Allen School News

The latest installment of our Undergrad Spotlight features Pooja Sethi, a native of Granite Falls, Washington who graduated from the Allen School with honors last month. Sethi received her bachelor’s degree in computer engineering and was recognized as one of two winners of our Best Senior Thesis Award, which she earned for “Respeak: A Voice-based, Crowd-powered, and Accessible Speech Transcription System” that she worked on with professor Richard Anderson and Ph.D. student Aditya Vashistha in the Allen School’s Information & Communication Technology for Development Lab.

In addition to building a reputation as an outstanding undergraduate researcher, during the course of her studies Sethi participated in five internships, collaborated on research with the Allen Institute of Artificial Intelligence, served as an undergraduate teaching assistant, and served as an officer for the local chapters of ACM and ACM-W.

Sethi plans to spend the summer working with professor Yejin Choi of the Allen School’s Natural Language Processing research group. After that, she will head to Menlo Park for full-time employment with Facebook. The Allen School took an opportunity, before Sethi leaves campus for California, to find out more about what attracted her to computer science, what she looks forward to next, and what advice she would give to students following in her footsteps.

Allen School: Why did you choose to study CSE?

Pooja Sethi: It’s kind of funny, but growing up, I thought the last thing I would ever want to be was a software engineer. The title always conjured up images of people sitting in lonely cubicles staring at blinking lights and yawning. I’ve also always wanted to do something that would help other people, so since I was a kid I thought I would be a doctor.

In high school, I discovered I really loved math and physics and being able to understand the logic behind how the world works. That motivated me to take my first programming class, and I realized how fun it was to be able to “speak” to computers in code. CSE was also really appealing because it has applications to so many facets of life: people here work on everything from finding security vulnerabilities in self-driving cars to using smartphones to detect if a newborn has jaundice. Computers power everything in our lives, and as I was learning to program, it felt empowering to not only understand how computers work but also to be able to create new things with them.

Allen School: What was your favorite CSE course?

PS: That’s so hard — there were so many CSE classes that I loved! I’m going to list a few since I have a hard time updating weights in a priority queue. CSE 332 (Data Structures) was my gateway into fundamental topics and made me feel like a “real” CSE student. My favorite systems courses were CSE 444 (Database Internals) and CSE 452 (Distributed Systems), because let’s be real, it sounds pretty cool to say you’ve implemented a Query Optimizer or a Paxos-based Key Value Service. I also loved CSE 517 (Natural Language Processing) and CSE 573 (Artificial Intelligence), since they introduced me to my current research area of language generation using deep learning. Last but not least, I would highly recommend CSE 599 (Entrepreneurship) with professor Ed Lazowska and Madrona Venture Group’s Greg Gottesman. It was really fun to build a product from the ground-up and hear from amazing entrepreneurs in the Seattle area.

Allen School: What did you like most or what will you miss most about being a CSE undergraduate?

PS: The people in CSE are hands down what I will miss the most. I’ve found that there is something about being trapped in a basement with tea, underflowing snacks, Linux machines, and buggy code that is very conducive to building lifelong friendships. I’m also really thankful to all of the advisers, grad students, and professors I worked with who made CSE feel awe-inspiring but also very welcoming. And of course, the gorgeous view of Lake Washington from the Allen Center balcony will be sorely missed!

Allen School: Are there any people in particular you’d like to mention, who helped shape your experience as a student?

PS: A huge thank you to all of these wonderful people: First, the “Never Stop Dreaming” family of my fellow students: Karishma Mandyam, Aishwarya Mandyam, Naomi Musgrave, Hasanthi Neti, Huong Vo, Grant Timmerman, Dan Radion, Karan Goel, Anna Pendleton, Lilian Liang, Michael Petrochuk, and Bran Hagger. They filled my college experience with so much joy, code, and chocolate milk. To my big sisters in the Bay Area: Vinaya Polamreddi and Arathi Mani, for their constant inspiration, goddess-level AI prowess, and (literal) sunshine in my life.

I also want to thank the amazing grad students and faculty who guided me through research: Aditya Vashistha, Richard Anderson, Gaetano Borriello, Yejin Choi, Ari Holtzman, Max Forbes, Talia Ringer, James Wilcox, and Zach Tatlock. Also, the lovely academic advisers — Raven Alexander, Jenifer Hiigli, and Maggie Ryan — for their kindness and for answering my many questions throughout the years.

