We are happy to announce that Lawrence Saul has accepted a position as Associate Professor with the Artificial Intelligence group. Professor Saul's interests are in machine learning and its applications, and he is particularly well known for his work on nonlinear dimensionality reduction. He will be joining CSE in July from the University of Pennsylvania's Department of Computer and Information Science, and will be continuing his research in machine learning, pattern recognition, and voice processing. Prior to joining U Penn, Lawrence worked at AT&T Labs, and received an A.B. from Harvard and a Ph.D. from MIT.

On April 1st, US News and World Report released its 2006 reputation rankings of graduate programs in the United States. UCSD's computer science and engineering department was elevated to the 13th position overall -- the largest jump of any program in the top 30. In addition, UCSD was ranked among the top twenty in all computer science specialties (9th in Systems, 14th in Theory, 17th in Programming Languages and 19th in Artificial Intelligence). Finally, UCSD's interdisciplinary program in Genomics, Genetics and Bioinformatics was ranked 6th in the nation. Over the twelve years in which US News has ranked graduate computer science programs, UCSD's rise has been unprecedented and unmatched by any program in the country. This recognition has mirrored the tremendous growth of the department over this time, the enthusiasm of its students, staff and faculty and the widespread impact of our research. We invite you to peruse our recent activity and achievements in our 2005 departmental brochure.

Faculty, staff, and grad students recently took a break from work to celebrate the end of the academic year. The fiesta featured carne asada, pollo, and carnitas tacos grilled in the engineering courtyard. Rice and beans, along horchata and jamaica drinks rounded out the menu. Keith added a multicultural flair with a quick ukulele sing-along. You can view photos from the event by clicking here. Thanks for attending; have a great summer!

CSE's Undergraduate Affairs Coordinator, Pat Raczka, was nominated for the University's Exemplary Staff Employee of the Year award. Pat was one of five people selected from the Jacobs School, and the only person from CSE. In nominating Pat, lecturer Susan Marx said: "(Pat) has exceeded her job duties by extending her caring assistance to help the CSE undergraduate faculty." The full list of nominees is available here.

The CSE department is excited to welcome Steve Swanson as our newest faculty member! Professor Swanson recently completed doctoral work at the University of Washington, and will be joining our faculty as an Assistant Professor with the Computer Architecture and Compilers research group. His interests lie primarily in unconventional processor architectures, and their inherent problems of performance, power, and programmability. From 2004-2005, Swanson held a University of Washington Microsoft Endowed Fellowship. Prior to this, he was awarded fellowships from Intel (2002-2003), and the National Science Foundation (1999-2002).

Professor Joseph Amadee Goguen passed away peacefully in the early morning of July 3, 2006. He was in the company of his wife Ryoko, daughter Alice, and a few close family friends. He is also survived by another daughter Heather and a son Healfdene. You can read more about Professor Goguen and his life's accomplishments here.

CSE graduate Jon Sundt ('86) has given UCSD's Recreation department its first major financial donation. The gift was made in honor of three of Sundt's relatives. His two brothers succumbed to drug use, and Sundt hopes enhancements to the Recreation department will be a healthy outlet for students dealing with stress and problems. Sundt's father, who recently lost a battle with cancer, is also included in the tribute. UCSD Recreation is a department within Academic Affairs that aims to provide a broad scope of recreational experiences for students, staff, faculty, and the University community. Sundt is founder and president of Altegris Investments in San Diego; the press release announcing his gift is available here.

The department welcomes 19 high school students who are taking part in our COSMOS (California State Summer School for Mathematics and Science) cluster. Entitled "Adventures in Media computing," students will use computer programming to creatively manipulate graphics, audio, video, and text in an integrated way. The students will master media programming concepts, and ultimately through this experience get a taste for some of the exciting, innovative implementations of computer science. As a final project, students will work in teams to create presentations that will be shown in spectacular form in UCSD's state-of-the-art Calit2 digital theater. More information about the program can be found on websites for the UCSD COSMOS program and the CSE Cluster.

