Middle-Schoolers Are Ready, Ready, Ready for Programming Adventure

A RESEARCH AND ALUMNI NEWS MAGAZINE DEPARTMENT OF COMPUTER SCIENCE BROWN UNIVERSITY

Also inside: ■ CS Women Take Exception To Being Typecast ■ Tunnels, Bunkers and Nukes: My Underground Vacation Spring | Summer 2011

Van Hentenryck on their new books: Tom’s Notes from the Chair: Operating Systems in Depth: Design and Pro- the Latest News from gramming and Pascal’s Hybrid Optimization: The Ten Years of CPAIOR. My book Introduc- 115 Waterman tion to Computer Security (coauthored with Mi- chael Goodrich) was also recently published. We are thrilled to Greetings to all CS alums, supporters and add these three vol- friends. umes to the department’s library The spring semester is flying by and the CIT is of faculty-penned bustling with activity. Wonderful things continue books. More on to happen in the department and I am thrilled Pascal and Tom’s to be able to share the highlights with you. books can be found As part of a review of all departments and cen- on page 14. ters being conducted by the university, our de- It is with mixed partment underwent a review late last semester. feelings that I announce the departures of Mi- We are encouraged that strengths were found in chael Black and Meinolf Sellmann. Both have all major dimensions of research, teaching, ad- moved on to exciting opportunities: Michael ministration, and outreach. Based on feedback is a Director of a newly established Max Planck from the reviewers and from the university’s Ac- Institute in Tübingen, Germany and Meinolf ademic Priorities Committee, we plan to broad- is the Group Leader of AI for Optimization at en the horizon of our strategic planning efforts IBM Research in Yorktown Heights, New York. and to experiment with new models of depart- We will miss them as colleagues and we wish mental governance. them continued success in their new endeavors. I am excited to report that our enrollments We’d also like to congratulate Lawrence Lar- continue to climb. Overall enrollment is up son on his appointment as the School of Engi- 12% from the previous academic year and up neering’s founding Dean, effective July 1, 2011. a whopping 38% from the 2007-08 academic Dr. Larson is currently the Chair of the Depart- year. We are thrilled that so many students have ment of Electrical and Computer Engineering taken an interest in our program and hope to at the University of California, San Diego and is continue to see that number climb over time. the first holder of the Communications Industry Congratulations are in order for Philip Klein, Chair. He is an expert in microelectronics tech- who has been named a Fellow of the Associa- nology and wireless communications. The de- tion for Computing Machinery for his work on partment looks forward to a strong partnership graph and network algorithms. We are delight- with the School of Engineering. ed to see his research leadership recognized by Finally, please share your professional and per- this prestigious honor. sonal stories for inclusion in upcoming issues of Several new courses are being offered this se- Conduit. Your support of and participation in mester, including Computational Topology with departmental activities are always appreciated John “Spike” Hughes, Creating Modern Web and we are grateful to have such a close commu- Applications with Steve Reiss, and Cybersecuri- nity—thank you! ty and International Relations with John Savage. Also, Pascal Van Hentenryck’s course on Solving Roberto Tamassia Hard Problems in Combinatorial Optimization Plastech Professor of Computer Science has been redesigned. You can read more about Chair, Department of Computer Science Pascal’s and Spike’s courses on page 20. Look for more information on John’s course in the next issue of Conduit. Congratulations to Tom Doeppner and Pascal Volume 20, Number 1 Spring | Summer 2011

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Publisher Industrial Partners Program, fe atures Department of Computer Science CS Women Take Exception...... Page 4 Bootstrap...... page 6 Editor-in-Chief Amy Tarbox Travelogue...... page 8

Gr aphic De sign Facult y Brown Graphic Services The Faculty Speak Out...... page 12 Faculty Notes...... page 13 Fe at ured columnis t s Books...... page 14 Nell Elliott and Alexandra Schultz Richard Lewis Jennie Duggan DEPARTMENT ne ws AND HAPPENINGS Tom Doeppner Çagatay Demiralp Department Awards and Honors...... page 15 Carleton Coffrin 10th Annual Kanellakis Memorial Lecture...... page 19 Recent Ph.D.s...... page 19 Condu¡t on the web New Courses...... page 20 John Bazik Kathy Kirman alumni

Prin t ing and Distribution Alumni Update...... page 22 Brett Turner, Information Services Ping!...... BACK COVER Brown Graphic Services

25% Conduit is printed on Burgo’s ChorusArt, an acid free and elemental chlorine free paper containing Cert no. SCS-COC-001154 50% recycled content and 15% post-consumer waste. You are the difference – reduce, reuse, recycle.

3 Condu¡t Spring | Summer 2011 Faculty

CS Women take exception

to being typecast By Nell Elliott and Alexandra Schultz

(We wrote this piece to address misconceptions carried out through the use of computing pow- in the Brown Daily Herald’s February 16 article er. It’s much more than sitting at a computer and programming – it requires an understand- “Algorithms Can’t Solve CS Gender Gap,” by ing of how to store and manipulate information; Sahil Luthra. Note that “we” refers to the co- how to model both real-world and abstract, the- authors, not “every woman in Brown’s CS oretical problems; and techniques to solve these department”—we two don’t claim that all female problems in practice. In discussing an introductory CS class at Harvey Mudd, Luthra claims that computer scientists feel exactly the way we “the focus of the class switched from Java pro- do. However, the number of professors and gramming to computer-based problem solv- students who asked us to write this, as well as ing.” This misguided statement only perpetuates the amount of positive response we received, the misconception that CS is equivalent to programming, and that programming and problem speak to the widespread discontent at the solving are discrete entities. In fact, one writes Herald’s gross misrepresentation of Brown’s CS programs as a problem-solving tool; for example, department, being a female computer scientist, students in CSCI0150, Brown’s largest introduc- and the field of Computer Science in general.) tory CS class, formulate and implement problem solutions as programs in Java. The Herald illustrates a national deficit of wom- Next, we want to clarify what it’s actually like en in computer science by citing the CS enroll- to study Computer Science at Brown; fantas- ments at Brown and other schools. There’s no ar- tic! Being a computer scientist is incredibly chal- guing with the numbers, but speculating about lenging, fun, and rewarding. Despite the wide- the cause of the problem through numbers alone ly propagated stereotype that programmers are is an inherently misguided and error-prone ap- Mountain Dew-guzzling, Dorito-inhaling, anti- proach. Thus, it’s not surprising that the Herald’s social hermits, our department is a close-knit article lacked an eye-opening, fair, or even accu- group of genuinely friendly, passionate people. rate depiction of being a female CS student. Like Between the two of us we have TAed nearly every many writings on this topic, the article discusses incoming student over the past three years, and the underrepresentation of women in the scienc- an overwhelming number of our students have es, and how it can be difficult to be a woman in a remarked upon the department’s sense of com- field largely comprised of men. Yet it says nothing munity. When surrounded by such a welcoming about the positive experiences of female CS stu- atmosphere and immersed in fascinating proj- dents – students like us. ects, why should it matter that fellow females are Before we address the “women in CS” topic, it’s few and far between? important that readers understand what exact- Which brings us to the question: what is it like ly CS is. Put simply, CS is problem solving that is

4 Condu¡t Spring | Summer 2011 Faculty

to be a woman in CS at Brown? Honestly, being women in the department simply does not de- fine our experiences here. In fact, the top five groups within the CS department with which we identify do not include “women in CS.” We two identify more strongly with, for example, other TAs and Microsoft interns: engaged and passionate members of the department. Only things like the Herald’s distorted characterization of the gender imbalance make us feel stigmatized or like outsiders. Rather than heeding a report- er who has no personal experience as a woman in science or as a CS concentrator, but who nev- ertheless labels women as people fighting to be- long in a field where they are underrepresented, we encourage you to consider some facts:

Nell Elliot and Alex Schultz have been known to consume The eight women graduating from the CS de- Doritos and Mountain Dew on Occasion. partment this year have 33 total semesters of TA- ing experience. All eight have been a TA for at There are fewer women than men in Brown’s least one CS class, five have been a Head TA at CS department. Yet, quantity and quality are not least once, and for the last two years one has one and the same. The excellence of female stu- been a “Meta TA,” responsible for facilitating dents’ departmental contributions is in no way the program of ninety TAs. Additionally, three limited by the number of female students—nor work as consultants who fix technical problems is our love for the subject. Articles that broad- that students encounter in the computer lab. cast the unflattering statistics regarding wom- This is not to say that our department lowers its en in CS and fixate on the trials and tribula- standards for women and other minorities – all tions they face, but that do not also mention eight have accepted jobs at major tech compa- their joys and successes, is a damaging and re- nies for next year, and all are esteemed by peers actionary way to dishearten potential comput- and professors alike as noteworthy department er scientists. The two of us love what we do and members. This substantiates our claim that be- want others to join us, not for the sake of boost- ing a woman isn’t a handicap: our fellow fe- ing the numbers, but so that they can experi- male CS students all excel and stand out as high- ence first-hand a subject that is uniquely excit- achievers in one way or another. ing and rewarding. We sincerely hope that after reading this piece, no student – male or female – feels discouraged from exploring the fascinating field of CS.

