Allen School Ph.D. students Deepali Aneja and Eric Whitmire have been named 2018 Adobe Research Fellows. The Adobe Research Fellowship program recognizes outstanding graduate students with exceptional technical and personal leadership skills who are engaged in creative, high-impact research. Aneja and Whitmire are among a total of 10 graduate students around the world to be recognized in this year’s fellowship competition.
Aneja works with Allen School professor Linda Shapiro in the Graphics and Imaging Laboratory (GRAIL) and Creative Director Barbara Mones in the Animation Research Labs. Her research focuses on computer vision, the intersection of vision and machine learning, and computer graphics and animation.
Aneja previously spent two summers as an intern in Adobe Seattle’s Creative Intelligence Lab, where she contributed to the team’s efforts to enhance lip sync accuracy for 2D animation in Adobe Character Animator 2018, part of the company’s Creative Cloud lineup. Previously, she completed a computer vision research internship at Lawrence Livermore National Laboratory as part of its Data Heroes intern program. At last year’s Allen School open house and poster session, Aneja and her collaborators captured the People’s Choice Award for “Learning Stylized Character Expressions from Humans.” The winning poster presented the team’s work on DeepExpr, a data-driven framework that uses deep learning to map human facial expressions to animated characters in a way that is both perceptually valid and geometrically correct.
Whitmire works with Allen School and Electrical Engineering professor Shwetak Patel in the UbiComp Lab, where his research focuses on the intersection of hardware and software to enable new capabilities in wearable sensors, interaction, and mixed-reality systems.
Whitmire has completed multiple internships at Oculus Research, where he worked on alternative input techniques for augmented reality applications and a wearable scleral coil eye-tracking system for virtual reality displays. He earned the Best Paper Award for his work on the latter, called EyeContact, at the Association for Computing Machinery’s International Symposium on Wearable Computers (ISWC) in 2016. Whitmire spent last summer working with a team at Microsoft Research on a new handheld controller with haptic feedback for virtual reality applications. Other recent projects include DigiTouch, a reconfigurable glove that enables thumb-to-figure touch interaction for general input and text entry on head-mounted AR and VR displays, and PupilScreen, a smartphone app currently under development that will enable accurate, on-the-spot assessment of traumatic brain injury.
The Adobe Research Fellowship comes with a financial award, an Adobe Research mentor, and the opportunity to spend a summer as an intern at Adobe. Past Allen School recipients include Ph.D. students Julian Michael, who works with professor Luke Zettlemoyer in the Natural Language Processing group, and Pavel Panchekha, who works with professors Michael Ernst and Zachary Tatlock in the Programming Languages & Software Engineering (PLSE) group.
Congratulations, Deepali and Eric!
That’s a question that researchers in the University of Washington’s Molecular Information Systems Laboratory (MISL) hope will inspire people around the world to submit original photos to the #MemoriesInDNA Project. The project — the result of a partnership between Allen School, UW Department of Electrical Engineering, Microsoft, and Twist Bioscience — aims to build a robust dataset of 10,000 images to develop exciting new capabilities for DNA-based data storage and processing.
The MISL launched in 2015 to develop synthetic DNA as an archival storage medium for digital data that is denser and more durable than existing technologies. Now, backed by a $6.3 million grant from the U.S. Defense Advanced Research Projects Agency (DARPA) as part of its Molecular Informatics program, MISL researchers plan to build upon their prior work. Using the trove of visual data that will be assembled as part of the #MemoriesInDNA Project, the team will explore new ways to process and search for data still encoded in DNA — without having to retrieve and convert the images back into their electronic form. It’s the next frontier in the evolution of DNA as a viable — and truly useful — solution for the world’s growing data storage needs.
“Let’s suppose you have a trillion images encoded in DNA and want to find all the photographs that have a red car in them,” Allen School professor Luis Ceze explained in a UW News release. “We want to be able to do that information processing in DNA directly — to search in a smart way and make the molecules themselves carry out that computer vision work.”
