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  • Recent Faculty Recruit on Importance of Microbiome

    The TED Talks website has posted a much-awaited presentation by UC San Diego professor of pediatrics as well as computer science, Rob Knight. Actually, it was recorded at TED 2014 nearly a year ago, when Knight  was still a Howard Hughes Medical Institute Early Career Scientist at the University of Colorado Boulder. Knight made the switch to UC San Diego early this year, and the TED organization finally lifted the free-viewing curtain on the video of his March appearance at TED 2014 in Vancouver.

    Then, in just over 24 hours, approximately 125,000 visitors viewed Knight's talk on "How our microbes make us who we are." What's more, TED Books began to sell the hardcover as well as Kindle and audio CD editions, all through Amazon. The book based on Knight's presentation, now dubbed "Follow Your Gut: The Enormous Impact of Tiny Microbes" (see photo below), will be released on April 7.

    In his original TED presentation, now available for free on the TED website and via TED apps or iTunes, Knight is described as a "microbial ecologist", which, while true, is an understatement of his impressive credentials. After earning his Ph.D. from Princeton, he became an expert in the human microbiome, mgicrobial community ecology and what he now calls "multi-omics". In joining UC San Diego's Biomedical Sciences (BMS) Graduate Program in the focus areas of bioinformatics and glycobiology, Knight simultaneously agreed to spend part of his time working closely with the team of bioinformatics faculty in the Computer Science and Engineering department.

    "A major challenge in microbiome research is in computation," said Knight.  "The ability to generate the data has greatly outstripped a lot of people's ability to analyze the data." Knight's decision to join the UC San Diego faculty is owed, at least in part, to the university having "a unique combination of high-performance computing, immunology... " as well as other companies, institutions and hospitals.

    "Ninety percent of the cells in your body are not human," said Calit2 Director Larry Smarr, quoted in the San Diego Union-Tribune when the hire of Rob Knight was announced. "They are bacteria located in places like your large intestine. Medicine has been ignoring those microbes. But that's changing, and UCSD will be a leader in this transformation. Indeed, Smarr hopes to move his own research into Knight's larger lab once it is fully established.

    Watch the webcast of Rob Knight's TED 2014 talk or read the Interactive Transcript.

  • CSE Chair Comments on First U.S. Chief Data Scientist

    When the San Diego Union-Tribune looked for an assessment of incoming White House chief data scientist DJ Patil, the newspaper turned to CSE chair and professor Rajesh Gupta for a comment: "DJ perfectly reflects UCSD's core: young and [on the] leading edge of science." In the article about President Obama elevating Patil to be the first-ever U.S. Chief Data Scientist, the reporter noted that the CSE department, "which has more than 2,500 students, has been straining to meet enrollment demand, partly because of soaring interest in data science."

    Patil received his undergraduate degree from UCSD in 1996, but from mathematics, not computer science. At the time, the computer science program was much smaller than it is today. Patil later earned his Ph.D. in 2001 from the University of Maryland, where he also began his teaching career. At various points Patil has served in industry, including stints at eBay as a distinguished research scientist, and as chief scientist for social-media giant, LinkedIn. Most recently, Patil was a data scientist in residence at one of the oldest venture-capital firms in Silicon Valley, Greylock Partners.

    In his first memo as U.S. Chief Data Scientist, DJ Patil noted that "'big data' has become a regular part of our daily lives. In 2013 researchers estimated that there were about four zettabytes of data worldwide: That's approximately the total volume of information that would be created if every person in the United States took a digital photo every second of every day for over four months!" But Patil was upbeat in hs first official memo, titling it: "Unleashing the Power of Data to Serve the American People."  The good news for Patil is that he doesn't have to move. He is already deputy Chief Technology Officer for Data Policy in the White House Office of Science and Technology Policy, and Patil has assumed the Chief Data Scientist as well. His most immediate priority is in President Obama's Precision Medicine Initiative (tapping medical and genomic data to transition from one-size-fits-all to truly personalized medicine).

