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Institute for Applied Computational ScienceHarvard School of Engineering and Applied Sciences

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The IACS Report2010–13

The Promise of Computational Science

IACS Timeline

Harvard’s Applied Computation Institute

IACS by the Numbers

People

Seminars and Symposia

May 2014

http://iacs.seas.harvard.edu

http://seas.harvard.edu

IACS Report2010–132

Harvard’s reputation in the academic disciplines within its intellectual sweep is unparalleled. In the first decade of the 21st century, however, the university’s portfolio still did not include a

convincingly robust effort in the modern and dynamic discipline of Computational Science and Engineering (CSE).

The confluence of computer science, applied mathematics and a broad range of established disciplines, CSE was being practiced by individuals at several departments and schools within Harvard but lacked coherence and recognition as a field of study. As the Report of the Task Force on Applied Mathematics and Computational Science (authored by a committee co-chaired by Professors M. P. Brenner and D. C. Parkes) pointed out in January 2010, these activities were present but undersupported and uncoordinated at Harvard. The Task Force wrote:

While Harvard has made great strides in recent years in building up computer science, the university’s investment in computational science has been falling behind.... there are very few core practitioners and there is no concerted effort among faculty.... This is a field that is essential to the future of science and the social sciences, and is one in which Harvard is uniquely positioned to play a leading role [emphasis in original].

It had been evident for quite a while that the exceptional talents and contributions of faculty from computer science and applied math, combined with the knowledge and expertise of Harvard colleagues from various scientific disciplines, could elevate the field of CSE to a whole new level of intellectual prowess and produce exciting new developments and results. These notions coalesced into a proposal, first put forward at faculty retreats of the School of Engineering and Applied Sciences in January 2010 and discussed in more depth in May 2010. The proposal for creating the Institute for Applied Computational Science noted that its lack of disciplinary barriers, its broad intellectual leadership, and its inherently inter-disciplinary structure made the School of Engineering and Applied Sciences the natural administrative unit to take the leading role in CSE activities within the entire University.

It is my pleasure to present the very first IACS Report, put together by 2010–13 Director Efthimios (Tim) Kaxiras and 2010–13 Executive Director Rosalind (Ros) Reid. IACS was founded in 2010 by Dean Cherry A. Murray to foster graduate training and research in applied computational science, infuse the SEAS curriculum with new courses and student research opportunities, and create an intellectual home for faculty and students applying computational methods to major challenges in science and the world.

This report tells the founding story of IACS, a remarkable achievement at Harvard that I have been privileged to participate in. I am humbled by the talent and commitment of the many people who came together to create this important new program, one that responds to the demands and opportunities of a fast-changing world. A key element of our success has been purposeful collaboration with practitioners and thought leaders in industry and in government. By bringing those two sectors together with academia, we ensure that our educational objectives and research agendas are in sync. And together we advance the state of knowledge.

Tim and Ros have played a crucial role in the founding and success of IACS, and they have been invaluable mentors and friends to me. I thank them both for their dedication and hard work to put IACS on a path to success, and I am excited to continue to realize that vision.

Hanspeter PfisterAn Wang Professor of Computer ScienceDirector, IACS

The Promise of Computational Science


Institute for Applied Computational ScienceHarvard School of Engineering and Applied Sciences 3

The proposal for IACS described the role it might play in filling an important gap in Harvard’s intellectual activities. Our faculty committee noted that even though the definition of Computational Science and Engineering can still be a matter of debate, CSE is widely viewed as the third pillar of scientific inquiry, complementing the traditional pillars of theory and experiment. A 2001 report by the Working Group on CSE Education of the Society for Industrial and Applied Mathematics noted that:

Computer models and computer simulations have become an important part of the research repertoire, supplementing (and in some cases replacing) experimentation. Going from application area to computational results requires domain expertise, mathematical modeling, numerical analysis, algorithm development, software implementation, program execution, analysis, validation and visualization of results.

Another report, issued by a National Research Council committee in 2008, focused on the impact of computation on fields where data-gathering capabilities are outstripping the capacity of analyzing and understanding large and complex data sets.

These reports and others emphasized the huge range of applications and areas of knowledge where computation has the potential to provide dramatic advances. The SIAM report listed weather and climate prediction, combustion, nuclear stockpile stewardship, simulation, design and control of vehicles, aircraft design, electronic design automation, astrophysics, molecular biology, materials, bioengineering, and quantum chemistry.

Over the period marking the creation and development of IACS, these predictions have been borne out. Examples of current trends that promise exciting new discoveries are the development of special-purpose hardware and domain-specific languages matched to scientific problems requiring massive computation. Algorithms can be thought of as “burned into” hardware or system architecture in these special-purpose machines designed for tackling huge problems such as protein folding efficiently and with much smaller power budgets. Meanwhile, in the domain of data-intensive science, there is a new focus on finding patterns and meaning in large datasets, where understanding and accounting for the uncertainty and heterogeneity of data from multiple sources is among the daunting tasks to be faced.

The first step in the creation of IACS was to develop pioneering educational activities, including new courses and graduate degree programs to address future needs. To support our students and nurture new collaborations, an ambitious program of activities to build skill and nucleate the new intellectual community was also essential. These unique programs, driven by student and faculty enthusiasm, along with the growth of collaborative interdisciplinary research that will yield scientific insights and extract new knowledge from data, will earn Harvard a prominent place in the field of CSE, enhancing and broadening its academic mission and its societal impact.

The rest of the present Report documents the steps that were taken toward these goals during the first three years of the Institute’s life. I am grateful to Dean Murray for her leadership in this endeavor, to Ros Reid and Joy Sircar for their invaluable contributions in establishing the IACS, and to all my SEAS faculty colleagues for their unwavering support and encouragement.