5 Condu¡t Spring | Summer 2011 Bootstrap

Middle-schoolers are school children. ready, ready, ready By: Richard Lewis, Brown PAUR

The thing about video games: they’re complicated Kurt Spindler, right, and Shaopeng Zhang work with Diamon Curry, a student at Gilbert Stuart Middle School, during a lesson on programming. Credit: Mike Cohea/Brown University for programming adventure Bootstrap, a nonprofit educational organization, pairs Brown undergraduates with middle-school students in Brown computer classrooms. The kids show up after school to learn how to make animations, video games, and other cool stuff. What they’re actually getting is substantial help with mathematics.

Madavin Vong’s eyes lit up as the blue rocket spewed a puff of cartoonish smoke and lifted off on her computer screen.

“Yeah!” she exclaimed. “We did it!”

The 11-year-old Vong was excited because she had mastered the computer and math skills necessary to make the rocket soar. She was do- Madavin Vong, a student at Gilbert Stuart Middle School, wanted ing the programming on the Brown University to see how video game characters are made — and made to move. campus through a class taught by Brown Credit: Mike Cohea/Brown University undergraduate students for Providence-area

6 Condu¡t Spring | Summer 2011 Faculty

Vong loves video games. Her favorites are ones styled on adventure, fighting, and—perhaps in an odd twist for someone so young—on time management. Now, through a program run by a nonprofit educational outfit called Bootstrap, she was getting a chance to create her own video game.

“Basically, I want to see how they make them,” said Vong, who is in sixth grade at Gilbert Stuart Middle School. “To make [characters] move is a really cool thing.”

The creative possibilities of programming For about 10 weeks, up to a dozen middle-school students from Providence-area schools ride a bus after school to Brown to fulfill their dreams of creating their own superheroes, villains, mon- sters, stellar athletes, or super-organized genius- es. The video game, while real, is the hook to ex- Kidai Kwon, right, works with middle-school students Devante King, left, and Wesley Cabral during pose the children to computer science and to an after-school Bootstrap session. Credit: Mike Cohea/Brown University deepen their mathematics skills, according to Shriram Krishnamurthi, associate professor of needed to create shapes and animation. They computer science at Brown and a pivotal back- seem vaguely aware of, yet little deterred, by the er of the Bootstrap class. Enticing them with a algebra and computer science as they furiously straight-on programming class would be “a hin- complete exercises in their workbooks. drance, rather than a help,” he says.

“The pitch is, Wouldn’t you like to write your Focused on programming, unfazed by algebra own video game?” said Krishnamurthi, who That’s the goal behind Bootstrap, said Emman- made Bootstrap’s video-game software accessible uel Schanzer, a Providence native and the pro- via the Web and has helped with fundraising. gram’s creator. While teaching math and computer science classes in Boston-area schools, For the students who filed into a computer room Schanzer found that his students reacted coo- at the Center for Information Technology for the ly to algebra and computer programming. So first class last month, the answer would appear to Schanzer, who studied computer science in col- be yes. These kids, with backgrounds from Cam- lege and worked for a while at Microsoft, devised bodia, Haiti and El Salvador, were eager to get a curriculum that effectively masked the fact started. Their teacher, Brown sophomore Kurt that his students were tackling heavy math and Spindler, urged caution. “We’re here to make computer programming. That curriculum led to video games,” he assured them, “but the thing Bootstrap, now in its fifth year and running af- about video games, is they’re complicated.” ter-school classes for urban schoolchildren in The students soon learn that’s the case. They Austin, Texas, the Bay Area in California, Boston, get drilled on x and y coordinates and, in a lat- New York, and Providence. “I had my life plan,” er class, are introduced to programming code Schanzer related. “I’d make my millions and

7 Condu¡t Spring | Summer 2011 FacultyTravelogue

We met up with a local man who maps and ex- Tunnels, Bunkers and plores the former mines, Eugene Lata. We spent Nukes: a day hiking through a hundred years of mining as he told us about the local history. It is amaz- My Underground Va- ing how mining technology has progressed from the era of pulling stones out of the ground with cation hand saws and horses. We saw many artifacts of By Jennie Duggan, PhD Student old mining equipment that had been abandoned and even photographed hundred-year old graf- In the first two weeks of September 2010, my fiti from miners depicting early locomotives. We husband Matthew and I took a trip to the camped for one night on furniture constructed Ukraine and Moscow, Russia. We started in Cher- from limestone within the caverns. It is the quiet- nobyl, progressed south until we reached the est place I have ever slept. Black Sea and continued on to the Russian capital. I was determined to experience as much of the culture as possible, so I extensively researched where we were going and planned everything possible by myself. It was a tight sched- ule traversing most of the largest country in Europe and experiencing Moscow in the time allotted, but very rewarding.

We started with a two-day stay in Chernobyl, the site of the 1986 soviet nuclear disaster. Cher- nobyl is neighbored by Pripyat, a city for 50,000 people that was slated to be the example of an “atomic city”. Everything was very modern for Boiling tea at our campsite in the Odessa Catacombs. the time and built around the power plants. Af- The catacombs also played a part for many ter Reactor 4 melted down, everyone was forced WWII battles in the area. On our second day, we to vacate in under 48 hours, leaving a veritable saw where the soldiers had created makeshift time capsule of the mid ‘80s Russia. beds in the mines, meeting places and a well. We Visiting the amusement park at Pripyat It was exciting to get to explore this city at our finished at our friend’s other camp where a sec- in the Chernobyl Exclusion Zone. own pace. My husband and I took rooftop pho- ond catacomber showed us some of their finds tos from abandoned skyscrapers, checked out from within the mines. They have a personal col- period literature in the schools and wandered lection of war artifacts including period Stahl- through an amusement park that was slated to helms (steel helmets), a rifle and grenades from open just 3 days after the disaster. We even got both sides of the conflict. to meet some of the wildlife that has now taken We next took an overnight train to the Republic over the 30 km exclusion zone around the disas- of Crimea. Our destination was the city of Sev- ter. Przewalksi’s horses were extinct in nature for astopol, which includes Balaklava. Balaklava is a years, but as we found, now thrive in the zone. town built around a secret submarine base. Un- We then spent a couple of days in Kiev and then til the late 1990’s, the entire area was off-limits progressed on to Odessa. Here we ventured into to people outside of the workers at the base and the world’s largest man-made tunnel system, the their immediate families. Odessa Catacombs. The catacombs are estimat- The submarine base itself is an engineering ed to be about 2500 km long (the maps no lon- marvel. From the outside it looks like a normal ger exist) and are a product of limestone min- mountain, but inside it is a teeming mini-city. It ing. They form a spider web under the city and was built by carving channels into a mountain. surrounding villages.

8 Condu¡t Spring | Summer 2011 Faculty

Chernobyl Music Hall

Balaklava Bunker Train Station

Odessa Catacomb WWII Artifacts

9 Condu¡t Spring | Summer 2011 Travelogue

The system was designed such that a submarine During our stay in Moscow, we also attended could return to Balaklava and reach its port with- the Yury Nikulin circus. In Moscow the circus- out ever surfacing. The inner channel has a lock es are still primarily run by a small set of fami- designed to bring the submarines into dry dock lies, where performers pass down the expertise for maintenance. The complex also has an in- ternal train network and a nuclear bunker. This complex has been used as the inspiration for a video game and after walking through it, I can appreciate why.