  • CSE's Lovett Is Only UC Computer Scientist Honored with 2015 Sloan Research Fellowship

    This year five faculty from UC San Diego, and 18 from the system-wide University of California are being honored by the Arthur P. Sloan Foundation with Sloan Research Fellowships for 2015. And only 16 computer scientists from the U.S. and Canada made the cut.
    Indeed, only one professor of computer science among the 18 UC honorees was named, when the foundation singled out UC San Diego's Shachar Lovett. The expert in computational complexity studies the foundations of computer science, and how computational problems can be efficiently solved. "As the scientific, engineering and life sciences communities continue to be transformed by new, ever larger data sets, the motivation for designing very efficient algorithms to manipulate, store and transfer data is becoming ever more clear," said Lovett in his research statement to the Foundation. "Specifically I study how the interplay between structure and randomness plays a central role in algorithm design and analysis."
    The Sloan Research Fellowships seek to stimulate fundamental research by early-career scientists and scholars of outstanding promise. The two-year fellowships are awarded yearly to 126 researchers in recognition of distinguished performance and a unique potential to make substantial contributions to their field, in Lovett's case, computer science. Other UC San Diego researchers named Sloan Fellows included Padmini Rangamini (Computational and Evolutionary Molecular Biology), Paul Niehaus (Economics), Andrea Tao (Chemistry) and Bradley Voytek (Neuroscience). 
    "Their achievements and potential place them among the next generation of scientific leaders in the U.S. and Canada," noted the Foundation in a full-page New York Times advertisement, adding that since 1955, "Sloan Research Fellows have gone on to win 43 Nobel Prizes, 16 Fields Medal, 65 National Medals of Science" and numerous other honors.
    In addition to Lovett. the CSE department claimed another of its own in the form of University of Wisconsin-Madison professor Thomas Ristenpart, a relatively recent alumnus from UC San Diego (Ph.D,, 2010). Ristenpart also is a frequent co-author on cyber security or cryptography papers with current CSE faculty including Hovav Shacham, Mihir Bellare and Stefan Savage.
  • CSE Professor Partners with Instagram Co-Founder on Coursera

    Coursera is pushing further into specialized sequences of courses that may be more attractive to people looking to boost their career prospects. The largest network offering massive open online courses, or MOOCs, Coursera is also partnering with companies to help shape the curriculum.

    Case in point: CSE and Cognitive Science professor Scott Klemmer will launch a sequence of online courses in Interaction Design, beginning June 16 with Klemmer's own introductory course on Human-Computer Interaction Design. In it, students will learn how to design great user experiences and to apply their skills in a capstone project. Klemmer has recruited a partner in industry: Michel (Mike) Krieger, a co-founder of Instagram. Following the sequence of six courses (some as short as three weeks, or as long as nine), students must do a capstone project in which they design a creative, end-to-end user experience using professional interaction design and "UX" (user experience) tools. Krieger has agreed to provide feedback to students about their projects, and some of the best students will earn the chance to get personalized feedback from Krieger as well as from Prof. Klemmer. The capstone project is only available to students who pay to take the full sequence of Interaction Design courses, while all six courses prior to the capstone can be taken at no cost, as long as the student does not require a verified certificate (which are reserved for paying customers). For his part, Krieger said that similar coursework he took in college had a lasting impact on his career and on the design of Instagram. "As our devices become increasingly powerful," he said, "it's essential that we create a generation of designers and builders who can help people around the world harness that power."

  • Lab-in-a-Box Takes Aim at Doctors’ Computer Activity

    They call it “the Lab-in-a-Box.” According to Nadir Weibel, a research scientist in the Computer Science and Engineering (CSE) department at the University of California, San Diego, inside the box are assorted sensors and software designed to monitor a doctor’s office, particularly during consultations with patients. The goal is to analyze the physician’s behavior and better understand the dynamics of the interactions of the doctor with the electronic medical records and the patients in front of them. The eventual goal is to provide useful input on how to run the medical practice more efficiently.