Efthimios KaxirasJohn Hasbrouck Van Vleck Professorof Pure and Applied PhysicsIACS Director, September 2010–August 2013

Reports cited: SIAM Working Group on CSE Education, Graduate Education in CSE, SIAM Review 43 (2001) pp. 163–177; Committee on the Potential Impact of High-End Computing on Illustrative Fields of Science and Engineering, National Research Council, 2008, The Potential Impact of High-End Capability Computing on Four Illustrative Fields of Science and Engineering, The National Academies Press, Washington, D.C.



September IACS is launched under the direction of Efthimios Kaxiras, John Hasbrouck Van Vleck Professor of Pure and Applied Physics. Its mission:• to foster graduate training and research in applied computational science• to infuse the SEAS curriculum with new courses and student research opportunities that will focus

on the use of computation to power discovery and innovation• to create an intellectual home for faculty and students applying computational methods to major

challenges in science.Staffing for the new institute included a part-time Executive Director, Rosalind Reid; Joy Sircar, SEAS Associate Dean detailed to serve as Chief Technologist for IACS; and Natasha Baker, part-time Administrative Coordinator.November Dean Murray convenes the Applied Computational Science Curriculum Development

Advisory Group for a one-day meeting to develop the new curriculum. The group comprises:• 9 SEAS faculty• 10 other Harvard faculty• 12 computational science leaders representing National Labs, Goldman Sachs, IBM, Microsoft, Exa

Corp., Oracle, American Scientist magazine, NVIDIA, the Broad Institute and Intel Corp.; and four SEAS administrators.

January IACS launches ComputeFest, a program of skill- and knowledge-building events during the new January intersession. The first ComputeFest consists of four days of workshops on Matlab and Mathematica, with hands-on training provided by SEAS Instructional and Research Computing Services.

Pavlos Protopapas, a Research Associate at the Harvard-Smithsonian Center for Astrophysics, is appointed the first Lecturer in Computational Science. Hudong Chen, Vice President and Chief Scientist at Exa Corporation, is appointed the first Visiting Professor.

IACS offers its first courses: • Applied Math 205b, Advanced Scientific Computing: Stochastic Optimization Methods (later

AM207), Efthimios Kaxiras and Pavlos Protopapas, instructors.• Applied Math 272r, Kinetic Methods for Fluids, Hudong Chen, instructor.

IACS Timeline

2010

2011

From understanding the dynamics of blood flow to visualizing complex data to tethering low-cost hardware together to create virtual supercomputers, applied computation is at the core of science and engineering. We owe it to our students to ensure that SEAS is at the forefront of this exciting field.

Whether they go to work in industry or pursue research careers, graduate students will need to know how to leverage computer power to solve human problems and explore all aspects of nature and life, at scales and speeds that will require novel computational thinking.

— Dean Cherry A. Murray, 2010



February The SEAS Faculty endorses a faculty Task Force proposal for a new curriculum and:• A Master of Engineering research degree• A Master of Science, to be offered as a stand-alone degree or in combination with an A.B. degree• A Secondary Field, or graduate minor, for Ph.D. students

March IACS sponsors the launch of the Harvard College Mathematica Club.

May The FAS Graduate Policy Committee approves the SEAS proposal for a Graduate Secondary Field in Computational Science and Engineering.

June IACS’s first gift, an anonymous donation, enables the Institute to support its first undergraduate research projects.

July Two more Lecturers in Computational Science, Cristopher Cecka (Stanford University) and David Knezevic (MIT/Oxford), join IACS to provide instructional staffing and supervision of student research and work with faculty to develop the new curriculum.

September IACS celebrates its move into newly renovated space in Cruft Laboratory with an Open House for faculty, staff and students.

The core curriculum designed by the Task Force is launched. IACS now offers two core courses:• Applied Math 205, Advanced Scientific Computing: Numerical Methods, David Knezevic, instructor

(revision of existing course)• Computer Science 205, Computing Foundations for Computational Science, Hanspeter Pfister and

Cris Cecka, instructorsThe first IACS Seminars are offered.October The first cohort of seven Ph.D. students are accepted into the Secondary Field program.

(Another six are accepted in March 2012, for a total of 13 the first year.)

January ComputeFest is expanded to include:• a seminar series on

entrepreneurship, Computational Science Ventures (initial speakers include Dean Kamen and Stephen Wolfram)

• a Student Computational Challenge• a Mini-Symposium on the Future of Computation in Science and Engineering

IACS Open House September 2011

2012

Speakers at the 2012 mini-symposium, drawn from the IACS Advisory Board and representing Google, NVIDIA, IBM, Intel and AstraZeneca



(January)The Advisory Board reconvenes to review and endorse the revised IACS curriculum and degree plan.Zhenyu Zhang, Qian-Ren Professor at the University of Science and

Technology of China, is appointed the second Visiting Professor at IACS.Three new courses are launched for spring semester:• Applied Math 274, Computational Fluid Dynamics, David Knezevic,

instructor• Applied Math 275, Computational Design of Materials, Zhenyu

Zhang, instructor• Computer Science 207, Systems Design for Computational Science,

Eddie Kohler and Cris Cecka, instructorsFebruary Dean Murray presents the full master’s degree proposal to

the Graduate Policy Committee of the Faculty of Arts and Sciences. The committee endorses the proposal.

April The proposal for Master of Science and Master of Engineering degrees in Computational Science and Engineering wins FAS Faculty Council approval.

May IACS students present posters and videos of their course projects at the first SEAS Design and Project Fair.

June The new master’s degrees are announced. The Graduate School of Arts and Sciences prepares to accept applications for students wishing to enter in 2013.