To achieve this “smart” search capability, Ceze and his colleagues will leverage the tendency of certain nucleotides that make up DNA molecules to bind themselves to others — adenine (A) to thymine (T), and cytosine (C) to guanine (G). As part of the encoding process, MISL researchers convert the digital data of an image — 0s and 1s — to the A, T, C, and G molecules that make up strands of DNA. To retrieve only those images they are interested in out of the thousands that make up the dataset, without having to convert them back to binary, the researchers plan to introduce a query containing complementary DNA that will cause only those that meet their search criteria to bind to it. The inclusion of magnetic nanoparticles in the query will enable them to pull out the images bound to it with the help of a magnet. The team will also employ machine learning techniques to enable the detailed mapping and encoding of all visual features that may be contained in an image to enable scientists to perform meaningful data processing.
The MISL team has already set a world record for the amount of digital data stored in and successfully retrieved from DNA, from the hip (a video by the band OK Go) to the historic (the Universal Declaration of Human Rights in 100 languages). To develop a robust capability to search digital data within the DNA itself, however, the team needs a significantly larger volume and variety of images to work with. That’s where the #MemoriesInDNA social media campaign, also launched today, comes in.
“It’s your turn to show us what should be preserved in DNA forever,” Ceze said. “We want people to go out and take a picture of something that they want the world to remember — it’s a fun opportunity to send a message to future generations and help our research in the process.”
The team plans to eventually make this digital time capsule — stripped of any personally identifying information — available to researchers around the world.
“It is thrilling to bring computer science and molecular biology together in this project,” said Microsoft senior researcher Karin Strauss, an affiliate associate professor at the Allen School. “There has been amazing progress recently in both areas and, when combined, they can be very powerful in tackling problems created by the massive amounts of data we’ve been generating.”
Other lead contributors to the project include Allen School and Electrical Engineering professor Georg Seelig and Microsoft partner architect Douglas Carmean. Twist Bioscience will supply the synthetic DNA for the project.
Anyone can contribute to the data set by uploading an original photo via the website memoriesindna.com. Afterward, help the campaign go global and inspire others to participate by sharing your image on social media with the hashtag #MemoriesInDNA.
Allen School alumna Gail Murphy (Ph.D., ’96), professor of computer science and Vice President Research & Innovation at the University of British Columbia, has been recognized by the IEEE Computer Society with its Harlan D. Mills Award, which honors individuals for significant contributions to software engineering research and practice through the development and application of sound theory. Murphy earned the 2018 award for “outstanding research on understanding software-development practices and tools that improve the productivity of developers.”
Murphy’s research focuses on the development and evaluation of tools for to enable software developers to better identify, manage, and coordinate the information that matters most to their work. She also conducts empirical studies to better understand the software development process. Her focus was partly inspired by experience: Murphy started out as a senior software engineer at MPR Teltech before arriving at UW to earn her Ph.D. with the late David Notkin. She later co-founded Tasktop Technologies to commercialize this work and streamline software development at the enterprise level.
The Harlan D. Mills Award is the latest in a string of professional honors Murphy has collected over the years, including the AITO Dahl-Nygaard Junior Prize, which highlights promising contributions to the field of object-oriented programming, and the CRA-W Anita Borg Early Career Award in recognition of her professional contributions and her commitment to increasing the participation of women in computing. Murphy is a Fellow of the Royal Society of Canada and of the Association for Computing Machinery, and she has earned a number of Distinguished Paper and Most Influential Paper awards — a testament to the enduring impact of her work in the software engineering community and the field of computer science, generally. In addition to professional accolades, Murphy has also earned multiple honors from her alma mater, including the Allen School’s 2014 Alumni Achievement Award and a 2008 Diamond Award from the UW College of Engineering for early-career achievement.
Read the full Harlan D. Mills Award announcement here.
Professor Zachary Tatlock, a member of the Allen School’s Programming Languages & Software Engineering (PLSE) group, has earned a CAREER Award from the National Science Foundation to advance the development of a practical verification framework and other methods for improving the reliability of distributed software systems that form the backbone of modern computing applications.
Billions of people around the world rely on distributed systems every day for critical services, including banking, healthcare, transportation, and more. Such systems are designed for optimum scalability and availability, so that when load spikes, machines crash, or networks misbehave, the system is able to compensate for those failures and continue servicing user requests. But these systems are not infallible in practice, and failures can have devastating impacts in human and economic terms — halting essential services and causing significant data loss. On a single day in the summer of 2015, a series of software failures halted trading on the New York Stock Exchange, grounded the entire mainland fleet of United Airlines, and knocked out the website of the The Wall Street Journal. Four years previously, a widespread failure in Amazon’s Elastic Compute Cloud (EC2), part of Amazon Web Services, brought down sites such as Foursquare and Reddit and affected the functionality of others, such as The New York Times. In all, more than 70 sites were affected by that outage.