In the final leg of the journey, we flew to Mos- cow. This was the more relaxing part of our trip after spending so much time on the road. We saw Red Square and the Kremlin and spent con-

The submarine channel in the Balaklava Base The border guard statue in the Revolution Square metro station. It is said that if you rub the dog’s nose, you will have good luck on your next exam. siderable time admiring the massive metro system. Moscow has one of the grandest subway stations on the planet. Most of them are also buried to their children. Some of the acts we saw were very deeply (up to 100 meters!). Consequent- multigenerational, including acrobats, trained ly, they also have some of the fastest escalators in wild cats, dancing dogs and a strongman. the world, which required some getting used to. After this whirlwind week and a half, I grew to These deep subway stations are also designed appreciate what the cold war had been like for to double as nuclear shelters in the case of at- the opposing side. Having worked for years for tack. One of the stations is adjacent to a nuclear the US Navy had allowed me to see how business bunker used by the soviet air command during was done here (and how we are still reacting to the cold war that has recently been opened to some of its affects), but it was good to learn that tourists. Naturally, I could not resist. Its 75,000 the other side was just as worried as we were. square feet consisted of winding tunnels that Their methods were different, but at the end of were punctuated by four cylindrical bunkers. It the day we all just wanted the same thing: to live was so secretive that each of the bunkers was au- safely and be regarded with respect. tonomous and barely knew about the existence of the others. The museum was furnished with artifacts from its lifetime that we were allowed to experiment with, including a radiation detector and protective equipment.

10 Condu¡t Spring | Summer 2011 Chernobyl Outdoor Museum Bunker Under Moscow

Tiger cub at the circus

St. Basil’s Cathedral, Red Square Balaklava Military Base Entrance

Travel Fiascos of the Faculty Around two hours before our scheduled departure I left, only a couple hours late. On the plane, they gave us Tom Doeppner: thought it might be prudent to get closer to our gate. It a certificate saying that we were there on the airport’s was at this point that we discovered that none of the opening day… We had made the reservations months ahead of time, monitors were working – there was no indication from They neglected to tell the people at the arriving airport and it was sheer coincidence that we were to be chang- what gate our flight would depart. Not only that, there (LAX) that there might be problems. To a first approxi- ing planes in Hong Kong the day their new airport was were zero airline employees available to ask. So, being mation, no one’s luggage was on its flight (it’s not clear to open (in July 1998). The first sign of any problem was a computer scientist, I embarked on a depth-first search whose luggage was on the flight). They had one agent when we landed. It took a half hour or so for the plane to of the airport, looking for a gate that claimed to have standing by to deal with missing luggage, and pretty get to the gate, then another half hour for the jet bridge our flight. The new Hong Kong airport is not only beauti- much everyone on the flight lined up to talk to him. to be positioned so they could let us out. We had landed ful, it’s large. After close to an hour I found the gate. So The good news was that we didn’t have to deal with our more or less on time, and we had a five-hour layover, so we took our carry-ons over to it and encamped ourselves luggage on the flights back to Providence – it was finally we didn’t feel pressed for time. We found some comfort- there. After a half hour or so, an airline employee arrived delivered several days later. able chairs to sit in (we had already been informed that and made an announcement (by yelling – no PA system) the airport lounges weren’t yet open) and prepared to that our gate had been changed. So all 300 or so peo- I carefully read news reports of the opening when we wait for our next flight. We watched, with some bemuse- ple surged to the new gate. A bit later he came by again got back home. As it turns out, we were among the lucky ment, the hordes of people hurrying back and forth and to announce that it had moved again. It turned out that ones. Some arriving flights had to wait many hours be- listened to the numerous announcements of gate chang- this was something like the fifth time the gate was being fore letting people off the plane. One report said that es. After a while, it became clear that we were watching changed and a rebellion broke out. The poor guy was sur- someone on one of these planes used his cell phone to many of the same people hurrying back and forth. The rounded by irate passengers who were asking such tough call the police to say he’d been kidnapped. If Hong Kong first clear sign that something was wrong was when we questions as “do you know where your airplane is?”. He was your final destination, you didn’t see your bags until, tried to find a restroom and discovered that they weren’t survived by promising that this would be the last gate in some cases, weeks thereafter. working. Any of them. We went to a few restaurants seek- change. It was, primarily because the new gate was in an Avoid version 1.0 of airports… ing food, but not only were they all out of food, they area where you board buses to be taken to a plane that couldn’t handle cleaning up all the trays and dishes that was some distance away. There was a mob scene when Note from the editor: Please send any of your own travel were scattered about. we got on the buses, but we finally got on the plane and fiascos you’d like to share to conduit at cs.brown.edu

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The Faculty Speak Out Q&A with Eli Upfal

How did you first become interested in post-doc Fabio Vandin. Our work focuses on ad- computer science? vance statistical/machine learning techniques to My undergraduate majors were in Mathemat- identify mutations in sets of gens with statistical- ics and Statistics. Both subjects were taught in ly significant correlation to a particular disease. the most abstract, formal form with few exam- The ultimate goal of research in Computation- ples or applications, and obviously no experi- al Biology is to develop theoretically sound tools ments. Programming was a refreshing “practical” that are practically useful for biologists. It was subject, where one could actually see some con- very encouraging to see the interest of lab biol- crete results. That was in the late 70’s, there were ogists in applying our tools to their data and inno personal computers, the university had one corporating it into their publication. mainframe computer and having access to that machine was a great privilege. In my senior year How have you seen your field evolving over I took an inspiring theory of computing course the course of your career? that convinced me to move to that relatively new Technically, theory of algorithm has become and exiting field. Years later I learned that the much more mathematically sophisticated. In the instructor of that course was one of the most early 80’s most results were based on elementa- influential founders of computer science. ry combinatorics and graph theory. Today, algorithm design and analysis employs advance tech- How do you pick your research problems? niques borrowed and adapted from almost any Most of my work has been in theory of algo- sub-field in mathematics, ranging from probabil- rithms, where the goal is to design efficient ity theory to number theory, group theory and algorithms and give rigorous mathematical anal- modern algebra. ysis of their performance. I have been mostly The second important change is the growing interested in randomized algorithms, stochastic relevance of the theory research to industry. analysis of algorithm, and related applications of Prior to the emergence of the web, the Human probability and statistics theory to computing. Genome Project and other large scale data ap- Working in theoretical computer science is not plications, theoretical computer science was just very different than working in pure mathematics. theory. Students who specialized in theory could The quality of the work is mostly judged by the so- only work in academia, teaching theory cours- phistication and beauty of the mathematical argu- es. All that changed in the last 10–15 years. With ment and by its application to other theory work. applications that handled huge magnitudes of data, the asymptotic analysis of theory of algo- In recent years I became more interested in rithms, which studies the performance of algo- practical applications of algorithms, and, in par- rithms on very large data sets, became important ticular applications of probabilistic and statistical commercial questions. Thus, commercial appli- techniques to real life computing problems. In cations for web search or large data analysis use this line of research I have benefited from joint sophisticated mathematical tools designed by work with great colleagues in the department, theoreticians. The most noticeable consequence collaborations with industry research labs and of this change is in the employment of theoret- some consulting engagements with companies ically trained computer scientists. You see them at the frontiers of computing applications. holding leading positions is many successful companies, and you see theory professors in re- Do you have a favorite project that you’ve search collaboration with industry. worked on? I’m always excited about the project I’m cur- If you had enough extra time to study one rently involved in, and easily switch interest additional area, what would it be? to the next one. I’m particularly happy about Music - my Calavinova is waiting for better the outcome of a recent collaboration with my times... colleague Ben Raphael and our outstanding