July Ian Stokes-Rees joins IACS as Lecturer in Computational Science.September The first course to be offered under a new heading, Applied Computation, is AC 263,

Data and Computation on the Internet, Ian Stokes-Rees, instructor. October Daniel Weinstock joins the IACS staff as Assistant Director of Graduate Studies. The

application process for the Master of Science degree program opens.December Pavlos Protopapas and Rosalind Reid visit the University of Chile and ALMA

radioastronomy facility for a conference and extensive meetings to establish an exchange program.

January SEAS faculty review the first round of 151 applications for the master’s program.

ComputeFest grows to include:• A mini-symposium, Celebrating 100 Years of

Markov Chains• A full-day symposium, Computing @ Exascale• An expanded four-day workshop program

Another new course is launched: Applied Computation 298r, Interdisciplinary Seminar in Computational Science and Engineering, Efthimios Kaxiras and Daniel Weinstock, instructors.

2012 cont.

2013

Student presentation in CS 207

The heated final round of competition during the 2013 Student Computational Challenge



February Following several rounds of review, 39 students are recommended for admission to the master’s program. An additional four applications from Harvard College students with advanced standing, wishing to complete the Master of Science during their final year, are approved.

March Students offered admission to the first class attend a SEAS open house for admitted students.

June Six undergraduate students from Harvard and other institutions arrive for a pilot project at IACS to gain research experience working in mentored teams on computational problems presented by industry.

July Pavlos Protopapas is appointed Scientific Program Director at IACS.

August Sadasivan Shankar, an engineering executive and materials scientist at Intel Corp., joins IACS for a four-month stay as the first Distinguished Scientist in Residence. Brad Malone, a postdoctoral fellow, is appointed Lecturer.Shankar and Malone offer AC 275 (formerly AM 275), Computational Design of Materials.

September SEAS welcomes the first class of Master of Science students in CSE: 24 students planning to complete a “stand-alone” degree plus four Harvard College undergraduates with advanced standing, taking on a master’s in addition to their bachelor’s degree.

Founding Director Efthimios Kaxiras is honored as he hands the Directorship of IACS to Hanspeter Pfister, An Wang Professor of Computer Science.

SEAS and the Harvard Statistics Department launch a Data Science course; more than 300 students enroll.

Meg Hastings joins IACS as Interim Executive Director.

David Shaw of D. E. Shaw Research speaks during Computing @ Exascale

Graduate Dean Xiao-Li Meng (left) and Charles Alcock (right), Director of the Harvard-Smithsonian Center for Astrophysics, chat with Efthimios Kaxiras at an event celebrating his service as IACS Director and welcoming Hanspeter Pfister as the new Director.



The Institute for Applied Computational Science was launched by the Harvard School of Engineering and Applied Sciences on

September 1, 2010. Although entirely new, IACS pulled together important threads

of Harvard history. Decades earlier, Harvard and IBM had joined in launching the age of scientific computation with the creation of the pioneering Harvard Mark electromechanical computer to solve problems in physics. And so it was no surprise that two physicists devised a 21st-century reboot of the ideas that Howard Aiken and Thomas J. Watson had espoused.

The school’s incoming Dean, Cherry A. Murray, asked Efthimios Kaxiras, John Hasbrouck van Vleck Professor of Pure and Applied Physics, to lead the creation of a new curriculum and degree program that would vault Harvard into a position of 21st-century leadership in computational science and engineering. Funded by the new Dean’s discretionary funds, the institute was created as an academic organization that would connect with all of Harvard by leading the application of computational methods to fields across the sciences and engineering through a focus on graduate training.

Dr. Kaxiras requested the aid of SEAS Associate Dean Joy Sircar and Rosalind Reid, former Executive Director of Harvard’s Initiative in Innovative Computing, in launching the new Institute. IACS offices were established in Dr. Kaxiras’s research space in Cruft Laboratory. Ms. Reid and Dr. Sircar undertook an analysis of computational science programs

at other institutions to inform the new Harvard effort. As part of the initial research, Dr. Kaxiras and Ms. Reid visited Stanford’s Institute for Computational and Mathematical Engineering..

Dr. Kaxiras proposed to convene a meeting of Harvard faculty with leaders from industry and the National Laboratories to define the leading edge of the field, needs for graduate training, and a unique contribution for Harvard. This meeting was held November 11, 2010. It was attended by nine SEAS faculty, 10 other Harvard faculty, and 12 computational science leaders representing the National Laboratories, IBM Corp., Microsoft Research, Goldman Sachs, Intel Corp., NVIDIA, the Broad Institute, American Scientist magazine and Oracle.

Meanwhile, IACS designed and launched its first two new courses under the Applied Mathematics course heading and welcomed IACS’s first visiting faculty member from industry. Both courses launched in February 2011. Aware of the urgency of computational courses for Ph.D. students, Dean Murray had asked Dr. Kaxiras to develop and launch new courses as the first step in building a curriculum.

Recommendations from industry and facultyAt their initial meeting, the advisory group rapidly reached consensus on three points:•SEAS’s immediate goal should be to develop a master’s-level program in computational science

and engineering (CSE), a secondary field for Ph.D. students, and an A.B./S.M. program for Harvard College students with advanced standing.

•A Ph.D. program is a long-term, evolutionary goal depending on the development of computational science as an academic discipline.

Color image of a Time magazine cover cartoon depicting the Harvard Mark II on January 23, 1950. The subscript is “Can man build a superman?” From the Computer History Museum collection.

Harvard’s Applied Computation Institute



•The curriculum and degree programs should be outcome-based, ensuring that students acquire specific capabilities if they successfully complete their coursework.