And finally, to my mom, dad, and brother Aakash. I would not be anywhere I am today without my family.

Allen School: What is next for you after graduation?

PS: I’m really excited to be joining Facebook full-time as a software engineer in the fall in the Bay Area. During the summer, I’ll be at the Allen School working on conversational question generation in NLP, advised by Yejin. I’ll also be working part-time at a local startup called Cue doing NLP and machine learning consulting. I hope to go back to school for a Ph.D. in the semi-near future. I also plan on sleeping, climbing, and running more post-graduation; we shall see if I succeed.

Allen School: What advice do you have for younger CSE students coming after you?

PS: There is a stigma associated with talking about failures, especially in CSE where many students come in having gotten used to being top of their class and always getting things right. The truth is, there are many times where I did not get things right — I’ve been rejected from internships, received mediocre scores on exams, and questioned my ability to do this subject at three o’clock in the morning.

I’ve learned that what ends up mattering is not the failures themselves, but how you react to them and the perseverance you build by standing back up. So, to those students I say stand strong, remember that you are badass and brilliant (as a few of my friends like to say), and last but not least, stay humble and kind. There is always more to learn.

Allen School: Any final thoughts you’d like to share, as you get ready to start your next chapter?

PS: Thank you for an incredible four years. To new students coming in: you’re in for quite the adventure!

Good luck, Pooja, and thank you for being an exemplary member of the Allen School community — we look forward to seeing you at a future alumni event!

A team of researchers from the University of Washington and Microsoft Research Cambridge have achieved a breakthrough in the design of computational circuit boards using DNA molecules. The group, which was led by Allen School and Electrical Engineering professor Georg Seelig and Andrew Phillips, head of the Biological Computation Group at Microsoft Research, applied principles of spatial organization to create a new “DNA domino” architecture that reduced computation time from hours to minutes compared to existing approaches. The results of the team’s work, which could lead to important advances in molecular engineering and embedded circuit design, were published in the journal Nature Nanotechnology.

Spatial organization is at the heart of many human-engineered systems, including silicon circuitry. Spatial constraints — the proximity of a system’s components to one another — dictate the flow of information between those components, accelerating it among those close to each other and reducing interference from those that are positioned farther apart. In a departure from this organizing principle, synthetic molecular circuits have focused on chemical specificity — a biological interaction determined by the binding properties of proteins — over proximity to guide the interactions of diffusible components.

The team from UW and Microsoft opted for spatial organization over sequence specificity in devising its DNA domino architecture. As the name suggests, the circuits in this new system transmit information in a cascade, from one adjacent component to the next — akin to a line of dominoes. To construct their circuits, the team laid out short strands of DNA, called staples or hairpins, on long strands of DNA folded into a scaffold known as DNA origami. Using this approach researchers were able to construct elementary Boolean logic gates and transmission lines, as well as a two-input, dual-rail XNOR gate that demonstrated the potential for the domino architecture to serve as a building block for a molecular computer.

Georg Seelig

The domino effect resulted in significant improvements in speed and efficiency over current approaches. In one experiment, the domino circuits performed in just seven minutes what would take a circuit built with diffusible components four hours to complete. And because proximity, not specificity, controls the interactions in the domino architecture, components can be duplicated and reused across circuits — enabling more efficient, modular design of molecular control circuits.

Seelig is particularly interested in how this work will translate into novel applications in health care, from new biosensing capabilities to tiny, DNA therapy-delivery robots.

“This work brings moves us closer to being able to use molecular computing for novel therapeutics and diagnostics,” said Seelig. “Not only because computation in a localized circuit is over 10 times as fast as earlier, non-localized circuits, but also because co-localizing functional components on a molecular board will make them easier to deliver to cells.”

In addition to Seelig and Phillips, co-authors of the paper include UW Bioengineering Ph.D. alum Gourab Chatterjee, now a postdoc in the Seelig Quantitative Biology and DNA Nanotechnology Lab; scientist Neil Dalchau of the Biological Computation research group at Microsoft Research Cambridge; and Richard Muscat, former postdoc in the Seelig Lab and now Research Funding Manager at Cancer Research UK.

Learn more in the Nature Nanotechnology paper and related articles on the Microsoft Research Blog and in IEEE Spectrum.