12 Condu¡t Spring | Summer 2011 Faculty

Faculty Notes

Rodrigo Fonseca and a comprehensive library.) Sorin August proved to be a successful Rodrigo received two grants this se- helped commemorate the centennial month for Sorin’s research projects: The mester - a $15,000 Salomon Faculty by participating in the seminar as an National Science Foundation funded Research award for research in the area invited lecturer, delivering an invited talk his proposal “Haplotype Phasing Algo- of “Energy Efficiency Exploration in Sen- titled “Concepts of Mathematical Rigor rithms and Clark Consistency Graphs,” sory Network Protocols and a $148,000 for Algorithms in De-randomization, Sta- and the NSF IGERT funded “Reverse grant from the Rhode Island Science tistical Physics, and Molecular Biology.” Ecology: Computational Integration and Technology Advisory Council to de- In honor of one of his most beloved of Genomes, Organisms, and Environ- velop techniques to measure the perfor- professors, Sorin created the Calin Ignat ments” (David Rand – PI, Sorin Co-PI). mance of modern web applications. Fellowship – a research bridge between Also in August, Sorin welcomed new staff his alma mater and Brown University. members: executive assistant Angel Mu- Maurice Herlihy Ignat was the founding professor of his rakami and (with the CCMB faculty) Na- Maurice Herlihy is on sabbatical at the alma mater’s Department of Computer thaniel Gill, the new CCMB coordinator. Technion, in Haifa Israel. He just fin- Science. The first recipients of the fel- Sorin Istrail with Professor Ignat ished teaching a class on applications lowship are Ph.D. student Vasile Alaiba David Laidlaw of combinatorial topology to distributed and his advisor, Professor Cristian In August 2010, Sorin, Ryan and Derek David continues to mourn the end of his computing, and is working on a book on Masalagiu. The pair made their first re- traveled to Lisbon for the Fourteenth In- sabbatical year, where he discovered it is the same subject. search visit to Brown last October. After ternational Conference on Research in possible to have an entire thought with- this note was sent for publication, Sorin Computational Biology (RECOMB). The out multiple interruptions. This year has found out that Professor Calin Ignat just two doctoral students are the co-first been a bit like a very long Monday. This passed away. The above picture, the last authors of a RECOMB paper titled “The semester he is teaching CS16 for the picture with Professor Ignat, was taken Clark Phase-able Sample Size Problem: first time, compounding the Monday ef- in 2005 when Sorin, who just arrived at Long-range Phasing and Loss of Hetero- fect somewhat. It’s been really fun work- Brown, visited Romania for the first time zygosity in GWAS.” Derek did a great job ing with and getting to know the TA team 22 years after his emigration to US. presenting the paper. that makes Brown CS classes what they are. It has also been a chance for some With his graduate students Ryan Tar- In September, Ryan traveled to Germany personal growth, learning how to pro- pine and Derek Aguiar and under- where, as the winner of the grand prize of duce 3 hours of class content for 60 stu- graduate student Kyle Schutter, Sorin the 2010 Worldwide APL Programming dents every week. Whew! In the remain- co-authored “Practical Computational Contest, he delivered a lecture at the APL ing 3 minutes each week, he continues Methods for Regulatory Genomics: A Conference. Ryan, the lead Ph.D. student to work with his graduate students on cis-Lexicon and cis-Browser for Gene on the Cyrene project, has been working applications of visualization and interac- Regulatory Networks,” a chapter in the also on the CLOSE (cis Lexicon Ontology tion to scientific areas. Tools for studying newly-released Computational Biology Search Engine) software system. This wrist bones will be the subject of funding of Transcription Factor Binding (Methods system focuses on literature extraction to begin in April. Tools for studying gene- (The family picture was taken at Petra, in Molecular Biology) (Humana Press/ of all published papers that report the expression data continue to advance. Jordan.) Spring Verlag). Kyle, a bioengineering results of cis-regulatory analysis of tran- And tools for studying brain white matter major, is the first undergraduate Sorin scription factors encoding genes based are the focus of several students getting Sorin Istrail has collaborated with on a paper/chap- on the Davidson criteria. close to finishing their dissertations. In This past June, Sorin Istrail traveled to ter, and his contribution was significant: the remaining 10 seconds each week, his native Romania to receive an hon- He led Sorin’s “small army of undergrad- In January, Sorin traveled to Hawaii for David is heading up the team building a orary professorship (professor hono- uate biologists” working on the Cyrene the Pacific Symposium on Biocomputing. replacement for the 1998 virtual reality ris causa) from Alexandru Ioan Cuza project’s cisGRN Lexicon. This lexicon is His lab contributed the paper, “Haplotype room known as The Cave. The new “Cave” University, where Sorin earned his B.S. devoted to the regulatory architecture Phasing by Multi-Assembly of Shared will be brighter, crisper, more contrasty, in computer science in 1975. The uni- of transcription factor encoding genes Haplotypes: Phase-Dependent Interac- faster, and able to leap tall buildings in a versity, which was celebrating its 150th that were validated experimentally using tions Between Rare Variants” coauthored single bound. If nothing else, it will make anniversary, was also celebrating the the most stringent experimental tests, with Derek and Sorin’s long-term col- for some killer demos! In the remaining centennial of its Alexandru Myller Math- known as the Davidson criteria. Working laborator Bjarni Halldorsson. Derek also 5 milliseconds each week, David is co- ematical Seminar. (Myller earned his with Sorin, Kyle also finished a very suc- completed the first Loss of Heterozygos- ordinating everything for the upcoming doctorate at Gottingen University, where cessful honors thesis. This past summer, ity genome-wide map of the Multiple VisWeek 2011 set of conferences, to be he worked with some of the greatest Sorin welcomed computational biology Sclerosis GWAS data set. Working with held in Providence in October. Maybe mathematicians of the time under the undergraduate James Hart to his lab. a matrix of 3 billion entries containing he’ll see you at the Rhode Island Con- supervision of David Hilbert and a Ph.D. James succeeds Kyle as the new leader data from 1,000 MS patients, each with vention Center then! committee of Herman Minkowski and of the Cyrene project’s “small army.” their two parents, Derek’s algorithm uses Felix Klein. He modeled the eponymous backtracking to construct the LOH map. seminar after one at Gottingen, which offered a 24-hour oasis of mathematics

13 Condu¡t Spring | Summer 2011 Faculty

Claire Mathieu The work on this question weaves togeth- John Savage government service and admiration for Claire spent the Winter break at Insti- er the most sophisticated tools currently In the fall, John Savage returned to Federal employees. tut Henri Poincare in Paris, where she at our disposal, revealing previously hid- campus after spending an exciting and In the spring of 2011 he is profiting from taught a mini-course on semi-definite den connections. It’s an exciting time for rewarding year in the U.S. State Depart- his year in DC by offering a new course programming in approximation algo- theoretical computer science! ment as a Jefferson Science Fellow. He entitled “Cybersecurity and International rithms, and attended an exciting work- Barb Meier served in the Cyber Affairs Office in the Relations” to an audience of 24 stu- shop on metric embeddings, algorithms Bureau of Intelligence and Research dents evenly divided between computer I’m back to teaching the second and the hardness of approximation. and on a variety of committees including science and policy concentrators. course in my two-semester animation There have been a series of break- two that coordinate research within the sequence after taking a break from throughs recently, bringing algorithmic Federal government, one for classified Peter Wegner it last spring. My students are busy design and lower bounds ever closer work and another for unclassified work. Peter Wegner, who continues as Editor putting together demo reels for job to each other. The object that seems He also sat on a White House commit- of the Faculty Bulletin, has contributed and internship applications. One of to lie smack at the meeting point, and tee that drafted a national strategy for a personal appreciation of the late Sir their frequent questions is, “Why don’t is currently the object of intense study, trusted identities in cyberspace (NSTIC) Maurice Wilkes, who was his thesis su- more production studios, especially is the unique games conjecture. Given and served as a subject matter expert pervisor at Cambridge, and an article smaller ones, recruit at Brown?” We a collection of linear equations whose on cybersecurity and identity manage- on Stephen Hawking’s recent book on love the attention from Pixar and Sony, variables are integers mod p, and where ment as a member of the US delegation scientific design. He is the current chair our main recruiters, but the students’ each equation is of the form xi-xj=a mod to a meeting of Study Group 17 of the of the ACM committee to select the win- question is a good one. Campus visits p, what fraction of the equations can si- International Telecommunications Union ner of the 2011 Kanellakis prize, to be and recruiting in general are expensive multaneously be satisfied, at best? in Geneva. The work was very interest- awarded this summer. He is working on and hosting internships requires a an autobiography that will include a dis- According to that conjecture, it is NP- ing, broad-ranging and provided many variety of resources, but I would urge cussion of his Holocaust experience as hard to distinguish between instances opportunities to develop a good sense our friends and alumni in industry to a child, as well as his technical research that are 90% feasible or more, and in- of the functioning of the Federal govern- consider giving a student the chance on Curriculum 68, programming lan- stances that are 10% feasible or less. ment. It was a great experience and left to experience your world. Get in touch guages, object-oriented programming The research community seems evenly him with a very favorable impression of if you’d like to discuss this further: bjm and interactive computing. split on whether the conjecture holds. at cs.brown.edu.

