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  • At Research Expo, M.S. Student Selected for Best CSE Poster

    Twenty CSE graduate students presented their research to an estimated 650 people attending the Jacobs School's Research Expo on April 16.

    Among all CSE entries, the computer science best poster award went to Narendran Thangarajan (pictured at left), a Master's student advised by CSE research scientist Nadir Weibel. The poster focused on Thangarajan's work analyzing social media to characterize HIV at-risk populations in San Diego. The researcher went beyond existing research on the feasibility of using Twitter to study HIV spread in the United States.  He took the approach further, "identifying and characterizing HIV at-risk populations locally in the San Diego are at a more granular scale in terms of both demographics and communities." He used dynamic visualizations, social network analysis, graph algorithms and machine-learning techniques to combine information from Twitter and data on HIV-infected patients provided by UC San Diego's AntiViral Research Center. The goal: to "learn how actual HIV-infected users behave on Twitter and build a computational model that can then be applied to other users to investigate similarities in their behaviors." Thangarajan expects to graduate with his M.S. degree this June. [Photo by Erik Jepsen/UC San Diego Publications]

    The jury also selected three other CSE posters deserving of Honorable Mentions:

    • Automated Annotation of Coral Reef Survey Images, by Oscar O. Beijbom (advised by David Kriegman and Serge Belongie)
    • Design Guidelines and Optimization of DRAM Interconnect, by Mulong Luo (advised by Andrew B. Kahng)
    • Gadgetron: Synthesizing Electronic Gadgets, by Devon James Merrill (advised by Steven Swanson)
  • Center for Visual Computing Makes Debut at 2015 Research Expo

    The new Center for Visual Computing, an 'agile' research center based in the CSE department, had its official unveiling April 16 during the 2015 Research Expo of the Jacobs School of Engineering. Making it official, CSE Prof. Ravi Ramamoorthi (pictured) presented an outline of the center's current and future activities. He also confirmed that VisComp has lined up Sony as its lead sponsor, with additional partners Qualcomm, Pixar and Adobe. Ramamoorthi said the center hopes to grow membership to at least six companies from a variety of industries, including communication, entertainment, health, 3D printing and more. On the faculty side, VisComp includes Ramamoorthi as director, as well as CSE professors David Kriegman and Henrik Jensen, Qualcomm Institute research scientist Jurgen Schulze, and Zhuowen Tu, an expert in computer vision from Cognitive Science. "The motivation for this agile research center is that computer vision, graphics and imaging are still at a formative stage," said Ramamoorthi, "and they affect all areas of the computing stack from hardware to software to output, and they will have a major impact on our everyday lives."

    Under the banner of "visualizing the way we capture, image and display the visual world," Ramamoorthi spelled out a three-part research agenda for the center: mobile visual computing and digital imaging; interactive digital (augmented) reality (to blend real and virtual scenes seamlessly in real time); and computer vision to understand people and their surroundings, from the individual- to the city-level. "We're witnessing the coming of age of computer vision, where every mobile phone has a camera and is doing fairly complicated processing based on a face detector," said Ramamoorthi. "Every mobile phone will also have access to Internet-scale visual databases, so we can enable semantic understanding of people's gestures, habits and similarities." He showed evidence that computer vision can be used to scan a crowd to detect "tribes" of people with like interests, such as bikers or surfers.

    The VisComp director spelled out some of the innovations that are rapidly changing photography and imaging, notably with virtual-reality devices such as the Oculus Rift, and perhaps more importantly, in the current commercialization of full 4D lightfield cameras, passive devices that capture the entire field of light, so that a photographer can capture an entire scene and choose later which angle, or what part of the image to refocus on. Light-field can also potentially be used to reconstruct three-dimensional (3D) scenes, one of the hottest new areas of interest that is pushing 3D from Hollywood down to the level of the mobile phone. "This enables a number of 3D applications," explained Ramamoorthi. "You can reconstruct 3D surfaces and couple it with the 3D printing industry to create an entire pipeline of 3D capture - just from the capture of a single shot image."