CSE staff members gathered for a kanikapila, or social gathering where Hawaiian style music is played. The recital was the culmination of 10 weeks of ukulele lessons given by CSE Chair Keith Marzullo. Over the course of the class, students learned chords and finger-picking to play both traditional Hawaiian and contemporary "western" songs. Accompanying the students on bass was Lecturer Paul Kube. The kanikapila's program featured such varied songs as the C&H Sugar Cane jingle, Bob Marley's "No Woman, No Cry," and a selection of traditional Hawaiian tunes. Photos available here. Great job, everyone!

CSE faculty, staff, and grad students gathered for a Hawaiian-themed party that included sushi, veggies, pineapple, potato salad, and punch. The only thing missing was loco moco! Photos from the fall party are available here. Also announced during the fete was the weekly Friday social hour to be hosted by rotating labs during the school year. Be sure to check the first one beginning Friday, October 6! Have a great year!

CSE continues to grow with the addition of 182 new fall 2006 undergrads. A student orientation was held on September 16 to welcome them and included Frieder Seible, Dean of the Jacobs School of Engineering; Paul Kube, Vice Chairman for Undergraduate Affairs; lecturer Rick Ord; and staff members Patricia Raczka and Viera Kair. Along with all the essential information (like where the building's paint colors can be purchased for the coolest dorm room on campus), the new course requirements for the Computer Engineering degree (administered jointly with the Department of Electrical and Computer Engineering) were announced.

A rousing afternoon of Office Olympics kicked off CSE's first Friday social hour. Billed as "a yearly festival of free beer, free food, and intense athletic competition," the organizers made good on their no-holds-barred promise with such games as chair(iot) racing, rubber band archery, soda can jenga, and pen javelin. For those unable to attend, photos are available here. Office 3260, consisting of programming languages and architecture students, was responsible for this week's fun; offices will take turns planning the weekly event with $1,000 going to the hosts of the year's best event. Friday socials are held on the fourth floor terrace at three o'clock and are open to faculty, staff, and grad students.

Bioformatics Ph.D. student Noah Zaitlen has been awarded a Microsoft Research Fellowship! The award will support his research into the development of methods to better understand the genetics of common human diseases. Zaitlen is advised by CSE professor Eleazar Eskin, and is currently undecided about pursuing a career in academia or the private sector. Begun in 1997, Microsoft Research's Graduate Fellowship program provides outstanding graduate students with tuition and fees, a TabletPC, a stipend, and a conference allowance. The program is open to students at U.S. and Canadian universities who are pursuing studies in the fields of computer science, electrical engineering, or math. Each year, the award is given to approximately 12 students for a two-year period, and may be extended for a third. More information about the Fellowship program is available here. Congratulations, Noah!

The Alfred P. Sloan Foundation has recognized CSE's Alin Deutsch with a prestigious research Fellowship! The distinction is one of 116 given annually to young U.S. and Canadian faculty who show "the most outstanding promise of making fundamental contributions to new knowledge." Deutsch is a member of CSE's database group, and his research focuses on providing infrastructure for publishing and consuming data on the Web, particularly by exploiting the Extended Markup Language (XML). Deutsch's Sloan award is the second in as many years given to CSE researchers; Serge Belongie was honored last year. The full press release is available here, and the complete list of this year's awardees can he found on the Sloan website. Congratulations, Alin!

Full-time lecturer Rick Ord was recently named Outstanding Faculty of the Year by our campus chapter of Tau Beta Pi, a nation-wide engineering honor society. The award will be given at the Jacobs School of Engineering's Recognition Banquet on May 19, and also announced at Tau Beta Pi's end-of-the-year banquet. Ord is a popular professor who is also a three-time winner of the Jacobs School of Engineering Teacher of the Year award for the CSE department, the most recent being last year (2004-2005). Way to go, Rick!