    Very often physicians pay attention to information on a computer screen, rather than looking directly at the patient. “With the heavy demand that current medical records put on the physician, doctors look at the screen instead of looking at their patients,” says Weibel (pictured below). “Important clues such as facial expression, and direct eye-contact between patient and physician are therefore lost.”

    The first findings from the project are just-published in the February 2015 edition of the journal, Personal and Ubiquitous Computing* and have been highlighted by the New Scientist magazine.  The Lab-in-a-Box solution could capture multimodal activity in many real-world settings, but the researchers focused initially on medical offices and the problem of the increasing burden on physician introduced by digital patient records.

    The Lab-in-a-Box has been developed as part of Quantifying Electronic Medical Record Usability to Improve Clinical Workflow (QUICK), a running  study funded by the Agency for Healthcare Research and Quality (AHRQ) and directed by Zia Agha, MD. The system is currently being deployed at the UC San Diego Medical Center, and the San Diego Veterans Affairs (VA) Medical Center.  

    The compact suitcase contains a set of tools to record activity in the office. A depth camera from a Microsoft Kinect device records body and head movements. An eye tracker follows where the doctor is looking. A special 360-degree microphone records audio in the room.  The Lab-in-a-Box is also linked to the doctor’s computer, so it can keep track of keyboard strokes, movements of the mouse, and pop-up menus that may divert the doctor’s attention.

    The greatest value of the Lab-in-a-Box, however, is in the software designed to merge, synchronize and segment data streams from the various sensors – assessing the extent to which a certain confluence of activity may lead to distraction on the part of the physician. For example, says Weibel, lots of head and eye movement would suggest that the doctor is multitasking between the computer and the patient.

    Weibel and the UC San Diego/VA team will compare data from different settings and different types of medical practice to pinpoint those factors that lead to distraction across the board, or that affect only specific medical specialties. Their findings could help software developers write less-disruptive medical software. The researchers envision also deploying the Lab-in-a-Box permanently in a doctor’s office to provide real-time prompts to warn the physician that he or she is not paying enough attention to a patient. “In order to intervene effectively, we need to first understand the complex system composed by patients, doctors, and electronic medical record in depth, and this is what our study will finally yield.” says Weibel. Ultimately, as Weibel and his co-authors state in their original Personal and Ubiquitous Computing article, the Lab-in-a-Box “has the potential to uncover important insights and inform the next generation of Health IT systems.”

  • How UC San Diego and CSE Fare in R&D Spending

    The latest authoritative statistics on university research and development (R&D) expenditures show that UC San Diego overall came in fifth place among all U.S. institutions of higher learning, with just over $1 billion in total R&D. Of that, $630,000 came from the federal government. UC San Diego ranked #5 following the universities of Wisconsin, Washington, Michigan and at #1, Johns Hopkins University.

    Looking at R&D in the computer sciences only, UC San Diego ranked #10 in the nation for R&D spending, down from #8 the previous year. That drop reflected a 22 percent decline in computer-science R&D expenditures from fiscal 2012 to fiscal 2013 (pictured at right). Total R&D expenditures at UC San Diego in the computer sciences were just under $38 million in fiscal 2013, when less than half of the computer-science R&D came from federal sources (only $17.7 million). 

    It's worth noting that after pulling out of a slump in the early 2000s, total R&D expenditures in higher education went up in each of the past five years, from $1.5 billion in 2008 to just over $2 billion as of fiscal 2013.  But it's also worth pointing out some comparisons which show how computer science stacks up with other fields when it comes to universities in search of R&D funding. The $2 billion total for the computer sciences in fiscal 2013 was less than what went to the social sciences, less than what went to the physical or environmental sciences, and less than one-tenth of what sent to the life sciences. 

    The Higher Education Research and Development Survey is the primary source of information on R&D spending at the 645 U.S. colleges and universities that reported at least $1 million a year on R&D in the latest year (which together account for more than 99 percent of total higher education R&D expenditures nationwide in fiscal 2013). Another talking point for UC San Diego: among the seven universities boasting at least $1 billion a year in R&D spending, UC San Diego received more funding from industry -- over $68 million -- than its six rivals.