Books Operating Systems In Depth: Design and Programming Hybrid Optimization Thomas W. Doeppner van Hentenryck, Pascal; Milano, Michela (Eds.) This book is designed for a one-semester This volume focuses on the integration of arti- operating-systems course for advanced under- ficial intelligence and constraint programming graduates and beginning graduate students. to solve problems in operations research and Prerequisites for the course generally include combinatorial optimization. This volume col- an introductory course on computer architec- lects the contributions of experts from various ture and an advanced programming course. research areas including decision theory, The goal of this book is to bring together and systems engineering, propositional satisfiabil- explain current practice in operating systems. ity, mathematical optimization, and artificial This includes much of what is tradition- intelligence. These invited scholars describe ally covered in operating-system textbooks: and demonstrate some of the most important concurrency, scheduling, linking and loading, topics and results from the last ten years storage management (both real and virtual), of research related to hybrid optimization. file systems, and security. However, the book Hybrid Optimization can serve as a valuable also covers issues that come up every day in resource for graduate students, researchers operating-systems design and implementation but are not often taught in under- and practitioners studying artificial intel- graduate courses. For example, the text includes: ligence or operations research who are interested in investigating or applying constraint • Deferred work, which includes deferred and asynchronous procedure programming techniques. calls in Windows, tasklets in Linux, and interrupt threads in Solaris. • The intricacies of thread switching, on both uniprocessor and multiprocessor systems. • Modern file systems, such as ZFS and WAFL. • Distributed file systems, including CIFS and NFS version 4. The book and its accompanying significant programming projects make students come to grips with current operating systems and their major operating-system components and to attain an intimate understanding of how they work.

14 Condu¡t Spring | Summer 2011 Department News and Happenings

Department Awards and Honors

Sorin Istrail awarded NSF grant to of individuals. The algorithms will employ the develop graph models and algorithms graph theory structure of long common hap- for genome-wide haplotype phasing lotype regions, identical by descent, that are shared by the individuals in the sample. This “Improving data quality is crucial, because if a approach is based on the algorithmic model human genome cannot be independently as- pioneered by Andy Clark (1990) and elaborat- sembled then the sequence data cannot be sort- ed through graph theory via Clark Consisten- ed into the two sets of parental chromosomes, or cy Graphs introduced by Sharan, Halldorsson haplotypes. This process; haplotype phasing will and Istrail (2006) and the long-range phasing become one of the most useful tools in genom- graphs employed by deCODE Genetics (Kong ic medicine. Establishing the complete set of ge- et al., 2008). netic information that we received from each parent is crucial to understanding the links be- One major application for haplotype phasing tween heritability, gene function, regulatory se- is in genome-wide association studies (GWAS), quences and our predisposition to disease.” J. C. whose current samples have data sets with billions of items, i.e., containing thousands of in- Venter, “Multiple personal genomes await,” Na- Sorin Istrail ture, April 2010 dividuals genotyped at a half-million to one million single-nucleotide polymorphisms each. For more than a decade, Sorin has been a re- Unlike the Icelandic population, for example, search leader in the area of haplotype phasing which was successfully phased due to its well-re- and inference. corded pedigree structure, the U.S. population, In 2001, his group at Celera published the first with its very complex and less-known pedigree paper on haplotype assembly. (The phasing al- structure, requires practical phasing algorithms gorithms developed by his Celera group were infor a sample of about one million individuals. strumental in the genome-wide haplotype phas- The first beneficiary of this project’s outcome is ing of the first diploid individual genome in expected to be the International Multiple Scle- 2007.) In 2002, he proposed a research program rosis Genetic Consortium, whose GWAS Analysis on the haplotype phasing problem akin to one Group includes Sorin’s lab. in computer science that resolved the problem of characterizing the class of computable func- Philip Klein, Claire Mathieu and tions. The goal was to develop a unifying statistical-algorithmic theory of the haplotype phasing Ph.D. Alum Glencora Borradaile Receive models proposed in the literature: parsimony NSF Grant to Develop New Algorithms phasing, maximum likelihood phasing, coales- for Solving Optimization Problems on cent phasing, and Bayesian phasing. Planar Networks

Sorin’s latest NSF grant supports his work on The National Science Foundation (NSF) has “Clark Consistency Graphs and Haplotype Phas- awarded a research grant, in the expected ing Algorithms”—a project devoted to unifying amount of $800,000, to Philip Klein, Claire Ma- algorithmic strategies for the long-range haplo- thieu and Ph.D. alum Glencora Borradaile (now type phasing problem, i.e., the computational Assistant Professor in the School of Electrical inference of the mother and father haplotypes Engineering and Computer Science at Oregon for each genotyped member in a sample from State University), to develop new algorithms for a population of individuals. The goal of the solving fundamental optimization problems on project is to develop practical haplotype phas- planar networks. Many optimization problems ing algorithms applicable to a very large sample in networks are considered computationally

15 Condu¡t Spring | Summer 2011 Department News and Happenings

difficult; some are even difficult to solve approx- Optimization: Theory and Systems (with Pascal imately. However, problems often become easi- Van Hentenryck) and Secrets and Promises: A er when the input network is restricted to be pla- Course on Cryptography for Non-Majors.) nar, i.e., when it can be drawn on the plane so Philip received his Ph.D. and S.M. in Computer that no edges cross each other. Such planar in- Science from Massachusetts Institute of Technol- stances of optimization problems arise in several ogy and his A.B., summa cum laude in Applied application areas, including logistics and route Mathematics, from Harvard College. He has planning in road maps, image processing and worked with several startup companies, served as computer vision, and VLSI chip design. a consultant for NEC Research Institute and Xe- The team plans to develop algorithms that rox Palo Alto Research Center and was a visiting achieve faster running times or better approx- scholar/scientist at MIT and Princeton. He was imations by exploiting the planarity of the in- also a post-doctoral fellow at Harvard University. put networks. In addition, in order to address The ACM Fellows Program was established in Philip Klein the use of optimization in the discovery of some 1993 to recognize and honor outstanding ACM ground truth, the investigators will develop al- members for their achievements in comput- gorithms not just for the traditional worst-case er science and information technology and for input model but also for models in which there their significant contributions to the mission is an unusually good planted solution; for a of the ACM. The ACM Fellows serve as distin- model of this kind, the investigators expect to guished colleagues to whom the ACM and its find algorithms that produce even more accu- members look for guidance and leadership as rate answers. the world of information technology evolves. In addition, new algorithms and techniques re- Philip joins the department’s eight other ACM sulting from this research might enable people Fellows: Tom Dean, Maurice Herlihy, Fran- to quickly compute better solutions to problems co Preparata, John Savage, Eli Upfal, Andy van arising in diverse application areas such as com- Dam, Peter Wegner and Stan Zdonik. puter vision. Further research has the potential to be useful, for example, in the design of networks, the planning of routes in road maps, and Ben Raphael Awarded NSF CAREER Grant Claire Mathieu the processing of images. Ben Raphael is the latest faculty recipient of an NSF CAREER award, a highly selective grant that Philip Klein Named ACM Fellow the National Science Foundation awards to junior faculty members who are likely to become The Association for Computing Machinery academic leaders of the future. (ACM) recently elevated Philip Klein to Fellow for his work in graph and network algorithms. The project funded by Ben’s CAREER grant aims to develop algorithms for new and emerg- Philip, who joined the department in 1989, fo- ing high-throughput DNA sequencing technolo- cuses on algorithms, especially for optimization gies. These technologies are lowering the cost of and for graphs. He is the recipient of the 2007 DNA sequencing by orders of magnitude, there- Philip J. Bray Award for Excellence in Teaching by enabling a variety of new biological applica- in the Sciences. He created six courses for the tions. Ben plans to: department: The Matrix in Computer Science, Computer Science: An Integrated Introduction • Develop novel algorithms for assembling com- I and II (with Leslie P. Kaelbling), Design and plete genome sequences from billions of Ben Raphael Analysis of Algorithms, Topics in Advanced Algo- shorter DNA sequences produced by high- rithms, Solving Hard Problems in Combinatorial throughput DNA sequencing machines.