We have no idea how the Seattle PI chose these 58 UW graduates and near graduates …

The Paul G. Allen School can’t claim credit for Bruce Lee, Anna Faris, or Kenny G. Not Ted Bundy either, thank goodness.

But we’re delighted to claim:

• Tim Paterson ’78 (QDOS -> MSDOS)
• Loren Carpenter ’74 ’76 (Pixar)
• Gary Kildall ’66 ’72 (CP/M, Digital Research)
• The other half of Chris DeWolfe ’88 (his Myspace co-founder, Aber Whitcomb, is a 2000 ACMS alum)

Professor Ira Kemelmacher-Shlizerman of the Allen School’s Graphics & Imaging Laboratory (GRAIL) flies her geek flag high in this week’s edition of GeekWire’s “Geek of the Week.” Kemelmacher-Shlizerman is one of the brains behind a series of high-profile research projects that combine facial recognition, modeling and 3-D reconstruction — including a new technique to create photorealistic videos of people from audio files, as demonstrated by a lip-syncing Obama.

The goal of her work, Kemelmacher-Schlizerman explains to GeekWire, is to transform how we interact with one another and the world around us through advancements in computer vision, computer graphics, and augmented and virtual reality technologies.

“Our photos and videos tell a ton of about ourselves, our histories, how people grow, age, learn to walk, and change over time,” she said. “Exploring and learning from that data will enable magical applications in telepresence, health, sports, entertainment and many other unexpected ones.”

Read the full article here, and also check out recent Allen School “Geeks of the Week” Shyam Gollakota, director of the Networks & Mobile Systems Lab, and Ph.D. alumna Irene Zhang.

DawgBytes is the Allen School’s K-12 outreach program. One component of DawgBytes is a series of girls and co-ed computer science summer day camps for middle school and high school students. Always wildly over-subscribed, they’re in full swing now. This was the second week of a two-week “High School Girls Leadership Camp,” during which the students were joined by (and mentored) students in the Middle School Girls Creative Coding Camp.

More photos here. Info on our summer camps here. Info on DawgBytes here. DawgBytes Facebook page here.

“With the nation’s fastest-growing economy and an all-star business roster of household names and up-and-comers, Washington — the Evergreen State — soars above the competition as America’s Top State for Business in 2017.

“The home of Amazon and Costco, Boeing and Expedia, as well as rising stars like Adaptive Biotechnologies, online marketplace OfferUp and space company Blue Origin, Washington has the old and new economies covered — as well as pretty much everything in between.

“But the success story does not end there. At a time when the best workforce rules, Washington boasts the nation’s largest concentration of STEM (science, technology, education and math) workers. Nearly 1 in every 10 Washington workers is in those professions, according to the U.S. Bureau of Labor Statistics. The University of Washington’s computer science school — recently named for one of the state’s most famous natives, Microsoft co-founder Paul Allen — is world class. There is no brain drain here; no state does better at hanging on to its college graduates. And the state is consistently a magnet for investment capital. Washington businesses attracted nearly $1.6 billion in venture capital last year, the sixth-highest total in the nation.”

Professor Michael Ernst of the Allen School’s Programming Languages & Software Engineering group (PLSE) has been recognized by the International Conference on Software Engineering with its Most Influential Paper Award for 2017. Ernst — along with co-authors Carlos Pacheco of Google, and Shuvendu Lahiri and Thomas Ball of Microsoft Research — earned the award for their ICSE 2007 paper, “Feedback-directed random test generation.”

Each year, ICSE selects a paper from 10 years earlier that it judges to have had “the most influence on the theory or practice of software engineering during the 10 years since its original publication.” In their winning paper, Ernst and his colleagues presented a test generation tool, Randoop, which generates tests for programs written in object-oriented languages such as Java and .NET. The technique put forward by the team generates one test at a time, executes the test, and classifies it as (probably) a normal execution, a failure, or an illegal input. Based on this information, it biases the subsequent generation process to extend good tests and avoid bad tests.

By contrast, a typical test generation technique would generate many tests and then try to determine which ones were of value. For example, an error-revealing test is one that makes legal calls that yield incorrect results. Without a formal specification, it is difficult to know whether a given call is legal and whether its outcome is desired. Furthermore, multiple generated tests might fail for the same reason.