    Read more about the Higher Education Research and Development Survey.

  • UW-UCSD Project Demonstrates Wireless Car Hacking for TV Newsmagazine

    If you watched CBS's 60 Minutes program on Sunday, Febrary 8, you missed seeing the CSE logo. As part of a broader feature on information security research undertaken with support from the Defense Advanced Research Projects Agency (DARPA), the TV newsmagazine showcased the joint research on automotive hacking undertaken by researchers at the University of Washington and faculty in the Computer Science and Engineering department at UC San Diego, which together created the Center for Automotive Embedded Systems Security. The car hacking portion of the 60 Minutes program was filmed entirely in Seattle, so members of the San Diego team (including CSE professors Stefan Savage and Hovav Shacham) did not get any 'face time' in the TV report. Indeed, CBS producers decided in the end to delete all names of people and institutions, except for DARPA, so the CSE and UW logos on the test car used by correspondent Lesley Stahl were covered over in the final version of the broadcast.

    The demonstrations captured for CBS occurred last August, when 60 Minutes deployed  a phalanx of cameras on and around the test car to demonstrate an escalating level of threat scenarios involving wireless hacking of a car's computer system (what researchers called 'remote exploit control' in a landmark 2011 paper at the USENIX Security Symposium). For the 60 Minutes program, Lesley Stahl was in the driver's seat of the wirelessly-hacked automobile, and at various points, she lost control of the breaks, the steering wheel, the windshield wipers, even the speedometer (which showed the car in "park" even though it was clearly accelerating).

    As CSE's top expert on automotive hacking, Prof. Stefan Savage noted recently that there has been a lot of cross-over of personnel between UC San Diego and UW, in both directions. Case in point: UW professor Tadayoshi Kohno was an early collaborator on the project while he was finishing his Ph.D. at UC San Diego. In the other direction, the lead Ph.D. student at UW, Karl Koscher (right), recently graduated and is now a postdoctoral researcher in Savage's group at UC San Diego. (Koscher was visible in the 60 Minutes segment, playing the role of the hacker who wirelessly took control of the car's functions even as CBS's Lesley Stahl was driving.)

    Watch the DARPA segment on the CBS 60 Minutes website.
    Read the 2010 and 2011 papers from the Center for Automotive Embedded Systems Security.

  • Theory of Computation Expert to Give Inaugural Talk in New Lecture Series

    On Friday, Jan. 30 at 11am, CSE Profs. Mohan Paturi and Russell Impagliazzo will host computer scientist and mathematician Avi Wigderson, one of the most prolific and influential researchers in the theory of computation. Wigderson was invited to speak in the department's colloquium and Distinguished Lecture Series. His topic: "Randomness". The talk is aimed at a general scientific audience. Wigderson is a professor in the School of Mathematics at the Institute for Advanced Study, best known as the longtime intellectual home of Albert Einstein in the U.S. (from 1933 until his death in 1955), located in Princeton, NJ.

    According to the abstract, "Is the universe inherently deterministic or probabilistic? Perhaps more importantly - can we tell the difference between the two? Humanity has pondered the meaning and utility of randomness for millennia.  There is a remarkable variety of ways in which we utilize perfect coin tosses to our advantage: in statistics, cryptography, game theory, algorithms, gambling... Indeed, randomness seems indispensable! Which of these applications survive if the universe had no randomness in it at all? Which of them survive if only poor quality randomness is available, e.g. that arises from "unpredictable" phenomena like the weather or the stock market?" 

    Wigderson goes on to note that a "computational theory of randomness, developed in the past three decades, reveals (perhaps counter-intuitively) that very little is lost in such deterministic or weakly random worlds. In the talk I'll explain the main ideas and results of this theory." 