    "I believe the progress we will make in these three themes," he concluded, "have the potential to transform the way we interact with computers and, indeed, how we live our lives."

  • CSE Lecturer Wins Campus Academic Integrity Award

    CSE Prof. Gary Gillespie says it was an honor just to be nominated this year for the Academic Integrity Faculty Award, but this year it was much more than that: He is one of two UC San Diego faculty members to win the 2015 Integrity Award. It was announced on April 14 along with staff and student honors at the 5th Annual Integrity Awards Ceremony in the Student Services Center. The award is presented to a faculty member who has contributed significantly to creating a culture of academic integrity through research, teaching and/or service. Gillespie is the second CSE lecturer and teaching professor selected for the honor, after Paul Kube won the same award two years ago.

    [Pictured at right: Gillespie receiving his award from Executive Vice Chancellor of Academic Affairs Suresh Subramani; below, he gets moral support from fellow teaching professors Leo Porter and Rick Ord.]

    Gillespie considers himself a strong supporter of academic integrity for many years, having sent many students through the process. "I talk with them in my office and try to help them make better decisions for the betterment of their future," he adds. "It's not always a pleasant process, but if students can better consider their decisions, they'll be better ambassadors from UC San Diego when they eventually graduate."

    It may have been a sign of his diligence and attention to his students that Gillespie ended up arriving late to the award ceremony itself, because he had to finish teaching his Software Engineering class. "All year I've been spending all my time teaching classes," said Gillespie. "It's really an all-consuming task with hundreds of students, a large staff of tutors, and much to orchestrate."

    Gillespie is now looking forward to summer when school isn't in session. He will head back to iboss Network Solutions, the company founded and led by CSE alumnus Paul Martini (BS '01), where he will work as a consultant over the summer, before returning to the classroom in the fall.

  • Alumna and Incoming Student Cross Paths in B-Ball and Computer Science

    There must be something about hoops, Tritons and computer science. Meet Marissa Hing. The 18-year-old high school senior was on campus last weekend to attend Triton Day, when over 20,000 accepted students and their families converged on UC San Diego to get a taste of everything the university offers to its students-to-be. Despite her 5.1-inch height, Hing is also coming to play basketball on an athletic scholarship for the NCAA Division II team, after starring since her freshman year at Pinewood High School in Los Altos, CA. She has started for four years as a guard on the Pinewood team, and was just selected by the San Jose Mercury-News as its girls basketball player of the year for northern California. The paper noted that she played a leadership role in helping Pinewood reach the CCS Open Division championship game this season. 

    The newspaper was also impressed with what she plans to study at UC San Diego: Hing says she wants to major in computer science, even while juggling a career on the basketball court. “As of right now my major is cognitive science because the computer science major was too full,” says Hing. “But I will be trying to change my major to computer science when I can.”

    Hing says she is attracted to computer science because she likes to know how things work. “It also lets you be creative while also being logical at the same time, which is something that not a lot of other fields offer,” says Hing. “It helps you understand how things work instead of just assuming they do.”

    Given the demands of both b-ball and CS, it may seem an unusual pick on both counts. But someone has proved that it can be done.

    Indeed, Hing is not the first girls basketball star from Pinewood to major in computer science at UC San Diego. Former Pinewood player Rachel Marty arrived in 2010 and went on to play NCAA varsity basketball on the UCSD team while pursuing a degree in CSE with a specialization in bioinformatics. She graduated magna cum laude in four years, despite also playing ball.

    Marty says she played on the UCSD squad with fellow Pinewood graduate Miranda Seto, and she knows Marissa Hing well through the "Pinewood connection." "After I came to UCSD, our Pinewood coach formed a good relationship with the UCSD coaches," explains Marty. "But I have to admit that I didn't know Marissa was planning to study computer science. I can claim the basketball recruitment, not the computer science recruitment, but I'm really excited about it!"

    Now a Ph.D. student in CSE since 2014, Marty says she did recruit one of her fellow basketball team members, Taylor Tanita, to switch to computer science. "I'm a big fan of the program," she observes.