Automated test generation is a practically important research topic. In 2002, the National Institute of Standards and Technology (NIST) estimated the annual costs of inadequate infrastructure for software testing in the U.S. to be at least $22.2 billion and as high as $59.5 billion — with more than half of those costs borne by software users on error avoidance and mitigation.

Ernst and Pacheco first introduced feedback-directed test generation in their ECOOP 2005 paper, “Eclat: Automatic generation and classification of test inputs,” when Ernst was a member of the MIT faculty and Pacheco was his student. The ICSE 2007 paper expanded and improved upon the technique with the introduction of Randoop based on more extensive experiments. Randoop continues to be actively maintained 10 years on, and thanks to its scalability and simplicity, it remains the standard benchmark against which other test generation tools are measured.

Ernst and his colleagues were formally recognized at the ICSE 2017 conference held in Buenos Aires, Argentina in May.

Congratulations, Michael!

Researchers in the Allen School’s Graphics & Imaging Laboratory (GRAIL) have developed a new technique that enables them to generate photorealistic videos from audio clips. The team, which includes recent Ph.D. graduate Supasorn Suwajanakorn and professors Steven Seitz and Ira Kemelmacher-Shlizerman, demonstrated their approach by producing a video of former president Barack Obama lip-syncing audio on a range of topics, complete with natural-looking facial expressions and mouth movements.

To achieve such a lifelike result, the researchers had to overcome the “uncanny valley” problem that typically plagues synthesized human likenesses — giving them a creepiness factor that most viewers will find hard to look past.

“People are particularly sensitive to any areas of your mouth that don’t look realistic,” noted Suwajanakorn, lead author of the paper describing the team’s results. “People can spot it right away and it’s going to look fake…you have to render the mouth region perfectly to get beyond the uncanny valley.”

For its demonstration with Obama, the team trained a neural network to view existing videos of the former president and translate sounds into mouth shapes. They then superimposed and blended those shapes onto a reference video — drawing on their previous research in 3-D facial reconstruction and digital modeling — to depict Obama accurately lip syncing speeches from unrelated audio clips. According to Kemelmacher-Shlizerman, it is the first time researchers have achieved such realistic results in an audio-to-video conversion.

The team’s approach, which will be presented at the SIGGRAPH 2017 conference in Los Angeles, California next month, could yield significant advancements in video conferencing and virtual reality applications.

Read the UW News release here and visit the project page here. Also check out coverage of the project by The Atlantic, IEEE Spectrum, Wired, New Atlas, Engadget, GeekWire, PCMag, Variety, and The Verge.

The Allen School continues to build its expertise in leading-edge areas of the field with the recruitment of Kevin Jamieson as the Guestrin Endowed Professor in Artificial Intelligence & Machine Learning. Jamieson, whose research focuses on adaptive data collection algorithms for machine learning, will join the University of Washington this fall after completing a postdoc at University of California, Berkeley.

Jamieson’s research explores how to leverage already-collected data to inform what future measurements to make next, in a closed loop. In both theory and practice, Jamieson has demonstrated that adaptive data collection — or active learning — can extract considerably richer insights than any measurement plan fixed in advance, using the same statistical budget. This is particularly valuable for machine learning applications when training data is time-consuming or expensive to collect, such as when labeled examples are provided by humans. His work has been adopted in a range of applications, from measuring human perception in psychology studies, to numerical optimization and choosing hyperparameters for deep neural networks, to recommending what beer you should try next.

Keen to explore how applications and collaborations can inform his research questions, Jamieson also led the development of NEXT, an open-source software system that facilitates the development, testing, and deployment of active learning for online, real-time applications. The New Yorker magazine employs the NEXT platform to crowd-source its cartoon caption contest, in which readers view captions submitted by other readers for a fixed cartoon one at a time online and rate them as funny, somewhat funny, or unfunny. It’s a contest for the algorithms as well as the readers: behind the scenes, a suite of different active-learning algorithms compete against each other to identify the captions that are consistently rated as funny, and to stop showing those that are unfunny. The exercise provides Jamieson and his collaborators valuable information about which algorithms work best in practice, and which can be discarded.