Postdoc Ben Raphael, along with CSE's Pavel Pevzner, has developed algorithms to understand how a cancer genome breaks apart and gets put back together. The undertaking is a joint venture with the UC San Francisco Cancer Center, Wellcome Trust Sanger Institute, Amplicon Express, Evrogen JSC, Lawrence Berkeley National Laboratory, and the Joint Genome Institute. Raphael's technique is called End Sequence Profiling (ESP), and exploits the fact that the mutagenetic processes that result in a tumor are similar to that of evolutionary genomic rearrangements, except they occur on a vastly expedited timescale. ESP determines some of a tumor's DNA base pairs and infers the missing pieces from comparisons with the unchanged genome. These data then suggest areas of the genome that UCSF Cancer Center researchers should examine more closely. You can read more about Ben Raphael's research, which is published in this month's Genome Research here.

Professor Geoff Voelker has been honoroed with the Chancellor's Associates 2006 award for excellence in undergraduate teaching. The selection committee chose Voelker for his "fresh teaching approach, tireless advocacy for student efforts and exceptional contributions" to the CSE department. Voelker has consistently received outstanding student reviews, especially from those who participate in his wildly popular Software System Design and Implementation course. CSE 125 teams seniors in their final quarter on projects to build a multi-player, networked computer game over the course of ten weeks. Voelker's award was one of five bestowed on faculty members for their scholarship and overall contributions to the University and the community. Follow a link for more information about the Chancellor's Awards or to read the press release.

The National Science Foundation has awarded fellowships to three CSE graduate students. Current student Michael Vrable and entering students Krista Davis and Qing Zhang were each given fellowships that include three years of financial support. Additionally, current Ph.D. candidate Justin Ma and soon-to-be CSE student Nathan Bales were chosen for Honorable Mention awards. A total of 61 fellowships were awarded to U.S. students in the category of Computer and Information Science and Engineering for 2006; a full list of the winners is available here. Congratulations!

Undergraduate students Khawaja Shams, Son Dinh, and Darren Dao have been awarded one of two Best Poster awards at the Pt. Loma Nazarene Undergraduate Computer Science Conference. The poster highlighted the students' creation of InstaSEE, a process that allows instructors to automatically return paper documents via email through a scanner and paper-association process. With a prototype already built, and the students hope to offer the procedure to teaching assistants for the spring quarter. The conference's website can be found here.

CSE has been honored with one of 40 Technology for Teaching grants from HP. The award will provide expansion support for Ubiquitous Presenter (UP), a tablet-based educational technology system developed by professor William Griswold and lecturer Beth Simon. The $69,000+ gift will provide wireless equipment, other HP products, and a faculty stipend. These new resources will allow for the development of UP Note Blogger, a project that will explore the idea of treating traditional student note-taking in the classroom as blogging. Click here for the full press release.

CSE's Systems & Networking group authored five of the thirty-seven papers to appear at this year's ACM SIGCOMM -- the premiere networking research conference. The papers cover a range of topics including network modeling, high-speed traffic processing and large-scale analysis of wireless network activity.

The Howard Hughes Medical Institute (HHMI) has awarded CSE professor Pavel Pevzner a $1 million grant to be disbursed over four years. Pevzner is the first computer scientist to be named an HHMI professor. With these funds, Pevzner plans to introduce computer science and computational aspects of bioinformatics to all UCSD biology majors with a spring 2007 course on algorithmic biology. Additionally, he will develop collaborative research in bioinformatics for undergraduates by teaming them with grad students, postdoctoral researchers, and faculty. The HHMI developed the grant program in 2002 to "bring the excitement of scientific discovery to the undergraduate classroom." You may read more about Pavel's award here.

CSE's Fox Harrell was recently awarded a dissertation fellowship from the Ford Foundation. Fox's honor is one of only 35 given out annually to individuals who demonstrate superior academic achievement and are committed to a career in teaching at the college or university level. The fellowships provide one year of support for students working to complete a dissertation that will lead to a Ph.D. or Sc.D. degree. The program is administered by the National Research Council of the National Academies; you can find out more about the fellowship here.

Grad student Barath Raghavan has been honored with the Jacobs School's 2006 R.B. Woolley Leadership Award. The award was established to recognize outstanding leadership and productivity in engineering students, and includes a $5,000 award. Richard "Buzz" Woolley, a local retired venture capitalist, is the president of the Girard Foundation and a UCSD benefactor. Students are nominated by their advisor and department chair, based on criteria of demonstrated leadership in the department or beyond as well as substantive research accomplishments. A press release is available here.