    Marty (pictured at right as an undergraduate varsity basketball player) continues to be a strong career example for young women, athletes and computer scientists (whether from Pinewood High School or not). Last week, she was one of only three UC San Diego computer science graduate students selected in 2015 to receive NSF Graduate Research Fellowships, a three-year award carrying a stipend of $34,000 per year (plus a $12,000 annual cost-of-education allowance that goes directly to the campus). Some 16,500 students nationwide competed for roughly 2,000 fellowships. 

    The CSE alumna is pursuing her Ph.D. in bioinformatics, and her research interests include cancer genomics, genomic algorithms and population genetics. Marty has done bioinformatics internships at Thermo Fisher Scientific (and Life Technologies, which it acquired) as well as at Illumina, where she developed an "application to centralize the experience of gene exploration for researchers." She has also done research with both CSE Prof. Vineet Bafna (in the field of genomic algorithms) and with Hannah Carter at the UC San Diego School of Medicine's Division of Medical Genetics (on cancer genomics). "I will likely choose one of them to be my advisor at the end of the year," she says. That's when the rotation period of her doctoral program ends. 

    But Marty has also won fans off the court and away from bioinformatics. CSE Prof. Andrew Kahng recommended her for the fellowship. She took an algorithms class with him as an undergraduate, and Kahng also supervised an independent study project when she interned at Life Technologies. "He has played a prominent role in getting me where I am," says Marty. She plans to finish her Ph.D. in 2019.

  • Marriage of Big Data and Medicine Yields Top New Faculty for UC San Diego

    According to an article in the San Diego Union-Tribune, "San Diego is quickly becoming the focal point of a nationwide effort to use high-speed computers and smart software to sift through mountains of biomedical data for clues about why people develop everything from cancer to Alzheimer's disease." Science reporter Gary Robbins ask CSE Chair Rajesh Gupta what is driving the recent recruitment of top big-data researchers to UC San Diego and the nearby J. Craig Venter Institute. "Computers are the new microscopes," said Gupta, "and data is the new blood draw."

    While not yet official, the paper confirmed that the School of Medicine has recruited the chief informatics officer at MIT/Harvard's Broad Institute. Jill Mesirov (at left) will join the school in July if her appointment is approved by the Academic Senate. Given her background in high-performance computing, and current interactions with CSE professors Pavel Pevzner and Vineet Bafna, Gupta anticipates that the CSE faculty will apply to grant Mesirov faculty-affiliate status in the CSE department once she has arrived in San Diego. The same happened earlier this year, the CSE awarded faculty-affiliate status to Rob Knight (pictured at right), after he joined the department of pediatrics in the School of Medicine, where he works in bioinformatics as "one of the most respected microbiome experts in the world," according to the Union-Tribune article. Talking about hiring Knight and Mesirov, School of Medicine dean David Brenner said he wants the campus to lead in the field of precision medicine and computational biology. "We're going to leverage all of the strengths of this campus," said Brenner, "from Calit2 to the San Diego Supercomputer Center to Moores Cancer Center to computer science and bioengineering. That means we need to be able to handle large data sets." CSE's Gupta told the newspaper that in bioinformatics, the term 'big data' has become an understatement. "New discoveries show that the genome is but a small part of the overall makeup that spans epigenetic data as well as 100 times more individual-specific microbiome data," Gupta said. "The 'big data' is a tsunami now."

  • CSE Faculty Affiliate Honored with Vilcek Prize

    CSE faculty-affiliate Rob Knight is a newcomer to UC San Diego, but now he is also being honored as a (relative) newcomer to the United States. The Vilcek Foundation has named Knight the winner of a Creative Promise Prize in Biomedical Science for his "groundbreaking research on microbial communities and the development of computational tools that honed the analysis of microbial data." The Vilcek Foundation honors and supports foreign-born scientists and artists who have made outstanding contributions to society in the United States. Rob Knight was born in New Zealand, where he earned his bachelor's degree from the University of Otago in 1996, before going on to do his Ph.D. at Princeton University. While at the University of Colorado, Knight also became a Howard Hughes Medical Institute Early Career Scientist (2009-2014).