Tatlock aims to reduce the likelihood and severity of such failures by applying a practical verification-based approach that makes it easier for programmers to implement reliable, high-performance distributed systems. Currently, the set of potential failures is so complex, and the rate of change in software so high, that it is infeasible to effectively test such systems against all scenarios. An alternative approach is to mathematically prove the system works correctly in all cases. But researchers typically only prove the correctness of high-level algorithms for simplified models of these systems, compelled by their complexity to ignore low-level implementation details. This can lead to mismatches between the simplified model and actual implementation which yield subtle errors that may result in large-scale failure. Furthermore, even the most painstakingly constructed proofs eventually become obsolete as the systems they are written for evolve to meet the increasing demand for scale and performance. Tatlock will address these shortcomings by designing compositional verification techniques for independently proving implementation correctness for applications and reliability for fault-tolerance components. This approach would enable programmers to verify the safety and reliability of distributed systems implementations when faced with a variety of network or machine failures — making them less likely in future to ground flights or grind financial markets to a halt.
The NSF’s Faculty Early Career Development Program recognizes and supports junior faculty who exemplify the role of teacher-scholar and demonstrate the potential to be lifelong leaders at the intersection of education and research. Tatlock is the 11th Allen School professor to earn a CAREER Award through the program in the past two years — an incredible success rate that is a testament to the high caliber of our young faculty. A total of 58 current or former Allen School faculty members have earned a CAREER Award or its predecessor, the Presidential/NSF Young Investigator Award.
Read Tatlock’s award abstract here.
Allen School Ph.D. students James Bornholt and Eunsol Choi have won 2018 Facebook Fellowships, which are designed to support and recognize promising doctoral students who are pursing innovative research in computer science and engineering. Only 17 students from around the globe were chosen out of more than 800 applicants to receive one of these competitive awards, which provide each fellow with up to two years of tuition, grant support, conference travel support, and multiple opportunities to engage with Facebook researchers.
Bornholt works with professors Emina Torlak, Dan Grossman, and Luis Ceze in the Allen School’s Programming Languages & Software Engineering (PLSE) research group. His research focuses primarily on programming languages and formal methods, with an emphasis on the development of automated program synthesis and verification tools.
Bornholt was the lead researcher on MemSynth, the first of a new class of synthesis-aided memory model tools for formalizing subtle details of computer processors. Bornholt also co-authored “Push-Button Verification of File Systems via Crash Refinement,” which earned the Best Paper Award at the 12th USENIX Symposium on Operating Systems Design and Implementation (OSDI 2016). In that paper, Bornholt and his colleagues presented Yggdrasil, a new file system automatically proven to be crash-safe. Bornholt branched out from his core research interests to contribute to “A DNA-Based Archival Storage System,” in which a team of researchers in the Molecular Information Systems Lab — a collaboration between UW and Microsoft Research — designed a next-generation storage system for digital data using synthetic DNA.
Other recent projects to which Bornholt has contributed include Hyperkernel, an automatically verified OS kernel, and Ferrite, a toolkit for constructing crash-consistency models to improve file system performance and correctness.
Choi is a member of the Allen School’s Natural Language Processing group, where she works with professors Luke Zettlemoyer and Yejin Choi. Her research interests broadly span natural language processing, computational social science, and machine learning. She is particularly interested in developing methods for extracting structured representations of human information such as scientific findings, historical facts, and opinions, and retrieving them using natural language questions.
In “Truth of Varying Shades: Analyzing Language in Fake News and Political Fact-Checking,” which was presented at the Conference on Empirical Methods in Natural Language Processing (EMNLP 2017), Choi and a group of colleagues at the Allen School and Pacific Northwest National Laboratory analyzed the linguistic patterns of articles and political statements to identify cues that indicate whether a news story is trustworthy, unreliable, or satire. As an intern at Google, Choi was lead author on “Coarse-to-Fine Question Answering for Long Documents,” which presented a new framework for question answering that efficiently scales to longer documents while matching or exceeding the performance of current models.
