Monday, August 14, 2017
Design Lab Faculty to Launch NSF-Funded Graduate Education Project
On September 1, the Design Lab at UC San Diego will launch a new project to help teach incoming graduate students how to program in the era of big data. The project is funded by the National Science Foundation (NSF) Innovations in Graduate Education (IGE) program, and the Design Lab project is one of 10 new IGE grants awarded a total of $4.8 million to “pilot, test and validate innovative and potentially transformative ways to teach science, technology, engineering and mathematics (STEM).”
The UC San Diego team will receive approximately $500,000 over three years to develop a new data-science teaching approach via “Augmenting, Piloting and Scaling Computational Notebooks to Train New Graduate Researchers in Data-Centric Programming.”
The project's principal investigator and Design Lab co-founder is James Hollan, a distinguished professor of Cognitive Science with an adjunct appointment in Computer Science and Engineering (CSE). He leads a team including co-PIs Scott Klemmer, Philip Guo and Bradley Voytek. Design Lab co-founder Klemmer has a joint faculty appointment in CSE and Cognitive Science, while Guo and Voytek are professors of Cognitive Science (in Voytek’s case, with a joint appointment in Neuroscience).
The Design Lab team proposed to take the popular concept of introductory “bootcamps” for new grad students, and to scale that approach while exploiting the growing movement of computational notebooks. Specifically, the researchers propose to augment the Jupyter Notebook, a widely used open-source web application, with other pedagogical tools to support training in data-centric programming in a wide range of STEM disciplines.
“This has the potential to improve the efficacy of training graduate students in data-centric programming,” said Klemmer. “But the impact could be much greater in the long run because all of the new capabilities can be harnessed for teaching in other domains, and the open-source nature of the notebooks and tools will ensure that the technology will be widely available via the Web.”
In producing an open-source version of the Jupyter Notebook for teaching data-centric programming, the UC San Diego researchers plan to integrate other tools that have been widely used, particularly for massive open online courses (MOOCs). Co-PI Klemmer helped develop Talkabout and PeerStudio. “Both systems have been used by tens of thousands of students in dozens of MOOCs on the Coursera online education platform over the past four years,” said Klemmer. Indeed, students and other learners taking Klemmer’s widely-watched “Interactive Design” courses on Coursera already have access to the software tools to provide feedback (PeerStudio) and to enable discussion among widely-distributed course participants (Talkabout).
Co-PI Philip Guo developed Python Tutor for tutoring support. It has been available for seven years, and in that time, over 3.5 million people in over 180 countries have used Python Tutor to visualize over 30 million pieces of code, either directly online or via Python Tutor’s integration into MOOCs from edX, Coursera and Udacity.
PI Hollan developed analysis tools – notably Traces and ChronoViz – to support the education of graduate students at scaleBoth are software tools widely used in analyzing video of real-world activity.
“Our team,” noted Hollan, “has deep experience in implementing, deploying and maintaining these tools over extended periods of time.”
Co-PI Bradley Voytek, a professor of Computational Cognitive Science and Neuroscience, has been teaching Introduction to Data Science (COGS 9) since 2014, when he joined the UC San Diego faculty..
He notes that COGS 9 class size has ballooned since then, from 24 students that first quarter, to 280 students in the latest quarter. In spring 2017, Voytek launched his first course for upper division students, Data Science in Practice (COGS 108), with approximately 420 students.
Voytek’s classes have used the Jupyter Notebook, and he will employ iterative versions of the augmented version to assess its utility in university classrooms, in comparison with the augmented notebook’s use in MOOCs and other distributed learning environments. The resulting system will be available online through a GitHub repository. “This will enable it to be widely shared, evolved and tailored to specific discipline requirements,” said Hollan.