After breaking into small-group discussions and reconvening, participants identified learning outcomes for the new program. These outcomes were defined as answers to the question: “What should a graduate of this program be able to do?”

Realizing the outcomesTaking the learning outcomes and the full Advisory Board discussion as guidance, a Curriculum Task Force of SEAS faculty began work on a curriculum to achieve the desired goals.

Typically, academic experts from other institutions are engaged as advisors as a new academic program is developed. In the case of CSE, there were few related graduate programs. Further, Dr. Kaxiras told the members of the Task Force and Advisory Board that he preferred to devise a program unique to Harvard, tapping the wisdom of the faculty and responding to their needs.

Within Harvard’s Graduate School of Arts and Sciences, the Master of Science (S.M.) degree is unique to SEAS. SEAS also offers the only Master of Engineering (M.E.) degrees at Harvard. The S.M. degree is earned by taking eight courses, or a full-time load for two semesters. The M.E. is a two-year degree requiring a thesis in the second year.

The Task Force outlined a four-course core for the program. Building on SEAS’s academic strengths in Applied Math and Computer Science, the core courses would all require projects and student collaboration to achieve and assess the specified learning outcomes. (These courses would be open to all Harvard graduate students and advanced undergraduates.) Master’s students were to be encouraged to put together individual plans of study in which they would pursue independent project courses with faculty; take additional upper-level courses in Applied Math, Statistics and Computer Science; and seek out computation-intensive courses in application domains. An important component was a “mini-oral,” or a requirement that each student present project work to demonstrate mastery of the program content and learning outcomes.

The task force met twice and presented its proposal on February 8, 2011 to the SEAS faculty, which approved it unanimously. Faculty discussion resulted in a number of modifications to the proposal. For example, the degree requirements were redefined to facilitate dual degrees for students wishing to combine the S.M. in CSE with a Ph.D. in a field of application.

In addition to the degree programs, the Task Force devised a four-course Secondary Field (graduate minor) program to be offered to all Harvard Ph.D. students. Whereas master’s students would be required to take at least three of the core courses, the Secondary Field would require two core courses in addition to a pair of electives or and elective and independent project.

The CSE Program Learning Outcomes

1. Produce a computational solution to a problem that is reproducible and can be comprehended by others in the same field.

2. Communicate across disciplines and collaborate in a team.

3. Model complex systems appropriately with consideration of efficiency, cost, and data availability.

4. Use computation for advanced data analysis.

5. Create or enable a breakthrough in a science domain.

6. Take advantage of parallel and distributed computing and other emerging modes of computation, both in algorithms and in code implementation.

7. Evaluate and compare multiple computational approaches to a scientific challenge and choose the most appropriate and efficient one.

8. Apply techniques and tools from software engineering to build robust, reliable, and maintainable software.

A graduate of this program should be able to:



Implementing a new curriculumUpon reviewing the initial proposal from the SEAS faculty, the Graduate Policy Committee of the Faculty of Arts and Sciences asked Dean Murray to implement the Secondary Field as a first step while further refining the master’s degree program design. The Secondary Field was announced in May 2011. To ensure that Secondary Field students would have strong academic advising and be integrated into the IACS community, SEAS established an application process for second-year graduate students and scheduled spring and fall Advising Fairs for prospective students.

With a curriculum design in place, IACS began launching and staffing core and elective courses in computational science and adapting existing courses. SEAS had already established courses in scientific computing (Applied Math 205) and parallel programming (Computer Science 264). These topics were folded into the IACS core curriculum; AM 205 was updated, and CS 264 was replaced by CS 205, Computing Foundations for Computational Science. A course on stochastic optimization methods was launched as AM 205b in the spring of 2011 and was subsequently renumbered AM 207. The fourth core course, Systems Design for Computational Science, was launched in the spring of 2012 as CS 207. Thus the full core curriculum was in place as the first students entered the Secondary Field program in spring 2012.

In proposing a new degree program, SEAS had also committed to faculty recruitment in computational science. In order to develop and launch the new curriculum, IACS recruited Lecturers. These positions were created to combine teaching and research responsibilities, in order to ensure that graduate teaching in this fast-developing field would be informed by research, and students would have supervision for research projects. Pavlos Protopapas, a Research Associate at the Harvard-Smithsonian Center for Astrophysics, was recruited to develop AM 207 with Dr. Kaxiras; Cristopher Cecka, a new Stanford Ph.D., was recruited to develop CS 205, with Hanspeter Pfister, and CS 207, with Eddie Kohler. David Knezevic, a postdoc at MIT, was hired to teach AM 205 and develop an elective in computational fluid dynamics.

Dr. Kaxiras also proposed that IACS recruit experts from industry as visitors who would teach special electives and serve as a resource for graduate students developing computational projects. The first Visiting Professor was Hudong Chen, Chief Scientist at Exa Corporation, who visited in spring 2011 to teach AM 272r, Kinetic Methods for Fluids.

By the time the master’s program was approved and announced in spring 2012, IACS had in place a core curriculum and a high-quality teaching staff as well as a modest number of electives and activities in support of the emerging computational science community. A new course heading, AC or Applied

Computation, had been created to enable the flexible development of discipline-spanning courses focused on the application of computation.

Building an intellectual home for computational science at HarvardWhen Cherry Murray arrived to become Dean of Harvard’s newest school in 2009, she emphasized the role of engineering and applied sciences as a bridge between disciplines. In line with this mission, IACS’s founders hoped to build a matrix of connections through discipline-spanning computational methods and ideas. Faculty expressed interest in workshops, seminars and symposia as ways to exchange ideas, build collaboration and train students and researchers in

Simulation image courtesy Hudong Chen

Ethimios Kaxiras, Institute Fellow Alex Wissner-Gross, and Stephen Wolfram of Wolfram Research during the first Computational Science Ventures program in January 2012.



important new tools. Dr. Kaxiras proposed to launch a regular seminar series and also take advantage of the January intersession period opened up by Harvard’s new academic calendar.