Choi’s research contributions also include TriviaQA, a robust, large-scale reading comprehension data set, and “Zero-Shot Relation Extraction via Reading Comprehension,” which demonstrated how reducing relation extraction to a reading comprehension problem allows generalization to unseen relations that are defined on-the-fly in natural language.
Past Allen School winners of the Facebook Fellowship include Aditya Vashistha (2016), for his work on social media tools for people in developing communities; Lydia Chilton and Nicki Dell (2013), for their work on crowdsourcing algorithms and applications for improving quality of life in low-resource communities, respectively; and Adrian Sampson (2012), for his work in energy-efficient computing.
Congratulations, James and Eunsol!
Allen School professor and undergraduate alumnus Kurtis Heimerl (B.S., ’07) has been recognized with a 2018 Diamond Award from the University of Washington’s College of Engineering. Each year, the Diamond Awards recognizes alumni and friends of the college who have made significant contributions to the field of engineering. The college is honoring Heimerl with its Early Career Achievement Award, which is given each year to an outstanding graduate of the college who has made exceptional professional contributions through research, teaching or service within the first 10 years of their career.
Heimerl is a member of the Allen School’s Information & Communication Technology for Development ICTD) Lab, which focuses on improving the lives of underserved populations in low-income communities through technology. He is particularly interested in harnessing the potential for technology to alleviate poverty by bringing mobile internet access to people in some of the most remote regions on earth.
“Growing up in Alaska, I developed a deep understanding and appreciation of rural life and the difficulties of connectivity in these environments. This background, in areas where people are forced to improvise and resolve their local issues, has always informed my research,” Heimerl explained. “I’m happy and grateful that UW was there to foster my technical skills as a student and now continues to support my work to empower people and communities to own their infrastructure.”
That work began in earnest during his time as a Ph.D. student at the University of California, Berkeley working with professors Eric Brewer and Tapan Parikh (Ph.D., ’07). There, Heimerl became known for his efforts to develop community-based cellular networks. These small-scale networks, which he designed to be locally owned and operated, brought the benefits of cellular connectivity to people in resource-constrained areas that previously lacked coverage. Heimerl founded the startup Endaga, Inc. to commercialize his “cell network in a box,” deploying the technology in rural Pakistan, Indonesia, the Philippines, and other areas without existing wireless infrastructure.
“Cellular communication has revolutionized the way people communicate and connect to essential services, and the benefits are particularly important for people in developing countries,” noted Allen School professor Richard Anderson. “But cell towers are expensive, and if the ‘economic density’ is too low, telecommunication companies won’t invest in connecting those communities. So what can be done to connect the billion people who are still outside of cellular coverage? That’s where Kurtis comes in, developing a ‘local cellular’ technology to address this inequality and bring the benefits of connectivity to more people around the globe.”
In 2014, Heimerl’s efforts earned him the notice of MIT Technology Review, which recognized his contributions with a TR35 Humanitarian Award. Endaga raised $1.2 million in seed funding before eventually joining forces with Facebook in 2015, which gave Heimerl the opportunity to continue his work as a visiting scientist focused on the company’s rural access initiatives. The following year, he joined the UW faculty, where he continues his focus on increasing connectivity and improving economic opportunity for people living in underserved areas.
Most recently, Heimerl and his colleagues began investigating the increasing adoption of smartphones in rural areas that currently lack the bandwidth to support many of the features that are built into those devices. By developing a better understanding of subscribers’ behavior and motivation, the team aims to provide useful guidance for the deployment of new or upgraded cellular infrastructure to support the preferences of people living in these communities.
“Kurtis combines a thorough knowledge of computer systems and infrastructure with creativity and a strong commitment to a set of social values. This allows him to identify and work on research problems that can have a deep and lasting impact on society,” observed Parikh, now a faculty member at Cornell Tech. “Kurtis has frequently challenged my ideas and perspective, and often he has been right. He is also willing to listen and adapt, which is a testament to his maturity as a researcher and the personal ideals for which he works.”