    Wigderson has made fundamental contributions to circuit complexity, parallel algorithms,cryptography (in particular, to zero-knowledge proofs and private multi-party computation), the role of randomness in computation, proof complexity, and connections between complexity and combinatorics. He earned his Ph.D. in computer science at Princeton University in 1983, studying with Prof. Richard Lipton.  He was a professor at Hebrew University from 1986 to 2003, and has been on the faculty of the Institute for Advanced Study since 2003. Among many other honors, Wigderson is the recipient of the Nevanlinna Prize (1994), awarded every four years for outstanding contributions in mathematical aspects of information sciences; and the Gödel Prize (2009), jointly with Omer Reingold and Salil Vadhan, for their work on the zig-zag graph product. In 2013 Wigderson was elected to the National Academy of Sciences. 

  • Déjà Vu: CSE's Vianu Passes the Test of Time... Again

    For the second time in five years, CSE Prof. Victor Vianu is the recipient of the ACM PODS Alberto O. Mendelzon Test-of-Time Award. The annual award goes to the author or co-authors of a paper published in the proceedings of the Principles of Database Systems (PODS) ten years earlier. The award goes to the paper that had "the most impact in terms of research, methodology, or transfer to practice over the intervening decade." After winning the Test-of-Time Award in 2010, Vianu will be honored at the 2015 SIGMOD PODS conference in Australia this May, when he accepts his second Test-of-Time Award.

    The 2015 award will cite Vianu's influential 2005 paper, titled "Views and Queries: Determinacy and Rewriting." The paper explores a scenario that is not uncommon in query processing, security and privacy, data integration and query pricing. "The paper considers a seemingly simple question," explains Vianu, who will share the award with co-author Luc Segoufin from INRIA. "Suppose you know the answer to a query Q on a database and you wish to answer another query R. Does Q provide enough information to answer R? If so, how can the answer to R be obtained from Q?" According to Vianu, the problem turned out to be unexpectedly challenging even for the simplest queries used in relational database systems, and some of the basic questions raised in 2005 remain open today.

    [Editor's Note: Vianu is not the first CSE professor to receive two test-of-time awards from the same conference. For two years in a row, the International Symposium on Computer Architecture (ISCA) gave its Influential Paper Award in 2010 and 2011 to simultaneous multithreading-related papers by Dean Tullsen and colleagues 15 years earlier. The papers originally appeared in ISCA proceedings for 1995 and 1996.] 

    There is little doubt that Vianu's paper from ten years ago had an out-sized impact in the research arena. "This first paper spawned a whole line of follow-up research on this and related problems," says Vianu, noting that this year's Best Student Paper awardee at the 18th International Conference on Database Theory (ICDT) contributed to the same line of research (and cited Vianu's 10-year-old paper). "I think our paper received the award because the questions it raised were novel and widely relevant, and some of the answers it provided challenged conventional wisdom by going against widely accepted 'folklore' assumptions."

    (The Best Student Paper Award at ICDT 2015 will be awarded this March to "Asymptotic Determinacy of Path Queries using Union-of-Paths Views," by Nadime Francis, a graduate student at France's École Normale Supérieure de Cachan. Francis is also a collaborator with Vianu's co-author, Luc Segoufin, from the PODS paper.)

    In 2010 Vianu and his co-authors Dan Suciu and Tova Milo won the Mendelzon Test-of-Time Award for their work a decade earlier on type-checking for XML transformation languages. Vianu's paper studied the problem of checking whether or not an XML transformation is well-typed -- which would be essential for manipulating XML documents. The paper proved that typechecking for k-pebble transducers is decidable and, consequently, it could be performed for a broad range of XML transformation languages.

    Victor Vianu received his Ph.D. in Computer Science from the University of Southern California in 1983 and joined UC San Diego in 1984. Aside from UCSD, he has taught at the Ecole Normale Superieure and Ecole Nationale Superieure des Telecommunications in Paris, as well as the Sorbonne. He has spent numerous sabbaticals as an invited professor at INRIA, where he now holds an International Chair. Vianu's interests include database theory, computational logic, and Web data. His most recent research focuses on specification and verification of data‐driven Web services and workflows. Vianu's publications include over 100 research articles and a graduate textbook on database theory.

