing University Technology and the Office of Public Tanner Schmidt Systems Affairs and Government Relations. Teoman Yavuzkurt Students were challenged to come up Gang Luo Chi Zhang with innovative and Duke-centric Hauzhong University of Science applications to add to the DukeMobile Machine Learning, AI suite of apps for iPhone and iPod Touch devices (www.medu.com/duke/). Cafaro will develop his winning idea—a narrated, illustrated campus tour—with another Duke student, Matthew Isabel, and Christoph Guttentag, Dean of Undergraduate Admissions. student publications/presentations

Nedyalko Borisov Mingyu Guo Anita Lungu Why Did My Query Slow Down?, Biennial Combinatorial Prediction Markets for Event Multicore Power Management Ensuring Conference on Innovative Data Systems Hierarchies, 8th International Conference Robustness via Early-Stage Formal Research (CIDR 2009) on Autonomous Agents and Multiagent Verification, 41st Annual IEEE/ Systems (AAMAS 2009) ACM International Symposium on

DiaDS: Addressing the “my-problem-or- students Microarchitecture 2008 (MICRO-41) yours?” Syndrome with Integrated SAN and Welfare Dominated Groves Mechanisms, Database Diagnosis, 7th USENIX Conference 5th Workshop on Internet and Network

Constantin Pistol threads on File and Storage Technologies Economics (WINE 2009) Architectural Implications of Nanoscale 11 (FAST 2009) Integrated Sensing and Computing, 14th Xin Guo DiaDS: A Problem Diagnosis Tool for International Conference on Architectural Domain-oriented Edge-based Alignment Databases and Storage Area Networks, Support for Programming Languages and of Protein Interaction Networks, 17th 35th International Conference on Very Large Operating Systems (ASPLOS ’09) International Conference on Intelligent Databases (VLDB 2009) Systems for Molecular Biology (ISMB Nanoscale Integrated Sensing and 2009) & 8th European Conference on Processing: Architectures for a New Azbayar Demberel Computational Biology (ECCB 2009) Computational Domain, 6th Conference on Reflective Control for an Elastic Cloud Foundations of Nanoscience (FNANO 2009) Application: An Automated Experiment Herodotos Herodotou Workbench, HotCloud ’09 Workshop with the Automated SQL Tuning through Trials and Sharath Raghvendra 2009 USENIX Annual Technical Conference (Sometimes) Error, 2nd International Approximate Euclidean Shortest-path Workshop on Testing Database Systems Amid Convex Obstacles, ACM/SIAM Songyun Duan (DBTest 2009) Symposium on Discrete Algorithms Fa: A System for Automating Failure (SODA 2009) Diagnosis, 25th International Conference Josh Letchford on Data Engineering (ICDE 2009) An Ethical Game-Theoretic Solution Risi Thonangi Concept for Two-Player Perfect-Information Weighted Proximity Best-joins for Shashidhara Ganjugunte Games, 4th Workshop on Internet and Information Retrieval, 25th International Efficient Sensor Placement for Surveillance Network Economics (WINE 2008) Conference on Data Engineering Problems, 5th IEEE International (ICDE 2009) Conference on Distributed Computing in Harold Lim Sensor Systems (DCOSS 2009) Automated Control in Cloud Computing: Yi Zhang Challenges and Opportunities, 1st RIOT: I/O-Efficient Numerical Computing Peter Gilbert Workshop on Automated Control for without SQL, 4th Biennial Conference on Experimenting in Mobile Social Contexts Datacenters and Clouds (ACDC09) Innovative Data Systems Research Using JellyNets, 10th International (CIDR 2009) Workshop on Mobile Computing Systems and Applications (HotMobile 2009)

Keep in Touch! Congratulations to the following alumni who have recently received awards or taken new jobs.

Julia Foran (BS, ‘09) Christopher LaPilla (MS, ‘08) Jeff Phillips (PhD, ‘09) Andrew Waterman (BS, ‘08) Comscore Modality Inc. Postdoctoral Researcher Graduate School Seattle, WA Durham, NC University of Utah University of California Salt Lake City, UT Berkeley, CA Dan Garrison (BS, ‘09) Chaz Lever (BS, ‘06) Cisco Systems Masters Program Jaidev Patwardhan (PhD, ‘06) Congyi Wu (BS, ‘09) San Jose, CA Wake Forest University Apple Computer Microsoft Winston-Salem, NC Sunnyvale, CA Research Triangle Park, NC Raluca Gordan (PhD, ‘09) Postdoctoral Researcher Anita Lungu (PhD, ‘09) Constantin Pistol (PhD, ‘09) Tiffany Yam (BS, ‘09) Brigham & Women’s Hospital PhD Program Apple Computer Citigroup Boston, MA Sunnyvale, CA New York City, NY Seattle, WA Matt Johnson (BS, ‘08) Alex Schearer (BS, ‘08) Aydan Yumerefendi (PhD, ‘09) Graduate Program Urmi Majumder (PhD, ‘09) Microsoft Blue Stripe Software University of Illinois Oracle Corporation Seattle, WA Morrisville, NC at Urbana-Champaign Redwood Shores, CA Urbana, IL David Zhang (BS, ‘09) Microsoft If you received a degree from the Department of Computer Science, please fill out our Redmond, WA online alumni registration form (www.cs.duke.edu/people/alumni). Non-Profit Org US Postage paid Durham, NC Permit 60 Department of Computer Science Duke University Box 90129 Address Service Requested Durham, NC 27708-0129 threads threads 2009 fall

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graduation 2009

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