Heimerl and his fellow Diamond Awards honorees will be formally recognized at a gala hosted by the college on May 10th. He joins a distinguished list of past Allen School recipients, including recent Early Career Achievement winners Ben Hindman, founder of Mesosphere (2016), big data pioneer Christophe Bisciglia (2015), LiveJournal creator Brad Fitzpatrick (2014), and consumer technology leader Greg Badros (2012); Distinguished Service winners Yaw Anokwa, one of the creators of Open Data Kit (2015), and Washington FIRST Robotics volunteer Kevin Ross (2013); and Anne Condon, professor at University of British Columbia, who was recognized for Distinguished Achievement in Academia (2012).
Read more about the 2018 Diamond Award recipients here.
Allen School professor Jennifer Mankoff is an award-winning researcher in human-computer interaction and accessibility. But her road to a successful academic research career was bumpier than most promising young faculty. In addition to navigating the demands of teaching and research while raising a young family — she and spouse Anind Dey, the new Dean of the University of Washington’s Information School, have two children — she had another obstacle to overcome: her health.
According to the U.S. Centers for Disease Control and Prevention, roughly half of all adults in the United States have one or more chronic illnesses — some of which may be “invisible” to others yet are no less debilitating. A little over a decade ago, Mankoff was diagnosed with Lyme disease, a tick-borne illness that is tricky to diagnose and just as tricky to manage, with symptoms that over time ranged from extreme fatigue, to loss of hearing, memory, and fine motor control. She recently spoke with Nature as part of the journal’s in-depth look at how scientists balance the demands of research with long-term illness. It’s a topic that has received very little attention — a situation Mankoff and the other featured researchers hope to rectify by speaking out about their experiences.
As the article makes clear, chronic illness takes a heavy emotional as well as physical toll. Although Mankoff continued doing those things that define success in academic research circles — writing grants, publishing research, and earning tenure — her battle with Lyme cause her to question who she is and what she is capable of.
“My image of who I could or should be didn’t match up with reality in terms of my productivity,” she explained.
For Mankoff and the others who went on the record for the story, finding their way often means finding a way around the limitations brought on by their condition. Mankoff says she “long ago learned that one aspect of managing a chronic illness is accepting the ‘disability’ label and working within that structure to make things easier.”
For example, she requests a classroom near her office so she does not have to contend with a long trek across campus on days when her Lyme-induced fatigue is particularly acute. She also has become adept at prioritizing tasks and at breaking down large tasks into smaller ones, both of which help her to take full advantage of times when her illness takes a back seat.
Mankoff, who arrived at the Allen School last fall after 12 years on the faculty of Carnegie Mellon University, in part credits her colleagues’ support for enabling her to carve out a career that works for her.
“I’ve been lucky to receive a tremendous amount of positive support from the faculty at CMU and again at UW during my interview and since I arrived,” Mankoff told the Allen School News. “Equally important was the support I received at home from my family. That said, negotiating something like this is a personal process, and one for which there are no easy answers.”
Mankoff points out that the lines between work and personal life can get blurred. From her perspective, that is not a bad thing — in fact, she says, it has made her a better researcher. It also opened up new avenues of inquiry that she may not have considered otherwise, including the impact of chronic disease on quality of life, the development of tools for managing chronic illness and physical therapy, and predictors of trust in health care content based on whether it was produced by practitioners or peers.
“Life outside work sometimes – often – impacts work, and for me it has never made sense to keep them separate,” she explained. “My research is often inspired and driven by my personal experiences, and that in turn helped my motivation to get through this.”
Speaking of motivation, Mankoff believes it is important to talk about her journey to give hope and support to others who find themselves in a similar position. While in Pittsburgh, she blogged about Lyme disease and helped to organize local support group efforts. She also has taken on a prominent role in the academic community leading an accessibility group that advocates for access to conferences and online materials.
Although going public can be scary, Mankoff says she does it because, “If my story, or any of the other information in this well researched article, can help someone, then I hope it reaches them.”
Christine Betts, a computer science major who earlier this week received the inaugural Allen Institute for Artificial Intelligence (AI2) Outstanding Software Engineer Scholarship for underrepresented groups, is profiled in GeekWire’s latest “Geek of the Week” feature.
Betts, who hails from Kansas City, Missouri, is an active contributor to the Allen School community, serving as a teaching assistant for our popular introductory programming courses and engaging in undergraduate research in the Molecular Information Systems Lab. In talking about her chosen field, she likes to point out that programming is inherently a creative endeavor — and that people don’t necessarily have to be the “STEM type” to be good at it. She is especially eager to engage more young people from underrepresented groups in computer science.