  • CSE Society Stages CSE Day 2015

    The Computer Science and Engineering Society (CSES) and its members turned out in force on Thursday, Jan. 22, for the 2015 version of the society's annual CSE Day event. Organizers estimate that roughly 250 students consistently attend at least one of the day's events (depending on their class schedules). Talks, activities and panel discussions throughout the day aimed to "inform students about the paths available to them in the computer science field by having them interact with students, alumni and faculty in the CSE Department, and members from industry." Sponsors of the event included Qualcomm, Microsoft, Google, ViaSat, and Visa (which also supplied one of its forensic investigators, John Camacho, to deliver a Tech Talk on enterprise-wide, risk-based security).

    Computer security was also on display when Prof. Stefan Savage (pictured at right) delivered a talk on "Buying Drugs for Science: Addressing the Economics of Cybercrime." Savage focused on the social and economic forces driving today's Internet attacks and deconstructing the underlying value chain for attackers. He sketched a picture of "economically-motivated, advertising-based e-crime." Savage and his collaborators spent roughly a year getting permission to use research funds to purchase $50,000 worth of counterfeit drugs and other merchandise sold through a patchwork of entities that make up the cyber-criminal ecosystem. The study, which included 600 orders of illicit drugs, turned up amazing evidence of the role that one type of pharmaceutical plays in the ecosystem: "Erectile dysfunction counterfeit drugs account for 75 percent of e-crime demand," said Savage, "and 80 percent of revenues." Tellingly, he added, between 20 and 40 percent of all sales of Viagra are ordered from consumers' spam folders, i.e., those consumers had to go into their spam folder to click on an offer of Viagra (usually at 20 percent of the regular price in the U.S.). The professor, who also directs the Center for Networked Systems, showed CSE students an example of ingenuity in packaging: the researchers received a shipment from Bangladesh that was supposed to have been for counterfeit RU-486 abortion pills. Instead they received an ornate woven textile that looked like a miniature carpet. With a little effort, they split apart the textile at the seams, only to find the pills stitched into the fabric.

    Other activities during the day included Startup 101, a panel on the growing phenomenon of computer science and engineering-based startup companies. Speakers included Moxie Center executive director Jay Kunin, who mentors students in the 40 companies already admitted to the Moxie Incubator, as well as two student entrepreneurs: Chesong (Daniel) Lee, co-founder of the earphone company called Hush, which raised nearly $600,000 on Kickstarter versus the $100,000 they were seeking; and Joseph Le, a second-year computer science student whose company StudentHero connects high school students to summer internships.

    Another popular session was the Alumni Panel, which gaves current students an oppportunity to ask the alumni for tips on interviewing, presenting, seeking internships, and so on. Speakers included: Patrick Johnson (BS '07), now a software engineer at Google; Qualcomm staff engineer and CSE lecturer Garo Bournoutian (BS '05, PhD '14); McKenzie Velia (BS '13), who parlayed a summer internship to a year-long internship and most recently, a full-time job working on network security, all at ViaSat; and CSE Alumni Board member Justin Allen (BS '10), who recently joined WebAction, a Palo Alto-based company in the real-time data streaming space.

    Among their recommendations in response to student questions:
    - Go to career fairs.
    - Get involved in student organizations (and student government, as Garo Bournoutian did as president of the Graduate Student Association).
    - Make yourself known to faculty members; they are often asked to recommend a student for hire.
    - Participate in the Jacobs School's Team Internship Program (like McKenzie Velia did at ViaSat).
    - Attend any event where you can get feedback and critique of your resume.
    - Consider studying a year abroad, preferably as a sophomore. (Justin Allen spent his year abroad in Scotland, and it was invaluable.)
    - Become a CSE Tutor: it's rewarding and looks great on your resume.

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