Thus was born ComputeFest, a January program of skill- and knowledge-building activities for the entire research and academic community.

The first ComputeFest, held in January 2011, consisted of four days of workshops on Matlab and Mathematica. The next year, ComputeFest grew to include additional workshops and the first Student Computational Challenge, in which two graduate student teams competed to solve an optimization problem. Institute Fellow Alexander Wissner-Gross organized three talks by entrepreneurs working on the frontiers of science and computation, called Computational Science Ventures. Finally, members of the IACS Advisory Board were tapped for the first Symposium on the Future of Computation in Science and Engineering, a half-day event held in conjunction with the board’s meeting.

Attendance at ComputeFest increased steadily as interest grew across Harvard and as IACS developed partnerships with workshop providers, including the Institute for Quantitative Social Science. By 2013, the program included two full days of symposia in addition to four days of workshops and the two-day student competition. In 2014, ComputeFest

outgrew SEAS’s tight space as audience size pushed events to the Northwest Building and Science Center, with nearly 500 people attending a “Weathering the Data Storm” symposium.

IACS began a program of Friday lunch seminars in September 2011; these became popular enough to be moved into SEAS’s largest auditorium space in 2012 and grew again as a special course, AC 298, was designed around the series. Today, IACS Seminars are presented by speakers from the Harvard faculty, other institutions and industry who often meet with students after their talks for closer examination of their topics.

A unique experience for undergraduatesAlthough IACS was created with a primary mission of enhancing graduate training, undergraduate students were quick to take advantage of IACS courses and workshops. IACS academic staff helped develop computational modules for undergraduate courses, and IACS sponsorship helped a group of students start the Harvard College Mathematica Club.

Late in 2012, Area Dean Michael Brenner asked IACS for help developing a summer program specifically aimed at undergraduates. Dr. Brenner, a member of the CSE Program Committee, was interested in adapting the model used by the RIPS program at the Institute for Pure and Applied Mathematics at UCLA, where undergraduates gain experience in real-life collaborative problem-solving by tackling summer team projects posed by industry.

Working with Margo Levine, Assistant Director of Undergraduate Studies in Applied Math, and Applied Math Preceptor Avi Shapiro, the IACS staff designed a pilot program with the QRI Group of Houston and the Akselos software company of Boston and Lausanne as industrial partners. QRI posed a data-analysis problem involving predicting oil-well production. Akselos asked another team to evaluate and compare two approaches to simulation widely used in structural engineering.

Pilot undergraduate collaborative research program participants and mentors, summer 2013

computefest 2013

guide to eventsJan 15–25

computefest.seas.harvard.edu


http://computefest.seas.harvard.edu/computefest-2013


Students with diverse backgrounds were recruited from the large pool of applicants to the SEAS program in Research Experiences for Undergraduates and experienced the full benefits of the REU summer program and community. Supported by Drs. Levine and Shapiro as mentors, six students participated on the two teams during a lively and challenging summer. IACS plans to seek funding and additional partners to repeat and expand this program helping students experience team problem-solving and real-life computational challenges.

Launching a master’s program at the dawn of data scienceAfter announcing the new CSE master’s program in June 2012, the Graduate School of Arts and Sciences opened up an online system for accepting applications for September 2013 admission. IACS began handling inquiries from hundreds of prospective students. Applications were taken only for the one-year Master of Science program during the first round, which ended in December 2012. Faculty had decided not to create a fixed number of admission slots because the nature and quality of the application pool for such a novel program, as well as the likelihood that students would matriculate if accepted, were difficult to predict.

By year’s end it was clear that the new program had attracted a high-quality group of applicants interested predominantly in careers working with large and complex data. Many were attracted by the new course in Data Science to be launched in the fall. After reviewing some 150 applications, the faculty chose to offer admission to 40 applicants. The accepted students were invited to a March visit day with other accepted graduate students at SEAS. Some 60% of the accepted students chose the Harvard CSE program, and in the end 24 students comprised the inaugural class.

Into the future: New directions and collaborationsA fundamental belief driving the creation and design of IACS’s programs is that today computation connects and propels the disciplines, just as it is an essential driver of progress in business and industry. Computation today also connects the world and is an essential driver of international collaboration. The IACS experience illustrates all these connections.

ComputeFest is an obvious example, drawing attendance from all of Harvard’s schools and neighboring institutions as well as the business community in Boston and beyond. Workshops on visualization and statistical analysis tools bring biologists, chemists and political scientists into the same room, and speakers at the big data science symposium

drew examples from fields as disparate as sports and journalism.Another important experiment for IACS has been a collaboration and academic exchange program

with the University of Chile. From the start, IACS has welcomed international visitors, hosting research visits by faculty and students from China, Russia, Italy, Scotland and Chile. The University’s Center for Mathematical Modeling invited Dr. Protopapas and Ms. Reid to visit in December 2012 to design and launch the program, an outgrowth of Dr. Protopapas’s astronomy research. Extensive discussions involved Harvard’s David Rockefeller Center for Latin American Studies (DRCLAS), two other Chilean universities, and others in the Chilean research and informatics community, which has built a substantial infrastructure for supporting large-scale astronomical observation and data analysis.