Professor and Associate Dean Jeanne Ferrante has been recognized by the Association for Computing Machinery for her work on the Static Single Assignment (SSA) form, a data structure that has led to more efficient and powerful transformations for optimizing compilers. The Programming Languages Achievement Award recognizes "individuals who have made a significant and lasting contribution to the field of programming languages" and includes a $5000 prize. Sharing the award are past colleagues Ron Cytron, Barry Rosen, Mark Wegman, and Kenneth Zadeck who jointly developed SSA with Ferrante at IBM in the 1980's. Among Ferrante's key contributions to the effort was the realization that her earlier work on control dependence could form the basis for an efficient construction algorithm. SSA is commonly used today in production compilers, and is considered required reading for those studying optimizing compiler technology.

Pavel Pevzner and a team of researchers led by Adam Godzik of the Burnham Institute for Medical Research have been awarded a $2.1M grant to create tools to better interpret information gleaned from the human genome project. The Joint Center for Molecular Modeling (JCMM) will develop innovative software to extract rules and trends of how protein structures change and evolve. The consortium will make its tools available to other scientists worldwide through open-source databases; they may ultimately be applied to the design of smarter drugs. You can read more about the JCMM and its work by clicking here.

CSE grad students have created a biometric vending machine as an expansion of Chez Bob, the department's food co-op. Chez Bob utilizes a barcode scanner to purchase snacks--everything from ice cream bars to bananas--and a computer program to track each user's account balance. With the new soda machine, users are logged in via a fingerprint reader and their purchases are deducted from a pre-paid account. Facial recognition via a modified webcam is also in beta testing. The project is a collaborative effort between students from systems and networking, vision, theory, and software engineering, and is overseen by Professor Stefan Savage. Read more about this unique project here.

CSE's Database group presented a record seven papers at this year's ACM SIGMOD/PODS conference, one of which was given an honorable mention award in the Best Paper competition. Click here read about the papers' research. Congratulations!

Sumeet Singh has been named one of the nation's top 35 innovators under age 35 by MIT's Technology Review magazine. Singh is being honored for research he started as a Ph.D. student in the CSE department. The project yielded a new way to identify worm and virus attacks across the Internet or other high-speed networks almost as soon as outbreaks occur. Click here to read the full press release.

Four undergrads have been awarded $12,500 to study distance tutoring, especially exploring the impact Tablet PCs might bring to such efforts. The students are: Morgane Botella, Mercedes R. Lopez, Stephanie Y. Lui, and Stephanie Mattingly. This work is funded under the Collaborative Research Environment for Undergraduates in Computer Science and Engineering (CREU), an initiative sponsored by the Computing Research Association Committee on the Status of Women in Computing Research (CRA-W) and the National Science Foundation. The project will be supervised by lecturer Beth Simon and graduate student Krista Davis.

Congratulations to Ross Tate for winning CSE's eighth annual fall programming contest. Students were given five hours to solve six algorithm problems and were allowed to submit answers in C, C++, or Java. To keep contestants fueled during the intense competition, pizza and soda were provided. Tate received $2,000 for first place and an extra $2,500 for solving all six puzzles within the time limit. Kei Shun Ma finished in second place and Eli Friedman took third. This year's contest results will be used to form teams for ACM's 2006 Southern California programming contest. Click here for a complete recap of the event. Thanks to The Dini Group for their continued, generous financial support.

Masters students Nathan Farrington and Jerry Fu have been awarded the DoD's 2006 Science, Mathematics, and Research for Transformation (SMART) scholarship. As recipients, the students will continue their graduate studies while working at the Space and Naval Warfare Systems Center in San Diego. Farrington and Fu are among 32 national recipients of the scholarship and will receive tuition reimbursment and a stipend while working for the Department of Defense. The complete press release is available here.