    In addition to his affiliation with the CSE department at UC San Diego, Knight (pictured center left with fellow recipients of Vilcek Prizes) is also a professor of pediatrics in the School of Medicine.  His computational and experimental approaches have led to rapid and cost-effective microbial DNA sequencing methods and data analysis platforms that help to understand similarities among microbial communities based on their evolutionary relationships.  Knight has used informatics to show how maps of distinct microbes thriving in different parts of the human body change over time, how human-associated microbes can influence metabolic health, and how microbes can be used as timekeepers to help establish the time of death in forensic examinations.  Knight is also continuing his work in bioinformatics, after a decade of developing software to analyze the abundance of microbial data that is now becoming available to researchers. Knight's recent book, "Follow Your Gut,"  was published by TED Books in April 2015.  Rob Knight was born in Dunedin, New Zealand. "New Zealanders tend to pride themselves on ingenuity and making do with whatever resources happen to be available," said Knight, but he is going beyond what's available to creating projects that encourage the public to contribute their individual microbiome data for future research and the greater good. He has set out to catalog the diverse kinds of microbes found in ecosystems across the globe in an ambitious, collaborative effort called the Earth Microbiome Project, but Knight is also a co-founder of the American Gut Project. For the latter project, anyone in the U.S. can contribute $99 and a personal sample to have their gut microbiome analyzed (and contributed to the growing store of data available to researchers).

  • CSE Alumni Brief Students on Profits, Perils in Tech Startups

    Lindsey Fowler (BS ’05), president of the CSE Alumni Advisory Board, moderated an April 2 panel of six alumni experts and Jay Kunin, executive director of the Moxie Center for Student Entrepreneurship at UC San Diego. The alumni included Taner Halicioglu (BS ’96), Jennifer Arguello (BS ’00), Chris Schulte (MS ’05), Aaron Liao (BS ’05), Erik Buchanan (BS ‘07), and Justin Allen (BS ’10), several of whom also sit on the alumni board.

    Justin Allen worked for Teradata after graduation, then joined a Bay Area startup called WebAction in 2014. He now works remotely from San Diego on purpose-built analytics applications in the growing real-time data streaming space. “I’m still a field engineer but I’m working on analytics applications and I get to live in San Diego while working for a startup,” said Allen. “It’s the best of both worlds.”

    Jennifer Arguello worked at four startups over the course of eight years. The last one (Tellme Networks) was acquired by Microsoft, where she worked for nearly five years before becoming a product manager at Mozilla. She says that she found a unique opportunity in a hybrid venture, combining some for-profit venture capital with non-profit activities to create positive social impact (along with economic value). Arguello calls her current employer, the Kapor Center for Social Impact, a “non-profit, social-good startup,” where she is a Senior Tech Advisor. Asked whether doing a non-profit startup is different from a for-profit venture, Arguello first points to what they have in common. “In both cases you’re begging for money,” she says, only half-jokingly.  “In fact, social entrepreneurism can be even more flexible and easier to do if it’s for profit.” Arguello also sits on the advisory boards of organizations that promote programming education, including Yes We Code, and Globaloria.

    When it comes to startups, advised the Moxie Center’s Kunin, both non-profits and for-profit companies need money in the bank. “Either way,” he said, “you need some kind of revenue model.”

    Chris Schulte was working at SAIC when he began to think about starting a company. “I was able to work on a startup in my spare time, mainly in the evening, while I was also working full-time for SAIC,” said Schulte. He became CTO and cofounder of MyCase, Inc., which made management software for law practices. Schulte stayed on when the company was acquired in 2012 by AppFolio. Recently, he left the company to think about the future. “Now I’m on an unspecified vacation,” he told the CSE students.

    Alumni Board president Fowler, who works for online retail giant Amazon, warned students to be careful about working on a startup from the comfort of a full-time company job: “You have to make sure that your employer doesn’t have any claim on your idea,” said Fowler, “especially if the future business is in some way related to your current job.”

    After graduating with a major in computer engineering, Aaron Liao worked at Microsoft for six years. He is currently the “evangelism director” at BitTorrent, and once again, he’s “starting to look for new startup opportunities.” Liao and others were asked about the biggest difference between working for a startup and working at a large, established company. “In a startup you wear many hats,” said Liao. “At Microsoft my job was very defined.”