Three students from Chile spent the summer of 2013 at IACS working with Dr. Protopapas and interacting with the undergraduates in the pilot summer program. In the fall of 2013, IACS secured funds from SEAS and the new Harvard-Chile Innovation Initiative to expand the collaboration by bringing a group of Harvard graduate students to Chile for an intensive joint research experience during

Alexander Isakov presenting his work in Applied Math 207 at the second SEAS Design and Project Fair, May 2013



the January term. Dubbed CHILE (Chile-Harvard Innovative Learning Exchange), the project brought together international teams to tackle a challenging big-data problem produced by the Dark Energy Camera, a novel astronomical instrument measuring the expansion of the universe.

Six Harvard students, chosen through a competitive application process, accompanied Dr. Protopapas and brought results back to share with attendees at the data science symposium. The group included three CSE master’s students, two astronomy Ph.D. students, and a Ph.D. student in statistics. All found that working with a large, noisy, imperfect data set in a diverse international team was a challenging and eye-opening experience in problem-solving.

Change and growthThe interest of master’s program applicants in data science careers was not the only signal that the data science portion of the IACS curriculum would be addressing a strong need in academia and industry. The data science course developed by Dr. Pfister and Joe Blitzstein, Professor of the Practice of Statistics, enrolled more than 300 graduate, undergraduate and extension students in the fall of 2013. Students had to be turned away when a SEAS advanced course on machine learning was oversubscribed the same semester. The third IACS Symposium, focusing on the promise and challenges of data science, was moved to the Harvard Science Center to accommodate a crowd of almost 500.

With the completion of a three-year term as IACS Director, Efthimios Kaxiras stepped down in mid-2013 to refocus on his research and teaching in physics and computational science. Appointed to succeed Dr. Kaxiras was Dr. Pfister, chief advocate for data science at SEAS. When Harvard Magazine asked the two IACS Directors to pose with the Harvard Mark I, it was clear that computational science at Harvard had been rebooted, retooled, and reinvigorated for a new century.

Pavlos Protopapas (right) on the University of Chile campus with IACS collaborators Eduardo Vera, Pablo Huijse and Karim Pichara during a site visit to establish the CHILE project, December 2012



IACS by the Numbers

SEAS investment in IACS

IACS course enrollment

ComputeFest participation

students admitted to the CSE Secondary Field program 2011–13, by field of study

recognition of IACS teaching

Cristopher CeckaSpring 2012 and 2013: CS 207Fall 2013: CS 205

David J. KnezevicFall 2011: AM 205Spring 2012 and 2013: AM 274

Two IACS Lecturers were each awarded the Harvard University Certificate of Teaching Excellence by the Derek Bok Center for Teaching and Learning three times, after receiving average course ratings of 4.5 or greater on a 5-point student evaluation scale.

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Members of the IACS Advisory Board and CSE Program CommitteeRyan Adams Harvard SEASAlán Aspuru-Guzik Harvard Chemistry & Chemical BiologyEdo Airoldi* Harvard StatisticsDavid Bear Goldman SachsKatia Bertoldi* Harvard SEASAlan Bishop Los Alamos National LaboratoryMichael Brenner* Harvard SEASDavid Brooks Harvard SEASDavid Brown Lawrence Berkeley LaboratoryJennifer Chayes Microsoft ResearchMarie Dahleh Harvard SEASBijan Davari IBMBrenda Dietrich IBMGeorges El-Fakhri Harvard Medical School/Brigham & Women’s HospitalOzlem Ergun Harvard SEAS/Georgia TechDoug Finkbeiner Harvard AstronomyBruce Fischl Harvard Medical School/Massachusetts General HospitalDavid Gilmour Blyth Capital PartnersFawwaz Habbal Harvard SEASJames Hurley IntelDaniel Jacob Harvard SEASEfthimios Kaxiras* Harvard SEAS/Harvard PhysicsGary King* Harvard Institute for Quantitative Social SciencesEddie Kohler Harvard SEASSamuel Kou Harvard StatisticsZhiming Kuang* Harvard SEAS/Earth & Planetary SciencesDavid Luebke NVIDIAL. Mahadevan Harvard SEASJoe Marks Disney LabsBrendan Meade Harvard Earth & Planetary SciencesXiao-Li Meng Harvard StatisticsGreg Morrisett Harvard SEAS

Cherry Murray Harvard SEASMichael Papka Argonne National LaboratoryDavid Parkes* Harvard SEASHanspeter Pfister* Harvard SEASBruce Rosen Harvard Medical School/Massachusetts General HospitalJeffrey Saltzman AstraZenecaJeffrey Schnapp* Harvard Romance Languages/Berkman Center for Internet and SocietyMargo Seltzer* Harvard SEAS

Sadasivan Shankar Intel

IACS People

*Member, CSE Program Committee



Guy Steele Oracle LabsFred Streitz Lawrence Livermore National LaboratoryChristopher Stubbs* Harvard Physics/AstronomyEli Tziperman Harvard SEAS/Earth & Planetary SciencesLeslie Valiant Harvard SEASJohn Wakeley Harvard Organismic & Evolutionary BiologyJim Waldo* Harvard SEASMatt Welsh GoogleKatherine Yelick Lawrence Berkeley Laboratory

*Member, CSE Program Committee

Administrative and Teaching StaffRosalind Reid Executive Director 2010–13Joy Sircar Chief Technologist 2010–13Natasha Baker Administrative Coordinator 2011–Pavlos Protopapas Lecturer 2011–

Scientific Program Director 2013–

Daniel Weinstock Assistant Director of Graduate Studies 2012–Lecturer 2013–

Meg Hastings Interim Executive Director 2013–14Cristopher Cecka Lecturer 2011–David Knezevic Lecturer 2011–14Hudong Chen Visiting Professor 2011Zhenyu Zhang Visiting Professor 2012Ian Stokes-Rees Lecturer 2012–13Brad Malone Lecturer 2013Sadasivan Shankar Distinguished Scientist in Residence 2013