Jamieson is returning to his roots by joining the UW, where he obtained his bachelor’s degree in electrical engineering before going on to earn his master’s at Columbia University and a Ph.D. from University of Wisconsin, Madison. He is the inaugural recipient of the Guestrin Endowed Professorship, which the Allen School created following Apple’s acquisition of Turi, the machine learning startup created by professor Carlos Guestrin.

Jamieson is the latest in a series of impressive new additions to the Allen School faculty: last week, the Allen School announced that two outstanding researchers in human-computer interaction — Jennifer Mankoff from Carnegie Mellon University and Jon Froehlich from University of Maryland, College Park — will arrive as part of a cluster hire that will make UW one of the leading centers of HCI research and education. Previously, the school revealed that leading robotics researcher Siddhartha “Sidd” Srinivasa of CMU and pioneering computer engineer Michael Taylor of University of California, San Diego would join the faculty this fall along with Yin Tat Lee, a rising star in theoretical computer science.

Jennifer Mankoff

The University of Washington is preparing to welcome outstanding new faculty hires who will bolster its reputation as a center of human-computer interaction research and teaching. Two of the impending arrivals, Jennifer Mankoff and Jon Froehlich, will join the Allen School faculty in advancing solutions to society’s greatest challenges, focusing on accessibility, education, health, sustainability, and more.

Jennifer Mankoff will join the Allen School as the Richard E. Ladner Endowed Professor in Computer Science & Engineering.  She is currently a Professor in Carnegie Mellon University’s Human Computer Interaction Institute, where she leads the Make4All Lab. Previously, Mankoff was a member of the faculty in Electrical Engineering & Computer Science at the University of California, Berkeley.

Mankoff’s research combines empirical methods and technical innovation to solve problems related to accessibility, health, and sustainability. Most recently, her work has focused on 3D printing and its potential for creating personalized assistive technologies for people with disabilities.

For example, Mankoff and her colleagues have shown that a 3D printed physical interface can augment a screen reader and improve interaction speed by a third. This do-it-yourself (DIY) theme is carried over into her work with e-NABLE, a collaborative effort to engage volunteers and clinicians in the design and fabrication of upper-limb assistive technologies. Mankoff’s assistive technology work also extends beyond fabrication. For example, she and her colleagues have explored navigation aids for the blind, and mobile sound capture and transcription tools for the deaf.

As is the case with a lot of accessibility research, Mankoff’s people-centric approach to technology and novel use of 3D printing will wind up benefiting everybody. Mankoff has studied and created solutions for addressing uncertainty in measurement during 3D printing, attaching adaptations to everyday objects (Encore and Reprise) and prototyping custom assistive technologies. Another stream of work aims to explore more natural materials, including embedding textiles in 3D printing, creating knitted objects programmatically, and printing using layers of fabric.

Mankoff’s work also extends to chronic illness. She has explored the impact of chronic disease on quality of life, predictors of trust in peer versus professionally produced health content, visualization techniques for infant oxygen monitoring, and the design of both mobile and web tools for managing chronic illness and physical therapy.

Mankoff has been recognized with an Alfred P. Sloan Fellowship, IBM Faculty Fellowship, and Best Paper awards from ASSETS, CHI, and Mobile HCI. She earned her B.A. in computer science from Oberlin College in 1995 and her Ph.D. in computer science from the Georgia Institute of Technology in 2001.

While she is eager to take advantage of new research opportunities as a member of the Allen School faculty and the university’s Design Use Build (DUB) group, Mankoff is particularly excited about the culture she encountered during her time on campus.

“I visited UW feeling that it would take a lot for me to leave my wonderful colleagues and position at CMU,” Mankoff admitted. “However, the wonderful welcome, fascinating research, many opportunities for collaboration, and warm community in the Allen School and DUB won me over.”

With Mankoff’s arrival, the Allen School adds an exciting new dimension to its accessibility research that will complement the existing efforts of its HCI research group and the Taskar Center for Accessible Technology.

Jon Froehlich’s arrival will be a homecoming of sorts. Froehlich, who earned his Ph.D. at the Allen School working with professors James Landay and Shwetak Patel, will return to his alma mater as an associate professor after having spent the past five years on the faculty of the computer science department at University of Maryland, College Park and director of the Makeability Lab.