Massry Prize Honors Microbiome Research Pioneers
Microbiome researcher Rob Knight, a professor with dual appointments in the Pediatrics as well as Computer Science and Engineering departments at UC San Diego, will receive the 2017 Massry Prize. He'll split the $200,000 honorarium with longtime colleagues and co-recipients of the prize, Jeffrey Gordon, MD, of the Washington University School of Medicine in St. Louis, and Norman Pace from the University of Colorado Boulder (where Knight worked before joining the UC San Diego faculty in 2015).
The three researchers lead a field that works to produce a detailed understanding of microbiomes — distinct constellations of bacteria, viruses and other microorganisms that live within and around us — and methods for manipulating microbiomes for the benefit of human and environmental health.
The Meira and Shaul G. Massry Foundation established the Massry Prize in 1996 to recognize outstanding contributions to the biomedical sciences and the advancement of health. The nonprofit foundation promotes education and research in nephrology, physiology and related fields. Shaul Massry, MD, is professor emeritus at the Keck School of Medicine of University of Southern California (USC). Twelve Massry Prize recipients have gone on to win Nobel Prizes.
Professor Knight and his co-honorees will each give the Massry Prize Lectures, scheduled for October on the USC Health Sciences campus in Los Angeles.
Pace developed a technique to sequence a bacterial gene called 16S rRNA and use that information to produce microbial “read outs” of what’s living in a mixed sample. Gordon found medical applications for the technique, using it to discover links between the human gut microbiome and obesity and malnutrition. Knight figured out how to scale up the approach, allowing researchers to perform high-throughput microbial gene sequencing, and made widely accessible tools that other researchers have now used in thousands of different environments, including the human body.
“I greatly appreciate this recognition for microbiome research — a scientific field that was relatively underappreciated until recent years,” said Knight, the founding director of the Center for Microbiome Innovation at UC San Diego, in addition to his academic appointments in the School of Medicine and Jacobs School of Engineering. “I’m honored and grateful to stand beside Jeff and Norm, true visionaries in the field and valued collaborators and mentors who have changed the way we think about the majority of the cells in our bodies and the vast majority of the cells on our planet.” The Center for Microbiome Innovation is part of the White House’s National Microbiome Initiative.
Knight’s research group and others are finding that the trillions of microbes living with us are critical contributors to human and environmental health. Allergies, inflammatory bowel disease, obesity and many other conditions have been linked to alterations in the human gut microbiome, and growing evidence suggests gut microbes also influence the brain, potentially affecting mood, behavior and psychiatric illnesses.
Knight’s team has also enhanced our understanding of microbes in environments ranging from the oceans to the tundra, and made high-throughput sequencing techniques accessible to thousands of researchers around the world.
“You would have a hard time finding a department or discipline anywhere on the UC San Diego campus that isn’t collaborating with Rob,” said David A. Brenner, MD, vice chancellor of Health Sciences and dean of the School of Medicine at UC San Diego. “He can make connections between seemingly unrelated topics and the scientific community as a whole has advanced thanks to him. Rob is extremely deserving of this award and I’m proud to call him a colleague and friend.”
Knight’s current research interests include relating the human microbiome to many human diseases and mental illnesses, spatial and temporal mapping of microbial communities on different scales, ranging from our bodies to our planet, and developing new data visualization methods and software tools that help resolve the challenges of microbial “Big Data.”
In one example project that leverages the interdisciplinary expertise provided by the Center for Microbiome Innovation, UC San Diego physicians, microbiome researchers, chemists, genomics experts and bioinformaticians are collaborating to build a 3D map of the chemistry associated with cystic fibrosis and how it shapes the lung microbiome. Their goal is to develop more effective, highly personalized treatments for potentially fatal lung infections that frequently affect people with this disease.
Knight also co-founded the Earth Microbiome Project; the American Gut Project, the world’s largest crowdsourced citizen science effort; and the company Biota, Inc., which uses DNA from microbes in the subsurface to guide oilfield decisions. He is a fellow of the American Association for the Advancement of Science and of the American Academy of Microbiology. In 2015, he received the Vilcek Prize in Creative Promise for the Life Sciences.