Computer Science & Engineering Ph.D. candidate Nuno Bandeira has won the Human Proteome Organization's 2006 Young Investigator Award for his work creating a new protein analysis technique. Developed for the proteins found in snake venom, Baneira's approach should be useful in studying a wide range of highly modified proteins that, due to technical limitations, was previously difficult. The approach is expected to aid drug development, increase understanding of cancer proteins and, perhaps, let scientists dive into dinosaur genetics. Bandeira was the only Ph.D. student among the award's five finalists. You can read more about Bandeira's research by clicking here.

Nine graduate programs and 13 departments are collaborating in a new graduate educational program at the crucial interface of biology, medicine, and physical and engineering sciences. The curriculum will include six new hands-on graduate laboratory courses taught by interdisciplinary teams of faculty members who will introduce students to state-of-the-art techniques studying living systems. In CSE, professors Vineet Bafna and Pavel Pevzner will each be teaching courses for the program. UCSD is one of 10 universities that will use $1 million each provided over three years by the Howard Hughes Medical Institute to initiate the new program. The Jacobs School press release can be found here.

Three Computer Science and Engineering graduate students play key roles in "Scalable City"--the high-profile interactive multimedia project led by Sheldon Brown, director of the Center for Research in Computing and the Arts (CRCA). It opened August 29 at Ars Electronica, the world's top new-media conference and a permanent museum in Linz, Austria. CSE grad student Joey Hammer was the 'buildmaster' on Scalable City--making him responsible for tying the various subsystems into a single software framework. Erik Hill took an algorithm for plant growth and applied it to the road construction. The game physics were handled by Daniel Tracy. For more, click here.

CSE recently took part in Operation College Freedom, a disaster exercise on the UCSD campus that tested new technologies designed for first-responders. Coordinated by San Diego's Metropolitan Medical Strike Team (MMST), the drill was a cooperative effort between Calit2, UCSD's School of Medicine, law enforcement, and first-responders. WIISARD, or the Wireless Internet Information System for Medical Response in Disasters, was one of 12 primary technologies deployed during the exercise. A system for the tracking of mass casualties, triage, and managing all medical information, WIISARD combines state-of-the-art networking, data collection, display devices and database services to produce a consistent, real-time view of the disaster scene. For more information about the drill and the technologies utilized, click here.

With the announcement of this year's COSMOS program, the department of Computer Science & Engineering will again be taking part in this program that gives talented high school students a taste of college life. COSMOS (California State Summer School for Mathematics and Science) is a month-long residential program designed to encourage students to continue their interest in science. The curriculum is broken into seven units known as clusters. This year's computer science cluster will be titled "Adventures in Media Computing" and will be overseen by Professor Joe Pasquale. CSE lecturers Paul Kube and Beth Simon (along with Christine Alvarado from Harvey Mudd College) will assist. Read the full article and visit the COSMOS website for more information.

Pavel Pevzner, together with JSOE colleagues Xiaohua Huang and Michael Heller, has been awarded a National Institutes of Health grant to create a breakthrough method that will radically streamline the way the human genome is sequenced. In order to sequence the 23 pairs of human chromosomes, its DNA must be cut into tens of million to hundreds of millions of pieces. Pevzner is developing techniques to computationally reassemble these chromosomes by piecing together the overlapping ends of all the fragments after they have been sequenced. The trio of researchers will attempt to simultaneously sequence more than 1 billion individual DNA molecules. You can read more about the research by clicking here.

Larry Smarr and Marv Frazier of the J. Craig Venter Institute are leading a new research project to help scientists study microbes in their natural ecosystems. CAMERA, or the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis, will build a state-of-the-art computational resource and develop software tools to decipher the genetic code of communities of microbial life in the world's oceans. UCSD's Calit2 (of which Smarr is director) will head the project in conjunction with the J. Craig Venter Institute, and UCSD's Center for Earth Observations and Applications. CSE's Ingolf Krueger is a co-PI on the project, which is funded by a grant from the Gordon and Betty Moore Foundation. Please see the San Diego Union-Tribune and Jacobs School of Engineering for complete coverage.

Online DVD rental company Netflix has created a competition to improve their movie recommendation program and tapped CSE's Charles Elkan to help design the system. A veteran organizer of data mining competitions, Elkan consulted for Netflix to create a leader board, design the competition's timeline, and advocated for data segregation to discourage systems geared specifically to the training data. Click here to read the full article.