16 Condu¡t Spring | Summer 2011 Department News and Happenings

• Design robust algorithms to characterize dif- In Genomes.” The proposed project will develop ferences between individual genomes within novel computational techniques to study structur- a species using an available reference genome al variation, an important class of differences that of the species. distinguish individual genome sequences. Struc- tural variants include duplications, insertions, de- • Introduce combinatorial algorithms for the letions, inversions, and translocations of large study of genome rearrangements in heteroge- blocks of DNA sequence. These differences have neous mixtures of DNA sequences. Examples been implicated in several human diseases includ- of such mixtures are a community of microbes ing autism and cancer. New genome technolo- from an environmental sample, or a collection gies are enabling large-scale measurement of these of cancer cells within a tumor. This image depicts the deployment of variants, but application of these technologies de- Carleton’s work in Los Alamos National The proposed research will be integrated with mand new methods to interpret the resulting data. Laboratory’s Logi-Sims tool. The image an educational component that includes the de- Ben and his collaborators will develop computa- presents the effects of hurricane landfall on velopment of an undergraduate seminar in per- Florida’s south-east shore. The shaded- tional approaches to facilitate the identification sonal genomics, a summer research experience concentric lines indicate the hurricane’s and characterization of structural variants. These in computational biology for high-school stu- wind speed, the small blue dots indicate approaches will be applied to data from human, dents, and the incorporation of a computational disaster relief shelters and the red bars cancer, mouse, and pathogen genomes in collab- biology module into the Artemis summer com- next to the dots show the amount of relief oration with several biomedical researchers. The supplies that are required at each shelter puting camp for 9th grade girls. proposed research will aid in the discovery of ge- location. The tables on left side of the The Faculty Early Career Development (CA- netic variants associated with various human diseas- window provide summary information REER) Program is a Foundation-wide activi- es, which in turn could lead to better diagnostics relating to necessary preparations and recovery actions for this potential disaster ty that offers the National Science Foundation’s and/or personalized treatments for these diseases. scenario, that were calculated using most prestigious awards in support of junior fac- Carleton’s work. ulty who exemplify the role of teacher-scholars through outstanding research, excellent edu- PhD Student Carleton Coffrin Finalist cation and the integration of education and re- in INFORMS Student Competition search within the context of the mission of their Carleton Coffrin, a Ph.D. student working with organizations. Such activities should build a firm Pascal Van Hentenryck, was chosen as one of foundation for a lifetime of leadership in inte- six finalists in the INFORMS 2010 Doing Good grating education and research. with Good OR Student Paper Competition for Besides his CAREER award, Ben has also re- his work on “Strategic Planning for Disaster Re- ceived a Sloan Research Fellowship and a Career covery with Stochastic Last Mile Distribution”, Award at the Scientific Interface from the Bur- which was presented this year as a paper in the roughs Wellcome Fund. Conference on Integration of Artificial Intelli- gence and Operations Research Techniques in Constraint Programming (CPAIOR) and as a Ben Raphael Awarded NIH Grant poster in the Conference on Heath and Human- to Develop Computational Techniques itarian Logistics. to Study Structural Variation Doing Good with Good OR Student Competi- Ben Raphael and his collaborators at Washing- tion is held each year to identify and honor out- ton University in St. Louis have been award- standing projects in the field of operations re- ed a five-year year grant from the National Insti- search and the management sciences conducted tutes of Health (NIH), in the expected amount by a student or student group that have a signif- of $2.5 million, for their project “Computation- icant societal impact. The competition is based al Approaches For Structural Variation Studies both on a written submission and a 25 minute

17 Condu¡t Spring | Summer 2011 Department FacultyNews and Happenings

talk. Carleton was recognized at the INFORMS Adrian Vladu Finalist in CRA’s 2011 2010 Annual Meeting in Austin, Texas. Undergraduate Researcher Award This work by Carleton in collaboration with Pas- Competition cal and PhD alum Russell Bent has been de- Undergraduate student Adrian Vladu was re- ployed at Los Alamos National Laboratory as part cently selected as a finalist in the Computing of the LogiSim project and is being used to aid Research Association’s Outstanding Undergrad- federal organizations such as DHS and DoE to uate Award competition for 2011. prepare for and recover from national disasters. Adrian’s main academic interests are centered Charalampos (Babis) Papamanthou around theoretical computer science, with a fo- Visits Mrs. Kanellakis cus on algorithms and data structures. He has On December 19th 2010, and while in Greece researched the problem of producing a global ranking of items given pairwise ranking infor- for the winter break, PhD student and Kanellakis Adrian Vladu fellow Charalampos (Babis) Papamanthou visited mation, when the items to be ranked arrive in Mrs Kanellakis in Athens. He was joined by previ- an online fashion. This work resulted in a paper ous Brown CS PhD alums Aris Anagnostopoulos published at the 8th Workshop on Approxima- and Yiannis Vergados, who were both Kanellakis tion and Online Algorithms. The paper was co- fellows in the past. All the fellows were delighted authored with Claire Mathieu. to see that Mrs Kanellakis is doing well, despite He has also worked in the area of Computation- the recent loss of General Kanellakis. al Biology, which resulted in the paper “An Effi- The visit was very interesting and enjoyable, with cient Algorithm for Alignment of Strobe Reads” Mrs Kanellakis going through many old archives (with Anna Ritz, Aparna Das, Benjamin J. Rapha- and stories referring to General Kanellakis’ life el), currently in submission. and achievements. Upon graduation in May, Adrian will be working The next day, on December 20th 2010, Babis toward a PhD in Theoretical Computer gave a talk at the Department of Informatics of Science. the University of Athens entitled “Efficient Veri- fication of Outsourced Data and Computations”. The talk was dedicated to the memory of Paris, on the occasion of the passing of exactly 15 years since his tragic loss.

Charalampos (Babis) Papamanthou

18 Condu¡t Spring | Summer 2011 Department FacultyNews and Happenings

Tenth Annual Paris C. Kanellakis Memorial Lecture

Distinguished Lecturer Moshe Y. Vardi of Rice University gave the 10th Annual lecture. Left to Right: Isabel Cruz, Alex Shvartsman, Dina Goldin, Shriram Krishnamurthi, He is shown here with Kanellakis Fellows Aggeliki Tsoli, Foteini Baldimtsi and Charalampos Scott Smolka, Moshe Vardi, and Roberto Tamassia. (Babis) Papamanthou. Recent Ph.D.s

Kiran Pamnay with advisor John Jannotti Alex Rasin with advisor Stan Zdonik Micha Elsner

Industrial Partners Program The IPP provides a Partners for their Start Ups For more information To learn more about the formal mechanism for support: Cloudera about the Industrial IPP visit: interactions between Delphix Partners Program, http://www.cs.brown. companies and Premier Partner DropBox contact: edu/industry students in the CS Adobe Mozilla Amy Tarbox Connect with the CS Department. Member NING Program Manager Department: companies benefit Affiliates Tel: (401) 863-7610 Vertica Systems Inc. Join the ‘Brown University from superior visibility Facebook [email protected] in the Department, Google Individuals Computer Science’ group on Facebook. exclusive access to GTECH Paul Edelman, Ugur Cetintemel Professor and IPP event/interview space Jane Street Capital Edelman & Associates Regional Groups: in the CIT Building and Microsoft Director Brown CS in Boston assistance with recruiting NABsys, Inc. Tel: (401) 863- events; students benefit Oracle 7600 from specific information TripAdvisor [email protected] Brown CS in Seattle about opportunities for VMware Brown CS in SF Bay Area summer internships and Brown CS in NYC permanent employment. Brown CS in LA/Southern California The department wishes to thank our Industrial 19 Condu¡t Spring | Summer 2011 Department News and Happenings