    “A startup company also means that you really own the company’s success or failure – you’re more invested in what happens,” added Erik Buchanan, engineering lead and “startup entrepreneur” at Connectifier, who worked at multiple large enterprises before the startup, including Microsoft, Intuit, and Google. “What happens at a big company still matters, but you don’t feel it so personally.”

  • Alvarado Receives Engagement Excellence Award

    CSE Prof. Christine Alvarado will be honored in late May at the Summit on Women and IT organized by the National Center for Women & Information Technology (NCWIT). The summit will take place in Hilton Head Island, South Carolina, where Alvarado and three former colleagues at Harvey Mudd College will share in NCWIT's Engagement Excellence Award. The annual award recognizes authors whose curricular materials have been submitted to the elite EngageCSEdu collection. Winners must demonstrate excellence in computer-science content and pedagogy while also using research-based engagement practices to make computer science relevant and meaningful for students.
    The award highlights the pioneering work that CSE's Alvarado (at right) did at Harvey Mudd prior to joining the UC San Diego faculty in 2012. Her co-winners of the award were fellow computer science faculty Geoff Kuenning, Ran Libeskind-Hadas and Zachary Dodds, all still at Harvey Mudd. "The work I did with my colleagues at HMC was both about rethinking curriculum as well as creating a supportive and relevant structure and community in which students can learn," says Alvarado, noting that the award-winning work is also reflected in various efforts that she has undertaken at UCSD. 
    Those efforts include the establishment of a curriculum for the new Summer Program for Incoming Students (SPIS). Alvarado and fellow teaching professor Mia Minnes based the SPIS computer science curriculum on Harvey Mudd's CS5.  Alvarado notes, "Using CS5 as the backbone for the SPIS CS curriculum was a great way to give students an overview of the big picture of computer science and math, and to show both the real-world relevance of the material and the connections across the ideas that are normally segregated into different classes."
    Another effort benefiting from Alvarado's previous experience at HMC is the Early Research Scholars Program, which places first- and second-year CSE students in research apprenticeships with active research projects in CSE. "We are trying to build community between early undergraduates and grad students and faculty," she adds. "This way, students can not only see the relevance of what they are learning in their early courses, but they also form a deeper sense of belonging within CSE."
  • NSF Graduate Research Fellowships to CSE Students

    Three current CSE students are among the 2,000 nationwide to be offered 2015 Graduate Research Fellowships from the National Science Foundation (NSF). Graduate students Rachel Marty and Alexandria Shearer and graduating senior Max Shen were selected from among roughly 16,500 applicants this year. In addition, CSE undergraduate Antonella Wilby was a runner-up in the national competition, receiving an Honorable Mention for work in the field of robotics and computer vision. Shearer and Wilby are both in CSE Prof. Ryan Kastner's research group, which is already home to three NSF graduate fellows: Dustin Richmond, Perry Naughton, and Alric Althoff. Max Shen works in the bioinformatics group of CSE Prof. Pavel Pevzner, while Rachel Marty is also pursuing a Ph.D. in bioinformatics.

    With its emphasis on support of individuals, the NSF program offers fellowship awards directly to graduate students selected through a national competition. If accepted, the award provides three years of financial support within a five-year fellowship period ($34,000 annual stipend and $12,000 cost-of-education allowance to the graduate institution) for graduate study that leads to a research-based master's or doctoral degree in science or engineering.

    Rachel Marty (left) is a CSE alumna (BS '14) who earned her computer science degree with a specialty in bioinformatics. She graduated magna cum laude even while playing varsity collegiate basketball. Marty has done bioinformatics internships at Thermo Fisher Scientific (and Life Technologies, which it acquired) as well as at Illumina, where she developed an "application to centralize the experience of gene exploration for researchers." Her research interests include cancer genomics, genomic algorithms and population genetics. Marty has done research with both CSE Prof. Vineet Bafna (in the field of genomic algorithms) and with Hannah Carter at the UC San Diego School of Medicine's Division of Medical Genetics (on cancer genomics). "I will likely choose one of them to be my advisor at the end of the year," she says, when the rotation period of her doctoral program ends. Marty also CSE Prof. Andrew Kahng, who recommended her for the fellowship; as an undergrad, she took an algorithms class with Kahng, who also supervised an independent study project when she interned at Life Technologies. "He has played a prominent role in getting me where I am," notes Marty, who plans to finish her Ph.D. in 2019.