Knight is the author of “Follow Your Gut: The Enormous Impact of Tiny Microbes” (Simon & Schuster, 2015) and co-author of “Sustainable Shale Oil and Gas” (Elsevier, 2017) and “Dirt is Good: The Advantage of Germs for Your Child’s Developing Immune System” (St. Martin’s Press, 2017). He spoke at TED in 2014.
Knight received a BSc in Biochemistry in 1996 from the University of Otago in his native New Zealand, a PhD in 2001 from Princeton University in Ecology and Evolutionary Biology, and performed postdoctoral work at the University of Colorado, Boulder before becoming a faculty member in the interdisciplinary BioFrontiers Institute there in 2004, in 2009 becoming a Howard Hughes Medical Institute Early Career Scientist. He moved his lab to the UC San Diego School of Medicine in 2015.
Extending State-of-Art Techniques for Concurrency Verification to Distributed Setting
Professor Ilya Sergey, a lecturer in computer science at University College London in the UK was on campus Friday, August 11, to give a talk in the CSE department. Sergey is a member of the UCL Computer Science Department's Programming Principles, Logic and Verification group. The talk on "Dependent Types for Compositional Verification of Distributed Systems" reflected joint work by Sergey with University of Washington professor (and CSE alumnus) Zachary Tatlock (Ph.D. '14) and Tatlock's Ph.D. student at UW,. James R. Wilcox.
In his talk, Sergey presented Disel, the first framework for implementation and compositional verification of distributed systems and their clients, all within the mechanized and foundational context of the Coq proof assistant.
According to Sergey's abstract, Disel users implement distributed systems using a domain specific language shallowly embedded in Coq and providing both high-level programming constructs as well as low-level communication primitives. Components of composite systems are specified in Disel as protocols, which capture system-specific logic and disentangle system definitions from implementation details.
By virtue of Disel's dependent type system, well-typed implementations always satisfy their protocols' invariants and never go wrong, allowing users to verify system implementations interactively using Disel's Hoare-style program logic, which extends state-of-the-art techniques for concurrency verification to the distributed setting.
In May, Sergey, Tatlock and Wilcox presented a paper on "Programming Language Abstractions for Modularly Verified Distributed Systems" at the 2nd Summit on Advances in Programming Languages (SNAPL 2017).
CSE-Trained Expert on Program Verification Featured in Communications of the ACM
CSE alumnus Zachary Tatlock (Ph.D. '14) is now a professor of computer science at the University of Washington. In an article about "hacker-proof coding" in the August issue of Communications of the ACM, the publication notes that as Tatlock was finishing up his dissertation at UC San Diego, the then-Ph.D. candidate gave a talk at UW about his thesis research on program verification (under his advisor, Sorin Lerner). The lead engineer for the UW medical center's radiotherapy team was in the audience and asked Tatlock how they could apply verification to that system.
Recalling the event three years later, Tatlock reckons that the question "probably helped me get hired." He joined UW shortly after and has continued to work with the medical center. In the case of the radiotherapy system, he noted that because the system was written in a variety of languages, different techniques had to be deployed to verify the software in its entirety.
According to Esther Shein, who wrote the CACM article, "The system has about a dozen components, each with different levels of criticality." She quotes Tatlock saying that "software for logging an event, for example, is not as critical as software that verifies the beam power has not become too high. What we want to be able to do is ensure the reliability of all pieces. We want to make sure there are no bugs that can affect the parts that are critical."
The medical center wanted to prevent software errors that might prove fatal, given that the radiotherapy system "shoots high-powered radiation beams into the heads of patients to treat cancers of the tongue and esophagus," writes Shein. To check its heaviest-duty components, the medical center uses DeepSpec principles, which are costly and time-consuming because they require highly-trained technicians to prove they're functioning correctly.