Like topology, computational topology is a New Courses large and diverse field and the course sylla- bus is just a selection from it, reflecting, in part, Computational Topology Spike’s interests. Here are some examples from the course projects (See the course website Çagatay Demiralp, PhD student and TA for CS195H http://www.cs.brown.edu/courses/csci1950-h/ CS195H - Computational Topology is a new ad- for further details): dition to the department’s course offerings by • Homotopy: Show that every grid loop (a loop Spike (a.k.a. John F. Hughes) and taught first whose vertices are on the integer lattice, and time this spring (Spring 2011). As its name sug- whose edges are all vertical or horizontal) is gests, the course aims to introduce students to homotopic to a constant grid loop by writing various algorithmic problems that arise in the a program that takes a grid loop as input and computational study of topology. produces as output a sequence of grid-homo- Compared to other branches of mathematics, topy steps. (Grid homotopies are made of dis- such as geometry or analysis (e.g., calculus), com- crete steps that model continuous deforma- puter science students are often less familiar with tions). Modify this program to take any grid topology. One reason for this is that topology is loop in the punctured plane (a plane with a a relatively new field. Although its roots can be missing point) and deform it into one of the traced back to Euler and Gauss (well, that can be “standard” loops (or the constant loop if it said for almost every other branch of mathemat- doesn’t wind around the missing point). ics), topology is primarily a product of the 20th • Whitney-Graustein Theorem: Write a program century mathematics and was pioneered by Poin- that computes the turning number of a poly- caré. So, what is topology about? It is best un- gon. Given a polygon of n vertices and turn- derstood in a comparison with geometry. In the ing number k, construct a regular homotopy Euclidean geometry (one of many possible ge- Figure 1: Screenshots from student projects from the given polygon to the standard poly- ometries), one studies the congruence (or equiv- plotting regular homotopy steps between gon with n vertices and a turning number k. alence) of spaces (e.g., curves and surfaces) un- two smooth polygonal curves Figure 1 shows screenshots from student proj- der rigid motions, which preserves lengths and ects plotting regular homotopy steps between angles. On the other hand, in topology we study two smooth polynomial curves. the congruence of spaces under continuous de- formations. This means that we deem changes in • Immersions: Write a program that lets the user lengths and angles to be unimportant. For exam- click a polygon, and then determines wheth- ple, consider the two font curves “S” and “I”; al- er the polygon bounds an immersed surface. though they are not congruent in the Euclide- Enhance your program so that if the polygon an geometry, these two curves considered “the bounds one or more surfaces, you report the same” in topology (here is a continuous deforma- turning number of the polygon and the Euler tion that projects the curve S onto I: Pull the end- characteristic of each surface that it bounds. points of the curve S until it is straightened and then • Simplicial Homology: Write a program that shrink it from both ends to match with I). Intuitively, computes the bases for the groups of cycles this added “flexibility” in the transformation un- that do not bound for a given triangulated der which the congruence is considered should surface (e.g., torus, Klein bottle, RP2, etc.) make it easier for different spaces to be congru- or a higher-dimensional simplicial complex ent. So, in topology, one should expect a smaller with coefficients in Z/2Z (binary numbers) number of equivalence classes of spaces. or Z (integers). Both topology and computational topology are The course is primarily aimed at Junior/Se- very active research fields. For example, Grigori nior Math/CS concentrators who have taken Perelman’s proof of the Poincaré conjecture and a 100-level math course that involves some to- the drama surrounding the subsequent events pology (e.g., MA106, MA141, and MA126) and are very recent memories. Similarly, computa- who know how to program, and preferably have some experience with Matlab. However, in my Figure 2: Snapshots from the Thurston tional topology has recently started finding in- corrugations demo used in CS195H. creasing number of applications in a wide range experience as a TA so far, it is also a great way of areas such as low-level vision, global (or quali- to learn topology for those who have not taken tative) data analysis, and sensor networks. any related math courses because concepts are

20 Condu¡t Spring | Summer 2011 Department News and Happenings

introduced very intuitively and programming potable water disaster recovery problem. I was projects force students to think about the under- able to spend the summer continuing this work lying ideas and theorems at a depth that these on site at Los Alamos National Laboratory, and ideas and theorems often demand. integrated it into their fast response pipeline. Each time a category three or higher hurricane Spike is very excited about the course and has al- is projected to make land fall on US soil, the fast ready written more demo code than we the TAs response pipeline is executed and cutting-edge (Andrew Furnas, a stellar math concentrator with algorithms are used to provided decision sup- accumulated accomplishments such as Goldwa- port to US government officials. It seems that my ter and Marshall Scholarships, is the HTA for the dreams of “changing the world” with comput- course). Figure1 shows snapshots from the inter- er science were coming true within just one year face for his Matlab code to demonstrate regular of starting my graduate studies. “Changing the homotopy via Thurston corrugations. Well, you will world” maybe a bit of an exaggeration, but I am need to take the course to learn what that means. still excited help save lives during natural disasters. CS2580 Providing decision support to by Carleton Coffrin, PhD Student & TA for CS2580 the US government is just the Back in the summer of 2007 I was working out of beginning. We also must share my apartment in NYC and coding web sites for our knowledge with the broad- anyone willing to pay. Of course there were ad- er community. We often do vantages to freelancing: sleeping in every day, this through academic publi- working in my pajamas, having no boss, but the cations, but we have also cho- work just wasn’t exciting for me. I spent my after- sen to disseminate our research Results from the weekly class tournament noons debugging cross-browser css compatibili- directly to the Brown community through Pas- where green boxes highlight the top ties and dreamed all night of writing algorithms cal’s graduate course, “Solving Hard Problems.” performers. The competition is fierce! to “change the world”! (I will admit that just one Solving Hard Problems is not new to the course year out of undergrad, my youthful optimism was catalogue and the weekly class tournaments re- as strong as it ever had been.) I had heard whis- main, but we have adjusted the curriculum to fo- pers in my last year of undergrad of optimization cus on problems in the field of humanitarian lo- tools, and the prospects of using this technolo- gistics. We have added two more projects to the gy for solving real-word problems were very excit- course and changed the others to be focused on ing. So I decided to return to school and master decision-support applications. Some of the new these optimization technologies. I imagined that projects include: “Supply Chain,” where a trans- my time in academia would focus on toy prob- portation network must be optimized to deliver lems such as sudoku or magic squares, but lit- relief supplies; “Green Zone,” where security forc- tle did I know that I would be solving real-world es must be efficiently deployed to cover an urban problems as soon as I arrived at Brown. area; and “Special Operations,” where medical supplies must be packaged efficiently while min- I joined Pascal’s lab (Brown’s Optimization Lab- imizing the risk of contamination. So far the re- oratory) in the fall of 2008, and before the new sponse to the new curriculum has been positive, student orientation had finished Russell Bent and we hope that some of the students will have [‘05] had already given an exciting talk about a the opportunity to take their experience outside series of disaster recovery problems that his di- the classroom and use it to solve real-world prob- vision faces at Los Alamos National Laborato- lems. In fact, two students, Nell Elliott and Ben ry. This was the beginning of a collaboration be- Simon, are already working in the Optimization tween Brown’s Optimization Laboratory and Los Laboratory on disaster-recovery projects. Alamos’s Energy and Infrastructure Analysis divi- sion that is still thriving today. In my first year at the Optimization Laborato- ry we successfully developed an algorithm for a