“Now that I’ve started programming, I can’t imagine doing anything else in a career, but more broadly I’m motivated by the voices I hope to lift up in whatever capacity I can,” Betts told GeekWire. “There are so many perspectives that aren’t being heard because of how poorly the field as a whole reflects the larger population, which is why in the future, no matter what I do, I hope to mentor and lift up young women.”
Betts knows first-hand how uplifting such support can be as one of the TUNE Scholars, a program that supports undergraduate women pursuing computer science and other tech-focused degrees at the University of Washington with housing, mentorship, and networking opportunities.
“I find inspiration in all of the young women I’ve gotten to work with, the awesome, hard-working and motivated women I get to live with as a TUNE Scholar, and in thinking about how much I have to be grateful for.”
Vikram Iyer, a Ph.D. student in Electrical Engineering who works with professor Shyam Gollakota in the Allen School’s Networks & Mobile Systems Lab, has earned a prestigious Microsoft Research Ph.D. Fellowship. He is one of only 10 graduate students from across North America to be selected as a member of the class of 2018 fellows.
The Microsoft Research Ph.D. Fellowship program is designed to promote the careers of promising student researchers in computer science, electrical engineering, mathematics, and related fields. For the class of 2018 fellows, the company specifically sought applicants in two key areas of interest: systems and networking, and artificial intelligence. Iyer has already made significant contributions to the former through his work on wireless power, communication, and localization.
In one recent, high-profile example, printed Wi-Fi, Iyer and his colleagues demonstrated how to create smart objects made entirely out of 3D printed plastic parts. To enable the objects to communicate over Wi-Fi without the need for batteries, the team relied on an ingenious combination of old and new techniques. They harvested power from the physical action of gears, coil springs, and other components — not unlike how a mechanical watch keeps time — and leveraged the lab’s pioneering work on backscatter, a method of wireless communication in which devices reflect ambient radio frequency signals that can be decoded by a Wi-Fi receiver.
Backscatter formed the basis of Iyer’s work on another project, interscatter, that enables implantable and other devices to communicate with smartphones and smartwatches by converting Bluetooth transmissions into Wi-Fi and Zigbee-compatible signals. Iyer and his colleagues built several prototypes to demonstrate the technology’s potential, including the first smart contact lens that can monitor and transmit information on the wearer’s medical condition and an implantable neural recording interface. The team, which included Allen School and EE professor Josh Smith of the Sensor Systems Lab, earned the Best Paper Award at SIGCOMM 2016, the annual flagship conference of the Association for Computing Machinery’s Special Interest Group on Data Communication.
In addition to unlocking new applications in battery-free communication, Iyer helped demonstrate that wireless signals can literally unlock a door through on-body transmissions. In this project, Iyer and his colleagues developed a way to securely transmit passwords via the human body using low-frequency signals generated by fingerprint sensors and touchpads on mobile devices. The technology has the potential to do more than open doors; it would also make it easier to link a medical device such as a glucose monitor or insulin pump with a smartphone by eliminating the need to manually type complicated serial numbers or passwords. Other projects that illustrate the range and impact of Iyer’s contributions include FM backscatter, which introduces connectivity to everyday objects using FM radio signals to enable smart fabrics and smart cities applications, and FingerIO, a system for fine-grained finger tracking on mobile devices using sonar that earned an Honorable Mention at CHI 2016, the ACM’s flagship conference on human-computer interaction.
“These are incredibly talented students, the top students from North America,” said Microsoft Principal Researcher and Research Manager Bill Dolan, director of the fellowship program, in a blog post announcing the class of 2018. “We really do want to promote the careers of these great students. It is good for all of us.”
The Microsoft Ph.D. Fellowship provides tuition support, an annual stipend, and funding to cover attendance at professional conferences and seminars. Fellows also have an opportunity to pursue an internship with Microsoft researchers in their field of study. The company has a history of supporting students engaged in leading-edge research at the Allen School, including past fellowship winners Kira Goldner (2017) in theory of computation; Lilian de Greef (2015), Mayank Goel (2014), and Gabe Cohn (2012) in ubiquitous computing; Irene Zhang in computer systems (2015); Yoav Artzi (2014) in natural language processing, and Franziska Roesner (2012) in security and privacy.