The Jacobs School of Engineering's annual awards banquet recognized several current and former CSE affiliates at this year's festivities. Lecturer Rick Ord was honored with the Tau Beta Pi Teacher of the Year Award. Rick is a popular instructor who has previously been honored with a slew of previous teaching awards at UCSD. The Digital Nursing Project, overseen by CSE's Bill Griswold, was recognized with the Teams in Engineering Service Award. Digital Nursing replaces hand-written logs with software to track patient information. JSOE also honored Dogan Koslu, '90, with the Outstanding Alumnus Award. Koslu is the founder of Treyarch, an Activision studio that produces computer games. A full list of awardees can be found online here.

Associate Professor Lawrence Saul's work recently achieved the distinction of being in the top 1% of citations in the field of Engineering, according to Essential Science Indicators. Saul's interest is machine learning and his most frequently cited paper, published in Science in 2000, proposed a nonlinear approach to analyzing and visualizing high-dimensional data. in-cites, a website that provides commentary and analysis on the most influential modern-day scientific discoveries, recently interviewed Saul about the work that has proven so important.

Researchers from Calit2's WIISARD project (Wireless Internet Information System for Medical Response in Disasters) successfully demonstrated their mass-casualty patient tracking system during the California EMS Authority's annual Rough and Ready on May 7, the largest state-wide emergency preparedness exercise. WIISARD enables the creation of real-time electronic medical records of victims triaged at disaster scenes. This information, both aggregated and individually, is available to medical personnel throughout a deployed WIISARD system: supervisors at the scene, the command center, and at the receiving hospital. WIISARD brings together broad-based participation from UCSD's School of Medicine and Jacobs School of Engineering, industry, the military, and emergency responders from the City and County of San Diego. Click hereto read more about the disaster drill.

CSE professor Serge Belongie is leading a computer vision research initiative to create tools that give better independence to the visually impaired. A collaborative effort with Calit2 and the University of Kentucky, the project is still in an early development phase. If it receives sufficient funding, Belongie and collaborators hope to create portable devices that "see" and help the visually impaired do things such as shop for groceries by themselves. More information about this project is available here.

Jeanne Ferrante, CSE professor and Associate Dean at the Jacobs School of Engineering, and Francine Berman, CSE professor and Director of the San Diego Supercomputer Center, sat down together to talk about pressing issues facing women in engineering in anticipation of the Grace Hopper Celebration of Women in Computer 2006 conference in San Diego. You can read a transcript of the conversation here.

It was in his mother's frustration with digital camera software that CSE alumnus Ryan Sit ('02) found his master's thesis. And from that research came DropShots, a website that automatically organizes, formats, and uploads a user's photos and videos to the Web. Users and invited guests can then view the photos and post comments online. More about the genesis of DropShots is available here.

UCSD's William J. von Liebig Center for Entrepreneurism and Technology Advancement has awarded approximately $430,000 to nine projects led by Jacobs School of Engineering faculty, including three from CSE. Pavel Pevzner and Vineet Bafna will be collaborating on a software project to process the data sets that result from mass spectrometry, or the measurement of wavelengths of light or other electromagnetic radiation. Yannis Papakonstantinou will use his award to develop app2you, a platform for the construction of innovative web applications. David Kriegman plans to leverage the financial resources of his award to develop a powerful suite of software products for processing human faces in digital images and videos. The von Liebig Center was set up in 2001 to foster entrepreneurism education and to provide funding and advisory services to technology projects at the Jacobs School that show strong commercial potential. More information about the awards is available here.

Researchers will convene at UCSD this week for a trio of conferences, Algorithmic Biology and RECOMB's Satellite Workshops on Systems Biology and Computational Proteomics. The Algorithmic Biology conference is the first in a series to be organized by the newly-established Center for Algorithmic and Systems Biology (CASB) at Calit2. Faculty from UCSD's CSE and Bioengineering departments will chair the conferences that run from November 30 to December 3. Registration is still open.