Research Visitors and Student Researchersby appointment date

2011

Dmitri Vinichenko Research Intern William Juan Research InternKunal Tiwari Research Intern Ayub Hanif FellowMauro Bisson Postdoctoral Fellow Pablo Huijse Heise FellowDae-Won Kim ResearcherOnyekwelu Okeke Postdoctoral Fellow 2013Gao Han Research Intern Nicholas Jin Research InternBrian Hayes Associate Daniel Acuña Research InternAlexander Wissner-Gross Institute Fellow Ruth Ashley Research Intern

Eduardo Lopez Beeche Research Intern2012 Wesley Chen Research InternJimmy Zhu Research Intern Jordan Dodson Research InternFei Gao Fellow Michelle Len Research InternWei Chen Fellow Gavin McCauley Research InternKarim Pichara Postdoctoral Fellow Marcelo Stöckle Research InternCaroline Scott Fellow Darragh Tobin Research InternXiaoguang Li Fellow Isadora Nun Fellow

IACS Advisory Board and CSE Program Committee (cont.)



IACS Seminars and Symposia

2011–12 Seminars

Planetary-Scale Computing Alexander Wissner-Gross

Research Affiliate, MIT Media Laboratory

The Future of Computing Systems and Technology Bijan Davari IBM Fellow and Vice President, Next Generation Computing Systems and Technology

The Reduced Basis Method for Fast and Accurate Solutions of Parametrized Partial Differential Equations

David Knezevic Lecturer in Computational Science, SEAS

The Fast Multipole and Tree Methods in High-Performance Computing

Cris Cecka Lecturer in Computational Science, SEAS

Molecular Movies: Exploring Hollywood’s Tools for Biovisualization

Gael McGill Director of Molecular Visualization, Harvard Medical School; founder and CEO, Digizyme, Inc.

Scaling Lattice QCD Calculations Beyond 100 GPUs Mike Clark Research Associate, Harvard-Smithsonian Center for Astrophysics

The Harvard Clean Energy Project: Finding Renewable Energy Materials One Screensaver at a Time

Alan Aspuru-Guzik Associate Professor of Chemistry and Chemical Biology, Harvard

Rethinking Randomness: Alternative Characterizations of Uncertainty in the Real World

Jeffrey Buzen Founder, BGS Systems

New Approaches in Period Finding for Irregular Time Series: Looking for Periodic Signals from the Cosmos

Pavlos Protopapas Research Associate, Harvard-Smithsonian Center for Astrophysics; Lecturer in Computational Science, SEAS

Solving Differential Equations with Chebfun Nick Trefethen Professor of Numerical Analysis and Head of the Numerical Analysis Group, University of Oxford

Interatomic Potentials, Forces and the Uniqueness of Stress

Ellad Tadmor Professor of Aerospace Engineering and Mechanics, University of Minnesota

Metamaterials for Wave Engineering: A Novel Computational Paradigm

Hossein Mosallaei Associate Professor and Director, Computational EM and Photonics Laboratory, Northeastern University

Aerodynamics and Fluid-Structure Interaction Modeling of Wind Turbines: Methods and Applications

Yuri Bazilevs Assistant Professor of Structural Engineering, UC San Diego

Visual Computing in Connectomics Hanspeter Pfister Gordon McKay Professor of Computer Science, SEAS

Efficient Modeling of Solid Phases: From Thermodynamics to Kinetics

Axel van de Walle Associate Professor of Engineering, Brown University

Squeezing Electrons in Conventional Metal Films and Topological Insulator Heterostructures

Zhenyu Zhang University of Science and Technology of China

Computation and the Human Predicament Brian Hayes Senior Writer, American Scientist

Electrons Moving Atoms in Nanoelectronics Kirk Bevan Assistant Professor, McGill University

Markov Chain Monte Carlo Methods for Machine Learning

Ryan Adams Assistant Professor of Computer Science, SEAS

Can Research Computing Teach Us Anything? Christopher Hill Principal Research Engineer, MIT

Frontier Cosmology and GPU Computing Lincoln Greenhill Lecturer, Department of Astronomy, and Senior Research Fellow, Harvard; Radio Astronomer, Smithsonian Astrophysical Observatory

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Applications-Driven Systems Design Bijan Davari IBM Fellow and Vice President, Next Generation Computing Systems and Technology

How Cloud Computing Changes Everything Matt Welsh Software Engineer, Google Inc.

The Democratization of Parallel Computing David Luebke Director of Research, NVIDIA Corp.

In Silico Paradigm for Virtual Prototyping in Materials and Chemistry

Sadasivan Shankar Senior Principal Engineer, Program Leader for Materials Design, Technology and Manufacturing Group, Intel Corp.

Toward In Silico Integrated Design in the Pharmaceutical Industry

Jeffrey Saltzman Senior Director, Predictive Computational Sciences Research and Development Information, AstraZeneca Pharmaceutical

Efficient Simulation of Multiscale Kinetic Transport Nicolas Hadjiconstatinou

Professor of Mechanical Engineering; Director of Computation for Design and Optimization, MIT

Scientific Computing for Movie Special Effects and Virtual Surgery

Joseph Teran Associate Professor of Applied Mathematics, UCLA

Leveraging High-Performance Parallel Computing for Biologically Inspired Object and Face Recognition

David Cox Assistant Professor, Molecular and Cellular Biology and Center for Brain Science, Harvard

Sequential Monte Carlo Methods for Computational Finance and Astrophysics

Ayub Hanif IACS Fellow; Research Student, Doctoral Centre in Financial Computing, University College London

Overview of Scientific Activities at D. E. Shaw Research

Paul Maragakis and Zhou Fan

Research Scientist and Scientific Programmer, D. E. Shaw Research

A Computational Engineer Combusts Margot Gerritsen Professor ofEnergy Resources Engineering; Director, Institute for Computational and Mathematical Engineering, Stanford

Design and Analysis of Experiments that Leverage Social Structure and Interactions

Edoardo Airoldi Assistant Professor of Statistics and Systems Biology, Harvard

Will “Big Data” Yield Big Insights about Human Society?