To assess less-critical parts of the system, the medical center uses "lighter-weight, less powerful techniques to ensure the correctness," said Tatlock. "So the guarantees for those parts aren't as strong, but it's a better engineering trade-off."
The CACM article goes on to note that Tatlock and colleagues have built a suite of tools the engineers use in their regular development process. "They include a checker that allows them to formally describe the entire radiotherapy system to a computer and ensure the key components are individually correct. The researchers are now working on building verified replacements for those parts of the system." The system is also checked daily. "We want to make sure the code written by the engineers on that team will correctly turn off the beam if anything goes wrong," Tatlock told the publication. "The work is similar to DeepSpec's; it just emphasizes a different degree of automation."
New Graduate Course in Automated Reasoning in Artificial Intelligence
This fall CSE professor Sicun Gao -- who joined the faculty July 1 from a postdoctoral position in MIT's Computer Science and Artificial Intelligence Lab (CSAIL) -- is launching a new CSE 291 course on "Automated Reasoning in AI."
"It will be an introduction to reasoning-based methods in AI, and practical combinatorial search methods for NP-complete problems in general," noted Gao in the announcement. "Students are encouraged to use the AI methods and tools to solve problems in their own respective research areas."
The first half of the course will focus on SAT solving. The course will guide students to build their own SAT solvers from scratch. The second half will survey more general combinatorial search and constraint-solving methods, some theory, and applications in AI and other areas.
The course does not require any prior knowledge in logic or AI.
WEDNESDAY, SEPTEMBER 13, 2017
Virtual Reality in the Classroom
Mark your calendars. That's when CSE associate adjunct professor Jurgen Schulze, who teaches both computer graphics and virtual reality in the department, will be on a panel of experts at a special community event in connection with the Sally Ride Science STEAM Series. The event is organized by UC San Diego Extension and the San Diego Public Library, which is hosting the panel discussion.
Date: Wednesday, September 13
Time: 5-7 p.m.
Location: San Diego Central Library, Shiley Suite, 330 Park Boulevard, San Diego
Abstract: Why just read about ancient Rome when you can walk the cobbled streets as if you were really there? That's the promise of virtual reality, augmented reality and mixed reality in today's classrooms. While the idea of strapping on goggles to virtually visit the Colosseum or go inside a molecule sounds like the stuff of science fiction, the technology to do just that is becoming more popular and available every day. While there are plenty of obstacles -- from cost to teacher training -- that are impeding the growth of virtual reality as an educational tool, it offers considerable benefits. Not only can it boost visual and technology literacy, but it also improves students' attention and engagement.
To explore how this technology has the possibility of transforming K-12 education, a panel of educators and technologists will discuss both the promise and peril of using virtual reality in the classroom. The panel will be moderated by Scott Lewis, CEO of Voice of San Diego. Panelists will include: Qualcomm Institute research scientist and CSE associate adjunct professor Jurgen Schulze; UC San Diego NanoEngineering alumnus Steve McCloskey, CEO and Founder of Nanome, a startup located in QI's Innovation Space; Rodney Guzman, Co-founder, Director of Design and CEO of InterKnowlogy; and Julie A. Evans, CEO of Project Tomorrow.
Bios: Jürgen Schulze, Ph.D., Associate Research Scientist, UCSD's Qualcomm Institute, and Associate Adjunct Professor, Computer Science and Engineering, teaches computer graphics and virtual reality in the CSE department. His research interests at UC San Diego Qualcomm Institute include applications for virtual and augmented reality systems, 3D human-computer interaction and medical data visualization. Dr. Schulze holds an M.S. degree from the University of Massachusetts and a Ph.D. from the University of Stuttgart, Germany. After graduation, he spent two years as a postdoctoral researcher in the Computer Science Department at Brown University working on real-time volume rendering in virtual reality. (For short bios of the other speakers on the VR in the Classroom panel, click here.)