    Alexandria Shearer (right) is a Ph.D. student working on applications in heterogeneous computing. Less than two weeks ago, she was selected to receive a one-year UC San Diego Frontiers of Innovation Scholarship to continue her work on aerial LiDAR scanning of Mayan ruins. The FISP fellowship will cover Shearer over the summer and partially cover some equipment and travel costs related to her research, while the NSF stipend covers her primary expenses during the school year and the tuition allowance is paid directly to UCSD. Shearer arrived at UC San Diego in 2013 after getting her B.S. in computer science and engineering from Santa Clara University's School of Engineering, where she graduated as the top senior in computer engineering. Shearer expects to complete her Ph.D. in 2018. Among past honors, she was a SWE ViaSat Scholar in 2012, and a Google Anita Borg Memorial Scholar in 2011, the same year she won an NSF Grace Hopper Celebration Scholarship.

    Max Shen (left) will graduate this June with a B.S. in computer science and a specialization in bioinformatics. He is a research assistant in the group of CSE Prof. Pavel Pevzner, and for the past year has been a content contributor to Pevzner's Rosalind platform for learning bioinformatics and programming through problem-solving. For Rosalind, Shen designs and implements bioinformatics programming assignments onto a live website with randomized input generation and scoring. Rosalind is used in undergraduate bioinformatics courses, and also by students enrolled in Pevzner's massive open online courses on Coursera, including courses on bioinformatics algorithms. In addition to being a research assistant, Shen has also been a TA and tutor in CSE, a software engineering intern at Qualcomm, and a software engineer at Illumina. He was also a research assistant in the UC San Diego School of Medicine's Radiology Imaging Laboratory, thanks to which Shen may be the only computer science student who is also certified to operate a magnetic resonance imaging (MRI) machine.    

    Honorable Mention recipient Antonella Wilby is a graduating senior. She has been active for over two years in the Engineers for Exploration program co-directed by CSE's Kastner. Wilby graduates in June and will start grad school in CSE this fall, having just accepted an invitation to join Shearer in Kastner's research group. She also recently received a National Geographic Young Explorer grant for her work to document the endangered vaquita, a rare species of porpoise found primarily in the Gulf of California.

  • Society Honors Computer Scientist and Mathematician Fan Chung Graham

    CSE Prof. Fan Chung Graham and 30 others worldwide have been named as the Class of 2015 Fellows of the Society for Industrial and Applied Mathematics (SIAM). She was cited for her contributions to “combinatorics, graph theory and their applications,” and those applications have included Internet computing, communication networks, software reliability and more.

    The Distinguished Professor has joint appointments in CSE and the Department of Mathematics, where she holds the Paul Erdös Chair in Combinatorics. In the early 1990s, Chung Graham served on the council of SIAM.

    She is not the only Graham to be honored by SIAM – not even in the Graham household. That’s because her husband and fellow CSE professor, Ronald Graham, was honored in 2009 to be included in the inaugural class of SIAM Fellows. Ron Graham is also Chief Scientist in the California Institute for Telecommunications and Information Technology (Calit2).

    In 2013, Chung Graham and her husband were recruited to the inaugural class of Fellows of the American Mathematical Society. Both are experts in theoretical computer science and combinatorics.  Among her other honors, Chung Graham received the Allendoerfer Award from the Mathematical Association of America in 1990, and she is one of three CSE professors awarded membership in the American Academy of Arts and Sciences. (The others? Larry Smarr and... Ron Graham).

    Chung Graham earned her Ph.D. in mathematics from the University of Pennsylvania in 1974. She went on to work at Bell Labs in its Mathematical Foundations of Computing department.

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