Jon Froehlich

Froehlich focuses on the design of interactive tools and techniques that span the virtual and the physical to address pressing global challenges in accessibility, education, and environmental sustainability. He aims to invent or reappropriate methods for sensing physical or behavioral phenomena, leveraging techniques in computer vision and machine learning to interpret and characterize the data. He then builds software and hardware tools that are uniquely enabled by this approach for people of different ages and abilities.

One of Froehlich’s most recent projects, MakerWear, earned him a CAREER Award from the National Science Foundation. MakerWear is a modular toolkit that enables children without prior programming knowledge to create their own interactive wearables using tangible plug-and-play modules. Froehlich and his colleagues won a Best Paper at CHI 2017 for demonstrating how children between the ages of five and 12 can use MakerWear to create their own diverse, personally meaningful designs while developing computational thinking. Another project developed for children, BodyVis, explores how wearable sensing technology can help develop scientific inquiry skills and knowledge of anatomy and physiology. Froehlich and his team created a custom e-textile shirt that senses the wearer’s physiology in real-time and then visualizes this information via responsive anatomical models.

Froehlich is also interested in developing assistive technologies that support independent living. For example, as part of the HandSight project, Froehlich and his colleagues repurposed tiny, endoscopic cameras to augment a blind person’s hand with computer vision. The technology enables users to sense non-tactile information about the world — such as color, texture, and printed text — to support the activities of daily living and increase their independence. Froehlich also initiated Project Sidewalk to collect street-level accessibility information and develop new location-based tools to assist people with disabilities in navigating their communities.

Similar to Mankoff, Froehlich identified the collaborative culture — exemplified by the interdisciplinary DUB group, of which Froehlich was a founding member during his student days — as a motivating factor in his decision to join the UW faculty.

“I am delighted to rejoin the Allen School — a place that helped shape and support my desire to work on applied problems with social relevance,” Froehlich said. “The school has a reputation not just of research excellence and creative innovation, but of collegiality and a unique collaborative culture.”

“UW is a world-leader in HCI research and education, with top experts in nearly every facet of the discipline,” he continued. “I am excited to once again have the opportunity to work with the fantastic faculty and students not just in computer science and engineering, but also in art, geography, social science, HCDE, and the iSchool. Cross-campus collaborations like DUB are what make UW one of the top HCI institutions in the world.”

With the arrival of Froehlich and Mankoff, the Allen School adds leading-edge expertise in wearable technology, personal fabrication, and pervasive computing — and reinforces the school’s reputation as a destination for rising stars in HCI and accessibility research.

Mankoff and Froehlich will be accompanied by Anind K. Dey and Leah Findlater, respectively, in their moves to UW.

Anind K. Dey (left) and Leah Findlater

Dey, who currently serves as the Director and Charles M. Geschke Chair of CMU’s Human Computer Interaction Institute, will join UW as Dean of the Information School. Dey’s research spans human-computer interaction, ubiquitous computing, machine learning, and sensing, with projects focused on intelligibility and end-user control in context-aware computing, active learning to improve usability and performance, modeling and predicting human behavior, and development of programming support for context-aware and sensor-rich environments.

Findlater, currently a faculty member in the University of Maryland College of Information Studies and Institute for Advanced Computer Studies, will join the faculty of UW’s Department of Human Centered Design & Engineering (HCDE). At UMD, Findlater leads the Inclusive Design Lab, where her research focuses on the design of new mobile and wearable technologies that can be adapted to accommodate individual users’ needs and preferences — including novel interfaces and interactions that are accessible to people with visual and motor impairments.

In addition to their primary appointments, both Dey and Findlater will be adjunct faculty members of the Allen School.

Alexis Hiniker

The group announced today are part of a larger HCI cluster hire by UW that includes Alexis Hiniker, who is joining the iSchool faculty after earning her Ph.D. at UW in human-centered design and engineering. Hiniker is an HCI researcher and full-stack developer who builds technologies to empower users by reducing vulnerability and fostering well-being, especially among children, including work in child-computer interaction, technology use in families, and technology for supporting children with atypical patterns of development.

Together, this group of new hires will significantly expand UW’s capacity to develop novel solutions to some of the most pressing problems facing society today and advance the Seattle region’s reputation as a center of innovation and real-world impact.

The Allen School previously announced the impending arrival of two other game-changing faculty hires — leading robotics researcher Siddhartha “Sidd” Srinivasa from CMU, and pioneering computer engineer Michael Taylor from University of California, San Diego.