21 Condu¡t Spring | Summer 2011 Alumni

stereotype-promoting violent games. Even hands, he submitted to the Brown Entre- On Fantasy Hip when games started taking the turn towards preneurship Program’s Business Plan com- Hop, Inc. “social” in the Facebook scene, these hip- petition, taking home second place, as the hop games did little more than encourage only competing team that had both a com- The Problem the player to get as much “bling” as possible pleted product and several thousand dol- and earn “respect” by dissing others. lars in revenue. His player base grew faster For as long as he than he could actually deal with it, and after can remember, Jason’s disappointment with the hip-hop amassing over 16,000 players he finally dis- Jason Townes game offering quickly turned into the rec- connected the servers and figured he’d deal French, (Brown ognition of a big opportunity. To Jason with the game later (afterall — he had to Computer Sci- and many other hip-hop fans, hip-hop is so focus on passing CS 167!) ence ’08, shown much more than violence and bling. It is here) has al- a wildly polymorphic form of creative ex- After graduating, Jason moved out to Silicon ways liked two things: video games and mu- pression, and a multi-billion dollar industry Valley to work full time for Apple prepar- sic. His application essay to Brown was in that has spread far beyond the music itself. ing for their Snow Leopard release, and was fact written about his fascination with Su- Hip-hop has inspired global waves of graph- shortly hired to serve as CTO of a new finan- per Mario Bros., and wanting to figure out ic designers, graffiti artists, clothing lines, cial technology startup backed by venture what exactly made Mario jump whenever and other forms of media and merchandise capitalist Tim Draper called Xpert Finan- he pressed the “A” button. This question more than any other type of music. With so cial (www.xpertfinancial.com). It was there ultimately led him down the path of learn- much subject matter to build off of, surely where he synced up with California native ing to program, and teaching himself C in someone could think of a better game, no? Brent Vale — a University of Chicago alum, 6th grade. and former classmate of Jason at Phillips Enter Fantasy Hip Hop Academy. After working together for a year Somewhere along the path to geekism he While studying at Phillips Academy in An- learning about how businesses get funded, found time to stimulate the other half of dover, Massachusetts, Jason was itching the duo teamed up to formally found Fan- his brain with music. Coming from a family to create a game. His friends were play- tasy Hip Hop and bring it back as a full- of musicians, song and rhythm have been a ing fantasy football obsessively, and Jason, screen, 3D visual experience. With Brent’s part of his life since before he could talk. In not knowing jack about sports, figured that help and support, they received angel fund- particular, the catchy beats and witty rhymes maybe he could make a game about some- ing and set up shop in Silicon Valley’s most of hip-hop music caught his attention at a thing he knew — music. It wasn’t until af- renowned startup incubator — the Plug and young age, and he would frequently play it ter taking Steve Reiss’ CS 9: Building a Web Play Tech Center in Sunnyvale, California. in the background while defending his vir- Application course that Jason mustered tual ant farm in SimAnt, or racking up frags up the skills and courage to build his own Plug and Play in Unreal Tournament. web-based fantasy game. He called it Fan- “Working in the Plug and Play Tech Cen- It was only a matter of time before his tasy Hip Hop. It sported a PHP/MySQL ter is like being in the CIT all over again,” curiosities led him to seek out hip-hop backend, and a simple HTML front end. says Jason — except this time everyone was based video games, but he was sourly disap- No graphics, no color even — just reading working on a new startup. It’s a massive pointed at the offerings. While other genres a bunch of hip-hop stats on a screen. His complex filled with tons of web, mobile, of music had found their own ways of man- sophomore year, after a long coding ses- and gaming companies. Hot startups like ifesting in the game industry, the lack of sion in his dorm room in Grad Center Tow- Addmired and G6 Media are right down quality hip-hop games stuck out to him er B, Jason published his game live on the the hall from Fantasy Hip Hop, and all the like a sore thumb. “If you wanted to play a Internet at fantasyhiphop.com. What hap- startups get to enjoy Friday lectures from hip-hop video game, you pretty much had pened afterwards surprised him. Within the Silicon Valley’s top VCs (pizza and beer in- your choice between rhythm games like first 24 hours of launching the game he got cluded!) “It’s great being at Plug and Play”, Parappa the Rapper, fighting games like around 2,000 players. Where these players says Jason. “It has the right energy and cul- the Def Jam series, or urban crime sand- came from, to this day he does not know. ture to keep you inspired during those long box games like Grand Theft Auto: San An- No Google Analytics, no marketing strate- nights of coding. Plus technical help and dreas.” While these games had their ap- gy (he placed a poster up at Lupo’s down- new hires are just around the corner, pretty peal (who wouldn’t want to play as 50 town, and one in the Underground on cam- much 24 hours a day”. Cent shooting up terrorists in the Middle pus, but that was about it), but somehow East, like in 50 Cent: Blood on the Sand?), While the next generation of Fantasy Hip the players flooded in. there weren’t many options outside of awk- Hop is just now getting underway, Jason wardly implemented rhythm games, and Seeing that he had something special in his and Brent are very excited about their

22 Condu¡t Spring | Summer 2011 FacultyAlumni

outlook. “Having a previous version of the online to solve the mystery. Current MIT of classroom time. game to go off of took out a lot of the risk students will model good scientific prac- — we know what players liked before, and tice for the players and Smithsonian scien- we know how to make it better.” Their desk- tists will be available as resources for play- Danfeng (Daphne) top computer game is set to release on Win- ers trying to learn the science that will dows and Mac OS X late summer 2011. help them succeed. Yao PhD ’07

Hip-hop gamers — get ready for the game This work is heavily inspired by the suc- Danfeng (Daphne) Yao is now an assistant you’ve been waiting for! cess of ARGs (Alternate Reality Games), professor at Virginia Tech Computer but we’ve had to make some serious mod- Science Department. ifications to the design to make it encour- She moved from Rutgers CS to the beauti- Dana Tenneson, age active engagement from a wide range PhD ’08 of players. This has been a particularly exciting proj- For the last two years I’ve been working in ect for me as there are dozens of people at the Education involved and dozens of ‘moving parts’ to Arcade, an educational games research the mystery and I’m one of the two prima- lab at MIT within the ry implementers. newly formed ‘Me- dia Lab Complex.’ My One other exciting project I got to be a ful Blacksburg mountains in January 2010, job title is that of Se- part of was working on a game to help together with her daughter (Radia) who nior Programmer, but populations at risk of predatory lending is almost 4 years old. Her husband, Chang this is the sort of place to understand their finances. I worked Lu, also moved from Purdue University where everyone has with a few of my coworkers to put togeth- to VT Chemical Engineering as an associ- to be a bit of a one- er a design in our spare hours. Then, in ate professor. Daphne received her NSF man army. I do a fair a single code flurry weekend, I wrote a CAREER Award in January 2010 to sup- amount of game de- prototype for our game, ‘Farm Blitz.’ port her work on human-behavior driv- sign and managing of undergraduates in The design and prototype won fund- en malware detection. She holds a pat- addition to leading software development ing from the Social Security administra- ent (PCT) on the technology developed projects and generally making Adobe Flex tion and an outside game studio was con- on this project, which is licensed to Incu- do things it has never done before. tracted to make it. When all the funded bation Factory. Some of her other recent games were completed, there was a con- work received IT media attention, e.g., Getting a job here was a really great fit giv- gressional briefing about the games and NSF news reported her work on activity- en how my research at Brown was always ours was highlighted as the example for based authentication systems in November focused on educational uses of technol- demonstrating how players learn impor- 2009. She and her graduate students also ogy (Education was my outside minor se- tant finance basics through gameplay. grabbed a couple of best paper and poster quence) and that I was really interested in awards in conferences. Most recently, she games development in my limited spare http://financialentertainment.org/play/ started a new cyber-security project fund- time. Having been involved in Brown’s farmblitz.html ed by the Army Research Office (ARO) on Fantasy Gaming Society and Chad’s Inno- Also, readers might be interested to know designing personalized anomaly detection vating Game Development seminars really that I’m not the only Brown CS alum here. solutions. helped prepare me for the work I do now. I work with Louisa Rosenheck (class of For the last year, most of my time has been 2003, BA in CS) who is a Project Manag- devoted to the upcoming Smithsonian/ er. She went on to get a master’s degree MIT science mystery, Vanished in Education from Harvard and focus- (http://vanished.mit.edu). es more on game and curriculum design. Lately, she has been developing a series We’ve been creating a complex two- of biology games for high school students month scenario where middle school kids to play on smartphones (Android) outside across the country will have to collaborate

23 Condu¡t Spring | Summer 2011 Department of Computer Science Brown University Box 1910 Providence, RI 02912 USA

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