David Lazer Professor of Political Science and of Computer andInformation Science, Northeastern University

Exploring Energy Landscapes: From Molecules to Nanodevices

David Wales University Professor of Chemical Physics and Deputy Head, Department of Chemistry, University of Cambridge

The Giza Pyramids, 3D Technologies, and the Challenges of Archaeological Information Management

Peter Der Manuelian

Philip J. King Professor of Egyptology, Harvard

Multiphysics and Multiscale Modeling of Cardiac Dynamics

Boyce Griffith Assistant Professor of Medicine, NYU; Affiliate, Courant Institute of Mathematical Sciences

The Network Effect: Integrative Systems Approaches to Modeling Biological Processes

John Quackenbush Professor of Biostatistics and Computational Biology/Cancer Biology, Dana-Farber Cancer Institute; Computational Biology and Bioinformatics, Harvard School of Public Health

Multi-Scale Seizure Dynamics Mark Kramer Assistant Professor of Mathematics and Statistics, Boston University

Possible Infrastructures for Data Science Jeff Hammerbacher Chief Scientist, Cloudera; Assistant Professor, Mount Sinai School of Medicine

Designing Visualizations for Biological Research Miriah Meyer USTAR Assistant Professor, School of Computing and Scientific Computing and Imaging Institute, Universityof Utah

Evolution of the Cancer Genome Franziska Michor Associate Professor of Biostatistics and Computational Biology, Dana-Farber Cancer Institute; Biostatistics, Harvard School of Public Health

2012–13 Seminars

Mini-Symposium January 13, 2012: The Future of Computation in Science and Engineering

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http://computefest.seas.harvard.edu/future-computation-science-2012


First Links in the Markov Chain: Poetry and Probability

Brian Hayes Senior Writer, American Scientist

From Markov to Pearl: Conditional Independence as a Driving Principle for Probabilistic Modeling

Ryan Adams Assistant Professor of Computer Science, SEAS

Applications of Markov Chains in Science Pavlos Protopapas Lecturer in Computational Science, SEAS

Mini-Symposium January 23, 2013: Celebrating 100 Years of Markov Chains

Symposium January 25, 2013: Computing @ Exascale Molecular Simulation and the Future of Biology David E. Shaw Chief Scientist, D. E. Shaw Research; Senior Research Fellow,

Center for Computational Biology and Bioinformatics, Columbia University

The Promise of Urban Informatics Steven E Koonin Director, Center for Urban Science and Progress, New York University

If Exascale is the Answer, What Is the Question? Sadasivan Shankar Senior Principal Engineer, Program Leader for Materials Design, Technology and Manufacturing Group, Intel Corp.

Science in the Cloud Joseph L. Hellerstein Manager, Computational Discovery for Science, Google Inc.

Computational Science, Innovation, and International Competitiveness

David Turek IBM Vice President, Exascale Systems

Transforming Scientific Discovery with Commodity Technologies

Stephen Keckler Senior Director of Architecture Research, NVIDIA, and Adjunct Professor of Computer Science, University of Texas at Austin

Race to Exascale: Opportunities and Challenges Stephen S. Pawlowski Intel Senior Fellow; CTO, Intel Architecture Group; General Manager, Cross-IAG Architecture and Pathfinding, Intel Corp.

Computational Science Ventures Speakers2012

January 17 Dean Kamen Founder and President, DEKA Research & Development Corporation

January 18 Maria Lopez-Bresnahan Vice President and Global Head for Medical and Scientific Affairs, Pharmanet/i3

January 19 Luke Burns Partner, Ascent Venture Partners

January 20 Stephen Wolfram Founder and CEO, Wolfram Research

2013

January 24 Dan Cerutti General Manager of Watson Commercialization, IBM

Alexander Onik President, ScienceGL

Ben Vigoda General Manager and Technical Director, Analog Devices Research Labs

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Fall 2013 SeminarsMultiscale Hemodynamics: Using Computation to Diagnose and Predict Heart Disease

Efthimios Kaxiras John Hasbrouck Van Vleck Professor of Pure and Applied Physics, Harvard

Prediction, Renaissance, and Cognition—Three Questions for Computing

Sadasivan Shankar Distinguished Scientist in Residence, IACS

How the Brain Handles Big Data Dmitri Chklovskii Group Leader, HHMI Janelia Farm Research Campus

10 Simple Rules for the Care and Feeding of Scientific Data

Mercé Crosas Director of Data Science, Institute for Quantitative Social Science

Probabilistic Programming and Probability Processing

Ben Vigoda Director, Analog Devices Lyric Labs

Deep Learning for Distribution Estimation Hugo Larochelle Assistant Professor of Computer Science, Université de Sherbrooke


http://computefest.seas.harvard.edu/exascale-symposium

http://computefest.seas.harvard.edu/markov


CSE Secondary Field students with distinguished presenters and special guests gathered for lunch at the Computing @ Exascale symposium, 2013

Members of the inaugural class of CSE Master of Science students with IACS administrative and teaching staff

Helping launch a new generation of computational scientists

with special thanks to Eliza Grinnell for photography and design of the IACS logo


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